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https://microbewiki.kenyon.edu/index.php?title=Carbon_cycle&diff=132940
Carbon cycle
2018-04-05T04:07:03Z
<p>Kmscow: /* Reducing Carbon Losses */</p>
<hr />
<div>=='''Introduction'''==<br />
::Globally, carbon cycles among the oceans, atmosphere, terrestrial biosphere, ecosystem, and geosphere. This wiki page focuses on carbon dynamics in soil. Soil organic matter (SOM) is the largest terrestrial carbon pool and contains more than three times as much carbon as either the atmospheric or living plant pools<ref name="one">Fischlin, A. et al.(2007). Climate Change 2007: Impacts, Adaptation and Vulnerability. Cambridge Univ. Press, 211–272.</ref>. In section 2, the first part of the wiki, we describe how organic residues are broken down in soil, focusing on the role of microbes as decomposers. By emphasizing the role of microbes, we hope to build a better nexus of information between organic input decay and SOM formation. So, in the next section we discuss the importance, formation, and recent research of SOM. Topics covered in sections 2 and 3 are integrated into three SOM formation models in section 3.5. There have been a lot of recent discoveries and many newly developed models surrounding SOM. As such, the predominant views may well be subject to change. After decomposition and SOM, we move toward focusing on real world applications and impacts of the carbon cycle in soil. <br />
<br />
::The carbon cycle has a huge role in maintaining global climate and ecosystems. SOM, being the primary pool of carbon, is of crucial importance in climate change, as demonstrated in section 3. For thousands of years, humans have interacted with soil and the carbon cycle through agriculture. However, only now are we starting to properly understand the impact agricultural practices have on soil. Driven by the strong impetus to better understand carbon dynamics in agroecosystems, we discuss carbon management strategies in agricultural systems in section 4. Permafrost thaw and drainage of wetlands are presented in section 5, as two “case studies” of soil carbon cycle. <br />
<br />
::The carbon cycle, like most natural cycles and models, is not a system closed from outside influences. There are many interlocking elements throughout cycles of nutrients, carbon, and nitrogen in soils. The nitrogen cycle is especially closely linked to the carbon cycle in microbiology because of the importance of C/N ratios. A thorough understanding of the [[Nitrogen Cycle]] will greatly improve our understanding of the carbon cycle in turn.<br />
<br />
=='''Decomposition of Organic Residues'''==<br />
::The formation of SOM and the decomposition of residue are intimately associated. Decomposition of organic residue is one of the major functions of microorganisms in the soil. The soil microorganisms utilize the residue components for energy and carbon source to synthesize the new cells. The organic materials added to soil are primarily plant residues from either cultivated crops or native vegetation, which are the source of energy stored in the carbon compounds. The crop agricultural ecosystems primarily include the combination of leaf, stem, and root tissues remaining after harvest. On the other hand, the residues that undergo decomposition in the natural ecosystems are derived from native prairie and forest vegetation. There are two types of plant residue that assimilate into the soil<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. One is above ground residue, which is derived from falling debris and other plant that are above the soil surface. The second type is deposited from root systems that complete their life cycle throughout the course of a particular season. These residue with the root exudates supply the substrate carbon input into the soil. The decay process of above-ground residue begin and initiate due to different agricultural management systems and practices<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. A portion of these substrate goes into microbial mass as it is used by the soil microorganisms for reproduction and metabolic activity and a larger part of it is lost as carbon dioxide due to the energy yielding metabolic processes of the microbial community. Recent studies<ref name="three">M. Francesca Cotrufo et al. (2013) The Microbial Efficiency-Matrix Stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization: do labile plant inputs form stable soil organic matter? Global Change Biology,19, 988–995.</ref><ref name="four">M. Francesca Cotrufo, et al. (2015) Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nature Geoscience 8, 776–779.</ref> emphasize that not all the litter Carbon loss are mineralized to carbon dioxide, but a part of these Carbon loss is transferred to mineral soil, where it contributes to the formation of soil organic matter through the two main pathways, dissolved organic matter-microbial path and physical transfer path.<br />
<br />
====Chemical Constituents====<br />
::The composition of the crop residues added to and decaying in soil are varied. Plant residues are comprised of many complex polymers such as lignin and cellulose and contains water-soluble organic compounds such as proteins, carbohydrates, and organic acidsl.<br />
<br />
=====<span style="color:black">Carbohydrates</span>=====<br />
::From 5-25% of soil organic matter is combined in the form of carbohydrates, which include simple sugars, cellulose, and hemicellulose <ref name="five">Baldock J (2007).Composition and cycling of organic C in soil. In: Nutrient Cycling in Terrestrial Ecosystems.Springer,pp. 1–35.</ref>. These carbohydrates are rapidly degraded by varied microorganisms in the soil including bacteria, archaea, actinomycetes, and fungi. During degradation soil microorganisms synthesize extracellular polysaccharides. These polysaccharides bind soil into water stable aggregates so that the aggregates are more permeable to water and air. Polysaccharides also affect the cation exchange capacity of soil and act as an energy source for other microorganisms<ref name="five">Baldock J (2007).Composition and cycling of organic C in soil. In: Nutrient Cycling in Terrestrial Ecosystems.Springer,pp. 1–35.</ref>. <br />
::Heterotrophic microbes can easily metabolize simple sugars. Plants link glucose molecules (and other sugar monomers) into long chains to produce polymers such as cellulose, which requires more specialized organisms to degrade.<br />
::For example: Starch is made of amylose (alpha 1,4 bonded glucose) and amylopectin (alpha 1,6 bonded glucose), and is relatively easy for most organisms to degrade. Cellulose, however, is a polysaccharide of glucose connected with beta 1,4 bonds, and is more difficult to degrade. No animal can degrade cellulose, so bacteria can frequently be found in mutualistic relationships with detritivores: the bacteria degrade the cellulose enough that the animal is able to digest it. <br />
<br />
======<span style="color:black">Cellulose</span>======<br />
::[[Image:CelluloseDecomp_edited.jpg|center|thumb|200px|The Decomposition of Cellulose <ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>,]]<br />
<br />
::Cellulose is the most abundant carbon input in soil. It’s a structural polysaccharide that is made of 1400 to 10000 glucose units. In order to access the glucose monomer, the cellulose must be cleaved by extracellular enzymes. These pieces are then transported into the cell for energy generation (catabolism) or production of biomass (anabolism). Cellulose is used by a diverse group of soil organisms including fungi such as Penicillium and [[Aspergillus]] and bacteria such as [[Streptomyces]] and [[Pseudomonas]]. Fungi and bacteria are important participants in the extracellular cleavage of cellulose<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>.<br />
<br />
======<span style="color:black">Hemicellulose</span>======<br />
::[[Image:HemicelluloseDecomp edited.jpg|center|thumb|200px|The Decomposition of Pectin (a Hemicellulose)<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>,]] <br />
::Hemicellulose is the next most common carbohydrate in plants. It is a branched polymer with varied sugar monomers (glucose, mannose, and galactose) and bonds. The decomposition of hemicellulose is similar to that of cellulose in that the initial depolymerization step takes place outside of the cell, and the sugars produced are then transported into the cell for catabolism or anabolism. Even though hemicellulose decomposition is much quicker than cellulose decomposition, cells will utilize simple sugars as substrates before hemicellulose<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>.<br />
<br />
======<span style="color:black">Chitin</span>======<br />
:::[[Image:ChitinDecomposition_edited.jpg|center|thumb|200px|The Decomposition of Chitin and Chitosan Under Aerobic Soil Conditions<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>]]<br />
:::Chitin is a special compound which can be found in the integument of arthropods and the cell walls of fungi. Chitin is one of the cell-wall component of many common soil fungi (e.g., [[Aspergillus]] and [[Penicillium]]) as around 3% to 25% of these soil fungal biomass are chitin<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. Chitin is usually protected from degradation by the protein-chitin complex in its natural normal stage in soil. Due to this type of protection, chitin is an important component in soil organic matter formation. The polymer is not easily degraded and requires a variety of enzymes to do so. The dominant chitin degraders are the Actinomycetes, [[Streptomyces]] and Nocardia. Less important than Actinomycetes, fungi such as Trichoderma and [[Verticillium]] and bacteria, such as [[Bacillus]] and [[Pseudomonas]] can also degrade chitin<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>.<br />
<br />
=====<span style="color:black">Lignin</span>=====<br />
:::[[Image:LigninDecomp2_edited.jpg|center|thumb|200px|One Possible Pathway of Lignin Decomposition<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>]]<br />
::Lignin is the main component of wood in trees. Lignin has a varied, unique, and complicated chemical structure which contains many aromatics. Aromatics are part of the reason why lignin is more difficult to be decomposed. Even with strong acid treatment, the plant residues are not solubilized due to the complex ring structure.These aromatics can be released from the lignin structure by fungal enzymes such as peroxidases and oxidases. The enzymes utilize H2O2 and OH radicals to break the bonds in the lignin. Lignin is decomposed through groups of specialized fungi. Common types of fungi which depolymerize lignin are white rot ("[[Phanerochaete chrysosporium]]"), brown rot, and soft rot<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. Once the aromatics are released from the original lignin structure they are incorporated into the metabolic pathway as pyruvate, acetyl CoA, and into the TCA cycle.<br />
<br />
=====<span style="color:black">Proteins</span>=====<br />
::Proteins are one of the most important components of plant residue added to soil. Protein is a polymers of amino acids linked by peptide bonds. A variety of microorganisms in soil can produce proteolytic enzymes such as protease and peptidase, which can break the peptide bond of the protein and hydrolyze it into individual amino acids. These amino acid monomers can then be utilized by microbes for either catabolism or for the synthesis of new essential proteins<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>.<br />
<br />
=====<span style="color:black">Fats & Waxes</span>=====<br />
::More than 2% of soil organic matter is cultivated in the forms, fats and waxes. Unlike cellulose and sugar, fats and waxes are much harder for microorganisms to breakdown. They are decomposed very slowly into CO2, water and energy which can be used by microorganisms<ref name="six">Osman, Khan Towhid. (2013). Soils’: Principle, Properties, and Management. Springer Dordrecht Heidelberg New York London, 93-95.</ref> Very little investigation has been done so information regarding this is limited.<br />
<br />
=='''Soil Organic Matter'''==<br />
====SOM and Climate Change====<br />
::The carbon cycle in soil is a dynamic balance between photosynthesis, the respiration of decomposing organisms, and the stabilization of carbon. Soil stores at least three times as much carbon (in SOM) as is found in either the atmosphere or in living plants<ref name="one">Fischlin, A. et al.(2007). Climate Change 2007: Impacts, Adaptation and Vulnerability. Cambridge Univ. Press, 211–272.</ref>. The total global carbon stock in soil is about 2500 Pg C, including approximately 1550 Pg in organic carbon, and 950 in inorganic carbon. Soils act as a buffer against the increase of atmospheric CO2. There is growing interest that it is possible to remove a significant amount of CO2 from the atmosphere by sequestering carbon in soil. It is estimated that 16-30% atmospheric CO2 can be removed when SOM concentrations increase 5-15% in soil up to 2m depth<ref name="seven">Baldock J (2007).Composition and cycling of organic C in soil. In: Nutrient Cycling in Terrestrial Ecosystems.Springer,pp. 1–35.</ref><ref name="eight">Kell DB (2011).Breeding crop plants with deep roots: their role in sustainable carbon nutrient and water sequestration. Annals of Botany, 108, 407–418.</ref>. It is also believed that soil respiration rates could cause a positive feedback in global warming. There are more nutrient based, plant-oriented interests in SOM, however, it seems that concerns about the changing climate “have now overtaken these other justifications”<ref name="nine">Sollins, P., Swanston, C. & Kramer, M. (2007).Stabilization and destabilization of soil organic matter—a new focus. Biogeochemistry 85, 1–7.</ref>.<br />
<br />
====New Insights on SOM====<br />
::For a long time, the scientific community described SOM in terms of humic substances. With the help of advanced analytical techniques, a growing body of research indicates that the importance of the biotic and abiotic environments in soil outweighs that of the molecular structure of plant inputs and organic matter in the process of OM stabilization. Factors such as rate of decay, SOM pools, stability, or ‘recalcitrance’ are not sufficient to describe the “ecosystem property”<ref name="ten">Schmidt MWI, Torn MS, Abiven S et al. (2011) Persistence of soil organic matter as an ecosystem property. Nature, 478, 49–56.</ref> of SOM; rather, texture, mineralogy, water solubility, molecular size, functionalization, and perhaps most important, climate change conditions should be incorporated into our understanding (and modeling) of carbon.<br />
<br />
=====<span style="color:black">History of Humic Substances</span>=====<br />
::Historically soil chemists use alkali and acid extraction methods and observations of the extracted (or residual) functional group chemistry to describe the soil organic matter, or humus<ref name="ten">Schmidt MWI, Torn MS, Abiven S et al. (2011) Persistence of soil organic matter as an ecosystem property. Nature, 478, 49–56.</ref>. When protons are added to the solubilized organic materials, the dark color solid that precipitates is called ‘humic acid’. ‘Fulvic acid’ is the organic matter that remains soluble after reacidification treatment. The organic matter that does not respond to the extraction treatment is called ‘humin’. Long-standing theory suggests that humic substances are comprised of large and complex macromolecules which are the most stable SOM. Recently, by direct high-resolution observations, people understand that only a small portion of total organic matter is represented by humic substances. Smaller and simpler molecular structures are observed, as shown in Fig.1. The formation of humic polymers is not necessary related with humus formation in soils. A comprehensive review of traditional approach and critique of ‘humification’ model is conducted in the paper<ref name="eleven">Johannels Lehmann, Markus Kleber. (2015). The contentious nature of soil organic matter. Nature, 528, 60–68.</ref>.<br />
<br />
=====<span style="color:black">Decomposition and Molecular Structure</span>=====<br />
:[[Image:SOM_models.png|center|thumb|350px|Historically view vs emerging understanding of SOM<ref name="fourteen">Anja Miltner et al, (2012) SOM genesis: microbial biomass as a significant source. Biogeochemistry,111,41–55.</ref>.]]<br />
::Historically SOM is thought to be made of stable and chemically unique compounds. The decomposition rate of plant residues largely depends on its biochemical composition, especially the C/N ratio and lignin content. Accordingly, people believe that the molecular structure of biomass and organic material controls the long-term decomposition rates in soil. Recent studies find that this is not true. Lignin and plant lipids (‘recalcitrants’) can turn over very rapidly<ref name="twelve">.Marschner, B. et al. (2008). How relevant is recalcitrance for the stabilization of organic matter in soils? J. Plant Nutr. Soil Sci. 171, 91–110.</ref><ref name="thirteen">Amelung, W., Brodowski, S., Sandhage-Hofmann, A. & Bol, R. (2008).Combining biomarker with stable isotope analysis for assessing the transformation and turnover of soil organic matter. Adv. Agron. 100, 155–250.</ref>. Moreover, sugar and other potential labile compounds have been shown to persist for decades---much longer than a couple weeks.<br />
<br />
====<span style="color:black">Role of Microbes in SOM Formation</span>==== <br />
:'''''“The role of microorganisms in SOM dynamics must be considered beyond the context of simple decomposition of fresh residues and extended to environment.” ---Jessica Chiartas, respectful TA of SSC111'''''<br />
<br />
::[[Image:Microbes_in_SOM_formation.png|center|thumb|350px|The roles of soil microbes in SOM formation.<ref name="fourteen">Anja Miltner et al, (2012) SOM genesis: microbial biomass as a significant source. Biogeochemistry,111,41–55.</ref>]]<br />
<br />
::Soil microorganisms serve not only as decomposers, but also as important components of SOM. Although plant residue contributes most of the carbon to soil, a large proportion actually ‘filters’ through microbial biomass before being transformed into SOM. It is now widely accepted that the contributions of microbial biomass to SOM formation seem to be much higher than the 1-5% estimation. A recent study shows that the living microbial biomass and necromass (the microbial residue after cell death) together account for 80% of the soil organic <ref name="fifteen">Liang C, Balser TC (2010) Microbial production of recalcitrant organic matter in global soils: implications for productivity and climate policy. Nat Rev Microbiol 9:75.</ref>. Bacteria and fungi comprise > 90% of the microbial biomass in soil<ref name="sixteen">Six J, Frey SD, Thiet RK, Batten KM (2006) Bacterial and fungal contributions to carbon sequestration in agroecosystems. Soil Sci Soc Am J 70:555–569.</ref>. Microbes also contribute to soil aggregate formation, and soil structure. For instance, fungi help build microaggregates by connecting soil particles with their hyphae and extracellular components<ref name="sixteen">Six J, Frey SD, Thiet RK, Batten KM (2006) Bacterial and fungal contributions to carbon sequestration in agroecosystems. Soil Sci Soc Am J 70:555–569.</ref>.<br />
<br />
::[[Image:SUE.png|center|250px|]]<br />
<br />
::The turnover of microbial biomass can be described by microbial substrate use efficiency (SUE). Factors that affect SUE include 1) substrate quality ( molecular weight, solubility, structural complexity, C:N ratio), and 2) the degradative efficacy of microbes<ref name="seventeen">Lekkerkerk LJA, Lundkvist H, Agren G, Ekbohm G, Bosatta E (1990) Decomposition of heterogeneous substrates: an experimental investigation of a hypothesis on substrate and microbial properties. Soil Biology & Biochemistry, 22, 161–167.</ref>(microbial community composition and structure, protection of organic compounds, other physiochemical environment). SUE is also a measure of the amount of ATP released through catabolism vs. the formation of biomolecules through anabolic activity, which is controlled by stoichiometric, chemical, and physiological factors[1]. Microbes and SUE, being the eye of the needle through which carbon moves in soil, are good indicators of SOM formation. However, SUE does not equate to SOM stabilization. Details will be discussed in next section. <br />
<br />
::Recently, the similar compositions between SOM spectra and microbial biomass are observed by the NMR approach<ref name="eighteen>Simpson AJ, Simpson MJ, Smith E, Kelleher BP (2007) Microbially derived inputs to soil organic matter: are current estimates too low? Environmental Science & Technology, 41, 8070–8076.</ref>. Technology to 1) track the fate of specific labelled organic compounds, and 2) directly observe microbes under high resolution scopes have extended our ability to understand soil microbial activity and diversity. Nevertheless, the quantitative linkages to ecosystem function remain uncertain<ref name="nineteen">Raes, J. & Bork, P. (2208) Molecular eco-systems biology: towards an understanding of community function. Nature Rev. Microbiol. 6, 693–699.</ref><ref name="twenty">Morales, S. E.&Holben,W. E.(2011). Linkingbacterial identitiesandecosystemprocesses:can ’omic’ analyses be more than the sumof their parts? FEMS Microbiol. Ecol. 75, 2–16.</ref>.<br />
<br />
====Carbon Stability and Turnover====<br />
:'''''“Rather than describing organic matter by decay rate, pool, stability or level of ‘recalcitrance’—as if these were properties of the compounds themselves—organic matter should be described by quantifiable environmental characteristics governing stabilization, such as solubility, molecular size and functionalization.” ---Michael W.I. Schmidt'''''<br />
<br />
::Historically, SOM has been grouped into active, intermediate, and passive pools based on stabilization mechanisms and turnover time<ref name="twenty-one">Sollins, P., Homann, P., Caldwell, B. A. (1996): Stabilisation and destabilisation of soil organic matter: mechanisms and controls.Geoderma 74, 65–105.</ref>. SOM stability is controlled by accessibility rather than recalcitrance<ref name="twenty-two">Jennifer A. J. Dungait, et al. (2012) Soil organic matter turnover is governed by accessibility not recalcitrance. Global Change Biology, 18, 1781-1796.</ref>. Stabilization is the protection of OM from mineralization. Stabilization refers to processes and mechanisms that can prolong C turnover times in soil. Detailed SOM stabilization mechanisms based on this knowledge have been well developed and summarized<ref name="twenty-three">Margit von Lützow et al. (2008) Stabilization mechanisms of organic matter in four temperate soils:Development and application of a conceptual model. J. Plant Nutr. Soil Sci, 171, 111–124.</ref>. However, a few mechanisms have been challenged in recent years<ref name="ten">Schmidt MWI, Torn MS, Abiven S et al. (2011) Persistence of soil organic matter as an ecosystem property. Nature, 478, 49–56.</ref><ref name="eleven">Johannels Lehmann, Markus Kleber. (2015). The contentious nature of soil organic matter. Nature, 528, 60–68.</ref>.<br />
<br />
::Managements of the size and the turnover rate of soil C pools can mitigate global climate change. Carbon pools with a fast turnover rate (<1 year) are important for short term nutrients availability in soil. SOM pools with slower turnover rate (decades, or even centuries) are important for soil structure and are believed to be more sensitive to climate change<ref name="twenty-four">Davidson, E. A. & Janssens, I. A. (2006).Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature 440, 165–173.</ref><ref name="twenty-five">Conant, R. T. et al. (2008).Sensitivity of organic matter decomposition to warming varies with its quality. Glob. Change Biol. 14, 868–877.</ref>.<br />
<br />
::After moving through the ‘microbial filter’<ref name="twenty-six">Wickland KP, Neff JC, Aiken GR (2007) Dissolved organic carbon in Alaskan boreal forest: sources, chemical characteristics and biodegradability. Ecosystems, 10,1323–1340, doi: 10.1007/s10021-007-9101-4</ref>, the fate of SOM is heavily dependent on environmental conditions and soil properties (pH, soil texture, and mineralogy).Generally speaking, SOM stabilization is controlled by interactions of SOM with the mineral soil matrix through 1) phyllosilicates; 2) polyvalent cations (e.g., Ca2+); 3) Fe-, Al-, Mn-oxides; 4) spatial occurrence/accessibility<ref name="three">M. Francesca Cotrufo et al. (2013) The Microbial Efficiency-Matrix Stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization: do labile plant inputs form stable soil organic matter? Global Change Biology,19, 988–995.</ref><br />
<br />
====<span style="color:black">Recent SOM formation models</span>====<br />
<br />
::Three fairly modern conceptual models of SOM formation are selected and presented in this section. No single model is perfect. Advanced technology and previous knowledge are always “the shoulders of giant[s]” we stand on to help us see further. Thus, models in this section should not be evaluated by comparing them with each other; rather, they should be viewed collectively to help us to explore the world of soil carbon, where many things remain uncertain. <br />
=====<span style="color:black">SOM as Ecosystem Property</span>=====<br />
::[[Image:SOM_formation_models.png|center|thumb|500px|A combination of recent insights, contrasting historical and emerging views of carbon cycling in soil<ref name= "ten">Schmidt MWI, Torn MS, Abiven S et al. (2011) Persistence of soil organic matter as an ecosystem property. Nature, 478, 49–56.</ref>,pg52.]]<br />
<br />
::From a respectful article<ref name="ten">Schmidt MWI, Torn MS, Abiven S et al. (2011) Persistence of soil organic matter as an ecosystem property. Nature, 478, 49–56.</ref>, this model suggests that carbon stability should be viewed as an ecosystem property. The influence of compound chemistry largely depends on environmental factors such as reactive soil mineral matrix, water solubility, soil redox state, pH, and climate. Physical disconnection refers to the spatial inaccessibility between microbial decomposers and substrate, which causes SOM sequestration in aggregates and physical protection from decomposition. Sorption/desorption refers to the organo-mineral associations, mainly controlled by the amount and quality of silt and clay. The Fe-, Al-, and Mn-oxides act as clay coatings, interacting with, and physically protecting organic matter. Thawing is expected to become more widespread due to climate change. It refers to the mineralization of previously stable SOM. Freezing, on the other hand, refers to the stabilization process owing to low temperatures. Microbial activity and products (necromass) affect the fate of SOM along the whole carbon cycle in soil.<br />
<br />
=====<span style="color:black">Soil Continuum Model (SCM)</span>=====<br />
::[[Image:SCM.png|center|thumb|500px|Fate of residues into a consolidated view of the SCM mode<ref name="eleven">Johannels Lehmann, Markus Kleber. (2015). The contentious nature of soil organic matter. Nature, 528, 60–68.</ref>,pg 63.]]<br />
::SCM is an evidence-based approach that focuses on the ability of decomposer organisms to access SOM and the protection of organic matter from decomposition. In the SCM model, the molecular size of residues become smaller through the biotic transformation (microbial decomposer community), and the oxidation state of SOM increases. Consequently, the water solubility increases. At the same time, larger mineral surfaces and aggregate incorporation protects SOM against further decomposition. The SCM model includes both abiotic and biotic processes as functions of temperature, moisture, and the biota present. SOM is viewed as “a continuum of progressively decomposing organic compounds”<ref name="eleven">Johannels Lehmann, Markus Kleber. (2015). The contentious nature of soil organic matter. Nature, 528, 60–68.</ref>.<br />
<br />
=====<span style="color:black">Biochemical and Physical Pathways---Nexus Between Plant Input and SOM Formation</span>=====<br />
:::[[Image:DOC_pathway.png|center|thumb|400px|Schematic representation of DOC and physical pathways<ref name="four">M. Francesca Cotrufo, et al. (2015) Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nature Geoscience 8, 776–779.</ref>.]]<br />
::Two major pathways of SOM formation are proposed. 1) Under the SOM-microbial pathway, SOM is formed by organo-mineral interactions<ref name="twenty-seven">Kleber, M., Sollins, P. & Sutton, R.(2007). A conceptual model of organo-mineral interactions in soils: Self-assembly of organic molecular fragments into zonal structures on mineral surfaces. Biogeochemistry 85, 924.</ref><ref name="four">M. Francesca Cotrufo, et al. (2015) Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nature Geoscience 8, 776–779.</ref>, and labile litter components (non-structural, celluloses, hemicelluloses) are decomposed during the early stages of decomposition. The SOM-microbial pathway has high SUE, and leads to new, net SOM formation. 2) Under the Physical transfer pathway, litter fragments are incorporated into a light fraction, and stabilized by chemical recalcitrance. With low DOC leaching, low SUE, and low SOM formation, the physical transfer pathway stabilizes carbon by promoting aggregation and spatial inaccessibility<ref name="four">M. Francesca Cotrufo, et al. (2015) Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nature Geoscience 8, 776–779.</ref>.<br />
<br />
====Roles of SOM====<br />
:Any change in soil carbon pools potentially impacts the atmospheric CO2 concentration and the global climate. However, the changing climate is not the only reason why SOM is important. More functions of SOM are listed here to emphasize the importance of SOM as an ecosystem property. <br />
<br />
::*'''Nutrient Cycling''': Soil organic matter contributes 20% to 80% of the cation exchange capacity (CEC), which increases the ability of mineral soil to retain nutrients. SOM itself is a pool of nutrients for plant and microbes. SOM also enhances chelation (organic compounds forming complexes with cations like iron) and thus increase the bioavailability of trace elements to plants and other soil microbes<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. <br />
<br />
::*'''Water Dynamics''': Improves water infiltration. SOM takes an important part in decreasing evaporation by enhancing the total water-holding capacity and strength of holding water in soil<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>.<br />
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::*'''Structure''': SOM contributes to improve soil structure and aggregation. Humic substances produced by fungi and polysaccharide produced by bacteria stabilize and improve aggregation. As aggregation improves, the infiltration rate increases, reducing runoff and soil erosion<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. SOM also helps to prevent compaction by decreasing bulk density and increasing percentage pore space.<br />
<br />
::*'''Other Effects of SOM''': Pesticides break down more quickly and can be "tied-up" by organic matter. Dark, bare soil may warm more quickly than light-colored soils, but heavy residue may slow warming and drying in spring. Plant residues and other organic material may support some diseases and pests, as well as predators and other beneficial organisms.<br />
<br />
====Factors Affecting SOM====<br />
:Instead of calling mechanisms, and integrating into models, different factors are discussed separately in this section to summarize SOM dynamics from another perspective. Some factors are thought to be dominant but being challenged by recent insights. <br />
:A huge variety of factors can affect SOM. Countless organisms and chemical interactions affect its production and use. Understanding the many factors that contribute to the production, and state of SOM will give insight into everything from carbon sequestration and improving agricultural practices to the lives of microbial organisms.<br />
::*'''Quantity of Carbon''': Carbon inputs are essential to soil as microbes are constantly respiring and releasing carbon from the soil. Low carbon inputs means there is less for microbes to metabolize and less carbon to be converted into organic matter there is more carbon available to be converted. <br />
::*'''Quality of Carbon''': (Old view) Easier to break down carbon sources will be fully converted to SOM faster. Though more complicate forms of carbon often produce a greater yield over time, and persist for longer.<br />
::*'''Temperature''': Colder weather in general means more soil organic matter. The cold slows microbial respiration so less carbon is metabolized.<br />
::*'''Moisture''': Higher moisture leads to the same result. More water filled pores and less oxygen availability reduces microbial respiration and means less carbon released as carbon dioxide.<br />
::*'''Texture''': High clay content means there is more surface area for carbon compounds to be attached to and more space for organomineral interaction. Furthermore, soil which is well aggregated can contain aggregates full of organic matter that are harder to reach for microbes to consume.<br />
::*'''Microbial Community''': As shown in a lot of factors above, high microbial activity can lead to carbon being lost as a product of respiration. However, microbes are necessary as degraders of complex organic material, facilitating carbon mineralization, and are a large portion of organic matter itself as dead microbial biomass. Microbes have a specific C/N/P ratio and the more carbon there is the more carbon microbes will release as carbon dioxide. As a result, more proper carbon ratios more efficiently convert carbon into SOM.<br />
::*'''Disturbance''': Soil disturbance such as tilling or erosion exposes protected pocket of organic matter and introduces oxygen reducing organic matter.<br />
::*'''Fire''': Black carbon, carbon that has been burned and turned into charcoal, is integrated into soils by wildfires or human burning. This black carbon is being increasingly recognized as an important factor in SOM formation and retention. The charcoal particles have high surface area and surface charges. These factors give black carbon soils higher cation exchange capacities<ref name="twenty-eight">B. Liang, J. Lehmann, D. Solomon, J. Kinyangi, J. Grossman, B. O’Neill, J. O. Skjemstad, J. Thies, F. J. Luizao, J. Petersen, and E. G. Neves. (2006). Black carbon increases cation exchange capacity in soils. Soil Science Society of America, 70, 1719-1730.</ref>. A high charge means black carbon is very easily incorporated into SOM through mineralization.<br />
<br />
=='''Soil Organic Carbon in Agricultural System'''==<br />
Successful farming requires good, healthy soil. Good agricultural soil means lots of soil carbon and organic matter. The very nature of farming, growing and removing plants from soil again and again, removes a certain amount of carbon and other resources from the soil. However, a lot of the conventional practices around farming serve to damage soil and alter the carbon cycle far more than necessary. Many modern sustainable farming methods have been shown to greatly increase soil health. There are two different ways of approaching the problem, decreasing the amount of carbon lost and increasing the amount of carbon input.<br />
<br />
===Reducing Carbon Losses=== <br />
:[[Image:Stratification_ratio_of_SOM_over_time.png|right|thumb|400px|Change in stratification ratio of soil organic carbon with time under different tillage systems in Spain<ref name="thirty">Franzluebbers, A. J. (2013). Pursuing robust agroecosystem functioning through effective soil organic carbon management. Carbon Management, 4(1), 43–56.</ref>.]] <br />
:Carbon being lost from an agricultural system because crop harvesting is unavoidable. Crops differ in the amount of residue they return to soil. Corn has high biomass remaining after harvest associated with the husks and stalks of the plant: this is either removed for other uses or returned to the soil.<br />
Tillage: Tillage is the practice of mixing and aerating soil by breaking it apart and turning it. Tilling practices increase oxygen availability to microbes and exposes aggregate bound organic matter to microbes. As a result, high tillage gives microbes access to previously soil bound carbon which is released as carbon dioxide into the atmosphere. Tilling also damages soil structure, increasing erosion and removing yet more valuable organic carbon from fields. The increased attention on sustainable farming practices over the past decades has led to an increase in “no till” farming. In no till and reduced till systems levels of soil organic carbon, microbial biomass, and mineralizable nitrogen are significantly higher in the surface layer, but not necessarily deeper layers, of the soil. In fact, gains in SOC were 250 kg/ha/yr higher in minimal till than in conventional systems<ref name="thirty-one">X. Liu1, S.J. Herbert, A.M. Hashemi, X. Zhang, G. Ding. (2006) Effects of agricultural management on soil organic matter and carbon transformation – a review. Plant Soil Environment, 52(12), 531-543.</ref>. Soil structure also improves greatly under no till farming. A reduction in tilling from conventional to no or minimal till increases macro aggregation by 21% - 42%<ref name="thirty-one">X. Liu1, S.J. Herbert, A.M. Hashemi, X. Zhang, G. Ding. (2006) Effects of agricultural management on soil organic matter and carbon transformation – a review. Plant Soil Environment, 52(12), 531-543.</ref>. The chart below shows the difference in the stratification ratio, a measure of organic matter at the surface of the soil over organic matter a bit deeper. No till systems have far more surface organic matter which helps fend off erosion and better facilitates seedling growth and root growth<ref name="thirty">Franzluebbers, A. J. (2013). Pursuing robust agroecosystem functioning through effective soil organic carbon management. Carbon Management, 4(1), 43–56.</ref>.<br />
<br />
===Increasing Carbon Inputs===<br />
:Practices for increasing carbon inputs have been used in traditional farming for a long time. Native americans often farmed polycultures, and crop rotations have been in use for hundreds of years. However, in modern conventional farming, where convenience of harvesting has outstripped the benefits of these techniques, there are very few carbon inputs to agricultural systems. While harder to implement in large scale farming these techniques are very important in practicing a sustainable model of agriculture.<br />
::*'''Monocultures, Crop Rotations, Polycultures, and Cover Crops''': Monocultures, the system of growing a single crop continuously in the same soil, are common because of the simplicity of dealing with a single crop. However monoculture systems lead to lowered carbon, nitrogen, microbial biomass and diversity, and soil enzyme levels. One alternative to a monoculture is a crop rotation. Crop rotations are when alternating crops are grown in the soil. The benefits of crop rotation depend on what crops are rotated. Crop rotations shown to be especially beneficial to SOC levels include legumes and sweet clover. Both of these are often used as cover crops. Cover crops are, instead of being harvested, either tilled into, or laid on top of the soil. Cover cropping provides an annual boon of plant residue to the soil, massively increasing carbon in soil. Another system, less commonly used is that of a polyculture. A polyculture is a system in which multiple crops are grown at the same time. The diversity of crops allows for more diverse microbial communities and a greater variety of plant residue in the soil.<br />
::*'''Carbon Sequestration''': The techniques that increase the amount of carbon in soil, no till with high carbon inputs, not only improve soil longevity in farming but also cause carbon sequestration. Carbon sequestration is the process by which carbon is taken from the atmosphere and stored long term, in this case as soil organic carbon. Switching from a conventional to a no till, organic system can sequester 22 gC/m2/yr<ref name="thirty-one">X. Liu1, S.J. Herbert, A.M. Hashemi, X. Zhang, G. Ding. (2006) Effects of agricultural management on soil organic matter and carbon transformation – a review. Plant Soil Environment, 52(12), 531-543.</ref>. There are movements all over the world to implement conservation farming methods. The sequestration of carbon in soil would not only increase the sustainability of farms, but also help reduce the carbon in the atmosphere, combating the buildup of greenhouse gases in the atmosphere.<br />
::*'''Recent Research''': Recent research into conserving soil organic matter in agricultural systems suggests that minimizing tillage and introducing plant residues isn’t what ultimately conserves more organic matter. Microbial biomass is what ultimately creates organic matter. Results drawn by Kallenbach, Grandy, Frey, and Diefendorf <ref name="thirty-two">C.M. Kallenbach , A.S. Grandy , S.D. Frey , A.F. Diefendorf. (2015). Microbial physiology and necromass regulate agricultural soil carbon. Soil Biology and Biochemistry, 91, 279-290.</ref> indicate that microbial growth rates and carbon use efficiency are associated with more conversion of carbon into microbial biomass and mineralized soil organic carbon. Enhancing the transformation of plant carbon to microbial biomass is a developing, exciting area of research that could lead to more effective agricultural management. Microbes, by breaking down organic molecules and facilitating the mineralization of carbon, are essential in storing carbon in soil for carbon sequestration.<br />
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==='''Case Study'''=== <br />
====<span style="color:black">Permafrost Thaw</span>====<br />
::[[Image:permafrost.png|right|thumb|300px|Permafrost Thaw and Carbon Balance<ref name="twenty-nine">Schuur, Ted. (2013): 117. "Permafrost Thaw Predictions." Science Experience Your America. Department of Botany, University of Florida, 2009. Web.</ref>.]]<br />
:::Permafrost is a subsurface soil layer that remains frozen throughout the year. When the permafrost is thawed or unfrozen, it can either increase greenhouse gas emissions or sequester more carbon in the carbon cycle. According to “Permafrost Thaw and Carbon Balance”, more than 50% of global terrestrial C is already stored in permafrost regions as soil organic matter<ref name="twenty-nine">Schuur, Ted. (2013): 117. "Permafrost Thaw Predictions." Science Experience Your America. Department of Botany, University of Florida, 2009. Web.</ref>. <br />
:::Carbon is naturally photosynthesized/uptaken by plants into the soil ecosystem and respired in the form of CO2 back into atmosphere by plants, animals, and microbes (bacteria). A carbon sink occurs when the uptake of CO2 by plants is greater than the emission of CO2 into the atmosphere by the process of respiration. A carbon source occurs when the emission of CO2 into the atmosphere by respiring microbes and plants is greater than the uptake of CO2 by plants. As reported from “Permafrost Thaw and Carbon Balance”, when the climate gets warmer, permafrost thaw can change the ecosystem carbon balance to a sink or a source<ref name="twenty-nine">Schuur, Ted. (2013): 117. "Permafrost Thaw Predictions." Science Experience Your America. Department of Botany, University of Florida, 2009. Web.</ref>. <br />
:::As stated by United Nations Environment Program, “[Thawing] of the Arctic permafrost is a “wild card” that could dramatically worsen global warming by releasing massive amounts of greenhouse gases…”<ref name="twenty-nine">Schuur, Ted. (2013): 117. "Permafrost Thaw Predictions." Science Experience Your America. Department of Botany, University of Florida, 2009. Web.</ref>. How does it do that? Well, the reason global warming is associated with permafrost thaw is because when permafrost is thawed, it can stimulate great amounts of microbial decomposition of soil organic matter. This stimulation of decomposition will decrease the C content stored in soil by releasing more CO2 into the atmosphere. The CO2 that is released into atmosphere contributes to the cycle of greenhouse gases involved in climate change.<br />
:::In an experiment conducted by researchers from the University of Florida, C balance was intensively measured during the growing seasons in three separate conditions (minimally thawed permafrost, moderately thawed permafrost, and extensively thawed permafrost). In the corresponding graph, the results of the study recorded accounted for both the growing and non-growing seasons. Researchers found that during non-growing seasons and minimal permafrost conditions, plants do not uptake C from the atmosphere but rather microorganisms release CO2 into the atmosphere indicated by the white bar in the graph. In moderately permafrost thawed, C uptake exceeded C emission because of stimulation in decomposition which signified a carbon sink occurrence. Lastly, extensive permafrost thaw observed a C emission that exceeded C uptake which signified a carbon source occurrence which released large amounts of greenhouse gases to the atmosphere. Based on the measurements, Schuur concluded that “the net release of C to the atmosphere in landscapes where there is advanced permafrost thaw adds to the existing problem of increasing greenhouse gases in the atmosphere. This C release from permafrost thaw may create a dramatic feedback that accelerates climate change”<ref name="twenty-nine">Schuur, Ted. (2013): 117. "Permafrost Thaw Predictions." Science Experience Your America. Department of Botany, University of Florida, 2009. Web.</ref>. <br />
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====Drainage of Wetlands====<br />
:::Drainage of wetlands could either increase or decrease methane production but will most certainly lose massive amounts of organic carbon sequestered in the soil from the carbon cycle. According to “The Role of Wetlands in the Carbon Cycle”, wetlands operate “six to nine percent of the Earth’s surface and contain about 35 percent of global terrestrial carbon”[30]. Wetlands are capable of high productivity meaning that they have a high capacity to sequester and store carbon. Wetlands sequester and store carbon into biomass and organic matter by photosynthesizing CO2 from the atmosphere. Like permafrost thaw, seasons can affect wetlands by turning it into either a carbon sink or carbon source. <br />
:::As reported by the Department of Sustainability, Environment, Water, Population and Communities, wetlands are subjected to seasonal “waterlogging” conditions that induce anaerobic conditions<ref name="thirty-three">Foster, .John, Lisa Evans, Alison Curtin, and Brydie Hill. (2012) The Role of Wetlands in the Carbon Cycle. Issues Paper The Role of Wetlands in the Carbon Cycle. pag. Department of Environment. Australian Government, 2012. Web.</ref>. When the wetlands are subjected to inundated/anaerobic conditions, the emission of greenhouse gases (N2O and CH4) and carbon or methane sinks are created. It is because wetlands naturally store significant amounts of carbon, that during drainage conditions, wetlands emit a significant amount of greenhouse gases. However, it is also noted that these drainage of channels also contribute to emission of methane to atmosphere. These “so-called” channels are hydrological connections that exist between watercourses and designated pathways to saturate wetlands with carbon and nutrients. During aerobic conditions, soil levels are oxygenated and methane production is decreased.<br />
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====Climate Change on Wetland Carbon Cycles====<br />
::As predicted by the Department of Sustainability, Environment, Water, Population and Communities, climate can play a part in the methane emission and carbon storage in wetland soils. Natural disturbances such as drainage of wetland soils will oxidize/aerate soils which decreases methane production which lead to large net losses of sediment organic carbon. In addition, depending on the climate change, wetland carbon cycle can altered in the following number of ways:<br />
<br />
::*Warmer climates will accelerate the rate of CO2 and methane production from wetland soils<br />
::*Wetter climates will increase wetland surface areas and promote carbon sequestration and increased primary production, but may increase methane emissions.<br />
::*Drier climates will increase the oxidation of carbon stores but reduce methane emissions.<br />
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====Policies and Programs====<br />
::[[Image:Wetland_Carbon_Cycle.png|right|thumb|400px|Wetland Carbon Cycle<ref name="thirty-three">Foster, .John, Lisa Evans, Alison Curtin, and Brydie Hill. (2012) The Role of Wetlands in the Carbon Cycle. Issues Paper The Role of Wetlands in the Carbon Cycle. pag. Department of Environment. Australian Government, 2012. Web.</ref>.]] <br />
::A number of policies and outreach programs have been place to provide a positive feedback towards degradation of wetlands and emission of greenhouse gases by offsetting carbon sequestration and sources.. One of such policy called the Carbon Farming Initiative is currently carried out by the Department of Climate Change and Energy Efficiency. The policy is to implement change within the farmers’ lands. By storing excess greenhouse gas emission from wetlands into their lands, the farmers are able to earn carbon credits. Other organizations such as Regional Natural Resource Management Planning for Climate Change Fund and Biodiversity Fund are implementing policies to maintain healthy levels of greenhouse gas emission in wetlands.<br />
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==References==<br />
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Recently edited by students of [mailto:kmscow@ucdavis.edu Kate Scow], Winter 2016.<br />
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<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Carbon_cycle&diff=132939
Carbon cycle
2018-04-05T04:05:18Z
<p>Kmscow: /* Reducing Carbon Losses */</p>
<hr />
<div>=='''Introduction'''==<br />
::Globally, carbon cycles among the oceans, atmosphere, terrestrial biosphere, ecosystem, and geosphere. This wiki page focuses on carbon dynamics in soil. Soil organic matter (SOM) is the largest terrestrial carbon pool and contains more than three times as much carbon as either the atmospheric or living plant pools<ref name="one">Fischlin, A. et al.(2007). Climate Change 2007: Impacts, Adaptation and Vulnerability. Cambridge Univ. Press, 211–272.</ref>. In section 2, the first part of the wiki, we describe how organic residues are broken down in soil, focusing on the role of microbes as decomposers. By emphasizing the role of microbes, we hope to build a better nexus of information between organic input decay and SOM formation. So, in the next section we discuss the importance, formation, and recent research of SOM. Topics covered in sections 2 and 3 are integrated into three SOM formation models in section 3.5. There have been a lot of recent discoveries and many newly developed models surrounding SOM. As such, the predominant views may well be subject to change. After decomposition and SOM, we move toward focusing on real world applications and impacts of the carbon cycle in soil. <br />
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::The carbon cycle has a huge role in maintaining global climate and ecosystems. SOM, being the primary pool of carbon, is of crucial importance in climate change, as demonstrated in section 3. For thousands of years, humans have interacted with soil and the carbon cycle through agriculture. However, only now are we starting to properly understand the impact agricultural practices have on soil. Driven by the strong impetus to better understand carbon dynamics in agroecosystems, we discuss carbon management strategies in agricultural systems in section 4. Permafrost thaw and drainage of wetlands are presented in section 5, as two “case studies” of soil carbon cycle. <br />
<br />
::The carbon cycle, like most natural cycles and models, is not a system closed from outside influences. There are many interlocking elements throughout cycles of nutrients, carbon, and nitrogen in soils. The nitrogen cycle is especially closely linked to the carbon cycle in microbiology because of the importance of C/N ratios. A thorough understanding of the [[Nitrogen Cycle]] will greatly improve our understanding of the carbon cycle in turn.<br />
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=='''Decomposition of Organic Residues'''==<br />
::The formation of SOM and the decomposition of residue are intimately associated. Decomposition of organic residue is one of the major functions of microorganisms in the soil. The soil microorganisms utilize the residue components for energy and carbon source to synthesize the new cells. The organic materials added to soil are primarily plant residues from either cultivated crops or native vegetation, which are the source of energy stored in the carbon compounds. The crop agricultural ecosystems primarily include the combination of leaf, stem, and root tissues remaining after harvest. On the other hand, the residues that undergo decomposition in the natural ecosystems are derived from native prairie and forest vegetation. There are two types of plant residue that assimilate into the soil<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. One is above ground residue, which is derived from falling debris and other plant that are above the soil surface. The second type is deposited from root systems that complete their life cycle throughout the course of a particular season. These residue with the root exudates supply the substrate carbon input into the soil. The decay process of above-ground residue begin and initiate due to different agricultural management systems and practices<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. A portion of these substrate goes into microbial mass as it is used by the soil microorganisms for reproduction and metabolic activity and a larger part of it is lost as carbon dioxide due to the energy yielding metabolic processes of the microbial community. Recent studies<ref name="three">M. Francesca Cotrufo et al. (2013) The Microbial Efficiency-Matrix Stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization: do labile plant inputs form stable soil organic matter? Global Change Biology,19, 988–995.</ref><ref name="four">M. Francesca Cotrufo, et al. (2015) Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nature Geoscience 8, 776–779.</ref> emphasize that not all the litter Carbon loss are mineralized to carbon dioxide, but a part of these Carbon loss is transferred to mineral soil, where it contributes to the formation of soil organic matter through the two main pathways, dissolved organic matter-microbial path and physical transfer path.<br />
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====Chemical Constituents====<br />
::The composition of the crop residues added to and decaying in soil are varied. Plant residues are comprised of many complex polymers such as lignin and cellulose and contains water-soluble organic compounds such as proteins, carbohydrates, and organic acidsl.<br />
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=====<span style="color:black">Carbohydrates</span>=====<br />
::From 5-25% of soil organic matter is combined in the form of carbohydrates, which include simple sugars, cellulose, and hemicellulose <ref name="five">Baldock J (2007).Composition and cycling of organic C in soil. In: Nutrient Cycling in Terrestrial Ecosystems.Springer,pp. 1–35.</ref>. These carbohydrates are rapidly degraded by varied microorganisms in the soil including bacteria, archaea, actinomycetes, and fungi. During degradation soil microorganisms synthesize extracellular polysaccharides. These polysaccharides bind soil into water stable aggregates so that the aggregates are more permeable to water and air. Polysaccharides also affect the cation exchange capacity of soil and act as an energy source for other microorganisms<ref name="five">Baldock J (2007).Composition and cycling of organic C in soil. In: Nutrient Cycling in Terrestrial Ecosystems.Springer,pp. 1–35.</ref>. <br />
::Heterotrophic microbes can easily metabolize simple sugars. Plants link glucose molecules (and other sugar monomers) into long chains to produce polymers such as cellulose, which requires more specialized organisms to degrade.<br />
::For example: Starch is made of amylose (alpha 1,4 bonded glucose) and amylopectin (alpha 1,6 bonded glucose), and is relatively easy for most organisms to degrade. Cellulose, however, is a polysaccharide of glucose connected with beta 1,4 bonds, and is more difficult to degrade. No animal can degrade cellulose, so bacteria can frequently be found in mutualistic relationships with detritivores: the bacteria degrade the cellulose enough that the animal is able to digest it. <br />
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======<span style="color:black">Cellulose</span>======<br />
::[[Image:CelluloseDecomp_edited.jpg|center|thumb|200px|The Decomposition of Cellulose <ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>,]]<br />
<br />
::Cellulose is the most abundant carbon input in soil. It’s a structural polysaccharide that is made of 1400 to 10000 glucose units. In order to access the glucose monomer, the cellulose must be cleaved by extracellular enzymes. These pieces are then transported into the cell for energy generation (catabolism) or production of biomass (anabolism). Cellulose is used by a diverse group of soil organisms including fungi such as Penicillium and [[Aspergillus]] and bacteria such as [[Streptomyces]] and [[Pseudomonas]]. Fungi and bacteria are important participants in the extracellular cleavage of cellulose<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>.<br />
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======<span style="color:black">Hemicellulose</span>======<br />
::[[Image:HemicelluloseDecomp edited.jpg|center|thumb|200px|The Decomposition of Pectin (a Hemicellulose)<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>,]] <br />
::Hemicellulose is the next most common carbohydrate in plants. It is a branched polymer with varied sugar monomers (glucose, mannose, and galactose) and bonds. The decomposition of hemicellulose is similar to that of cellulose in that the initial depolymerization step takes place outside of the cell, and the sugars produced are then transported into the cell for catabolism or anabolism. Even though hemicellulose decomposition is much quicker than cellulose decomposition, cells will utilize simple sugars as substrates before hemicellulose<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>.<br />
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======<span style="color:black">Chitin</span>======<br />
:::[[Image:ChitinDecomposition_edited.jpg|center|thumb|200px|The Decomposition of Chitin and Chitosan Under Aerobic Soil Conditions<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>]]<br />
:::Chitin is a special compound which can be found in the integument of arthropods and the cell walls of fungi. Chitin is one of the cell-wall component of many common soil fungi (e.g., [[Aspergillus]] and [[Penicillium]]) as around 3% to 25% of these soil fungal biomass are chitin<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. Chitin is usually protected from degradation by the protein-chitin complex in its natural normal stage in soil. Due to this type of protection, chitin is an important component in soil organic matter formation. The polymer is not easily degraded and requires a variety of enzymes to do so. The dominant chitin degraders are the Actinomycetes, [[Streptomyces]] and Nocardia. Less important than Actinomycetes, fungi such as Trichoderma and [[Verticillium]] and bacteria, such as [[Bacillus]] and [[Pseudomonas]] can also degrade chitin<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>.<br />
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=====<span style="color:black">Lignin</span>=====<br />
:::[[Image:LigninDecomp2_edited.jpg|center|thumb|200px|One Possible Pathway of Lignin Decomposition<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>]]<br />
::Lignin is the main component of wood in trees. Lignin has a varied, unique, and complicated chemical structure which contains many aromatics. Aromatics are part of the reason why lignin is more difficult to be decomposed. Even with strong acid treatment, the plant residues are not solubilized due to the complex ring structure.These aromatics can be released from the lignin structure by fungal enzymes such as peroxidases and oxidases. The enzymes utilize H2O2 and OH radicals to break the bonds in the lignin. Lignin is decomposed through groups of specialized fungi. Common types of fungi which depolymerize lignin are white rot ("[[Phanerochaete chrysosporium]]"), brown rot, and soft rot<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. Once the aromatics are released from the original lignin structure they are incorporated into the metabolic pathway as pyruvate, acetyl CoA, and into the TCA cycle.<br />
<br />
=====<span style="color:black">Proteins</span>=====<br />
::Proteins are one of the most important components of plant residue added to soil. Protein is a polymers of amino acids linked by peptide bonds. A variety of microorganisms in soil can produce proteolytic enzymes such as protease and peptidase, which can break the peptide bond of the protein and hydrolyze it into individual amino acids. These amino acid monomers can then be utilized by microbes for either catabolism or for the synthesis of new essential proteins<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>.<br />
<br />
=====<span style="color:black">Fats & Waxes</span>=====<br />
::More than 2% of soil organic matter is cultivated in the forms, fats and waxes. Unlike cellulose and sugar, fats and waxes are much harder for microorganisms to breakdown. They are decomposed very slowly into CO2, water and energy which can be used by microorganisms<ref name="six">Osman, Khan Towhid. (2013). Soils’: Principle, Properties, and Management. Springer Dordrecht Heidelberg New York London, 93-95.</ref> Very little investigation has been done so information regarding this is limited.<br />
<br />
=='''Soil Organic Matter'''==<br />
====SOM and Climate Change====<br />
::The carbon cycle in soil is a dynamic balance between photosynthesis, the respiration of decomposing organisms, and the stabilization of carbon. Soil stores at least three times as much carbon (in SOM) as is found in either the atmosphere or in living plants<ref name="one">Fischlin, A. et al.(2007). Climate Change 2007: Impacts, Adaptation and Vulnerability. Cambridge Univ. Press, 211–272.</ref>. The total global carbon stock in soil is about 2500 Pg C, including approximately 1550 Pg in organic carbon, and 950 in inorganic carbon. Soils act as a buffer against the increase of atmospheric CO2. There is growing interest that it is possible to remove a significant amount of CO2 from the atmosphere by sequestering carbon in soil. It is estimated that 16-30% atmospheric CO2 can be removed when SOM concentrations increase 5-15% in soil up to 2m depth<ref name="seven">Baldock J (2007).Composition and cycling of organic C in soil. In: Nutrient Cycling in Terrestrial Ecosystems.Springer,pp. 1–35.</ref><ref name="eight">Kell DB (2011).Breeding crop plants with deep roots: their role in sustainable carbon nutrient and water sequestration. Annals of Botany, 108, 407–418.</ref>. It is also believed that soil respiration rates could cause a positive feedback in global warming. There are more nutrient based, plant-oriented interests in SOM, however, it seems that concerns about the changing climate “have now overtaken these other justifications”<ref name="nine">Sollins, P., Swanston, C. & Kramer, M. (2007).Stabilization and destabilization of soil organic matter—a new focus. Biogeochemistry 85, 1–7.</ref>.<br />
<br />
====New Insights on SOM====<br />
::For a long time, the scientific community described SOM in terms of humic substances. With the help of advanced analytical techniques, a growing body of research indicates that the importance of the biotic and abiotic environments in soil outweighs that of the molecular structure of plant inputs and organic matter in the process of OM stabilization. Factors such as rate of decay, SOM pools, stability, or ‘recalcitrance’ are not sufficient to describe the “ecosystem property”<ref name="ten">Schmidt MWI, Torn MS, Abiven S et al. (2011) Persistence of soil organic matter as an ecosystem property. Nature, 478, 49–56.</ref> of SOM; rather, texture, mineralogy, water solubility, molecular size, functionalization, and perhaps most important, climate change conditions should be incorporated into our understanding (and modeling) of carbon.<br />
<br />
=====<span style="color:black">History of Humic Substances</span>=====<br />
::Historically soil chemists use alkali and acid extraction methods and observations of the extracted (or residual) functional group chemistry to describe the soil organic matter, or humus<ref name="ten">Schmidt MWI, Torn MS, Abiven S et al. (2011) Persistence of soil organic matter as an ecosystem property. Nature, 478, 49–56.</ref>. When protons are added to the solubilized organic materials, the dark color solid that precipitates is called ‘humic acid’. ‘Fulvic acid’ is the organic matter that remains soluble after reacidification treatment. The organic matter that does not respond to the extraction treatment is called ‘humin’. Long-standing theory suggests that humic substances are comprised of large and complex macromolecules which are the most stable SOM. Recently, by direct high-resolution observations, people understand that only a small portion of total organic matter is represented by humic substances. Smaller and simpler molecular structures are observed, as shown in Fig.1. The formation of humic polymers is not necessary related with humus formation in soils. A comprehensive review of traditional approach and critique of ‘humification’ model is conducted in the paper<ref name="eleven">Johannels Lehmann, Markus Kleber. (2015). The contentious nature of soil organic matter. Nature, 528, 60–68.</ref>.<br />
<br />
=====<span style="color:black">Decomposition and Molecular Structure</span>=====<br />
:[[Image:SOM_models.png|center|thumb|350px|Historically view vs emerging understanding of SOM<ref name="fourteen">Anja Miltner et al, (2012) SOM genesis: microbial biomass as a significant source. Biogeochemistry,111,41–55.</ref>.]]<br />
::Historically SOM is thought to be made of stable and chemically unique compounds. The decomposition rate of plant residues largely depends on its biochemical composition, especially the C/N ratio and lignin content. Accordingly, people believe that the molecular structure of biomass and organic material controls the long-term decomposition rates in soil. Recent studies find that this is not true. Lignin and plant lipids (‘recalcitrants’) can turn over very rapidly<ref name="twelve">.Marschner, B. et al. (2008). How relevant is recalcitrance for the stabilization of organic matter in soils? J. Plant Nutr. Soil Sci. 171, 91–110.</ref><ref name="thirteen">Amelung, W., Brodowski, S., Sandhage-Hofmann, A. & Bol, R. (2008).Combining biomarker with stable isotope analysis for assessing the transformation and turnover of soil organic matter. Adv. Agron. 100, 155–250.</ref>. Moreover, sugar and other potential labile compounds have been shown to persist for decades---much longer than a couple weeks.<br />
<br />
====<span style="color:black">Role of Microbes in SOM Formation</span>==== <br />
:'''''“The role of microorganisms in SOM dynamics must be considered beyond the context of simple decomposition of fresh residues and extended to environment.” ---Jessica Chiartas, respectful TA of SSC111'''''<br />
<br />
::[[Image:Microbes_in_SOM_formation.png|center|thumb|350px|The roles of soil microbes in SOM formation.<ref name="fourteen">Anja Miltner et al, (2012) SOM genesis: microbial biomass as a significant source. Biogeochemistry,111,41–55.</ref>]]<br />
<br />
::Soil microorganisms serve not only as decomposers, but also as important components of SOM. Although plant residue contributes most of the carbon to soil, a large proportion actually ‘filters’ through microbial biomass before being transformed into SOM. It is now widely accepted that the contributions of microbial biomass to SOM formation seem to be much higher than the 1-5% estimation. A recent study shows that the living microbial biomass and necromass (the microbial residue after cell death) together account for 80% of the soil organic <ref name="fifteen">Liang C, Balser TC (2010) Microbial production of recalcitrant organic matter in global soils: implications for productivity and climate policy. Nat Rev Microbiol 9:75.</ref>. Bacteria and fungi comprise > 90% of the microbial biomass in soil<ref name="sixteen">Six J, Frey SD, Thiet RK, Batten KM (2006) Bacterial and fungal contributions to carbon sequestration in agroecosystems. Soil Sci Soc Am J 70:555–569.</ref>. Microbes also contribute to soil aggregate formation, and soil structure. For instance, fungi help build microaggregates by connecting soil particles with their hyphae and extracellular components<ref name="sixteen">Six J, Frey SD, Thiet RK, Batten KM (2006) Bacterial and fungal contributions to carbon sequestration in agroecosystems. Soil Sci Soc Am J 70:555–569.</ref>.<br />
<br />
::[[Image:SUE.png|center|250px|]]<br />
<br />
::The turnover of microbial biomass can be described by microbial substrate use efficiency (SUE). Factors that affect SUE include 1) substrate quality ( molecular weight, solubility, structural complexity, C:N ratio), and 2) the degradative efficacy of microbes<ref name="seventeen">Lekkerkerk LJA, Lundkvist H, Agren G, Ekbohm G, Bosatta E (1990) Decomposition of heterogeneous substrates: an experimental investigation of a hypothesis on substrate and microbial properties. Soil Biology & Biochemistry, 22, 161–167.</ref>(microbial community composition and structure, protection of organic compounds, other physiochemical environment). SUE is also a measure of the amount of ATP released through catabolism vs. the formation of biomolecules through anabolic activity, which is controlled by stoichiometric, chemical, and physiological factors[1]. Microbes and SUE, being the eye of the needle through which carbon moves in soil, are good indicators of SOM formation. However, SUE does not equate to SOM stabilization. Details will be discussed in next section. <br />
<br />
::Recently, the similar compositions between SOM spectra and microbial biomass are observed by the NMR approach<ref name="eighteen>Simpson AJ, Simpson MJ, Smith E, Kelleher BP (2007) Microbially derived inputs to soil organic matter: are current estimates too low? Environmental Science & Technology, 41, 8070–8076.</ref>. Technology to 1) track the fate of specific labelled organic compounds, and 2) directly observe microbes under high resolution scopes have extended our ability to understand soil microbial activity and diversity. Nevertheless, the quantitative linkages to ecosystem function remain uncertain<ref name="nineteen">Raes, J. & Bork, P. (2208) Molecular eco-systems biology: towards an understanding of community function. Nature Rev. Microbiol. 6, 693–699.</ref><ref name="twenty">Morales, S. E.&Holben,W. E.(2011). Linkingbacterial identitiesandecosystemprocesses:can ’omic’ analyses be more than the sumof their parts? FEMS Microbiol. Ecol. 75, 2–16.</ref>.<br />
<br />
====Carbon Stability and Turnover====<br />
:'''''“Rather than describing organic matter by decay rate, pool, stability or level of ‘recalcitrance’—as if these were properties of the compounds themselves—organic matter should be described by quantifiable environmental characteristics governing stabilization, such as solubility, molecular size and functionalization.” ---Michael W.I. Schmidt'''''<br />
<br />
::Historically, SOM has been grouped into active, intermediate, and passive pools based on stabilization mechanisms and turnover time<ref name="twenty-one">Sollins, P., Homann, P., Caldwell, B. A. (1996): Stabilisation and destabilisation of soil organic matter: mechanisms and controls.Geoderma 74, 65–105.</ref>. SOM stability is controlled by accessibility rather than recalcitrance<ref name="twenty-two">Jennifer A. J. Dungait, et al. (2012) Soil organic matter turnover is governed by accessibility not recalcitrance. Global Change Biology, 18, 1781-1796.</ref>. Stabilization is the protection of OM from mineralization. Stabilization refers to processes and mechanisms that can prolong C turnover times in soil. Detailed SOM stabilization mechanisms based on this knowledge have been well developed and summarized<ref name="twenty-three">Margit von Lützow et al. (2008) Stabilization mechanisms of organic matter in four temperate soils:Development and application of a conceptual model. J. Plant Nutr. Soil Sci, 171, 111–124.</ref>. However, a few mechanisms have been challenged in recent years<ref name="ten">Schmidt MWI, Torn MS, Abiven S et al. (2011) Persistence of soil organic matter as an ecosystem property. Nature, 478, 49–56.</ref><ref name="eleven">Johannels Lehmann, Markus Kleber. (2015). The contentious nature of soil organic matter. Nature, 528, 60–68.</ref>.<br />
<br />
::Managements of the size and the turnover rate of soil C pools can mitigate global climate change. Carbon pools with a fast turnover rate (<1 year) are important for short term nutrients availability in soil. SOM pools with slower turnover rate (decades, or even centuries) are important for soil structure and are believed to be more sensitive to climate change<ref name="twenty-four">Davidson, E. A. & Janssens, I. A. (2006).Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature 440, 165–173.</ref><ref name="twenty-five">Conant, R. T. et al. (2008).Sensitivity of organic matter decomposition to warming varies with its quality. Glob. Change Biol. 14, 868–877.</ref>.<br />
<br />
::After moving through the ‘microbial filter’<ref name="twenty-six">Wickland KP, Neff JC, Aiken GR (2007) Dissolved organic carbon in Alaskan boreal forest: sources, chemical characteristics and biodegradability. Ecosystems, 10,1323–1340, doi: 10.1007/s10021-007-9101-4</ref>, the fate of SOM is heavily dependent on environmental conditions and soil properties (pH, soil texture, and mineralogy).Generally speaking, SOM stabilization is controlled by interactions of SOM with the mineral soil matrix through 1) phyllosilicates; 2) polyvalent cations (e.g., Ca2+); 3) Fe-, Al-, Mn-oxides; 4) spatial occurrence/accessibility<ref name="three">M. Francesca Cotrufo et al. (2013) The Microbial Efficiency-Matrix Stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization: do labile plant inputs form stable soil organic matter? Global Change Biology,19, 988–995.</ref><br />
<br />
====<span style="color:black">Recent SOM formation models</span>====<br />
<br />
::Three fairly modern conceptual models of SOM formation are selected and presented in this section. No single model is perfect. Advanced technology and previous knowledge are always “the shoulders of giant[s]” we stand on to help us see further. Thus, models in this section should not be evaluated by comparing them with each other; rather, they should be viewed collectively to help us to explore the world of soil carbon, where many things remain uncertain. <br />
=====<span style="color:black">SOM as Ecosystem Property</span>=====<br />
::[[Image:SOM_formation_models.png|center|thumb|500px|A combination of recent insights, contrasting historical and emerging views of carbon cycling in soil<ref name= "ten">Schmidt MWI, Torn MS, Abiven S et al. (2011) Persistence of soil organic matter as an ecosystem property. Nature, 478, 49–56.</ref>,pg52.]]<br />
<br />
::From a respectful article<ref name="ten">Schmidt MWI, Torn MS, Abiven S et al. (2011) Persistence of soil organic matter as an ecosystem property. Nature, 478, 49–56.</ref>, this model suggests that carbon stability should be viewed as an ecosystem property. The influence of compound chemistry largely depends on environmental factors such as reactive soil mineral matrix, water solubility, soil redox state, pH, and climate. Physical disconnection refers to the spatial inaccessibility between microbial decomposers and substrate, which causes SOM sequestration in aggregates and physical protection from decomposition. Sorption/desorption refers to the organo-mineral associations, mainly controlled by the amount and quality of silt and clay. The Fe-, Al-, and Mn-oxides act as clay coatings, interacting with, and physically protecting organic matter. Thawing is expected to become more widespread due to climate change. It refers to the mineralization of previously stable SOM. Freezing, on the other hand, refers to the stabilization process owing to low temperatures. Microbial activity and products (necromass) affect the fate of SOM along the whole carbon cycle in soil.<br />
<br />
=====<span style="color:black">Soil Continuum Model (SCM)</span>=====<br />
::[[Image:SCM.png|center|thumb|500px|Fate of residues into a consolidated view of the SCM mode<ref name="eleven">Johannels Lehmann, Markus Kleber. (2015). The contentious nature of soil organic matter. Nature, 528, 60–68.</ref>,pg 63.]]<br />
::SCM is an evidence-based approach that focuses on the ability of decomposer organisms to access SOM and the protection of organic matter from decomposition. In the SCM model, the molecular size of residues become smaller through the biotic transformation (microbial decomposer community), and the oxidation state of SOM increases. Consequently, the water solubility increases. At the same time, larger mineral surfaces and aggregate incorporation protects SOM against further decomposition. The SCM model includes both abiotic and biotic processes as functions of temperature, moisture, and the biota present. SOM is viewed as “a continuum of progressively decomposing organic compounds”<ref name="eleven">Johannels Lehmann, Markus Kleber. (2015). The contentious nature of soil organic matter. Nature, 528, 60–68.</ref>.<br />
<br />
=====<span style="color:black">Biochemical and Physical Pathways---Nexus Between Plant Input and SOM Formation</span>=====<br />
:::[[Image:DOC_pathway.png|center|thumb|400px|Schematic representation of DOC and physical pathways<ref name="four">M. Francesca Cotrufo, et al. (2015) Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nature Geoscience 8, 776–779.</ref>.]]<br />
::Two major pathways of SOM formation are proposed. 1) Under the SOM-microbial pathway, SOM is formed by organo-mineral interactions<ref name="twenty-seven">Kleber, M., Sollins, P. & Sutton, R.(2007). A conceptual model of organo-mineral interactions in soils: Self-assembly of organic molecular fragments into zonal structures on mineral surfaces. Biogeochemistry 85, 924.</ref><ref name="four">M. Francesca Cotrufo, et al. (2015) Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nature Geoscience 8, 776–779.</ref>, and labile litter components (non-structural, celluloses, hemicelluloses) are decomposed during the early stages of decomposition. The SOM-microbial pathway has high SUE, and leads to new, net SOM formation. 2) Under the Physical transfer pathway, litter fragments are incorporated into a light fraction, and stabilized by chemical recalcitrance. With low DOC leaching, low SUE, and low SOM formation, the physical transfer pathway stabilizes carbon by promoting aggregation and spatial inaccessibility<ref name="four">M. Francesca Cotrufo, et al. (2015) Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nature Geoscience 8, 776–779.</ref>.<br />
<br />
====Roles of SOM====<br />
:Any change in soil carbon pools potentially impacts the atmospheric CO2 concentration and the global climate. However, the changing climate is not the only reason why SOM is important. More functions of SOM are listed here to emphasize the importance of SOM as an ecosystem property. <br />
<br />
::*'''Nutrient Cycling''': Soil organic matter contributes 20% to 80% of the cation exchange capacity (CEC), which increases the ability of mineral soil to retain nutrients. SOM itself is a pool of nutrients for plant and microbes. SOM also enhances chelation (organic compounds forming complexes with cations like iron) and thus increase the bioavailability of trace elements to plants and other soil microbes<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. <br />
<br />
::*'''Water Dynamics''': Improves water infiltration. SOM takes an important part in decreasing evaporation by enhancing the total water-holding capacity and strength of holding water in soil<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>.<br />
<br />
::*'''Structure''': SOM contributes to improve soil structure and aggregation. Humic substances produced by fungi and polysaccharide produced by bacteria stabilize and improve aggregation. As aggregation improves, the infiltration rate increases, reducing runoff and soil erosion<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. SOM also helps to prevent compaction by decreasing bulk density and increasing percentage pore space.<br />
<br />
::*'''Other Effects of SOM''': Pesticides break down more quickly and can be "tied-up" by organic matter. Dark, bare soil may warm more quickly than light-colored soils, but heavy residue may slow warming and drying in spring. Plant residues and other organic material may support some diseases and pests, as well as predators and other beneficial organisms.<br />
<br />
====Factors Affecting SOM====<br />
:Instead of calling mechanisms, and integrating into models, different factors are discussed separately in this section to summarize SOM dynamics from another perspective. Some factors are thought to be dominant but being challenged by recent insights. <br />
:A huge variety of factors can affect SOM. Countless organisms and chemical interactions affect its production and use. Understanding the many factors that contribute to the production, and state of SOM will give insight into everything from carbon sequestration and improving agricultural practices to the lives of microbial organisms.<br />
::*'''Quantity of Carbon''': Carbon inputs are essential to soil as microbes are constantly respiring and releasing carbon from the soil. Low carbon inputs means there is less for microbes to metabolize and less carbon to be converted into organic matter there is more carbon available to be converted. <br />
::*'''Quality of Carbon''': (Old view) Easier to break down carbon sources will be fully converted to SOM faster. Though more complicate forms of carbon often produce a greater yield over time, and persist for longer.<br />
::*'''Temperature''': Colder weather in general means more soil organic matter. The cold slows microbial respiration so less carbon is metabolized.<br />
::*'''Moisture''': Higher moisture leads to the same result. More water filled pores and less oxygen availability reduces microbial respiration and means less carbon released as carbon dioxide.<br />
::*'''Texture''': High clay content means there is more surface area for carbon compounds to be attached to and more space for organomineral interaction. Furthermore, soil which is well aggregated can contain aggregates full of organic matter that are harder to reach for microbes to consume.<br />
::*'''Microbial Community''': As shown in a lot of factors above, high microbial activity can lead to carbon being lost as a product of respiration. However, microbes are necessary as degraders of complex organic material, facilitating carbon mineralization, and are a large portion of organic matter itself as dead microbial biomass. Microbes have a specific C/N/P ratio and the more carbon there is the more carbon microbes will release as carbon dioxide. As a result, more proper carbon ratios more efficiently convert carbon into SOM.<br />
::*'''Disturbance''': Soil disturbance such as tilling or erosion exposes protected pocket of organic matter and introduces oxygen reducing organic matter.<br />
::*'''Fire''': Black carbon, carbon that has been burned and turned into charcoal, is integrated into soils by wildfires or human burning. This black carbon is being increasingly recognized as an important factor in SOM formation and retention. The charcoal particles have high surface area and surface charges. These factors give black carbon soils higher cation exchange capacities<ref name="twenty-eight">B. Liang, J. Lehmann, D. Solomon, J. Kinyangi, J. Grossman, B. O’Neill, J. O. Skjemstad, J. Thies, F. J. Luizao, J. Petersen, and E. G. Neves. (2006). Black carbon increases cation exchange capacity in soils. Soil Science Society of America, 70, 1719-1730.</ref>. A high charge means black carbon is very easily incorporated into SOM through mineralization.<br />
<br />
=='''Soil Organic Carbon in Agricultural System'''==<br />
Successful farming requires good, healthy soil. Good agricultural soil means lots of soil carbon and organic matter. The very nature of farming, growing and removing plants from soil again and again, removes a certain amount of carbon and other resources from the soil. However, a lot of the conventional practices around farming serve to damage soil and alter the carbon cycle far more than necessary. Many modern sustainable farming methods have been shown to greatly increase soil health. There are two different ways of approaching the problem, decreasing the amount of carbon lost and increasing the amount of carbon input.<br />
<br />
===Reducing Carbon Losses=== <br />
:[[Image:Stratification_ratio_of_SOM_over_time.png|right|thumb|400px|Change in stratification ratio of soil organic carbon with time under different tillage systems in Spain<ref name="thirty">Franzluebbers, A. J. (2013). Pursuing robust agroecosystem functioning through effective soil organic carbon management. Carbon Management, 4(1), 43–56.</ref>.]] <br />
:Carbon being lost from an agricultural system because crop harvesting is unavoidable. Crops differ in the amount of residue they return to soil. Corn has high biomass remaining after harvest associated with the husks and stalks of the plant: this is either removed for other uses or returned to the the soil.<br />
Tillage: Tillage is the practice of mixing and aerating soil by breaking it apart and turning it. Tilling practices increase oxygen availability to microbes and exposes aggregate bound organic matter to microbes. As a result, high tillage gives microbes access to previously soil bound carbon which is released as carbon dioxide into the atmosphere. Tilling also damages soil structure, increasing erosion and removing yet more valuable organic carbon from fields. The increased attention on sustainable farming practices over the past decades has led to an increase in “no till” farming. In no till and reduced till systems levels of soil organic carbon, microbial biomass, and mineralizable nitrogen are significantly higher in the surface layer, but not necessarily deeper layers, of the soil. In fact, gains in SOC were 250 kg/ha/yr higher in minimal till than in conventional systems<ref name="thirty-one">X. Liu1, S.J. Herbert, A.M. Hashemi, X. Zhang, G. Ding. (2006) Effects of agricultural management on soil organic matter and carbon transformation – a review. Plant Soil Environment, 52(12), 531-543.</ref>. Soil structure also improves greatly under no till farming. A reduction in tilling from conventional to no or minimal till increases macro aggregation by 21% - 42%<ref name="thirty-one">X. Liu1, S.J. Herbert, A.M. Hashemi, X. Zhang, G. Ding. (2006) Effects of agricultural management on soil organic matter and carbon transformation – a review. Plant Soil Environment, 52(12), 531-543.</ref>. The chart below shows the difference in the stratification ratio, a measure of organic matter at the surface of the soil over organic matter a bit deeper. No till systems have far more surface organic matter which helps fend off erosion and better facilitates seedling growth and root growth<ref name="thirty">Franzluebbers, A. J. (2013). Pursuing robust agroecosystem functioning through effective soil organic carbon management. Carbon Management, 4(1), 43–56.</ref>.<br />
<br />
===Increasing Carbon Inputs===<br />
:Practices for increasing carbon inputs have been used in traditional farming for a long time. Native americans often farmed polycultures, and crop rotations have been in use for hundreds of years. However, in modern conventional farming, where convenience of harvesting has outstripped the benefits of these techniques, there are very few carbon inputs to agricultural systems. While harder to implement in large scale farming these techniques are very important in practicing a sustainable model of agriculture.<br />
::*'''Monocultures, Crop Rotations, Polycultures, and Cover Crops''': Monocultures, the system of growing a single crop continuously in the same soil, are common because of the simplicity of dealing with a single crop. However monoculture systems lead to lowered carbon, nitrogen, microbial biomass and diversity, and soil enzyme levels. One alternative to a monoculture is a crop rotation. Crop rotations are when alternating crops are grown in the soil. The benefits of crop rotation depend on what crops are rotated. Crop rotations shown to be especially beneficial to SOC levels include legumes and sweet clover. Both of these are often used as cover crops. Cover crops are, instead of being harvested, either tilled into, or laid on top of the soil. Cover cropping provides an annual boon of plant residue to the soil, massively increasing carbon in soil. Another system, less commonly used is that of a polyculture. A polyculture is a system in which multiple crops are grown at the same time. The diversity of crops allows for more diverse microbial communities and a greater variety of plant residue in the soil.<br />
::*'''Carbon Sequestration''': The techniques that increase the amount of carbon in soil, no till with high carbon inputs, not only improve soil longevity in farming but also cause carbon sequestration. Carbon sequestration is the process by which carbon is taken from the atmosphere and stored long term, in this case as soil organic carbon. Switching from a conventional to a no till, organic system can sequester 22 gC/m2/yr<ref name="thirty-one">X. Liu1, S.J. Herbert, A.M. Hashemi, X. Zhang, G. Ding. (2006) Effects of agricultural management on soil organic matter and carbon transformation – a review. Plant Soil Environment, 52(12), 531-543.</ref>. There are movements all over the world to implement conservation farming methods. The sequestration of carbon in soil would not only increase the sustainability of farms, but also help reduce the carbon in the atmosphere, combating the buildup of greenhouse gases in the atmosphere.<br />
::*'''Recent Research''': Recent research into conserving soil organic matter in agricultural systems suggests that minimizing tillage and introducing plant residues isn’t what ultimately conserves more organic matter. Microbial biomass is what ultimately creates organic matter. Results drawn by Kallenbach, Grandy, Frey, and Diefendorf <ref name="thirty-two">C.M. Kallenbach , A.S. Grandy , S.D. Frey , A.F. Diefendorf. (2015). Microbial physiology and necromass regulate agricultural soil carbon. Soil Biology and Biochemistry, 91, 279-290.</ref> indicate that microbial growth rates and carbon use efficiency are associated with more conversion of carbon into microbial biomass and mineralized soil organic carbon. Enhancing the transformation of plant carbon to microbial biomass is a developing, exciting area of research that could lead to more effective agricultural management. Microbes, by breaking down organic molecules and facilitating the mineralization of carbon, are essential in storing carbon in soil for carbon sequestration.<br />
<br />
==='''Case Study'''=== <br />
====<span style="color:black">Permafrost Thaw</span>====<br />
::[[Image:permafrost.png|right|thumb|300px|Permafrost Thaw and Carbon Balance<ref name="twenty-nine">Schuur, Ted. (2013): 117. "Permafrost Thaw Predictions." Science Experience Your America. Department of Botany, University of Florida, 2009. Web.</ref>.]]<br />
:::Permafrost is a subsurface soil layer that remains frozen throughout the year. When the permafrost is thawed or unfrozen, it can either increase greenhouse gas emissions or sequester more carbon in the carbon cycle. According to “Permafrost Thaw and Carbon Balance”, more than 50% of global terrestrial C is already stored in permafrost regions as soil organic matter<ref name="twenty-nine">Schuur, Ted. (2013): 117. "Permafrost Thaw Predictions." Science Experience Your America. Department of Botany, University of Florida, 2009. Web.</ref>. <br />
:::Carbon is naturally photosynthesized/uptaken by plants into the soil ecosystem and respired in the form of CO2 back into atmosphere by plants, animals, and microbes (bacteria). A carbon sink occurs when the uptake of CO2 by plants is greater than the emission of CO2 into the atmosphere by the process of respiration. A carbon source occurs when the emission of CO2 into the atmosphere by respiring microbes and plants is greater than the uptake of CO2 by plants. As reported from “Permafrost Thaw and Carbon Balance”, when the climate gets warmer, permafrost thaw can change the ecosystem carbon balance to a sink or a source<ref name="twenty-nine">Schuur, Ted. (2013): 117. "Permafrost Thaw Predictions." Science Experience Your America. Department of Botany, University of Florida, 2009. Web.</ref>. <br />
:::As stated by United Nations Environment Program, “[Thawing] of the Arctic permafrost is a “wild card” that could dramatically worsen global warming by releasing massive amounts of greenhouse gases…”<ref name="twenty-nine">Schuur, Ted. (2013): 117. "Permafrost Thaw Predictions." Science Experience Your America. Department of Botany, University of Florida, 2009. Web.</ref>. How does it do that? Well, the reason global warming is associated with permafrost thaw is because when permafrost is thawed, it can stimulate great amounts of microbial decomposition of soil organic matter. This stimulation of decomposition will decrease the C content stored in soil by releasing more CO2 into the atmosphere. The CO2 that is released into atmosphere contributes to the cycle of greenhouse gases involved in climate change.<br />
:::In an experiment conducted by researchers from the University of Florida, C balance was intensively measured during the growing seasons in three separate conditions (minimally thawed permafrost, moderately thawed permafrost, and extensively thawed permafrost). In the corresponding graph, the results of the study recorded accounted for both the growing and non-growing seasons. Researchers found that during non-growing seasons and minimal permafrost conditions, plants do not uptake C from the atmosphere but rather microorganisms release CO2 into the atmosphere indicated by the white bar in the graph. In moderately permafrost thawed, C uptake exceeded C emission because of stimulation in decomposition which signified a carbon sink occurrence. Lastly, extensive permafrost thaw observed a C emission that exceeded C uptake which signified a carbon source occurrence which released large amounts of greenhouse gases to the atmosphere. Based on the measurements, Schuur concluded that “the net release of C to the atmosphere in landscapes where there is advanced permafrost thaw adds to the existing problem of increasing greenhouse gases in the atmosphere. This C release from permafrost thaw may create a dramatic feedback that accelerates climate change”<ref name="twenty-nine">Schuur, Ted. (2013): 117. "Permafrost Thaw Predictions." Science Experience Your America. Department of Botany, University of Florida, 2009. Web.</ref>. <br />
<br />
====Drainage of Wetlands====<br />
:::Drainage of wetlands could either increase or decrease methane production but will most certainly lose massive amounts of organic carbon sequestered in the soil from the carbon cycle. According to “The Role of Wetlands in the Carbon Cycle”, wetlands operate “six to nine percent of the Earth’s surface and contain about 35 percent of global terrestrial carbon”[30]. Wetlands are capable of high productivity meaning that they have a high capacity to sequester and store carbon. Wetlands sequester and store carbon into biomass and organic matter by photosynthesizing CO2 from the atmosphere. Like permafrost thaw, seasons can affect wetlands by turning it into either a carbon sink or carbon source. <br />
:::As reported by the Department of Sustainability, Environment, Water, Population and Communities, wetlands are subjected to seasonal “waterlogging” conditions that induce anaerobic conditions<ref name="thirty-three">Foster, .John, Lisa Evans, Alison Curtin, and Brydie Hill. (2012) The Role of Wetlands in the Carbon Cycle. Issues Paper The Role of Wetlands in the Carbon Cycle. pag. Department of Environment. Australian Government, 2012. Web.</ref>. When the wetlands are subjected to inundated/anaerobic conditions, the emission of greenhouse gases (N2O and CH4) and carbon or methane sinks are created. It is because wetlands naturally store significant amounts of carbon, that during drainage conditions, wetlands emit a significant amount of greenhouse gases. However, it is also noted that these drainage of channels also contribute to emission of methane to atmosphere. These “so-called” channels are hydrological connections that exist between watercourses and designated pathways to saturate wetlands with carbon and nutrients. During aerobic conditions, soil levels are oxygenated and methane production is decreased.<br />
<br />
====Climate Change on Wetland Carbon Cycles====<br />
::As predicted by the Department of Sustainability, Environment, Water, Population and Communities, climate can play a part in the methane emission and carbon storage in wetland soils. Natural disturbances such as drainage of wetland soils will oxidize/aerate soils which decreases methane production which lead to large net losses of sediment organic carbon. In addition, depending on the climate change, wetland carbon cycle can altered in the following number of ways:<br />
<br />
::*Warmer climates will accelerate the rate of CO2 and methane production from wetland soils<br />
::*Wetter climates will increase wetland surface areas and promote carbon sequestration and increased primary production, but may increase methane emissions.<br />
::*Drier climates will increase the oxidation of carbon stores but reduce methane emissions.<br />
<br />
====Policies and Programs====<br />
::[[Image:Wetland_Carbon_Cycle.png|right|thumb|400px|Wetland Carbon Cycle<ref name="thirty-three">Foster, .John, Lisa Evans, Alison Curtin, and Brydie Hill. (2012) The Role of Wetlands in the Carbon Cycle. Issues Paper The Role of Wetlands in the Carbon Cycle. pag. Department of Environment. Australian Government, 2012. Web.</ref>.]] <br />
::A number of policies and outreach programs have been place to provide a positive feedback towards degradation of wetlands and emission of greenhouse gases by offsetting carbon sequestration and sources.. One of such policy called the Carbon Farming Initiative is currently carried out by the Department of Climate Change and Energy Efficiency. The policy is to implement change within the farmers’ lands. By storing excess greenhouse gas emission from wetlands into their lands, the farmers are able to earn carbon credits. Other organizations such as Regional Natural Resource Management Planning for Climate Change Fund and Biodiversity Fund are implementing policies to maintain healthy levels of greenhouse gas emission in wetlands.<br />
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==References==<br />
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Recently edited by students of [mailto:kmscow@ucdavis.edu Kate Scow], Winter 2016.<br />
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<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Carbon_cycle&diff=132938
Carbon cycle
2018-04-05T04:02:46Z
<p>Kmscow: /* Chemical Constitutes */</p>
<hr />
<div>=='''Introduction'''==<br />
::Globally, carbon cycles among the oceans, atmosphere, terrestrial biosphere, ecosystem, and geosphere. This wiki page focuses on carbon dynamics in soil. Soil organic matter (SOM) is the largest terrestrial carbon pool and contains more than three times as much carbon as either the atmospheric or living plant pools<ref name="one">Fischlin, A. et al.(2007). Climate Change 2007: Impacts, Adaptation and Vulnerability. Cambridge Univ. Press, 211–272.</ref>. In section 2, the first part of the wiki, we describe how organic residues are broken down in soil, focusing on the role of microbes as decomposers. By emphasizing the role of microbes, we hope to build a better nexus of information between organic input decay and SOM formation. So, in the next section we discuss the importance, formation, and recent research of SOM. Topics covered in sections 2 and 3 are integrated into three SOM formation models in section 3.5. There have been a lot of recent discoveries and many newly developed models surrounding SOM. As such, the predominant views may well be subject to change. After decomposition and SOM, we move toward focusing on real world applications and impacts of the carbon cycle in soil. <br />
<br />
::The carbon cycle has a huge role in maintaining global climate and ecosystems. SOM, being the primary pool of carbon, is of crucial importance in climate change, as demonstrated in section 3. For thousands of years, humans have interacted with soil and the carbon cycle through agriculture. However, only now are we starting to properly understand the impact agricultural practices have on soil. Driven by the strong impetus to better understand carbon dynamics in agroecosystems, we discuss carbon management strategies in agricultural systems in section 4. Permafrost thaw and drainage of wetlands are presented in section 5, as two “case studies” of soil carbon cycle. <br />
<br />
::The carbon cycle, like most natural cycles and models, is not a system closed from outside influences. There are many interlocking elements throughout cycles of nutrients, carbon, and nitrogen in soils. The nitrogen cycle is especially closely linked to the carbon cycle in microbiology because of the importance of C/N ratios. A thorough understanding of the [[Nitrogen Cycle]] will greatly improve our understanding of the carbon cycle in turn.<br />
<br />
=='''Decomposition of Organic Residues'''==<br />
::The formation of SOM and the decomposition of residue are intimately associated. Decomposition of organic residue is one of the major functions of microorganisms in the soil. The soil microorganisms utilize the residue components for energy and carbon source to synthesize the new cells. The organic materials added to soil are primarily plant residues from either cultivated crops or native vegetation, which are the source of energy stored in the carbon compounds. The crop agricultural ecosystems primarily include the combination of leaf, stem, and root tissues remaining after harvest. On the other hand, the residues that undergo decomposition in the natural ecosystems are derived from native prairie and forest vegetation. There are two types of plant residue that assimilate into the soil<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. One is above ground residue, which is derived from falling debris and other plant that are above the soil surface. The second type is deposited from root systems that complete their life cycle throughout the course of a particular season. These residue with the root exudates supply the substrate carbon input into the soil. The decay process of above-ground residue begin and initiate due to different agricultural management systems and practices<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. A portion of these substrate goes into microbial mass as it is used by the soil microorganisms for reproduction and metabolic activity and a larger part of it is lost as carbon dioxide due to the energy yielding metabolic processes of the microbial community. Recent studies<ref name="three">M. Francesca Cotrufo et al. (2013) The Microbial Efficiency-Matrix Stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization: do labile plant inputs form stable soil organic matter? Global Change Biology,19, 988–995.</ref><ref name="four">M. Francesca Cotrufo, et al. (2015) Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nature Geoscience 8, 776–779.</ref> emphasize that not all the litter Carbon loss are mineralized to carbon dioxide, but a part of these Carbon loss is transferred to mineral soil, where it contributes to the formation of soil organic matter through the two main pathways, dissolved organic matter-microbial path and physical transfer path.<br />
<br />
====Chemical Constituents====<br />
::The composition of the crop residues added to and decaying in soil are varied. Plant residues are comprised of many complex polymers such as lignin and cellulose and contains water-soluble organic compounds such as proteins, carbohydrates, and organic acidsl.<br />
<br />
=====<span style="color:black">Carbohydrates</span>=====<br />
::From 5-25% of soil organic matter is combined in the form of carbohydrates, which include simple sugars, cellulose, and hemicellulose <ref name="five">Baldock J (2007).Composition and cycling of organic C in soil. In: Nutrient Cycling in Terrestrial Ecosystems.Springer,pp. 1–35.</ref>. These carbohydrates are rapidly degraded by varied microorganisms in the soil including bacteria, archaea, actinomycetes, and fungi. During degradation soil microorganisms synthesize extracellular polysaccharides. These polysaccharides bind soil into water stable aggregates so that the aggregates are more permeable to water and air. Polysaccharides also affect the cation exchange capacity of soil and act as an energy source for other microorganisms<ref name="five">Baldock J (2007).Composition and cycling of organic C in soil. In: Nutrient Cycling in Terrestrial Ecosystems.Springer,pp. 1–35.</ref>. <br />
::Heterotrophic microbes can easily metabolize simple sugars. Plants link glucose molecules (and other sugar monomers) into long chains to produce polymers such as cellulose, which requires more specialized organisms to degrade.<br />
::For example: Starch is made of amylose (alpha 1,4 bonded glucose) and amylopectin (alpha 1,6 bonded glucose), and is relatively easy for most organisms to degrade. Cellulose, however, is a polysaccharide of glucose connected with beta 1,4 bonds, and is more difficult to degrade. No animal can degrade cellulose, so bacteria can frequently be found in mutualistic relationships with detritivores: the bacteria degrade the cellulose enough that the animal is able to digest it. <br />
<br />
======<span style="color:black">Cellulose</span>======<br />
::[[Image:CelluloseDecomp_edited.jpg|center|thumb|200px|The Decomposition of Cellulose <ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>,]]<br />
<br />
::Cellulose is the most abundant carbon input in soil. It’s a structural polysaccharide that is made of 1400 to 10000 glucose units. In order to access the glucose monomer, the cellulose must be cleaved by extracellular enzymes. These pieces are then transported into the cell for energy generation (catabolism) or production of biomass (anabolism). Cellulose is used by a diverse group of soil organisms including fungi such as Penicillium and [[Aspergillus]] and bacteria such as [[Streptomyces]] and [[Pseudomonas]]. Fungi and bacteria are important participants in the extracellular cleavage of cellulose<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>.<br />
<br />
======<span style="color:black">Hemicellulose</span>======<br />
::[[Image:HemicelluloseDecomp edited.jpg|center|thumb|200px|The Decomposition of Pectin (a Hemicellulose)<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>,]] <br />
::Hemicellulose is the next most common carbohydrate in plants. It is a branched polymer with varied sugar monomers (glucose, mannose, and galactose) and bonds. The decomposition of hemicellulose is similar to that of cellulose in that the initial depolymerization step takes place outside of the cell, and the sugars produced are then transported into the cell for catabolism or anabolism. Even though hemicellulose decomposition is much quicker than cellulose decomposition, cells will utilize simple sugars as substrates before hemicellulose<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>.<br />
<br />
======<span style="color:black">Chitin</span>======<br />
:::[[Image:ChitinDecomposition_edited.jpg|center|thumb|200px|The Decomposition of Chitin and Chitosan Under Aerobic Soil Conditions<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>]]<br />
:::Chitin is a special compound which can be found in the integument of arthropods and the cell walls of fungi. Chitin is one of the cell-wall component of many common soil fungi (e.g., [[Aspergillus]] and [[Penicillium]]) as around 3% to 25% of these soil fungal biomass are chitin<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. Chitin is usually protected from degradation by the protein-chitin complex in its natural normal stage in soil. Due to this type of protection, chitin is an important component in soil organic matter formation. The polymer is not easily degraded and requires a variety of enzymes to do so. The dominant chitin degraders are the Actinomycetes, [[Streptomyces]] and Nocardia. Less important than Actinomycetes, fungi such as Trichoderma and [[Verticillium]] and bacteria, such as [[Bacillus]] and [[Pseudomonas]] can also degrade chitin<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>.<br />
<br />
=====<span style="color:black">Lignin</span>=====<br />
:::[[Image:LigninDecomp2_edited.jpg|center|thumb|200px|One Possible Pathway of Lignin Decomposition<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>]]<br />
::Lignin is the main component of wood in trees. Lignin has a varied, unique, and complicated chemical structure which contains many aromatics. Aromatics are part of the reason why lignin is more difficult to be decomposed. Even with strong acid treatment, the plant residues are not solubilized due to the complex ring structure.These aromatics can be released from the lignin structure by fungal enzymes such as peroxidases and oxidases. The enzymes utilize H2O2 and OH radicals to break the bonds in the lignin. Lignin is decomposed through groups of specialized fungi. Common types of fungi which depolymerize lignin are white rot ("[[Phanerochaete chrysosporium]]"), brown rot, and soft rot<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. Once the aromatics are released from the original lignin structure they are incorporated into the metabolic pathway as pyruvate, acetyl CoA, and into the TCA cycle.<br />
<br />
=====<span style="color:black">Proteins</span>=====<br />
::Proteins are one of the most important components of plant residue added to soil. Protein is a polymers of amino acids linked by peptide bonds. A variety of microorganisms in soil can produce proteolytic enzymes such as protease and peptidase, which can break the peptide bond of the protein and hydrolyze it into individual amino acids. These amino acid monomers can then be utilized by microbes for either catabolism or for the synthesis of new essential proteins<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>.<br />
<br />
=====<span style="color:black">Fats & Waxes</span>=====<br />
::More than 2% of soil organic matter is cultivated in the forms, fats and waxes. Unlike cellulose and sugar, fats and waxes are much harder for microorganisms to breakdown. They are decomposed very slowly into CO2, water and energy which can be used by microorganisms<ref name="six">Osman, Khan Towhid. (2013). Soils’: Principle, Properties, and Management. Springer Dordrecht Heidelberg New York London, 93-95.</ref> Very little investigation has been done so information regarding this is limited.<br />
<br />
=='''Soil Organic Matter'''==<br />
====SOM and Climate Change====<br />
::The carbon cycle in soil is a dynamic balance between photosynthesis, the respiration of decomposing organisms, and the stabilization of carbon. Soil stores at least three times as much carbon (in SOM) as is found in either the atmosphere or in living plants<ref name="one">Fischlin, A. et al.(2007). Climate Change 2007: Impacts, Adaptation and Vulnerability. Cambridge Univ. Press, 211–272.</ref>. The total global carbon stock in soil is about 2500 Pg C, including approximately 1550 Pg in organic carbon, and 950 in inorganic carbon. Soils act as a buffer against the increase of atmospheric CO2. There is growing interest that it is possible to remove a significant amount of CO2 from the atmosphere by sequestering carbon in soil. It is estimated that 16-30% atmospheric CO2 can be removed when SOM concentrations increase 5-15% in soil up to 2m depth<ref name="seven">Baldock J (2007).Composition and cycling of organic C in soil. In: Nutrient Cycling in Terrestrial Ecosystems.Springer,pp. 1–35.</ref><ref name="eight">Kell DB (2011).Breeding crop plants with deep roots: their role in sustainable carbon nutrient and water sequestration. Annals of Botany, 108, 407–418.</ref>. It is also believed that soil respiration rates could cause a positive feedback in global warming. There are more nutrient based, plant-oriented interests in SOM, however, it seems that concerns about the changing climate “have now overtaken these other justifications”<ref name="nine">Sollins, P., Swanston, C. & Kramer, M. (2007).Stabilization and destabilization of soil organic matter—a new focus. Biogeochemistry 85, 1–7.</ref>.<br />
<br />
====New Insights on SOM====<br />
::For a long time, the scientific community described SOM in terms of humic substances. With the help of advanced analytical techniques, a growing body of research indicates that the importance of the biotic and abiotic environments in soil outweighs that of the molecular structure of plant inputs and organic matter in the process of OM stabilization. Factors such as rate of decay, SOM pools, stability, or ‘recalcitrance’ are not sufficient to describe the “ecosystem property”<ref name="ten">Schmidt MWI, Torn MS, Abiven S et al. (2011) Persistence of soil organic matter as an ecosystem property. Nature, 478, 49–56.</ref> of SOM; rather, texture, mineralogy, water solubility, molecular size, functionalization, and perhaps most important, climate change conditions should be incorporated into our understanding (and modeling) of carbon.<br />
<br />
=====<span style="color:black">History of Humic Substances</span>=====<br />
::Historically soil chemists use alkali and acid extraction methods and observations of the extracted (or residual) functional group chemistry to describe the soil organic matter, or humus<ref name="ten">Schmidt MWI, Torn MS, Abiven S et al. (2011) Persistence of soil organic matter as an ecosystem property. Nature, 478, 49–56.</ref>. When protons are added to the solubilized organic materials, the dark color solid that precipitates is called ‘humic acid’. ‘Fulvic acid’ is the organic matter that remains soluble after reacidification treatment. The organic matter that does not respond to the extraction treatment is called ‘humin’. Long-standing theory suggests that humic substances are comprised of large and complex macromolecules which are the most stable SOM. Recently, by direct high-resolution observations, people understand that only a small portion of total organic matter is represented by humic substances. Smaller and simpler molecular structures are observed, as shown in Fig.1. The formation of humic polymers is not necessary related with humus formation in soils. A comprehensive review of traditional approach and critique of ‘humification’ model is conducted in the paper<ref name="eleven">Johannels Lehmann, Markus Kleber. (2015). The contentious nature of soil organic matter. Nature, 528, 60–68.</ref>.<br />
<br />
=====<span style="color:black">Decomposition and Molecular Structure</span>=====<br />
:[[Image:SOM_models.png|center|thumb|350px|Historically view vs emerging understanding of SOM<ref name="fourteen">Anja Miltner et al, (2012) SOM genesis: microbial biomass as a significant source. Biogeochemistry,111,41–55.</ref>.]]<br />
::Historically SOM is thought to be made of stable and chemically unique compounds. The decomposition rate of plant residues largely depends on its biochemical composition, especially the C/N ratio and lignin content. Accordingly, people believe that the molecular structure of biomass and organic material controls the long-term decomposition rates in soil. Recent studies find that this is not true. Lignin and plant lipids (‘recalcitrants’) can turn over very rapidly<ref name="twelve">.Marschner, B. et al. (2008). How relevant is recalcitrance for the stabilization of organic matter in soils? J. Plant Nutr. Soil Sci. 171, 91–110.</ref><ref name="thirteen">Amelung, W., Brodowski, S., Sandhage-Hofmann, A. & Bol, R. (2008).Combining biomarker with stable isotope analysis for assessing the transformation and turnover of soil organic matter. Adv. Agron. 100, 155–250.</ref>. Moreover, sugar and other potential labile compounds have been shown to persist for decades---much longer than a couple weeks.<br />
<br />
====<span style="color:black">Role of Microbes in SOM Formation</span>==== <br />
:'''''“The role of microorganisms in SOM dynamics must be considered beyond the context of simple decomposition of fresh residues and extended to environment.” ---Jessica Chiartas, respectful TA of SSC111'''''<br />
<br />
::[[Image:Microbes_in_SOM_formation.png|center|thumb|350px|The roles of soil microbes in SOM formation.<ref name="fourteen">Anja Miltner et al, (2012) SOM genesis: microbial biomass as a significant source. Biogeochemistry,111,41–55.</ref>]]<br />
<br />
::Soil microorganisms serve not only as decomposers, but also as important components of SOM. Although plant residue contributes most of the carbon to soil, a large proportion actually ‘filters’ through microbial biomass before being transformed into SOM. It is now widely accepted that the contributions of microbial biomass to SOM formation seem to be much higher than the 1-5% estimation. A recent study shows that the living microbial biomass and necromass (the microbial residue after cell death) together account for 80% of the soil organic <ref name="fifteen">Liang C, Balser TC (2010) Microbial production of recalcitrant organic matter in global soils: implications for productivity and climate policy. Nat Rev Microbiol 9:75.</ref>. Bacteria and fungi comprise > 90% of the microbial biomass in soil<ref name="sixteen">Six J, Frey SD, Thiet RK, Batten KM (2006) Bacterial and fungal contributions to carbon sequestration in agroecosystems. Soil Sci Soc Am J 70:555–569.</ref>. Microbes also contribute to soil aggregate formation, and soil structure. For instance, fungi help build microaggregates by connecting soil particles with their hyphae and extracellular components<ref name="sixteen">Six J, Frey SD, Thiet RK, Batten KM (2006) Bacterial and fungal contributions to carbon sequestration in agroecosystems. Soil Sci Soc Am J 70:555–569.</ref>.<br />
<br />
::[[Image:SUE.png|center|250px|]]<br />
<br />
::The turnover of microbial biomass can be described by microbial substrate use efficiency (SUE). Factors that affect SUE include 1) substrate quality ( molecular weight, solubility, structural complexity, C:N ratio), and 2) the degradative efficacy of microbes<ref name="seventeen">Lekkerkerk LJA, Lundkvist H, Agren G, Ekbohm G, Bosatta E (1990) Decomposition of heterogeneous substrates: an experimental investigation of a hypothesis on substrate and microbial properties. Soil Biology & Biochemistry, 22, 161–167.</ref>(microbial community composition and structure, protection of organic compounds, other physiochemical environment). SUE is also a measure of the amount of ATP released through catabolism vs. the formation of biomolecules through anabolic activity, which is controlled by stoichiometric, chemical, and physiological factors[1]. Microbes and SUE, being the eye of the needle through which carbon moves in soil, are good indicators of SOM formation. However, SUE does not equate to SOM stabilization. Details will be discussed in next section. <br />
<br />
::Recently, the similar compositions between SOM spectra and microbial biomass are observed by the NMR approach<ref name="eighteen>Simpson AJ, Simpson MJ, Smith E, Kelleher BP (2007) Microbially derived inputs to soil organic matter: are current estimates too low? Environmental Science & Technology, 41, 8070–8076.</ref>. Technology to 1) track the fate of specific labelled organic compounds, and 2) directly observe microbes under high resolution scopes have extended our ability to understand soil microbial activity and diversity. Nevertheless, the quantitative linkages to ecosystem function remain uncertain<ref name="nineteen">Raes, J. & Bork, P. (2208) Molecular eco-systems biology: towards an understanding of community function. Nature Rev. Microbiol. 6, 693–699.</ref><ref name="twenty">Morales, S. E.&Holben,W. E.(2011). Linkingbacterial identitiesandecosystemprocesses:can ’omic’ analyses be more than the sumof their parts? FEMS Microbiol. Ecol. 75, 2–16.</ref>.<br />
<br />
====Carbon Stability and Turnover====<br />
:'''''“Rather than describing organic matter by decay rate, pool, stability or level of ‘recalcitrance’—as if these were properties of the compounds themselves—organic matter should be described by quantifiable environmental characteristics governing stabilization, such as solubility, molecular size and functionalization.” ---Michael W.I. Schmidt'''''<br />
<br />
::Historically, SOM has been grouped into active, intermediate, and passive pools based on stabilization mechanisms and turnover time<ref name="twenty-one">Sollins, P., Homann, P., Caldwell, B. A. (1996): Stabilisation and destabilisation of soil organic matter: mechanisms and controls.Geoderma 74, 65–105.</ref>. SOM stability is controlled by accessibility rather than recalcitrance<ref name="twenty-two">Jennifer A. J. Dungait, et al. (2012) Soil organic matter turnover is governed by accessibility not recalcitrance. Global Change Biology, 18, 1781-1796.</ref>. Stabilization is the protection of OM from mineralization. Stabilization refers to processes and mechanisms that can prolong C turnover times in soil. Detailed SOM stabilization mechanisms based on this knowledge have been well developed and summarized<ref name="twenty-three">Margit von Lützow et al. (2008) Stabilization mechanisms of organic matter in four temperate soils:Development and application of a conceptual model. J. Plant Nutr. Soil Sci, 171, 111–124.</ref>. However, a few mechanisms have been challenged in recent years<ref name="ten">Schmidt MWI, Torn MS, Abiven S et al. (2011) Persistence of soil organic matter as an ecosystem property. Nature, 478, 49–56.</ref><ref name="eleven">Johannels Lehmann, Markus Kleber. (2015). The contentious nature of soil organic matter. Nature, 528, 60–68.</ref>.<br />
<br />
::Managements of the size and the turnover rate of soil C pools can mitigate global climate change. Carbon pools with a fast turnover rate (<1 year) are important for short term nutrients availability in soil. SOM pools with slower turnover rate (decades, or even centuries) are important for soil structure and are believed to be more sensitive to climate change<ref name="twenty-four">Davidson, E. A. & Janssens, I. A. (2006).Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature 440, 165–173.</ref><ref name="twenty-five">Conant, R. T. et al. (2008).Sensitivity of organic matter decomposition to warming varies with its quality. Glob. Change Biol. 14, 868–877.</ref>.<br />
<br />
::After moving through the ‘microbial filter’<ref name="twenty-six">Wickland KP, Neff JC, Aiken GR (2007) Dissolved organic carbon in Alaskan boreal forest: sources, chemical characteristics and biodegradability. Ecosystems, 10,1323–1340, doi: 10.1007/s10021-007-9101-4</ref>, the fate of SOM is heavily dependent on environmental conditions and soil properties (pH, soil texture, and mineralogy).Generally speaking, SOM stabilization is controlled by interactions of SOM with the mineral soil matrix through 1) phyllosilicates; 2) polyvalent cations (e.g., Ca2+); 3) Fe-, Al-, Mn-oxides; 4) spatial occurrence/accessibility<ref name="three">M. Francesca Cotrufo et al. (2013) The Microbial Efficiency-Matrix Stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization: do labile plant inputs form stable soil organic matter? Global Change Biology,19, 988–995.</ref><br />
<br />
====<span style="color:black">Recent SOM formation models</span>====<br />
<br />
::Three fairly modern conceptual models of SOM formation are selected and presented in this section. No single model is perfect. Advanced technology and previous knowledge are always “the shoulders of giant[s]” we stand on to help us see further. Thus, models in this section should not be evaluated by comparing them with each other; rather, they should be viewed collectively to help us to explore the world of soil carbon, where many things remain uncertain. <br />
=====<span style="color:black">SOM as Ecosystem Property</span>=====<br />
::[[Image:SOM_formation_models.png|center|thumb|500px|A combination of recent insights, contrasting historical and emerging views of carbon cycling in soil<ref name= "ten">Schmidt MWI, Torn MS, Abiven S et al. (2011) Persistence of soil organic matter as an ecosystem property. Nature, 478, 49–56.</ref>,pg52.]]<br />
<br />
::From a respectful article<ref name="ten">Schmidt MWI, Torn MS, Abiven S et al. (2011) Persistence of soil organic matter as an ecosystem property. Nature, 478, 49–56.</ref>, this model suggests that carbon stability should be viewed as an ecosystem property. The influence of compound chemistry largely depends on environmental factors such as reactive soil mineral matrix, water solubility, soil redox state, pH, and climate. Physical disconnection refers to the spatial inaccessibility between microbial decomposers and substrate, which causes SOM sequestration in aggregates and physical protection from decomposition. Sorption/desorption refers to the organo-mineral associations, mainly controlled by the amount and quality of silt and clay. The Fe-, Al-, and Mn-oxides act as clay coatings, interacting with, and physically protecting organic matter. Thawing is expected to become more widespread due to climate change. It refers to the mineralization of previously stable SOM. Freezing, on the other hand, refers to the stabilization process owing to low temperatures. Microbial activity and products (necromass) affect the fate of SOM along the whole carbon cycle in soil.<br />
<br />
=====<span style="color:black">Soil Continuum Model (SCM)</span>=====<br />
::[[Image:SCM.png|center|thumb|500px|Fate of residues into a consolidated view of the SCM mode<ref name="eleven">Johannels Lehmann, Markus Kleber. (2015). The contentious nature of soil organic matter. Nature, 528, 60–68.</ref>,pg 63.]]<br />
::SCM is an evidence-based approach that focuses on the ability of decomposer organisms to access SOM and the protection of organic matter from decomposition. In the SCM model, the molecular size of residues become smaller through the biotic transformation (microbial decomposer community), and the oxidation state of SOM increases. Consequently, the water solubility increases. At the same time, larger mineral surfaces and aggregate incorporation protects SOM against further decomposition. The SCM model includes both abiotic and biotic processes as functions of temperature, moisture, and the biota present. SOM is viewed as “a continuum of progressively decomposing organic compounds”<ref name="eleven">Johannels Lehmann, Markus Kleber. (2015). The contentious nature of soil organic matter. Nature, 528, 60–68.</ref>.<br />
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=====<span style="color:black">Biochemical and Physical Pathways---Nexus Between Plant Input and SOM Formation</span>=====<br />
:::[[Image:DOC_pathway.png|center|thumb|400px|Schematic representation of DOC and physical pathways<ref name="four">M. Francesca Cotrufo, et al. (2015) Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nature Geoscience 8, 776–779.</ref>.]]<br />
::Two major pathways of SOM formation are proposed. 1) Under the SOM-microbial pathway, SOM is formed by organo-mineral interactions<ref name="twenty-seven">Kleber, M., Sollins, P. & Sutton, R.(2007). A conceptual model of organo-mineral interactions in soils: Self-assembly of organic molecular fragments into zonal structures on mineral surfaces. Biogeochemistry 85, 924.</ref><ref name="four">M. Francesca Cotrufo, et al. (2015) Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nature Geoscience 8, 776–779.</ref>, and labile litter components (non-structural, celluloses, hemicelluloses) are decomposed during the early stages of decomposition. The SOM-microbial pathway has high SUE, and leads to new, net SOM formation. 2) Under the Physical transfer pathway, litter fragments are incorporated into a light fraction, and stabilized by chemical recalcitrance. With low DOC leaching, low SUE, and low SOM formation, the physical transfer pathway stabilizes carbon by promoting aggregation and spatial inaccessibility<ref name="four">M. Francesca Cotrufo, et al. (2015) Formation of soil organic matter via biochemical and physical pathways of litter mass loss. Nature Geoscience 8, 776–779.</ref>.<br />
<br />
====Roles of SOM====<br />
:Any change in soil carbon pools potentially impacts the atmospheric CO2 concentration and the global climate. However, the changing climate is not the only reason why SOM is important. More functions of SOM are listed here to emphasize the importance of SOM as an ecosystem property. <br />
<br />
::*'''Nutrient Cycling''': Soil organic matter contributes 20% to 80% of the cation exchange capacity (CEC), which increases the ability of mineral soil to retain nutrients. SOM itself is a pool of nutrients for plant and microbes. SOM also enhances chelation (organic compounds forming complexes with cations like iron) and thus increase the bioavailability of trace elements to plants and other soil microbes<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. <br />
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::*'''Water Dynamics''': Improves water infiltration. SOM takes an important part in decreasing evaporation by enhancing the total water-holding capacity and strength of holding water in soil<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>.<br />
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::*'''Structure''': SOM contributes to improve soil structure and aggregation. Humic substances produced by fungi and polysaccharide produced by bacteria stabilize and improve aggregation. As aggregation improves, the infiltration rate increases, reducing runoff and soil erosion<ref name="two">Sylvia, D.M., Fuhrmann, J.J., Hartel, P.G.,& Zuberer, D.A. (2005).Principles and Applications of Soil Microbiology, Second Edition. Prentice Hall, Upper Saddle River, NJ, 346,359,497-501 and 285-287 pp.</ref>. SOM also helps to prevent compaction by decreasing bulk density and increasing percentage pore space.<br />
<br />
::*'''Other Effects of SOM''': Pesticides break down more quickly and can be "tied-up" by organic matter. Dark, bare soil may warm more quickly than light-colored soils, but heavy residue may slow warming and drying in spring. Plant residues and other organic material may support some diseases and pests, as well as predators and other beneficial organisms.<br />
<br />
====Factors Affecting SOM====<br />
:Instead of calling mechanisms, and integrating into models, different factors are discussed separately in this section to summarize SOM dynamics from another perspective. Some factors are thought to be dominant but being challenged by recent insights. <br />
:A huge variety of factors can affect SOM. Countless organisms and chemical interactions affect its production and use. Understanding the many factors that contribute to the production, and state of SOM will give insight into everything from carbon sequestration and improving agricultural practices to the lives of microbial organisms.<br />
::*'''Quantity of Carbon''': Carbon inputs are essential to soil as microbes are constantly respiring and releasing carbon from the soil. Low carbon inputs means there is less for microbes to metabolize and less carbon to be converted into organic matter there is more carbon available to be converted. <br />
::*'''Quality of Carbon''': (Old view) Easier to break down carbon sources will be fully converted to SOM faster. Though more complicate forms of carbon often produce a greater yield over time, and persist for longer.<br />
::*'''Temperature''': Colder weather in general means more soil organic matter. The cold slows microbial respiration so less carbon is metabolized.<br />
::*'''Moisture''': Higher moisture leads to the same result. More water filled pores and less oxygen availability reduces microbial respiration and means less carbon released as carbon dioxide.<br />
::*'''Texture''': High clay content means there is more surface area for carbon compounds to be attached to and more space for organomineral interaction. Furthermore, soil which is well aggregated can contain aggregates full of organic matter that are harder to reach for microbes to consume.<br />
::*'''Microbial Community''': As shown in a lot of factors above, high microbial activity can lead to carbon being lost as a product of respiration. However, microbes are necessary as degraders of complex organic material, facilitating carbon mineralization, and are a large portion of organic matter itself as dead microbial biomass. Microbes have a specific C/N/P ratio and the more carbon there is the more carbon microbes will release as carbon dioxide. As a result, more proper carbon ratios more efficiently convert carbon into SOM.<br />
::*'''Disturbance''': Soil disturbance such as tilling or erosion exposes protected pocket of organic matter and introduces oxygen reducing organic matter.<br />
::*'''Fire''': Black carbon, carbon that has been burned and turned into charcoal, is integrated into soils by wildfires or human burning. This black carbon is being increasingly recognized as an important factor in SOM formation and retention. The charcoal particles have high surface area and surface charges. These factors give black carbon soils higher cation exchange capacities<ref name="twenty-eight">B. Liang, J. Lehmann, D. Solomon, J. Kinyangi, J. Grossman, B. O’Neill, J. O. Skjemstad, J. Thies, F. J. Luizao, J. Petersen, and E. G. Neves. (2006). Black carbon increases cation exchange capacity in soils. Soil Science Society of America, 70, 1719-1730.</ref>. A high charge means black carbon is very easily incorporated into SOM through mineralization.<br />
<br />
=='''Soil Organic Carbon in Agricultural System'''==<br />
Successful farming requires good, healthy soil. Good agricultural soil means lots of soil carbon and organic matter. The very nature of farming, growing and removing plants from soil again and again, removes a certain amount of carbon and other resources from the soil. However, a lot of the conventional practices around farming serve to damage soil and alter the carbon cycle far more than necessary. Many modern sustainable farming methods have been shown to greatly increase soil health. There are two different ways of approaching the problem, decreasing the amount of carbon lost and increasing the amount of carbon input.<br />
<br />
===Reducing Carbon Losses=== <br />
:[[Image:Stratification_ratio_of_SOM_over_time.png|right|thumb|400px|Change in stratification ratio of soil organic carbon with time under different tillage systems in Spain<ref name="thirty">Franzluebbers, A. J. (2013). Pursuing robust agroecosystem functioning through effective soil organic carbon management. Carbon Management, 4(1), 43–56.</ref>.]] <br />
:Carbon being lost from an agricultural system because of crop harvesting is unavoidable. The damage to soil can be reduced by growing less carbon intensive crops. Crops like corn return much of the plant carbon to the soil after a harvest from the husks and stalks of the plant. Another route by which carbon is lost from agricultural systems is via microbial respiration. Conventional farming greatly enhances these losses through tillage.<br />
:*'''Tillage''': Tillage is the practice of mixing and aerating soil by breaking it apart and turning it. Tilling practices increase oxygen availability to microbes and expose aggregate bound organic matter to microbes. As a result, high tillage increases microbial activity and soil respiration releasing previously soil bound carbon as carbon dioxide into the atmosphere. Tilling also damages soil structure, increasing erosion and removing yet more valuable organic carbon from fields. The increased attention on sustainable farming practices over the past decades has led to an increase in “no till” farming. In no till and reduced till systems levels of soil organic carbon, microbial biomass, and mineralizable nitrogen are significantly higher. In fact, gains in SOC were 250 kg/ha/yr higher in minimal till than in conventional systems<ref name="thirty-one">X. Liu1, S.J. Herbert, A.M. Hashemi, X. Zhang, G. Ding. (2006) Effects of agricultural management on soil organic matter and carbon transformation – a review. Plant Soil Environment, 52(12), 531-543.</ref>. Soil structure also improves greatly under no till farming. A reduction in tilling from conventional to no or minimal till increases macro aggregation by 21% - 42%<ref name="thirty-one">X. Liu1, S.J. Herbert, A.M. Hashemi, X. Zhang, G. Ding. (2006) Effects of agricultural management on soil organic matter and carbon transformation – a review. Plant Soil Environment, 52(12), 531-543.</ref>. The chart below shows the difference in the stratification ratio, a measure of organic matter at the surface of the soil over organic matter a bit deeper. No till systems have far more surface organic matter which helps fend off erosion and better facilitates seedling growth and root growth<ref name="thirty">Franzluebbers, A. J. (2013). Pursuing robust agroecosystem functioning through effective soil organic carbon management. Carbon Management, 4(1), 43–56.</ref>.<br />
<br />
===Increasing Carbon Inputs===<br />
:Practices for increasing carbon inputs have been used in traditional farming for a long time. Native americans often farmed polycultures, and crop rotations have been in use for hundreds of years. However, in modern conventional farming, where convenience of harvesting has outstripped the benefits of these techniques, there are very few carbon inputs to agricultural systems. While harder to implement in large scale farming these techniques are very important in practicing a sustainable model of agriculture.<br />
::*'''Monocultures, Crop Rotations, Polycultures, and Cover Crops''': Monocultures, the system of growing a single crop continuously in the same soil, are common because of the simplicity of dealing with a single crop. However monoculture systems lead to lowered carbon, nitrogen, microbial biomass and diversity, and soil enzyme levels. One alternative to a monoculture is a crop rotation. Crop rotations are when alternating crops are grown in the soil. The benefits of crop rotation depend on what crops are rotated. Crop rotations shown to be especially beneficial to SOC levels include legumes and sweet clover. Both of these are often used as cover crops. Cover crops are, instead of being harvested, either tilled into, or laid on top of the soil. Cover cropping provides an annual boon of plant residue to the soil, massively increasing carbon in soil. Another system, less commonly used is that of a polyculture. A polyculture is a system in which multiple crops are grown at the same time. The diversity of crops allows for more diverse microbial communities and a greater variety of plant residue in the soil.<br />
::*'''Carbon Sequestration''': The techniques that increase the amount of carbon in soil, no till with high carbon inputs, not only improve soil longevity in farming but also cause carbon sequestration. Carbon sequestration is the process by which carbon is taken from the atmosphere and stored long term, in this case as soil organic carbon. Switching from a conventional to a no till, organic system can sequester 22 gC/m2/yr<ref name="thirty-one">X. Liu1, S.J. Herbert, A.M. Hashemi, X. Zhang, G. Ding. (2006) Effects of agricultural management on soil organic matter and carbon transformation – a review. Plant Soil Environment, 52(12), 531-543.</ref>. There are movements all over the world to implement conservation farming methods. The sequestration of carbon in soil would not only increase the sustainability of farms, but also help reduce the carbon in the atmosphere, combating the buildup of greenhouse gases in the atmosphere.<br />
::*'''Recent Research''': Recent research into conserving soil organic matter in agricultural systems suggests that minimizing tillage and introducing plant residues isn’t what ultimately conserves more organic matter. Microbial biomass is what ultimately creates organic matter. Results drawn by Kallenbach, Grandy, Frey, and Diefendorf <ref name="thirty-two">C.M. Kallenbach , A.S. Grandy , S.D. Frey , A.F. Diefendorf. (2015). Microbial physiology and necromass regulate agricultural soil carbon. Soil Biology and Biochemistry, 91, 279-290.</ref> indicate that microbial growth rates and carbon use efficiency are associated with more conversion of carbon into microbial biomass and mineralized soil organic carbon. Enhancing the transformation of plant carbon to microbial biomass is a developing, exciting area of research that could lead to more effective agricultural management. Microbes, by breaking down organic molecules and facilitating the mineralization of carbon, are essential in storing carbon in soil for carbon sequestration.<br />
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==='''Case Study'''=== <br />
====<span style="color:black">Permafrost Thaw</span>====<br />
::[[Image:permafrost.png|right|thumb|300px|Permafrost Thaw and Carbon Balance<ref name="twenty-nine">Schuur, Ted. (2013): 117. "Permafrost Thaw Predictions." Science Experience Your America. Department of Botany, University of Florida, 2009. Web.</ref>.]]<br />
:::Permafrost is a subsurface soil layer that remains frozen throughout the year. When the permafrost is thawed or unfrozen, it can either increase greenhouse gas emissions or sequester more carbon in the carbon cycle. According to “Permafrost Thaw and Carbon Balance”, more than 50% of global terrestrial C is already stored in permafrost regions as soil organic matter<ref name="twenty-nine">Schuur, Ted. (2013): 117. "Permafrost Thaw Predictions." Science Experience Your America. Department of Botany, University of Florida, 2009. Web.</ref>. <br />
:::Carbon is naturally photosynthesized/uptaken by plants into the soil ecosystem and respired in the form of CO2 back into atmosphere by plants, animals, and microbes (bacteria). A carbon sink occurs when the uptake of CO2 by plants is greater than the emission of CO2 into the atmosphere by the process of respiration. A carbon source occurs when the emission of CO2 into the atmosphere by respiring microbes and plants is greater than the uptake of CO2 by plants. As reported from “Permafrost Thaw and Carbon Balance”, when the climate gets warmer, permafrost thaw can change the ecosystem carbon balance to a sink or a source<ref name="twenty-nine">Schuur, Ted. (2013): 117. "Permafrost Thaw Predictions." Science Experience Your America. Department of Botany, University of Florida, 2009. Web.</ref>. <br />
:::As stated by United Nations Environment Program, “[Thawing] of the Arctic permafrost is a “wild card” that could dramatically worsen global warming by releasing massive amounts of greenhouse gases…”<ref name="twenty-nine">Schuur, Ted. (2013): 117. "Permafrost Thaw Predictions." Science Experience Your America. Department of Botany, University of Florida, 2009. Web.</ref>. How does it do that? Well, the reason global warming is associated with permafrost thaw is because when permafrost is thawed, it can stimulate great amounts of microbial decomposition of soil organic matter. This stimulation of decomposition will decrease the C content stored in soil by releasing more CO2 into the atmosphere. The CO2 that is released into atmosphere contributes to the cycle of greenhouse gases involved in climate change.<br />
:::In an experiment conducted by researchers from the University of Florida, C balance was intensively measured during the growing seasons in three separate conditions (minimally thawed permafrost, moderately thawed permafrost, and extensively thawed permafrost). In the corresponding graph, the results of the study recorded accounted for both the growing and non-growing seasons. Researchers found that during non-growing seasons and minimal permafrost conditions, plants do not uptake C from the atmosphere but rather microorganisms release CO2 into the atmosphere indicated by the white bar in the graph. In moderately permafrost thawed, C uptake exceeded C emission because of stimulation in decomposition which signified a carbon sink occurrence. Lastly, extensive permafrost thaw observed a C emission that exceeded C uptake which signified a carbon source occurrence which released large amounts of greenhouse gases to the atmosphere. Based on the measurements, Schuur concluded that “the net release of C to the atmosphere in landscapes where there is advanced permafrost thaw adds to the existing problem of increasing greenhouse gases in the atmosphere. This C release from permafrost thaw may create a dramatic feedback that accelerates climate change”<ref name="twenty-nine">Schuur, Ted. (2013): 117. "Permafrost Thaw Predictions." Science Experience Your America. Department of Botany, University of Florida, 2009. Web.</ref>. <br />
<br />
====Drainage of Wetlands====<br />
:::Drainage of wetlands could either increase or decrease methane production but will most certainly lose massive amounts of organic carbon sequestered in the soil from the carbon cycle. According to “The Role of Wetlands in the Carbon Cycle”, wetlands operate “six to nine percent of the Earth’s surface and contain about 35 percent of global terrestrial carbon”[30]. Wetlands are capable of high productivity meaning that they have a high capacity to sequester and store carbon. Wetlands sequester and store carbon into biomass and organic matter by photosynthesizing CO2 from the atmosphere. Like permafrost thaw, seasons can affect wetlands by turning it into either a carbon sink or carbon source. <br />
:::As reported by the Department of Sustainability, Environment, Water, Population and Communities, wetlands are subjected to seasonal “waterlogging” conditions that induce anaerobic conditions<ref name="thirty-three">Foster, .John, Lisa Evans, Alison Curtin, and Brydie Hill. (2012) The Role of Wetlands in the Carbon Cycle. Issues Paper The Role of Wetlands in the Carbon Cycle. pag. Department of Environment. Australian Government, 2012. Web.</ref>. When the wetlands are subjected to inundated/anaerobic conditions, the emission of greenhouse gases (N2O and CH4) and carbon or methane sinks are created. It is because wetlands naturally store significant amounts of carbon, that during drainage conditions, wetlands emit a significant amount of greenhouse gases. However, it is also noted that these drainage of channels also contribute to emission of methane to atmosphere. These “so-called” channels are hydrological connections that exist between watercourses and designated pathways to saturate wetlands with carbon and nutrients. During aerobic conditions, soil levels are oxygenated and methane production is decreased.<br />
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====Climate Change on Wetland Carbon Cycles====<br />
::As predicted by the Department of Sustainability, Environment, Water, Population and Communities, climate can play a part in the methane emission and carbon storage in wetland soils. Natural disturbances such as drainage of wetland soils will oxidize/aerate soils which decreases methane production which lead to large net losses of sediment organic carbon. In addition, depending on the climate change, wetland carbon cycle can altered in the following number of ways:<br />
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::*Warmer climates will accelerate the rate of CO2 and methane production from wetland soils<br />
::*Wetter climates will increase wetland surface areas and promote carbon sequestration and increased primary production, but may increase methane emissions.<br />
::*Drier climates will increase the oxidation of carbon stores but reduce methane emissions.<br />
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====Policies and Programs====<br />
::[[Image:Wetland_Carbon_Cycle.png|right|thumb|400px|Wetland Carbon Cycle<ref name="thirty-three">Foster, .John, Lisa Evans, Alison Curtin, and Brydie Hill. (2012) The Role of Wetlands in the Carbon Cycle. Issues Paper The Role of Wetlands in the Carbon Cycle. pag. Department of Environment. Australian Government, 2012. Web.</ref>.]] <br />
::A number of policies and outreach programs have been place to provide a positive feedback towards degradation of wetlands and emission of greenhouse gases by offsetting carbon sequestration and sources.. One of such policy called the Carbon Farming Initiative is currently carried out by the Department of Climate Change and Energy Efficiency. The policy is to implement change within the farmers’ lands. By storing excess greenhouse gas emission from wetlands into their lands, the farmers are able to earn carbon credits. Other organizations such as Regional Natural Resource Management Planning for Climate Change Fund and Biodiversity Fund are implementing policies to maintain healthy levels of greenhouse gas emission in wetlands.<br />
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==References==<br />
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Recently edited by students of [mailto:kmscow@ucdavis.edu Kate Scow], Winter 2016.<br />
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Kmscow
https://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=132749
Bioremediation
2018-03-12T03:47:44Z
<p>Kmscow: /* Primary substrate utilization */</p>
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<div>{{Curated}}<br />
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Through agriculture, industry, and daily life, harmful chemicals have been released into the earth’s air, soil, and water. Depending on their concentrations, these substances can have destructive consequences on ecosystems, as well as cause severe damage to humans and other organisms nearby. Soil pollution is of special importance because of its impact on surface, groundwater and air contamination and can easily spread and be consumed by humans. <br />
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[[Image:Bioremediation_images.jpeg|upright=3|thumb|Retrieved from Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120.]]<br />
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<b>Biodegradation</b> is the biologically catalyzed modification of an organic chemical's structure. However, this modification can be through different metabolic pathways and does not necessarily mean a reduction in toxicity. Mineralization, one type of biodegradation, is defined as the conversion of an organic substance to its inorganic constituents, rendering the original compound harmless. [23]. Transformation is defined as any metabolically-induced change in the chemical composition of a compound [14].<br />
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<b>Bioremediation</b> refers to the use of microorganisms to degrade contaminants that pose environmental and human risks. Bioremediation processes typically involve the actions of many different microbes acting in parallel or sequence to complete the degradation process. Both in situ (in place) and ex situ (removal and treatment in another place) remediation approaches are used. The versatility of microbes to degrade a vast array of pollutants makes bioremediation a technology that can be applied in different soil conditions [3]. Though it can be inexpensive and in situ approaches can reduce disruptive engineering practices, bioremediation is still not a common practice [1].<br />
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A widely used approach to bioremediation involves stimulating naturally occurring microbial communities, providing them with nutrients and other needs, to break down a contaminant. This is termed <b>biostimulation.</b> Biostimulation can be achieved through changes in pH, moisture, aeration, or additions of electron donors, electron acceptors or nutrients. Another bioremediation approach is termed <b>bioaugmentation</b>, where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously.<br />
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Recent awareness of the dangers of many chemicals used in society has led to research on formulation of products that are more easily degraded in the environment.<br />
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From an ecological point of view, bioremediation depends on the various interactions between three factors: substrate (pollutant), organisms, and environment, as shown in the figure at right [4]. The interactions of these factors affect biodegradability, bioavailability, and physiological requirements, which are important in assessing the feasibility of bioremediation [4]. <b>Biodegradability</b>, or whether a chemical can be degraded or not, is determined by the presence or absence of organisms that are able to degrade a chemical of interest and how widespread these organisms are in the site [4]. The substrate (pollutant) can interact with its surrounding environment to change its <b>bioavailability</b>, or availability to organisms that are capable of degrading it; for example, substrate has low bioavailability if it is tightly bound to soil organic matter or trapped inside aggregates [4]. <b>Physiological requirements</b>, or set of conditions required by organisms to carry out bioremediation in the environment, include nutrient availability, optimal pH, and availability of electron acceptors, such as oxygen and nitrate [4]. Also, the environment needs to be habitable for organisms involved in bioremediation [4].<br />
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=='''Brief History'''==<br />
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[[Image:Wasterwater_treatment.png|upright=2.25|thumb|First Water Treatment Facility in Japan, 1934 Image from http://www.sewerhistory.org/grfx/trtmnt/trtmnt3.htm]] <br />
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Microorganisms in the environment have always broken down waste, and humans have always (knowingly or unknowingly) used them in agricultural, domestic, and industrial activities [24]. As the urbanized world shifted to a more industrial system, however, people began to take an active approach in bioremediation. In the late nineteenth century, wastewater treatment plants were formed, but even so, this was not officially called bioremediation .<br />
The project considered the initial spark of the bioremediation movement was the report “Beneficial Stimulation of Bacterial Activity in Groundwater Containing Petroleum Products” by R.L. Raymond et al. in 1975. By testing the relationship between oil presence and bacterial stimulation, Raymond found that adding nutrients to soil hastened the oil removal. This led to the development of in situ bioremediation [24].<br />
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Initial bioremediation projects focused on “pump and treat” (ex situ) methods in soil around gas stations and refinery spills to get oil out of groundwater sources, but soon cleaning up chlorinated hydrocarbons became a primary concern [24]. Chlorinated compounds were commonly used in pesticides, but when people learned it was a possible carcinogen and causing ozone depletion, research into bioremediation took off [24]. This was when anaerobic bacteria started being used, as it was discovered that they dechlorinate compounds much more quickly than do aerobic bacteria, and produce fewer damaging iron compounds that precipitate from the reactions [24].<br />
<br />
=='''Overview of Pollutants'''==<br />
Pollutants found in soils present a variety of different human health risks. Soil pollutants are typically classified as organic and inorganic pollutants. The remediation of some of these pollutants will be discussed in greater depth in the following sections.<br />
Below is a link to website with a list of examples of soil pollutants and their effects on human health:<br />
<br />
[http://www.environmentalpollutioncenters.org/soil/examples/ Summary of health effects of pollutants]<br />
<br />
==='''Organic Pollutants'''===<br />
Industrialization resulted in increased use of organic compounds that build up and persist in the environment [11]. Main sources of organic pollutants are through anthropogenic activities, including use of solvents, pesticides, and fuels [11]. Some of these organic compounds are highly toxic and they are associated with variety of health issues around the world [11].<br />
<br />
Table below lists some groups of contaminants, examples, and their sources.<br />
<br />
[[Image:Pollutants_list.png|center|upright=2.5|thumb|Retrieved from Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172.]]<br />
<br />
While organic pollutants are causing both environmental and health problems, bioremediation offers an effective solution to the pollution [11]. The table below lists some of the organic pollutants and microorganisms that are found to be able to degrade them.<br />
<br />
[[Image:Pollutants_and_organisms.png|center|upright=2.5|thumb|Retrieved from Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9]]<br />
<br />
==='''Inorganic Pollutants'''=== <br />
{| border="1" style="float:right; margin-left: 10px; text-align:center"<br />
|+ Most inorganic pollutants are due to human activities.<br />
!Pollutant<br />
!Source<br />
|-<br />
| [https://en.wikipedia.org/wiki/Arsenic Arsenic] || Pesticides, wood preservatives, biosolids, ore mining and smelting<br />
|- <br />
| [https://en.wikipedia.org/wiki/Cadmium Cadmium] || Paints and pigments, plastic stabilizers, electroplating, phosphate fertilizers<br />
|-<br />
| [https://en.wikipedia.org/wiki/Chromium Chromium] || Tanneries, steel industries, fly ash<br />
|- <br />
| [https://en.wikipedia.org/wiki/Copper Copper] || Pesticides, fertilizers, biosolids, ore mining and smelting<br />
|-<br />
| [https://en.wikipedia.org/wiki/Mercury_%28element%29 Mercury] || Gold and Silver mining, coal combustion<br />
|-<br />
| [https://en.wikipedia.org/wiki/Nickel Nickel] || Effluent, kitchen appliances, surgical instruments, automobile batteries<br />
|-<br />
| [https://en.wikipedia.org/wiki/Lead Lead] || Aerial emission from combustion of leaded fuel, batteries waste, insecticide and herbicides.<br />
|}<br />
<br />
A majority of heavy metal pollutants come from human sources that accumulate over time.<br />
<br />
There are also natural forms of contamination from normal biological processes, which include:<br />
<br />
1. Weathering of minerals over time<br />
<br />
2. [https://en.wikipedia.org/wiki/Erosion Erosion] and [https://en.wikipedia.org/wiki/Volcano volcanic activities]<br />
<br />
3. [https://en.wikipedia.org/wiki/Wildfire Forest fires] and biogenic source<br />
<br />
4. Particles released by vegetation<br />
<br />
Heavy metals can be absorbed by microbes at cellular binding sites. Extracellular polymers of these microbes can complex heavy metals through various mechanisms [21]. These specialized microorganisms can mineralize the organic contaminants to metabolic intermediates, which are used as primary substrates for cell growth. The microbes prevalent in heavily metal-contaminated soil can alter the oxidation state of the heavy metals by immobilizing them [21], allowing them to be easily removed. Bioremediation of heavy metals from microbes is not heavily researched, mostly due to an incomplete understanding of the genetics of the microbes used in metal adsorption. ''[https://microbewiki.kenyon.edu/index.php/Geomicrobiology Geomicrobiology]'' takes a better look at the interactions between microbes and inorganic material.<br />
<br />
=='''Organisms'''==<br />
As stated previously, bioremediation involves various microorganisms that are able to degrade and reduce toxicity of environmental pollutants [12]. Therefore, the interactions of microbes with the environment and pollutants are significant in determining effectiveness of bioremediation [4]. Those microbes can be either naturally present in the site of bioremediation or isolated from other sites and inoculated artificially [12]. Biodegradation often occurs as part of microbial metabolism and in some cases, microbes are able to directly harvest carbon and energy by breaking down pollutants [12]. Sections below go over bacteria and fungi, the commonly used organisms in bioremediation, and archaea, the more recently discovered group of organisms with unique potential in bioremediation.<br />
<br />
==='''Bacteria'''===<br />
Bacteria are widely diverse organisms, and thus make excellent players in biodegradation and bioremediation. There are few universal toxins to bacteria, so there is likely an organism able to break down any given substrate, when provided with the right conditions (anaerobic versus aerobic environment, sufficient electron donors or acceptors, etc.). Below are several specific bacteria species known to participate in bioremediation.<br />
<br />
===='''''[[Pseudomonas putida]]'''====<br />
[[Image:Pseudomonas_putida.png|upright=1|thumb|Pseudomonas putida, Image © http://www.denniskunkel.com/DK/Bacteria/23859D.html]]<br />
<br />
''Pseudomonas putida'' is a gram-negative soil bacterium that is involved in the bioremediation of toluene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===='''''[[Dechloromonas aromatica]]''' ====<br />
''Dechloromonas aromatica'' is a rod-shaped bacterium which can oxidize aromatics including benzoate, chlorobenzoate, and toluene, coupling the reaction with the reduction of oxygen, chlorate, or nitrate. It is the only organism able to oxidize benzene anaerobically. Due to the high propensity of benzene contamination, especially in ground and surface water, ''D. aromatic'' is especially useful for in situ bioremediation of this substance. [13]<br />
<br />
===='''Nitrifiers and Denitrifiers'''==== <br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage process that involves nitrification and denitrification. During nitrification, ammonium is oxidized to nitrite by organisms like <i>Nitrosomonas europaea</i>.Then, nitrite is further oxidized to nitrate by microbes like <i>Nitrobacter hamburgensis</i>.<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like <i>Paracoccus denitrificans </i>[2]. The result is N2 gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
===='''''[[Deinococcus radiodurans]]'''====<br />
''Deinococcus radiodurans'' is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered strain of Deinococcus radiodurans has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7].<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like ''[[Paracoccus denitrificans]]'' [2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
[[Image:Alcanivorax_borkumensis.png|upright=1|thumb|Alcanivorax borkumensis, Image©https://www.biotechnologie.de/BIO/Navigation/EN/Funding/foerderbeispiele,did=44848.html?view=renderPrint [25]]]<br />
<br />
===='''''[[Methylibium petroleiphilum]]'''====<br />
''Methylibium petroleiphilum'' (formally known as PM1 strain) is a bacterium capable of [https://en.wikipedia.org/wiki/Methyl_tert-butyl_ether methyl tert-butyl ether] (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
===='''''[[Alcanivorax borkumensis]]'''====<br />
''Alcanivorax borkumensis'' is a marine rod-shaped bacterium which consumes hydrocarbons, such as the ones found in fuel, and produces carbon dioxide. It grows rapidly in environments damaged by oil, and has been used to aid in cleaning the more than 830,000 gallons of oil from the [https://en.wikipedia.org/wiki/Deepwater_Horizon_oil_spill Deepwater Horizon oil spill] in the Gulf of Mexico [25].<br />
<br />
==='''Fungi (Mycoremediation)'''===<br />
Current bioremediation applications primarily utilize bacteria, with comparatively few attempts to use fungi. Fungi have fundamentally important roles because of their participation in the cycling of elements through decomposition and transformation of organic and inorganic materials. These characteristics can be translated into applications for bioremediation which could break down organic compounds and reduce the risks of metals. In some cases, fungi have an advantage over bacteria not just in metabolic versatility but also their environmental resilience.They are able to oxidize a diverse amount of chemicals and survive in harsh environmental conditions such as low moisture and high concentrations of pollutants. Therefore, fungi are potentially an extremely powerful tool in soil bioremediation and some versatile species such as <b>[https://en.wikipedia.org/wiki/Wood-decay_fungus#White_rot White Rot Fungi]</b> have been a hot topic of research. [16,17]<br />
<br />
===='''Biodegradation Capacities of White rot fungi'''====<br />
Using fungi as potential treatment of contaminants began in 1985 when the white rot species Phanerochaete chrysosporium was discovered to metabolize multiple key environmental pollutants. The most important feature of these fungi is their enzymatic functional ability to metabolize complex chemicals such as lignin. Similar abilities were later discovered in other white rot fungal species. In addition, white rot fungi are highly advantageous because they degrade lignin extracellularly through its hyphal extension. This allows them to access soil contaminants that other organisms are incapable of and maximize surface area for enzymatic interaction. These inexpensive fungi can tolerate extreme environmental conditions, such as pH, temperature, and moisture content. While many microbial organisms that are used for bioremediation require pre-conditioning of the environment for them to survive in, white rot fungi can directly be applied into most systems because they degrade based upon nutrient deprivation. [18]<br />
<br />
[[Image:040504062021.jpg|right|thumb|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x]]<br />
<br />
===='''''[[Phanerochaete chrysosporium]]'''====<br />
<i>P. chrysosporium</i> was the first fungi linked to degradation of organic pollutants. Extensive research has show this it has strong potential for bioremediation in pesticides, PAHs, dioxins, carbon tetrachloride, and many other pollutants. Among fungal systems, <i>P. chrysosporium</i> has become the model for bioremediation. Other notable species of white rot fungi include <i>Pleurotus ostreatus</i> and <i>Trametes versicolor</i>. [18]<br />
<br />
===='''Bioremediation of Hydrocarbon Pollutants'''====<br />
<br />
Hydrocarbons are stored deep underground but are brought up to the surface to be transformed and utilized, primarily as an energy source known as fossil fuels. The majority of pollution currently comes from these byproducts in the form Polycyclic Aromatic Hydrocarbons (PAHs), which are xenobiotic environmental pollutants that form when carbon materials are incompletely combusted. Some of examples of PAHs include burning wood, fossil fuels, and cigarette smoke. [19,20]<br />
Currently, bioremediation is only effective for soils contaminated with low-molecular weight PAHs because of bacterial commercial use. However, fungi are effective at PAH degradation in comparison to bacteria for a few reasons. Firstly, they are capable degrading PAH’s that are high in molecular weight, bacteria in comparison are better at degrading smaller molecules. Secondly, fungi can function well in non-aqueous environments and low oxygen conditions, both are conditions where PAH’s can accumulate. Many fungi have evolved mechanisms that allow the to target specific PAHs. Fungi produce extracellular enzymes that degrade lignin, a process called mineralization the produces carbon dioxide as the end product. [19,20]<br />
<br />
===='''Remediating Metals'''====<br />
<br />
Toxic metals can enter the environment all life cycle stages of metal compound. For example, metal leaching can occur from the mining process till the disposal of metal wastes. However in nature, the mobility of metals comes from the geological processes that can be released into the soil and aquatic environments. The environmental largest risk from metal contamination comes from the relationship between metals and compounds that are inherently of incapable of being degraded by any natural procedures. The best solution to treating contamination is transporting the metals to location where they cannot produce negative environmental effects. Fungi have various ways of interacting with metals, some of the techniques are increasing or decreasing the mobility of metals, sorption, or even cellular uptake. After the metals have been absorbed the fungus, they can chemically altered to be stored or translocated through the hyphae and into various plants that participate in symbiosis. [17]<br />
<br />
===='''Pesticide Degradation'''====<br />
<br />
Pesticide accumulation is an issue of great concern among the public, because they are directly associated with food products and water supplies. There are number of technologies used for pesticide clean-up; however, these technologies are generally expensive and inefficient because they require contaminated soil to be excavated and sent to a separate storage location for processing. Bioremediation offers a potential solution that treats contaminated soil and groundwater without needing excavation. Studies show that White Rot Fungi has high promise for soil bioremediation application; however, most tests have been conducted in the lab rather than in the actual environment. This fungi demonstrates the ability to transform and mineralize specific pesticides in soil. [18]<br />
<br />
===='''Environmental Applications'''====<br />
<br />
Although fungi demonstrate significant biochemical and ecological useful qualities, they are hardly utilized for biotechnological purposes. Instead, bacteria are most commonly used because they usually produce superior results in their numerous advantages ranging from their highly specific biochemical reactions to their capabilities of breaking down pollutants efficiently [17]. Fungi are underused primarily because of the costs that come from providing oxygen to fungi in polluted environments. However, filamentous fungi could be highly valuable in situations where bacteria cannot perform. For example, fungi are useful in situations where contaminants are physically blockaded and bacteria cannot reach or in circumstances of environmental extremes such as high acidity or dryness prevent bacteria from functioning. [17]<br />
<br />
==='''[https://en.wikipedia.org/wiki/Archaea Archaea]'''===<br />
The role of archaea in bioremediation has not been studied as commonly as that of bacteria [10]. Nevertheless, numbers of researchers have shown their ability to degrade various pollutants and scientists began to discover more about their potential in participating in bioremediation. Below lists some important facts regarding archaea’s potential role in bioremediation.<br />
<br />
- Biodegradation by extreme [https://en.wikipedia.org/wiki/Halophile halophilic] archaea was not recognized widely in the past, but scientists have found out that extreme halophilic archaea have greater catabolic diversity than expected [9]<br />
<br />
- Hydrocarbon-contamination is observed in some extreme environments, including hypersaline (high salt concentration), high or low temperature, or extreme pH [10]. Archaea’s adaptation to extreme environment gives them the potential to participate in biodegradation and bioremediation in these environments; in fact, microorganisms naturally adapted to the cold environments are known to be important degraders of hydrocarbons in those environments [10].<br />
<br />
- Extreme halophilic archaea has potential to biodegrade pollutants in hypersaline environment, in which bacteria typically used in bioremediation cannot survive or function properly. [5]<br />
<br />
- Some archaea are known to be resistant to variety of antibiotics, including penicillin, cycloheximide, streptomycin, etc, which gives them great advantage in participating in bioremediation in the presence of antibiotics [5].<br />
<br />
===='''Examples of studies of Archaea involved in bioremediation'''====<br />
<br />
Four extreme halophilic strains of archaea (belonging to genus ''[https://en.wikipedia.org/wiki/Halobacterium Halobacterium]'', ''[https://en.wikipedia.org/wiki/Haloferax Haloferax]'', and ''[https://en.wikipedia.org/wiki/Halococcus Halococcus]'') were studied to evaluate their potential to biodegrade crude oil and hydrocarbons. [5] All four strains could use various kinds of hydrocarbons as their carbon or energy sources [5]. Two strains of Haloferax grew on n-alkanes with different lengths, ranging from C8 to C34, and also benzene, toluene, biphenyl, and naphthalene. The research demonstrated the important fact that archaea have potential to carry out biodegradation at high temperatures, in the range of 40-45 °C [5], which is advantageous because hydrocarbons have higher solubility and bioavailability at these higher temperature [10]. The four strains studied were resistant to six different antibiotics, including penicillin, streptomycin, cycloheximide [5] and this gave them the potential to carry out biodegradation in conditions unfavorable for bacteria. Research suggests other genera of archaea are also capable of biodegrading in hypersaline environments [6]<br />
<br />
''[https://en.wikipedia.org/wiki/Halococcus Archaeglobus] fulgidus'', a [https://en.wikipedia.org/wiki/Hyperthermophile hyperthermophile] which can use sulfate as an electron acceptor, can also break down various aromatic hydrocarbons (Peeples, 2014).<br />
<br />
=='''Microbial Processes'''==<br />
<br />
Microorganisms use a wide range of processes to transform chemicals in their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor. This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. Below, several steps and details of the microorganisms’ actions are described.<br />
<br />
==='''Factors Affecting Rates of Biodegradation'''===<br />
Biodegradation may be influenced by pH, temperature, moisture, carbon sources, soil texture, aerobic versus anaerobic conditions, the number of substituents, and the concentration of the pollutant. It is impossible, however, to make a generalization about the best universal conditions for biodegradation. What’s toxic to some microbes is a nutrient to others, what might be a damaging pH to some is beneficial to others, and so on.<br />
<br />
A greater amount of substituents will cause slower degradation in aerobic environments, but faster degradation in anaerobic ones. Chlorine makes a molecule less degradable due to steric hindrance preventing access to necessary enzymes, therefore molecules with higher chlorination are slower to degrade in aerobic conditions. High concentration of a pollutant generally results in faster rates of degradation. If the concentration drops below a threshold concentration, the enzymes may not detect it and will cease to degrade it [26].<br />
<br />
Soil with small pores, especially clays, may cause biodegradation to take years due to the decrease in bioavailability. Chlorine makes a molecule less degradable due to steric hindrance preventing necessary enzymes from accessing the compound, therefore molecules with higher chlorination are slower to degrade. <br />
<br />
The rate at which a compound is transformed, as well as the curves that describe its transformation, is referred to as kinetics, and is affected by all factors listed above. First order kinetics (exponential decay) often describes biodegradation when the initial substrate concentration is low, while zero-order kinetics (linear biodegradation) is often observed when the substrate concentration is very high. In some cases if the concentration of the chemical falls below a critical threshold concentration, the microbes can no longer transform it and the chemical persists. <br />
<br />
The power rate model depicting the relationship between concentration and rate of degradation (first order decay here) is as follows:<br />
<br />
-dC/dt = kC^n<br />
<br />
C is substrate concentration, t is time, k is a rate constant for the chemical in question, and n is an appropriate parameter. The values of k and n are adjusted until a line is found to match experimental data [23].<br />
<br />
==='''Primary substrate utilization'''===<br />
<b>Primary substrate utilization</b> occurs when a microbe both transforms a substrate and uses it as an energy or carbon source. [15] An electron acceptor is required for these transformations. It can be anaerobic or aerobic, although the presence of oxygen tends to speed up reactions. This type of biodegradation is common in break down of petroleum compounds and some pesticides.<br />
<br />
==='''Cometabolism (Secondary Substrate Utilization)'''===<br />
<b>Cometabolism</b> involves the fortuitous transformation of a chemical by an organism while the organism uses a different substance as its primary energy or carbon source [14]. During the actual reaction degrading the substance, it appears that the organism involved has no net carbon or energy gain, and may even result in a product which is toxic to the cell [14]. <br />
<br />
A key example of cometabolism is fortuitous metabolism in the degradation of trichloroethylene, shown in the diagram below. An organic growth substrate such as propane or butane is required for the enzymatic activity that transforms TCE. [14]<br />
<br />
[[Image:Cometabolism.png|center|upright=3|thumb|Image from Kate Scow lecture, 2016]]<br />
<br />
==='''Reductive and Hydrolytic Dehalogenation'''===<br />
Chloride and other halogens are common components of pesticides and hazardous industrial wastes, and by removing them the toxic chemical can often be remediated [23]. If the halogen is replaced by a hydrogen (RCl -> RH), then it is <b>reductive dehalogenation</b>. If two halogens are replaced simultaneously, then the process is called <b>dihaloelimination</b>, although it still falls under reductive dehalogenation [14]. If the halogen is replaced by OH (RCl -> ROH) then it’s <b>hydrolytic dehalogenation</b>. In both cases, the halogen is released as its inorganic form into the environment [23].<br />
<br />
==='''Acclimation'''===<br />
An <b>acclimation period</b>, also called an <b>adaptation</b> or <b>lag period</b>, occurs when no destruction of a given chemical is observed [23]. It is caused by the microbes transitioning to their altered environment and shifting their metabolism to better suit it [14]. It can last for anywhere from hours (such as aromatic compounds in warm, oxygenated soils) to months (such as halobenzoates in anaerobic sediments) depending on the chemical in question and the environment [23]. Acclimation periods can be affected by temperature, the presence of oxygen, pH, and concentration of the substance. Although they are most often faster in warm, aerated, and fairly dry environments, there are few consistencies between what shortens or lengthens the period, even if the concentration is the same [23]. Insecticides including methyl parathion and azinphosmethyl; herbicides including 2, 4-D, MCPA, Mecoprop, TCA, and amitrole; the quaternary ammonium compound dodecyltrimethylammonium chloride; polycyclic aromatic hydrocarbons including naphthalene and anthracene; and other chemicals such as phenol, chlorobenzene, PCP, diphenyl-methane, and NTA have all been reported to have acclimation periods, and this can be of severe human concern [23]. The continued presence of these toxins extends human, plant, and animal exposure, and if the chemical is in water, it can allow the substance to flow further and impact environments distant to its site of origin before being degraded.<br />
<br />
==='''Detoxification and Activation'''===<br />
<b>Detoxication</b>, sometimes called <b>detoxification</b>, has been referred to as the “most important role of microorganisms in the transformation of pollutants” [23]. The process is the changing of a molecule into something less harmful to a species in question. There are a number of ways a molecule can be transformed, including hydrolysis, hydroxylation, dehalogenation, demethylation, methylation, and ether cleavage [23]. By breaking bonds, or adding or removing groups, the organism reduces its effect on the environment. Furthermore, although sometimes the resulting chemical is simply excreted as waste, the organism may also be able to use this new compound as a carbon source or further modifies it until it is released as CO2 [23].<br />
<br />
There are instances where the initial compound is harmless, and in fact the substance produced by microorganisms, or an intermediate in the degradation process, is a toxin [23]. This process is called activation. For this reason, it is important to test all steps of a reaction when determining how a compound is degrading. The new toxins may also be more or less mobile than its predecessor, so it can either stick around one area for extended periods of time or spread to other areas and increase damage [23]. A prevalent example of this is the dechlorination of TCE, which produces DCE (50 times more hazardous than TCE) and Vinyl Chloride (a known carcinogen) [14]. Commonly used insecticides in the past, like zinophos, trichloronat, and carbofuran, were all found to increase a soil’s toxicity with extended use [23].<br />
<br />
=='''Bioremediation treatment methods'''==<br />
In order for bioremediation to be successful, it requires sufficient proof for the degradation of contaminants. However, determining the effectiveness and completeness to reach sufficient results is one of the major issues. Natural attenuation relies on natural processes to clean up or attenuate pollution in soil and groundwater [27]. This remediation is done without human interaction, and is primarily used as a monitoring technique, to make sure more aggressive cleanup strategies are not needed. [https://en.wikipedia.org/wiki/Abiotic_component Abiotic] and [https://en.wikipedia.org/wiki/Biotic_component biotic] factors play a distinguishing factor of how effective bioremediation is.<br />
<br />
Current monitoring practices determine the disappearance of contaminants and their degradation products to regulatory levels that are monitored by toxicity testing, usually on single organisms or species to ensure there are no induced changes that may result in residual toxicity. The problem with these monitoring techniques is that the assessment of contaminants may result in an inaccurate indicator of residual toxicity[28]. Rather, studying the microbial community response may be a more comprehensive indicator of residual toxicity than a single species. Once sufficient evidence is provided, human intervention may be needed for a more effective cleanup process. <br />
<br />
There are two types of remediation that are done, ex situ: which is done by removing the contaminated soil or water and treating it outside the source, and in situ: which treatment takes place within the contaminated area. There are some treatments methods that can be either ex situ or in situ. Some techniques may deal with the mobilization of pollutants, to move them out of an area, or immobilized to keep them out of an area such as a water table.<br />
<br />
<br />
[[Image:Summary_of_bioremediation_strategies.png|center|upright=3|thumb|A comparative analysis of the different types of bioremediation. It can be used to find which remediation technique may be used in certain circumstances [12]]]<br />
<br />
<br />
[[Image:Biopiling.png|right|upright=1.5|thumb|Contaminated soil is mixed with amendments and piled on top of a liner, while a pipe with a blower controls aeration. [29]]]<br />
==='''Ex-situ'''===<br />
Ex-situ techniques are those that are applied to soil and groundwater which has been removed from the site via excavation or pumping [12]. The methods used include composting, biofilters, and biopiling. Ex-situ is used for smaller projects, primarily because larger excavation of soil is not prefered. The movement of the soil can be more detrimental by destroying the preestablish horizons in the soil.<br />
<br />
[[Image:Composting.png|right|upright=3|thumb|Composting is a very versatile remediation technique that can be used for either: a very broad treatment with many contaminants, or very specific treatment that utilizes particular microbes that target specific contaminants [30]. It can also be used to augment other treatment methods.]]<br />
<br />
===='''Biopiling'''====<br />
Excavated soils are mixed with soil amendments and placed on a treatment area. Biopiles are aerated with the use of perforated pipes and blowers in order to control the progression of biodegradation more efficiently by controlling the supply of oxygen [29], which in turn may affect other factors such as pH. This system is primarily used to remediate systems with oil and hydrocarbon contamination. The remediated soil is placed in a liner to prevent further contamination of the soil, they may also be covered with plastic to control runoff, evaporation, and [https://en.wikipedia.org/wiki/Volatilisation volatilization].<br />
<br />
===='''Composting'''====<br />
Nutrients are added to soil that is mixed to increase aeration and activation of indigenous microorganisms. Composting is done in a separate container, then when composting is complete it is incorporated into the soil. Bioremediation by the utilization of compost relies on the adsorption capabilities of organic matter and the degradation capabilities of microorganisms present[30]. Composting is recognized as as one of the most cost-effective technologies for soil bioremediation and it can be done on large and small scales. The use of composting is a very versatile technique for soil polluted by a wide range of organic pollutants and heavy metals, making it great for easier remediation involving various pollutants. The utilization of organic wastes for soil remediation is also helpful in decreasing the need for their storage and treatment. Organic matter that is generated from composting offers the benefit of improving soil quality and structure. Composting is primarily used for remediation over a longer period of time, as the nutrients for the microbes are released gradually and requrire more time compared to quicker treatments such as biostimulation.<br />
<br />
==='''In-situ'''===<br />
In-situ techniques are applied to soil and groundwater at the site with minimal disturbance[12]. These methods include biostimulation, bioleaching, biosorption, and bioventing. In-situ is preferred because it is often minimally invasive to the soil structure in comparison to ex-situ, but it can be expensive due to specialized equipment.<br />
<br />
===='''Biostimulation'''====<br />
This method involves the addition of nutrients to a polluted site in order to encourage the growth of naturally occurring chemical-degrading microorganisms[31]. Biostimulation is primarily done by the addition of various nutrients that are limited in the soil as well as electron acceptors, such as phosphorus, nitrogen and oxygen, or increasing the amount of available carbon in order to increase the population or activity of naturally occurring microorganisms. Other approaches are to optimize environmental conditions such as aeration, the addition of nutrients, altering pH and temperature control [32]. The primary advantage of biostimulation is that it is done by native microorganisms that are well-suited to the environment, and are already well distributed spatially. The challenge is delivering additives so they are readily available to the subsurface microbes.<br />
<br />
===='''Metal Biosorption'''====<br />
Adsorption of metals and other ions of an aqueous solution by the use of microbes. The biosorption process involves a solid phase and a liquid phase containing a dissolved species to be sorbed [34]. The process continues until equilibrium is established between the amount of solid-bound sorbate species and its portion remaining in the solution. The degree of affinity for the sorbate determines its distribution between the solid and liquid phases.<br />
<br />
Biosorption processes are very important in the environment, and has been utalized for conventional biotreatment processes. Biosorption is primarily aimed at the removal or recovery of organic and inorganic substances from solution [35]. The commercialization of biosorption technologies has been limited so far.<br />
<br />
[[Image:Bioventing.png|right|upright=2.5|thumb|Bioventing is primarily used for injecting air into specific remediation zones, adding oxygen as a readily available electron acceptor where it would otherwise be anaerobic. It can also be reversed to make a more anaerobic environment. Either technique can be applied depending on the remediating microbes would thrive in [36].]]<br />
<br />
===='''Bioventing'''====<br />
Bioventing is an In situ remediation technology that uses indigenous microorganisms to biodegrade organic constituents adsorbed to soils in the unsaturated zone[36]. The availability of oxygen generally controls the rate at which aerobic bioremediation proceeds. Bioventing is the coupling of soil venting and bioremediation. Bioventing can be successfully applied to compounds ranging from gasoline or diesel, to heavier hydrocarbons[36]. The addition of nutrients with the bioventing flow rates can achieve greater contaminant reductions than venting alone.<br />
<br />
==='''Ex-situ or In-situ'''===<br />
Some methods can be used by either in-situ or ex-situ methods. The soil or water can be removed from the contamination source and treated, or treated at the source, the method chosen can be based on many factors such as how expensive the project may be or how much contaminant needs to be treated. These methods include bioaugmentation, land farming and biofiltration.<br />
<br />
===='''Bioaugmentation'''====<br />
Bioaugmentation is the addition of non-native microorganisms that have the ability to degrade the contaminants that are recalcitrant to the indigenous microbiota. Bioaugmentation has been proven successful in cleaning organic pollutant, but still faces many environmental problems, such as the survival of strains introduced to soil[37]. The number of introduced microorganisms usually decreases shortly after soil inoculation. <br />
<br />
Bioaugmentation is ideal for soil:<br />
<br />
1. With low number of microbes that are capable of degrading targeted pollutants<br />
<br />
2. Containing compounds requiring multi stepped remediation.<br />
<br />
Augmentation techniques have a great potential for [https://en.wikipedia.org/wiki/Category:Aromatic_compounds aromatic compound] remediation. The most important step in successful bioaugmentation is selection of proper microbial strains. The success of bioaugmentation strongly depends on the ability of inoculants to survive in contaminated soil, which may vary due to predation and an environment that does provide all the conditions and nutrients that the organism needs to survive. In some cases the environment may be toxic to the added organism.<br />
<br />
===='''Land Farming'''====<br />
Contaminated soil is mixed with amendments such as nutrients, and then they are tilled into the earth, or the contaminated soil is applied into lined beds and periodically turned over or tilled to aerate the waste [38]. The topmost layer is the area of concentration for this method, so it is not ideal for deeper remediation. Land farming differs from composting because it actually incorporates contaminated soil into soil that is uncontaminated [38]. The higher zone of remediation will typically contain primarily lighter hydrocarbons that can be volatilized. The material is periodically tilled for aeration to hasten remediation of any nutrients and allow more oxygen to act as electron acceptors, as well as allowing volatilization to occur. Contaminants are degraded, transformed, and immobilized by microbiological processes and oxidation. Soil conditions are controlled to optimize the rate of contaminant degradation, moisture content, frequency of aeration, and pH are all conditions that may be controlled [38]. <br />
<br />
[[Image:Biofilter.png|right|upright=1.5|thumb|The application of a micro-algal/bacterial biofilter in the primary outflow of soil water [39]]]<br />
<br />
===='''Biofilter'''====<br />
Biofilters are primarily used for the filtration of contaminated groundwater in the soil. Biofilters can be used above soil, where the water will be pumped aboveground for treatment, or a filter can be placed in the soil near an outflow. A micro-algal/bacterial biofilter can be used for the detoxification of copper and cadmium metal wastes [22]. Biofilters have been used in larger industry environments to treat contaminated outflow of water. [https://en.wikipedia.org/wiki/Chromobacterium_violaceum Chromobacterium violaceum], is used to treat water and soil contaminated with silver nanoparticles, reducing its concentration.<br />
<br />
=='''Bioremediation Synopsis'''==<br />
<br />
==='''Advantages'''===<br />
1. Bioremediation that involves natural attenuation or biostimulation is a publicly accepted treatment of polluted soil because it is based upon natural processes. Microbes that metabolize contaminants often increase in population when the contaminant is present and thus rates of biodegradation may increase over time, up to a point. If biodegradation is complete (i.e. mineralization) the products from treatment are harmless; such as carbon dioxide, water, and cellular biomass. [12]<br />
<br />
2. In situ bioremediation can result in complete degradation of pollutants into harmless products on site. This removes the risks involved with transportation for treatment and elimination of contaminated substances. [12]<br />
<br />
3. Bioremediation can be a cheaper alternative to other technologies used for pollution mitigation. [12]<br />
<br />
==='''Disadvantages'''===<br />
1. Only biodegradable compounds are capable of undergoing bioremediation. Not every compound is capable of fully degrading quickly. [12]<br />
<br />
2. The products of biodegradation may potentially be even more persistent or toxic than the original contaminant. [12]<br />
<br />
3. Biological functions are usually extremely specific and require the presence of microbes that are capable of metabolizing the contaminants. In order for the correct microbes to be present, the appropriate environmental conditions, levels of nutrients, and contaminants need to be met. [12]<br />
<br />
4. Scaling up the size of studies from small initial studies to commercial-scale field operations is difficult.[12]<br />
<br />
5. The real environment contains contaminants that are mixed, unevenly distributed, and in different phases (solid, liquid, gas). More research needs to be completed to create technologies that can adapt. [12]<br />
<br />
6. Compared to other treatment technologies, bioremediation often takes more time. [12]<br />
<br />
7. Problems with ensuring adequate contact between the microbes and the contaminant. preferential pathway and soil structure can leave uncertainty in remediation dispersal.[12]<br />
<br />
=='''References'''== <br />
<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdf United States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120. <br />
<br />
5. Al-Mailem, D. M., Sorkhoh, N. A., Al-Awadhi, H., Eliyas, M., & Radwan, S. S. (2010). Biodegradation of crude oil and pure hydrocarbons by extreme halophilic archaea from hypersaline coasts of the Arabian Gulf. Extremophiles, 14(3), 321-328. doi: 10.1007/s00792-010-0312-9<br />
<br />
6. Fairley, D. J., Boyd, D. R., Sharma, N. D., Allen, C. C., Morgan, P., & Larkin, M. J. (2002). Aerobic metabolism of 4-hydroxybenzoic acid in Archaea via an unusual pathway involving an intramolecular migration (NIH shift). Appl Environ Microbiol, 68(12), 6246-6255.<br />
<br />
7. Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008<br />
<br />
8. Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008<br />
<br />
9. Le Borgne, S., Paniagua, D., & Vazquez-Duhalt, R. (2008). Biodegradation of organic pollutants by halophilic bacteria and archaea. J Mol Microbiol Biotechnol, 15(2-3), 74-92. doi: 10.1159/000121323<br />
<br />
10. Margesin, R., & Schinner, F. (2001). Biodegradation and biore<br />
mediation of hydrocarbons in extreme environments. Appl Microbiol Biotechnol, 56(5-6), 650-663.<br />
<br />
11. Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9<br />
<br />
12. Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172. <br />
<br />
13. "Dechloromonas Aromatica RCB." JGI Genome Portal, 16 Feb. 2016. [http://genome.jgi.doe.gov/decar/decar.home.html http://genome.jgi.doe.gov/decar/decar.home.html]<br />
<br />
14. King, R. Barry, John K. Sheldon, and GIlbert M. Long. (1998). Practical Environmental Bioremediation: The Field Guide. 2nd ed. Boca Raton: CRC, 1998.<br />
<br />
15. "Manual, Bioventing Principles and Practices." United States Environmental Protection Agency I (1995)<br />
<br />
16. Gadd, G. M. (Ed.). (2001). Fungi in bioremediation (No. 23). Cambridge University Press<br />
<br />
17. Harms, H., Schlosser, D., & Wick, L. Y. (2011). Untapped potential: exploiting fungi in bioremediation of hazardous chemicals. Nature Reviews Microbiology, 9(3), 177-192<br />
<br />
18. Fragoeiro, S. (2005). Use of fungi in bioremediation of pesticides. Applied Mycology Group Institute of Bioscience and Technology. Cranfield University<br />
<br />
19. Singh, H. (2006). Mycoremediation: fungal bioremediation. John Wiley & Sons. 283-285<br />
<br />
20. Norton, J. M. (2012). Fungi for Bioremediation of Hydrocarbon Pollutants. University of Hawai’i at Hilo. Hohonu, 10, 18-21<br />
<br />
21. Dixit, Ruchita, Emptyyn Wasiullah, Deepti Malaviya, Kuppusamy Pandiyan, Udai Singh, Asha Sahu, Renu Shukla, Bhanu Singh, Jai Rai, Pawan Sharma, Harshad Lade, and Diby Paul. "Bioremediation of Heavy Metals from Soil and Aquatic Environment: An Overview of Principles and Criteria of Fundamental Processes." Sustainability 7.2 (2015): 2189-212. Print.<br />
<br />
22. Bio-filters for Edge-of-Field Water Quality Management. (n.d.). Retrieved February 24, 2016, from [http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html]<br />
<br />
23. Alexander, Martin. (1999). Biodegradation and Bioremediation. San Diego: Academic Print. <br />
<br />
24. Litchfield, Carol. "Thirty Years and Counting: Bioremediation in Its Prime?" BioScience 55.3 (2005): 273.<br />
<br />
25. Biello, David. "Slick Solution: How Microbes Will Clean Up the Deepwater Horizon Oil Spill." Scientific American (n.d.): n. pag. 25 May 2010. <br />
<br />
26. Scow, Kate. “Lectures in Soil Microbiology.” UC Davis, Winter 2016.<br />
<br />
27 CLU-IN | Technologies Remediation About Remediation Technologies Natural Attenuation Overview. (n.d.). Retrieved February 24, 2016, from https://clu-in.org/techfocus/default.focus/sec/Natural_Attenuation/cat/Overview/<br />
<br />
28. Chauhan, Ashok K., and A. Varma. A Textbook of Molecular Biotechnology. New Delhi: I.K. International Pub. House, 2009. Print.<br />
<br />
29. Biopiles. (n.d.). Retrieved March 13, 2016, from [http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html]<br />
<br />
30. Chen, M., Xu, P., Zeng, G., Yang, C., Huang, D., & Zhang, J. (2015). Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: Applications, microbes and future research needs. Biotechnology Advances, 33(6, Part 1), 745–755.<br />
<br />
31. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. Retrieved March 13, 2016, from [http://www.sciencedirect.com/science/article/pii/S0944501309000585 http://www.sciencedirect.com/science/article/pii/S0944501309000585]<br />
<br />
32. Bioremediation, Biostimulation and Bioaugmention: A Review. (n.d.). Retrieved March 13, 2016, from http://pubs.sciepub.com/ijebb/3/1/5/<br />
<br />
33. Sulfur Oxides—Advances in Research and Application: 2013 Edition<br />
<br />
34. Fomina, M., & Gadd, G. M. (2014). Biosorption: current perspectives on concept, definition and application. Bioresource Technology, 160, 3–14. Retrieved February 24, 2016, from [https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application]<br />
<br />
35. Kotrba, Pavel, Martina Mackova, and Tomas Macek. (2011). Microbial Biosorption of Metals. Dordrecht: Springer Science Business Media Print.<br />
<br />
36. Bioventing » Water and Soil Bio-Remediation. (n.d.). Retrieved February 24, 2016, from [http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing]<br />
<br />
37. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. <br />
<br />
38. Land Farming. (n.d.). Retrieved March 13, 2016, from http://www.cpeo.org/techtree/ttdescript/lanfarm.htm<br />
<br />
<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=132748
Bioremediation
2018-03-12T03:46:43Z
<p>Kmscow: /* Cometabolism (Secondary Substrate Utilization) */</p>
<hr />
<div>{{Curated}}<br />
<br />
Through agriculture, industry, and daily life, harmful chemicals have been released into the earth’s air, soil, and water. Depending on their concentrations, these substances can have destructive consequences on ecosystems, as well as cause severe damage to humans and other organisms nearby. Soil pollution is of special importance because of its impact on surface, groundwater and air contamination and can easily spread and be consumed by humans. <br />
<br />
[[Image:Bioremediation_images.jpeg|upright=3|thumb|Retrieved from Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120.]]<br />
<br />
<b>Biodegradation</b> is the biologically catalyzed modification of an organic chemical's structure. However, this modification can be through different metabolic pathways and does not necessarily mean a reduction in toxicity. Mineralization, one type of biodegradation, is defined as the conversion of an organic substance to its inorganic constituents, rendering the original compound harmless. [23]. Transformation is defined as any metabolically-induced change in the chemical composition of a compound [14].<br />
<br />
<b>Bioremediation</b> refers to the use of microorganisms to degrade contaminants that pose environmental and human risks. Bioremediation processes typically involve the actions of many different microbes acting in parallel or sequence to complete the degradation process. Both in situ (in place) and ex situ (removal and treatment in another place) remediation approaches are used. The versatility of microbes to degrade a vast array of pollutants makes bioremediation a technology that can be applied in different soil conditions [3]. Though it can be inexpensive and in situ approaches can reduce disruptive engineering practices, bioremediation is still not a common practice [1].<br />
<br />
A widely used approach to bioremediation involves stimulating naturally occurring microbial communities, providing them with nutrients and other needs, to break down a contaminant. This is termed <b>biostimulation.</b> Biostimulation can be achieved through changes in pH, moisture, aeration, or additions of electron donors, electron acceptors or nutrients. Another bioremediation approach is termed <b>bioaugmentation</b>, where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously.<br />
<br />
Recent awareness of the dangers of many chemicals used in society has led to research on formulation of products that are more easily degraded in the environment.<br />
<br />
From an ecological point of view, bioremediation depends on the various interactions between three factors: substrate (pollutant), organisms, and environment, as shown in the figure at right [4]. The interactions of these factors affect biodegradability, bioavailability, and physiological requirements, which are important in assessing the feasibility of bioremediation [4]. <b>Biodegradability</b>, or whether a chemical can be degraded or not, is determined by the presence or absence of organisms that are able to degrade a chemical of interest and how widespread these organisms are in the site [4]. The substrate (pollutant) can interact with its surrounding environment to change its <b>bioavailability</b>, or availability to organisms that are capable of degrading it; for example, substrate has low bioavailability if it is tightly bound to soil organic matter or trapped inside aggregates [4]. <b>Physiological requirements</b>, or set of conditions required by organisms to carry out bioremediation in the environment, include nutrient availability, optimal pH, and availability of electron acceptors, such as oxygen and nitrate [4]. Also, the environment needs to be habitable for organisms involved in bioremediation [4].<br />
<br />
=='''Brief History'''==<br />
<br />
[[Image:Wasterwater_treatment.png|upright=2.25|thumb|First Water Treatment Facility in Japan, 1934 Image from http://www.sewerhistory.org/grfx/trtmnt/trtmnt3.htm]] <br />
<br />
Microorganisms in the environment have always broken down waste, and humans have always (knowingly or unknowingly) used them in agricultural, domestic, and industrial activities [24]. As the urbanized world shifted to a more industrial system, however, people began to take an active approach in bioremediation. In the late nineteenth century, wastewater treatment plants were formed, but even so, this was not officially called bioremediation .<br />
The project considered the initial spark of the bioremediation movement was the report “Beneficial Stimulation of Bacterial Activity in Groundwater Containing Petroleum Products” by R.L. Raymond et al. in 1975. By testing the relationship between oil presence and bacterial stimulation, Raymond found that adding nutrients to soil hastened the oil removal. This led to the development of in situ bioremediation [24].<br />
<br />
Initial bioremediation projects focused on “pump and treat” (ex situ) methods in soil around gas stations and refinery spills to get oil out of groundwater sources, but soon cleaning up chlorinated hydrocarbons became a primary concern [24]. Chlorinated compounds were commonly used in pesticides, but when people learned it was a possible carcinogen and causing ozone depletion, research into bioremediation took off [24]. This was when anaerobic bacteria started being used, as it was discovered that they dechlorinate compounds much more quickly than do aerobic bacteria, and produce fewer damaging iron compounds that precipitate from the reactions [24].<br />
<br />
=='''Overview of Pollutants'''==<br />
Pollutants found in soils present a variety of different human health risks. Soil pollutants are typically classified as organic and inorganic pollutants. The remediation of some of these pollutants will be discussed in greater depth in the following sections.<br />
Below is a link to website with a list of examples of soil pollutants and their effects on human health:<br />
<br />
[http://www.environmentalpollutioncenters.org/soil/examples/ Summary of health effects of pollutants]<br />
<br />
==='''Organic Pollutants'''===<br />
Industrialization resulted in increased use of organic compounds that build up and persist in the environment [11]. Main sources of organic pollutants are through anthropogenic activities, including use of solvents, pesticides, and fuels [11]. Some of these organic compounds are highly toxic and they are associated with variety of health issues around the world [11].<br />
<br />
Table below lists some groups of contaminants, examples, and their sources.<br />
<br />
[[Image:Pollutants_list.png|center|upright=2.5|thumb|Retrieved from Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172.]]<br />
<br />
While organic pollutants are causing both environmental and health problems, bioremediation offers an effective solution to the pollution [11]. The table below lists some of the organic pollutants and microorganisms that are found to be able to degrade them.<br />
<br />
[[Image:Pollutants_and_organisms.png|center|upright=2.5|thumb|Retrieved from Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9]]<br />
<br />
==='''Inorganic Pollutants'''=== <br />
{| border="1" style="float:right; margin-left: 10px; text-align:center"<br />
|+ Most inorganic pollutants are due to human activities.<br />
!Pollutant<br />
!Source<br />
|-<br />
| [https://en.wikipedia.org/wiki/Arsenic Arsenic] || Pesticides, wood preservatives, biosolids, ore mining and smelting<br />
|- <br />
| [https://en.wikipedia.org/wiki/Cadmium Cadmium] || Paints and pigments, plastic stabilizers, electroplating, phosphate fertilizers<br />
|-<br />
| [https://en.wikipedia.org/wiki/Chromium Chromium] || Tanneries, steel industries, fly ash<br />
|- <br />
| [https://en.wikipedia.org/wiki/Copper Copper] || Pesticides, fertilizers, biosolids, ore mining and smelting<br />
|-<br />
| [https://en.wikipedia.org/wiki/Mercury_%28element%29 Mercury] || Gold and Silver mining, coal combustion<br />
|-<br />
| [https://en.wikipedia.org/wiki/Nickel Nickel] || Effluent, kitchen appliances, surgical instruments, automobile batteries<br />
|-<br />
| [https://en.wikipedia.org/wiki/Lead Lead] || Aerial emission from combustion of leaded fuel, batteries waste, insecticide and herbicides.<br />
|}<br />
<br />
A majority of heavy metal pollutants come from human sources that accumulate over time.<br />
<br />
There are also natural forms of contamination from normal biological processes, which include:<br />
<br />
1. Weathering of minerals over time<br />
<br />
2. [https://en.wikipedia.org/wiki/Erosion Erosion] and [https://en.wikipedia.org/wiki/Volcano volcanic activities]<br />
<br />
3. [https://en.wikipedia.org/wiki/Wildfire Forest fires] and biogenic source<br />
<br />
4. Particles released by vegetation<br />
<br />
Heavy metals can be absorbed by microbes at cellular binding sites. Extracellular polymers of these microbes can complex heavy metals through various mechanisms [21]. These specialized microorganisms can mineralize the organic contaminants to metabolic intermediates, which are used as primary substrates for cell growth. The microbes prevalent in heavily metal-contaminated soil can alter the oxidation state of the heavy metals by immobilizing them [21], allowing them to be easily removed. Bioremediation of heavy metals from microbes is not heavily researched, mostly due to an incomplete understanding of the genetics of the microbes used in metal adsorption. ''[https://microbewiki.kenyon.edu/index.php/Geomicrobiology Geomicrobiology]'' takes a better look at the interactions between microbes and inorganic material.<br />
<br />
=='''Organisms'''==<br />
As stated previously, bioremediation involves various microorganisms that are able to degrade and reduce toxicity of environmental pollutants [12]. Therefore, the interactions of microbes with the environment and pollutants are significant in determining effectiveness of bioremediation [4]. Those microbes can be either naturally present in the site of bioremediation or isolated from other sites and inoculated artificially [12]. Biodegradation often occurs as part of microbial metabolism and in some cases, microbes are able to directly harvest carbon and energy by breaking down pollutants [12]. Sections below go over bacteria and fungi, the commonly used organisms in bioremediation, and archaea, the more recently discovered group of organisms with unique potential in bioremediation.<br />
<br />
==='''Bacteria'''===<br />
Bacteria are widely diverse organisms, and thus make excellent players in biodegradation and bioremediation. There are few universal toxins to bacteria, so there is likely an organism able to break down any given substrate, when provided with the right conditions (anaerobic versus aerobic environment, sufficient electron donors or acceptors, etc.). Below are several specific bacteria species known to participate in bioremediation.<br />
<br />
===='''''[[Pseudomonas putida]]'''====<br />
[[Image:Pseudomonas_putida.png|upright=1|thumb|Pseudomonas putida, Image © http://www.denniskunkel.com/DK/Bacteria/23859D.html]]<br />
<br />
''Pseudomonas putida'' is a gram-negative soil bacterium that is involved in the bioremediation of toluene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===='''''[[Dechloromonas aromatica]]''' ====<br />
''Dechloromonas aromatica'' is a rod-shaped bacterium which can oxidize aromatics including benzoate, chlorobenzoate, and toluene, coupling the reaction with the reduction of oxygen, chlorate, or nitrate. It is the only organism able to oxidize benzene anaerobically. Due to the high propensity of benzene contamination, especially in ground and surface water, ''D. aromatic'' is especially useful for in situ bioremediation of this substance. [13]<br />
<br />
===='''Nitrifiers and Denitrifiers'''==== <br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage process that involves nitrification and denitrification. During nitrification, ammonium is oxidized to nitrite by organisms like <i>Nitrosomonas europaea</i>.Then, nitrite is further oxidized to nitrate by microbes like <i>Nitrobacter hamburgensis</i>.<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like <i>Paracoccus denitrificans </i>[2]. The result is N2 gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
===='''''[[Deinococcus radiodurans]]'''====<br />
''Deinococcus radiodurans'' is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered strain of Deinococcus radiodurans has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7].<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like ''[[Paracoccus denitrificans]]'' [2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
[[Image:Alcanivorax_borkumensis.png|upright=1|thumb|Alcanivorax borkumensis, Image©https://www.biotechnologie.de/BIO/Navigation/EN/Funding/foerderbeispiele,did=44848.html?view=renderPrint [25]]]<br />
<br />
===='''''[[Methylibium petroleiphilum]]'''====<br />
''Methylibium petroleiphilum'' (formally known as PM1 strain) is a bacterium capable of [https://en.wikipedia.org/wiki/Methyl_tert-butyl_ether methyl tert-butyl ether] (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
===='''''[[Alcanivorax borkumensis]]'''====<br />
''Alcanivorax borkumensis'' is a marine rod-shaped bacterium which consumes hydrocarbons, such as the ones found in fuel, and produces carbon dioxide. It grows rapidly in environments damaged by oil, and has been used to aid in cleaning the more than 830,000 gallons of oil from the [https://en.wikipedia.org/wiki/Deepwater_Horizon_oil_spill Deepwater Horizon oil spill] in the Gulf of Mexico [25].<br />
<br />
==='''Fungi (Mycoremediation)'''===<br />
Current bioremediation applications primarily utilize bacteria, with comparatively few attempts to use fungi. Fungi have fundamentally important roles because of their participation in the cycling of elements through decomposition and transformation of organic and inorganic materials. These characteristics can be translated into applications for bioremediation which could break down organic compounds and reduce the risks of metals. In some cases, fungi have an advantage over bacteria not just in metabolic versatility but also their environmental resilience.They are able to oxidize a diverse amount of chemicals and survive in harsh environmental conditions such as low moisture and high concentrations of pollutants. Therefore, fungi are potentially an extremely powerful tool in soil bioremediation and some versatile species such as <b>[https://en.wikipedia.org/wiki/Wood-decay_fungus#White_rot White Rot Fungi]</b> have been a hot topic of research. [16,17]<br />
<br />
===='''Biodegradation Capacities of White rot fungi'''====<br />
Using fungi as potential treatment of contaminants began in 1985 when the white rot species Phanerochaete chrysosporium was discovered to metabolize multiple key environmental pollutants. The most important feature of these fungi is their enzymatic functional ability to metabolize complex chemicals such as lignin. Similar abilities were later discovered in other white rot fungal species. In addition, white rot fungi are highly advantageous because they degrade lignin extracellularly through its hyphal extension. This allows them to access soil contaminants that other organisms are incapable of and maximize surface area for enzymatic interaction. These inexpensive fungi can tolerate extreme environmental conditions, such as pH, temperature, and moisture content. While many microbial organisms that are used for bioremediation require pre-conditioning of the environment for them to survive in, white rot fungi can directly be applied into most systems because they degrade based upon nutrient deprivation. [18]<br />
<br />
[[Image:040504062021.jpg|right|thumb|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x]]<br />
<br />
===='''''[[Phanerochaete chrysosporium]]'''====<br />
<i>P. chrysosporium</i> was the first fungi linked to degradation of organic pollutants. Extensive research has show this it has strong potential for bioremediation in pesticides, PAHs, dioxins, carbon tetrachloride, and many other pollutants. Among fungal systems, <i>P. chrysosporium</i> has become the model for bioremediation. Other notable species of white rot fungi include <i>Pleurotus ostreatus</i> and <i>Trametes versicolor</i>. [18]<br />
<br />
===='''Bioremediation of Hydrocarbon Pollutants'''====<br />
<br />
Hydrocarbons are stored deep underground but are brought up to the surface to be transformed and utilized, primarily as an energy source known as fossil fuels. The majority of pollution currently comes from these byproducts in the form Polycyclic Aromatic Hydrocarbons (PAHs), which are xenobiotic environmental pollutants that form when carbon materials are incompletely combusted. Some of examples of PAHs include burning wood, fossil fuels, and cigarette smoke. [19,20]<br />
Currently, bioremediation is only effective for soils contaminated with low-molecular weight PAHs because of bacterial commercial use. However, fungi are effective at PAH degradation in comparison to bacteria for a few reasons. Firstly, they are capable degrading PAH’s that are high in molecular weight, bacteria in comparison are better at degrading smaller molecules. Secondly, fungi can function well in non-aqueous environments and low oxygen conditions, both are conditions where PAH’s can accumulate. Many fungi have evolved mechanisms that allow the to target specific PAHs. Fungi produce extracellular enzymes that degrade lignin, a process called mineralization the produces carbon dioxide as the end product. [19,20]<br />
<br />
===='''Remediating Metals'''====<br />
<br />
Toxic metals can enter the environment all life cycle stages of metal compound. For example, metal leaching can occur from the mining process till the disposal of metal wastes. However in nature, the mobility of metals comes from the geological processes that can be released into the soil and aquatic environments. The environmental largest risk from metal contamination comes from the relationship between metals and compounds that are inherently of incapable of being degraded by any natural procedures. The best solution to treating contamination is transporting the metals to location where they cannot produce negative environmental effects. Fungi have various ways of interacting with metals, some of the techniques are increasing or decreasing the mobility of metals, sorption, or even cellular uptake. After the metals have been absorbed the fungus, they can chemically altered to be stored or translocated through the hyphae and into various plants that participate in symbiosis. [17]<br />
<br />
===='''Pesticide Degradation'''====<br />
<br />
Pesticide accumulation is an issue of great concern among the public, because they are directly associated with food products and water supplies. There are number of technologies used for pesticide clean-up; however, these technologies are generally expensive and inefficient because they require contaminated soil to be excavated and sent to a separate storage location for processing. Bioremediation offers a potential solution that treats contaminated soil and groundwater without needing excavation. Studies show that White Rot Fungi has high promise for soil bioremediation application; however, most tests have been conducted in the lab rather than in the actual environment. This fungi demonstrates the ability to transform and mineralize specific pesticides in soil. [18]<br />
<br />
===='''Environmental Applications'''====<br />
<br />
Although fungi demonstrate significant biochemical and ecological useful qualities, they are hardly utilized for biotechnological purposes. Instead, bacteria are most commonly used because they usually produce superior results in their numerous advantages ranging from their highly specific biochemical reactions to their capabilities of breaking down pollutants efficiently [17]. Fungi are underused primarily because of the costs that come from providing oxygen to fungi in polluted environments. However, filamentous fungi could be highly valuable in situations where bacteria cannot perform. For example, fungi are useful in situations where contaminants are physically blockaded and bacteria cannot reach or in circumstances of environmental extremes such as high acidity or dryness prevent bacteria from functioning. [17]<br />
<br />
==='''[https://en.wikipedia.org/wiki/Archaea Archaea]'''===<br />
The role of archaea in bioremediation has not been studied as commonly as that of bacteria [10]. Nevertheless, numbers of researchers have shown their ability to degrade various pollutants and scientists began to discover more about their potential in participating in bioremediation. Below lists some important facts regarding archaea’s potential role in bioremediation.<br />
<br />
- Biodegradation by extreme [https://en.wikipedia.org/wiki/Halophile halophilic] archaea was not recognized widely in the past, but scientists have found out that extreme halophilic archaea have greater catabolic diversity than expected [9]<br />
<br />
- Hydrocarbon-contamination is observed in some extreme environments, including hypersaline (high salt concentration), high or low temperature, or extreme pH [10]. Archaea’s adaptation to extreme environment gives them the potential to participate in biodegradation and bioremediation in these environments; in fact, microorganisms naturally adapted to the cold environments are known to be important degraders of hydrocarbons in those environments [10].<br />
<br />
- Extreme halophilic archaea has potential to biodegrade pollutants in hypersaline environment, in which bacteria typically used in bioremediation cannot survive or function properly. [5]<br />
<br />
- Some archaea are known to be resistant to variety of antibiotics, including penicillin, cycloheximide, streptomycin, etc, which gives them great advantage in participating in bioremediation in the presence of antibiotics [5].<br />
<br />
===='''Examples of studies of Archaea involved in bioremediation'''====<br />
<br />
Four extreme halophilic strains of archaea (belonging to genus ''[https://en.wikipedia.org/wiki/Halobacterium Halobacterium]'', ''[https://en.wikipedia.org/wiki/Haloferax Haloferax]'', and ''[https://en.wikipedia.org/wiki/Halococcus Halococcus]'') were studied to evaluate their potential to biodegrade crude oil and hydrocarbons. [5] All four strains could use various kinds of hydrocarbons as their carbon or energy sources [5]. Two strains of Haloferax grew on n-alkanes with different lengths, ranging from C8 to C34, and also benzene, toluene, biphenyl, and naphthalene. The research demonstrated the important fact that archaea have potential to carry out biodegradation at high temperatures, in the range of 40-45 °C [5], which is advantageous because hydrocarbons have higher solubility and bioavailability at these higher temperature [10]. The four strains studied were resistant to six different antibiotics, including penicillin, streptomycin, cycloheximide [5] and this gave them the potential to carry out biodegradation in conditions unfavorable for bacteria. Research suggests other genera of archaea are also capable of biodegrading in hypersaline environments [6]<br />
<br />
''[https://en.wikipedia.org/wiki/Halococcus Archaeglobus] fulgidus'', a [https://en.wikipedia.org/wiki/Hyperthermophile hyperthermophile] which can use sulfate as an electron acceptor, can also break down various aromatic hydrocarbons (Peeples, 2014).<br />
<br />
=='''Microbial Processes'''==<br />
<br />
Microorganisms use a wide range of processes to transform chemicals in their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor. This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. Below, several steps and details of the microorganisms’ actions are described.<br />
<br />
==='''Factors Affecting Rates of Biodegradation'''===<br />
Biodegradation may be influenced by pH, temperature, moisture, carbon sources, soil texture, aerobic versus anaerobic conditions, the number of substituents, and the concentration of the pollutant. It is impossible, however, to make a generalization about the best universal conditions for biodegradation. What’s toxic to some microbes is a nutrient to others, what might be a damaging pH to some is beneficial to others, and so on.<br />
<br />
A greater amount of substituents will cause slower degradation in aerobic environments, but faster degradation in anaerobic ones. Chlorine makes a molecule less degradable due to steric hindrance preventing access to necessary enzymes, therefore molecules with higher chlorination are slower to degrade in aerobic conditions. High concentration of a pollutant generally results in faster rates of degradation. If the concentration drops below a threshold concentration, the enzymes may not detect it and will cease to degrade it [26].<br />
<br />
Soil with small pores, especially clays, may cause biodegradation to take years due to the decrease in bioavailability. Chlorine makes a molecule less degradable due to steric hindrance preventing necessary enzymes from accessing the compound, therefore molecules with higher chlorination are slower to degrade. <br />
<br />
The rate at which a compound is transformed, as well as the curves that describe its transformation, is referred to as kinetics, and is affected by all factors listed above. First order kinetics (exponential decay) often describes biodegradation when the initial substrate concentration is low, while zero-order kinetics (linear biodegradation) is often observed when the substrate concentration is very high. In some cases if the concentration of the chemical falls below a critical threshold concentration, the microbes can no longer transform it and the chemical persists. <br />
<br />
The power rate model depicting the relationship between concentration and rate of degradation (first order decay here) is as follows:<br />
<br />
-dC/dt = kC^n<br />
<br />
C is substrate concentration, t is time, k is a rate constant for the chemical in question, and n is an appropriate parameter. The values of k and n are adjusted until a line is found to match experimental data [23].<br />
<br />
==='''Primary substrate utilization'''===<br />
<b>Primary substrate utilization</b> occurs when a microbe both transforms a substrate and uses it as an energy or carbon source. [15] An electron acceptor is required for these transformations. It can be anaerobic or aerobic, although the presence of oxygen tends to speed up reactions. This form of biodegradation can be used for treating petroleum spills or the runoff of a number of pesticides. The rate of reaction follows the guidelines in the previous section, where a higher concentration leads to a higher rate. [15]<br />
<br />
==='''Cometabolism (Secondary Substrate Utilization)'''===<br />
<b>Cometabolism</b> involves the fortuitous transformation of a chemical by an organism while the organism uses a different substance as its primary energy or carbon source [14]. During the actual reaction degrading the substance, it appears that the organism involved has no net carbon or energy gain, and may even result in a product which is toxic to the cell [14]. <br />
<br />
A key example of cometabolism is fortuitous metabolism in the degradation of trichloroethylene, shown in the diagram below. An organic growth substrate such as propane or butane is required for the enzymatic activity that transforms TCE. [14]<br />
<br />
[[Image:Cometabolism.png|center|upright=3|thumb|Image from Kate Scow lecture, 2016]]<br />
<br />
==='''Reductive and Hydrolytic Dehalogenation'''===<br />
Chloride and other halogens are common components of pesticides and hazardous industrial wastes, and by removing them the toxic chemical can often be remediated [23]. If the halogen is replaced by a hydrogen (RCl -> RH), then it is <b>reductive dehalogenation</b>. If two halogens are replaced simultaneously, then the process is called <b>dihaloelimination</b>, although it still falls under reductive dehalogenation [14]. If the halogen is replaced by OH (RCl -> ROH) then it’s <b>hydrolytic dehalogenation</b>. In both cases, the halogen is released as its inorganic form into the environment [23].<br />
<br />
==='''Acclimation'''===<br />
An <b>acclimation period</b>, also called an <b>adaptation</b> or <b>lag period</b>, occurs when no destruction of a given chemical is observed [23]. It is caused by the microbes transitioning to their altered environment and shifting their metabolism to better suit it [14]. It can last for anywhere from hours (such as aromatic compounds in warm, oxygenated soils) to months (such as halobenzoates in anaerobic sediments) depending on the chemical in question and the environment [23]. Acclimation periods can be affected by temperature, the presence of oxygen, pH, and concentration of the substance. Although they are most often faster in warm, aerated, and fairly dry environments, there are few consistencies between what shortens or lengthens the period, even if the concentration is the same [23]. Insecticides including methyl parathion and azinphosmethyl; herbicides including 2, 4-D, MCPA, Mecoprop, TCA, and amitrole; the quaternary ammonium compound dodecyltrimethylammonium chloride; polycyclic aromatic hydrocarbons including naphthalene and anthracene; and other chemicals such as phenol, chlorobenzene, PCP, diphenyl-methane, and NTA have all been reported to have acclimation periods, and this can be of severe human concern [23]. The continued presence of these toxins extends human, plant, and animal exposure, and if the chemical is in water, it can allow the substance to flow further and impact environments distant to its site of origin before being degraded.<br />
<br />
==='''Detoxification and Activation'''===<br />
<b>Detoxication</b>, sometimes called <b>detoxification</b>, has been referred to as the “most important role of microorganisms in the transformation of pollutants” [23]. The process is the changing of a molecule into something less harmful to a species in question. There are a number of ways a molecule can be transformed, including hydrolysis, hydroxylation, dehalogenation, demethylation, methylation, and ether cleavage [23]. By breaking bonds, or adding or removing groups, the organism reduces its effect on the environment. Furthermore, although sometimes the resulting chemical is simply excreted as waste, the organism may also be able to use this new compound as a carbon source or further modifies it until it is released as CO2 [23].<br />
<br />
There are instances where the initial compound is harmless, and in fact the substance produced by microorganisms, or an intermediate in the degradation process, is a toxin [23]. This process is called activation. For this reason, it is important to test all steps of a reaction when determining how a compound is degrading. The new toxins may also be more or less mobile than its predecessor, so it can either stick around one area for extended periods of time or spread to other areas and increase damage [23]. A prevalent example of this is the dechlorination of TCE, which produces DCE (50 times more hazardous than TCE) and Vinyl Chloride (a known carcinogen) [14]. Commonly used insecticides in the past, like zinophos, trichloronat, and carbofuran, were all found to increase a soil’s toxicity with extended use [23].<br />
<br />
=='''Bioremediation treatment methods'''==<br />
In order for bioremediation to be successful, it requires sufficient proof for the degradation of contaminants. However, determining the effectiveness and completeness to reach sufficient results is one of the major issues. Natural attenuation relies on natural processes to clean up or attenuate pollution in soil and groundwater [27]. This remediation is done without human interaction, and is primarily used as a monitoring technique, to make sure more aggressive cleanup strategies are not needed. [https://en.wikipedia.org/wiki/Abiotic_component Abiotic] and [https://en.wikipedia.org/wiki/Biotic_component biotic] factors play a distinguishing factor of how effective bioremediation is.<br />
<br />
Current monitoring practices determine the disappearance of contaminants and their degradation products to regulatory levels that are monitored by toxicity testing, usually on single organisms or species to ensure there are no induced changes that may result in residual toxicity. The problem with these monitoring techniques is that the assessment of contaminants may result in an inaccurate indicator of residual toxicity[28]. Rather, studying the microbial community response may be a more comprehensive indicator of residual toxicity than a single species. Once sufficient evidence is provided, human intervention may be needed for a more effective cleanup process. <br />
<br />
There are two types of remediation that are done, ex situ: which is done by removing the contaminated soil or water and treating it outside the source, and in situ: which treatment takes place within the contaminated area. There are some treatments methods that can be either ex situ or in situ. Some techniques may deal with the mobilization of pollutants, to move them out of an area, or immobilized to keep them out of an area such as a water table.<br />
<br />
<br />
[[Image:Summary_of_bioremediation_strategies.png|center|upright=3|thumb|A comparative analysis of the different types of bioremediation. It can be used to find which remediation technique may be used in certain circumstances [12]]]<br />
<br />
<br />
[[Image:Biopiling.png|right|upright=1.5|thumb|Contaminated soil is mixed with amendments and piled on top of a liner, while a pipe with a blower controls aeration. [29]]]<br />
==='''Ex-situ'''===<br />
Ex-situ techniques are those that are applied to soil and groundwater which has been removed from the site via excavation or pumping [12]. The methods used include composting, biofilters, and biopiling. Ex-situ is used for smaller projects, primarily because larger excavation of soil is not prefered. The movement of the soil can be more detrimental by destroying the preestablish horizons in the soil.<br />
<br />
[[Image:Composting.png|right|upright=3|thumb|Composting is a very versatile remediation technique that can be used for either: a very broad treatment with many contaminants, or very specific treatment that utilizes particular microbes that target specific contaminants [30]. It can also be used to augment other treatment methods.]]<br />
<br />
===='''Biopiling'''====<br />
Excavated soils are mixed with soil amendments and placed on a treatment area. Biopiles are aerated with the use of perforated pipes and blowers in order to control the progression of biodegradation more efficiently by controlling the supply of oxygen [29], which in turn may affect other factors such as pH. This system is primarily used to remediate systems with oil and hydrocarbon contamination. The remediated soil is placed in a liner to prevent further contamination of the soil, they may also be covered with plastic to control runoff, evaporation, and [https://en.wikipedia.org/wiki/Volatilisation volatilization].<br />
<br />
===='''Composting'''====<br />
Nutrients are added to soil that is mixed to increase aeration and activation of indigenous microorganisms. Composting is done in a separate container, then when composting is complete it is incorporated into the soil. Bioremediation by the utilization of compost relies on the adsorption capabilities of organic matter and the degradation capabilities of microorganisms present[30]. Composting is recognized as as one of the most cost-effective technologies for soil bioremediation and it can be done on large and small scales. The use of composting is a very versatile technique for soil polluted by a wide range of organic pollutants and heavy metals, making it great for easier remediation involving various pollutants. The utilization of organic wastes for soil remediation is also helpful in decreasing the need for their storage and treatment. Organic matter that is generated from composting offers the benefit of improving soil quality and structure. Composting is primarily used for remediation over a longer period of time, as the nutrients for the microbes are released gradually and requrire more time compared to quicker treatments such as biostimulation.<br />
<br />
==='''In-situ'''===<br />
In-situ techniques are applied to soil and groundwater at the site with minimal disturbance[12]. These methods include biostimulation, bioleaching, biosorption, and bioventing. In-situ is preferred because it is often minimally invasive to the soil structure in comparison to ex-situ, but it can be expensive due to specialized equipment.<br />
<br />
===='''Biostimulation'''====<br />
This method involves the addition of nutrients to a polluted site in order to encourage the growth of naturally occurring chemical-degrading microorganisms[31]. Biostimulation is primarily done by the addition of various nutrients that are limited in the soil as well as electron acceptors, such as phosphorus, nitrogen and oxygen, or increasing the amount of available carbon in order to increase the population or activity of naturally occurring microorganisms. Other approaches are to optimize environmental conditions such as aeration, the addition of nutrients, altering pH and temperature control [32]. The primary advantage of biostimulation is that it is done by native microorganisms that are well-suited to the environment, and are already well distributed spatially. The challenge is delivering additives so they are readily available to the subsurface microbes.<br />
<br />
===='''Metal Biosorption'''====<br />
Adsorption of metals and other ions of an aqueous solution by the use of microbes. The biosorption process involves a solid phase and a liquid phase containing a dissolved species to be sorbed [34]. The process continues until equilibrium is established between the amount of solid-bound sorbate species and its portion remaining in the solution. The degree of affinity for the sorbate determines its distribution between the solid and liquid phases.<br />
<br />
Biosorption processes are very important in the environment, and has been utalized for conventional biotreatment processes. Biosorption is primarily aimed at the removal or recovery of organic and inorganic substances from solution [35]. The commercialization of biosorption technologies has been limited so far.<br />
<br />
[[Image:Bioventing.png|right|upright=2.5|thumb|Bioventing is primarily used for injecting air into specific remediation zones, adding oxygen as a readily available electron acceptor where it would otherwise be anaerobic. It can also be reversed to make a more anaerobic environment. Either technique can be applied depending on the remediating microbes would thrive in [36].]]<br />
<br />
===='''Bioventing'''====<br />
Bioventing is an In situ remediation technology that uses indigenous microorganisms to biodegrade organic constituents adsorbed to soils in the unsaturated zone[36]. The availability of oxygen generally controls the rate at which aerobic bioremediation proceeds. Bioventing is the coupling of soil venting and bioremediation. Bioventing can be successfully applied to compounds ranging from gasoline or diesel, to heavier hydrocarbons[36]. The addition of nutrients with the bioventing flow rates can achieve greater contaminant reductions than venting alone.<br />
<br />
==='''Ex-situ or In-situ'''===<br />
Some methods can be used by either in-situ or ex-situ methods. The soil or water can be removed from the contamination source and treated, or treated at the source, the method chosen can be based on many factors such as how expensive the project may be or how much contaminant needs to be treated. These methods include bioaugmentation, land farming and biofiltration.<br />
<br />
===='''Bioaugmentation'''====<br />
Bioaugmentation is the addition of non-native microorganisms that have the ability to degrade the contaminants that are recalcitrant to the indigenous microbiota. Bioaugmentation has been proven successful in cleaning organic pollutant, but still faces many environmental problems, such as the survival of strains introduced to soil[37]. The number of introduced microorganisms usually decreases shortly after soil inoculation. <br />
<br />
Bioaugmentation is ideal for soil:<br />
<br />
1. With low number of microbes that are capable of degrading targeted pollutants<br />
<br />
2. Containing compounds requiring multi stepped remediation.<br />
<br />
Augmentation techniques have a great potential for [https://en.wikipedia.org/wiki/Category:Aromatic_compounds aromatic compound] remediation. The most important step in successful bioaugmentation is selection of proper microbial strains. The success of bioaugmentation strongly depends on the ability of inoculants to survive in contaminated soil, which may vary due to predation and an environment that does provide all the conditions and nutrients that the organism needs to survive. In some cases the environment may be toxic to the added organism.<br />
<br />
===='''Land Farming'''====<br />
Contaminated soil is mixed with amendments such as nutrients, and then they are tilled into the earth, or the contaminated soil is applied into lined beds and periodically turned over or tilled to aerate the waste [38]. The topmost layer is the area of concentration for this method, so it is not ideal for deeper remediation. Land farming differs from composting because it actually incorporates contaminated soil into soil that is uncontaminated [38]. The higher zone of remediation will typically contain primarily lighter hydrocarbons that can be volatilized. The material is periodically tilled for aeration to hasten remediation of any nutrients and allow more oxygen to act as electron acceptors, as well as allowing volatilization to occur. Contaminants are degraded, transformed, and immobilized by microbiological processes and oxidation. Soil conditions are controlled to optimize the rate of contaminant degradation, moisture content, frequency of aeration, and pH are all conditions that may be controlled [38]. <br />
<br />
[[Image:Biofilter.png|right|upright=1.5|thumb|The application of a micro-algal/bacterial biofilter in the primary outflow of soil water [39]]]<br />
<br />
===='''Biofilter'''====<br />
Biofilters are primarily used for the filtration of contaminated groundwater in the soil. Biofilters can be used above soil, where the water will be pumped aboveground for treatment, or a filter can be placed in the soil near an outflow. A micro-algal/bacterial biofilter can be used for the detoxification of copper and cadmium metal wastes [22]. Biofilters have been used in larger industry environments to treat contaminated outflow of water. [https://en.wikipedia.org/wiki/Chromobacterium_violaceum Chromobacterium violaceum], is used to treat water and soil contaminated with silver nanoparticles, reducing its concentration.<br />
<br />
=='''Bioremediation Synopsis'''==<br />
<br />
==='''Advantages'''===<br />
1. Bioremediation that involves natural attenuation or biostimulation is a publicly accepted treatment of polluted soil because it is based upon natural processes. Microbes that metabolize contaminants often increase in population when the contaminant is present and thus rates of biodegradation may increase over time, up to a point. If biodegradation is complete (i.e. mineralization) the products from treatment are harmless; such as carbon dioxide, water, and cellular biomass. [12]<br />
<br />
2. In situ bioremediation can result in complete degradation of pollutants into harmless products on site. This removes the risks involved with transportation for treatment and elimination of contaminated substances. [12]<br />
<br />
3. Bioremediation can be a cheaper alternative to other technologies used for pollution mitigation. [12]<br />
<br />
==='''Disadvantages'''===<br />
1. Only biodegradable compounds are capable of undergoing bioremediation. Not every compound is capable of fully degrading quickly. [12]<br />
<br />
2. The products of biodegradation may potentially be even more persistent or toxic than the original contaminant. [12]<br />
<br />
3. Biological functions are usually extremely specific and require the presence of microbes that are capable of metabolizing the contaminants. In order for the correct microbes to be present, the appropriate environmental conditions, levels of nutrients, and contaminants need to be met. [12]<br />
<br />
4. Scaling up the size of studies from small initial studies to commercial-scale field operations is difficult.[12]<br />
<br />
5. The real environment contains contaminants that are mixed, unevenly distributed, and in different phases (solid, liquid, gas). More research needs to be completed to create technologies that can adapt. [12]<br />
<br />
6. Compared to other treatment technologies, bioremediation often takes more time. [12]<br />
<br />
7. Problems with ensuring adequate contact between the microbes and the contaminant. preferential pathway and soil structure can leave uncertainty in remediation dispersal.[12]<br />
<br />
=='''References'''== <br />
<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdf United States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120. <br />
<br />
5. Al-Mailem, D. M., Sorkhoh, N. A., Al-Awadhi, H., Eliyas, M., & Radwan, S. S. (2010). Biodegradation of crude oil and pure hydrocarbons by extreme halophilic archaea from hypersaline coasts of the Arabian Gulf. Extremophiles, 14(3), 321-328. doi: 10.1007/s00792-010-0312-9<br />
<br />
6. Fairley, D. J., Boyd, D. R., Sharma, N. D., Allen, C. C., Morgan, P., & Larkin, M. J. (2002). Aerobic metabolism of 4-hydroxybenzoic acid in Archaea via an unusual pathway involving an intramolecular migration (NIH shift). Appl Environ Microbiol, 68(12), 6246-6255.<br />
<br />
7. Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008<br />
<br />
8. Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008<br />
<br />
9. Le Borgne, S., Paniagua, D., & Vazquez-Duhalt, R. (2008). Biodegradation of organic pollutants by halophilic bacteria and archaea. J Mol Microbiol Biotechnol, 15(2-3), 74-92. doi: 10.1159/000121323<br />
<br />
10. Margesin, R., & Schinner, F. (2001). Biodegradation and biore<br />
mediation of hydrocarbons in extreme environments. Appl Microbiol Biotechnol, 56(5-6), 650-663.<br />
<br />
11. Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9<br />
<br />
12. Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172. <br />
<br />
13. "Dechloromonas Aromatica RCB." JGI Genome Portal, 16 Feb. 2016. [http://genome.jgi.doe.gov/decar/decar.home.html http://genome.jgi.doe.gov/decar/decar.home.html]<br />
<br />
14. King, R. Barry, John K. Sheldon, and GIlbert M. Long. (1998). Practical Environmental Bioremediation: The Field Guide. 2nd ed. Boca Raton: CRC, 1998.<br />
<br />
15. "Manual, Bioventing Principles and Practices." United States Environmental Protection Agency I (1995)<br />
<br />
16. Gadd, G. M. (Ed.). (2001). Fungi in bioremediation (No. 23). Cambridge University Press<br />
<br />
17. Harms, H., Schlosser, D., & Wick, L. Y. (2011). Untapped potential: exploiting fungi in bioremediation of hazardous chemicals. Nature Reviews Microbiology, 9(3), 177-192<br />
<br />
18. Fragoeiro, S. (2005). Use of fungi in bioremediation of pesticides. Applied Mycology Group Institute of Bioscience and Technology. Cranfield University<br />
<br />
19. Singh, H. (2006). Mycoremediation: fungal bioremediation. John Wiley & Sons. 283-285<br />
<br />
20. Norton, J. M. (2012). Fungi for Bioremediation of Hydrocarbon Pollutants. University of Hawai’i at Hilo. Hohonu, 10, 18-21<br />
<br />
21. Dixit, Ruchita, Emptyyn Wasiullah, Deepti Malaviya, Kuppusamy Pandiyan, Udai Singh, Asha Sahu, Renu Shukla, Bhanu Singh, Jai Rai, Pawan Sharma, Harshad Lade, and Diby Paul. "Bioremediation of Heavy Metals from Soil and Aquatic Environment: An Overview of Principles and Criteria of Fundamental Processes." Sustainability 7.2 (2015): 2189-212. Print.<br />
<br />
22. Bio-filters for Edge-of-Field Water Quality Management. (n.d.). Retrieved February 24, 2016, from [http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html]<br />
<br />
23. Alexander, Martin. (1999). Biodegradation and Bioremediation. San Diego: Academic Print. <br />
<br />
24. Litchfield, Carol. "Thirty Years and Counting: Bioremediation in Its Prime?" BioScience 55.3 (2005): 273.<br />
<br />
25. Biello, David. "Slick Solution: How Microbes Will Clean Up the Deepwater Horizon Oil Spill." Scientific American (n.d.): n. pag. 25 May 2010. <br />
<br />
26. Scow, Kate. “Lectures in Soil Microbiology.” UC Davis, Winter 2016.<br />
<br />
27 CLU-IN | Technologies Remediation About Remediation Technologies Natural Attenuation Overview. (n.d.). Retrieved February 24, 2016, from https://clu-in.org/techfocus/default.focus/sec/Natural_Attenuation/cat/Overview/<br />
<br />
28. Chauhan, Ashok K., and A. Varma. A Textbook of Molecular Biotechnology. New Delhi: I.K. International Pub. House, 2009. Print.<br />
<br />
29. Biopiles. (n.d.). Retrieved March 13, 2016, from [http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html]<br />
<br />
30. Chen, M., Xu, P., Zeng, G., Yang, C., Huang, D., & Zhang, J. (2015). Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: Applications, microbes and future research needs. Biotechnology Advances, 33(6, Part 1), 745–755.<br />
<br />
31. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. Retrieved March 13, 2016, from [http://www.sciencedirect.com/science/article/pii/S0944501309000585 http://www.sciencedirect.com/science/article/pii/S0944501309000585]<br />
<br />
32. Bioremediation, Biostimulation and Bioaugmention: A Review. (n.d.). Retrieved March 13, 2016, from http://pubs.sciepub.com/ijebb/3/1/5/<br />
<br />
33. Sulfur Oxides—Advances in Research and Application: 2013 Edition<br />
<br />
34. Fomina, M., & Gadd, G. M. (2014). Biosorption: current perspectives on concept, definition and application. Bioresource Technology, 160, 3–14. Retrieved February 24, 2016, from [https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application]<br />
<br />
35. Kotrba, Pavel, Martina Mackova, and Tomas Macek. (2011). Microbial Biosorption of Metals. Dordrecht: Springer Science Business Media Print.<br />
<br />
36. Bioventing » Water and Soil Bio-Remediation. (n.d.). Retrieved February 24, 2016, from [http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing]<br />
<br />
37. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. <br />
<br />
38. Land Farming. (n.d.). Retrieved March 13, 2016, from http://www.cpeo.org/techtree/ttdescript/lanfarm.htm<br />
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<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=132747
Bioremediation
2018-03-12T02:53:04Z
<p>Kmscow: /* Bioaugmentation */</p>
<hr />
<div>{{Curated}}<br />
<br />
Through agriculture, industry, and daily life, harmful chemicals have been released into the earth’s air, soil, and water. Depending on their concentrations, these substances can have destructive consequences on ecosystems, as well as cause severe damage to humans and other organisms nearby. Soil pollution is of special importance because of its impact on surface, groundwater and air contamination and can easily spread and be consumed by humans. <br />
<br />
[[Image:Bioremediation_images.jpeg|upright=3|thumb|Retrieved from Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120.]]<br />
<br />
<b>Biodegradation</b> is the biologically catalyzed modification of an organic chemical's structure. However, this modification can be through different metabolic pathways and does not necessarily mean a reduction in toxicity. Mineralization, one type of biodegradation, is defined as the conversion of an organic substance to its inorganic constituents, rendering the original compound harmless. [23]. Transformation is defined as any metabolically-induced change in the chemical composition of a compound [14].<br />
<br />
<b>Bioremediation</b> refers to the use of microorganisms to degrade contaminants that pose environmental and human risks. Bioremediation processes typically involve the actions of many different microbes acting in parallel or sequence to complete the degradation process. Both in situ (in place) and ex situ (removal and treatment in another place) remediation approaches are used. The versatility of microbes to degrade a vast array of pollutants makes bioremediation a technology that can be applied in different soil conditions [3]. Though it can be inexpensive and in situ approaches can reduce disruptive engineering practices, bioremediation is still not a common practice [1].<br />
<br />
A widely used approach to bioremediation involves stimulating naturally occurring microbial communities, providing them with nutrients and other needs, to break down a contaminant. This is termed <b>biostimulation.</b> Biostimulation can be achieved through changes in pH, moisture, aeration, or additions of electron donors, electron acceptors or nutrients. Another bioremediation approach is termed <b>bioaugmentation</b>, where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously.<br />
<br />
Recent awareness of the dangers of many chemicals used in society has led to research on formulation of products that are more easily degraded in the environment.<br />
<br />
From an ecological point of view, bioremediation depends on the various interactions between three factors: substrate (pollutant), organisms, and environment, as shown in the figure at right [4]. The interactions of these factors affect biodegradability, bioavailability, and physiological requirements, which are important in assessing the feasibility of bioremediation [4]. <b>Biodegradability</b>, or whether a chemical can be degraded or not, is determined by the presence or absence of organisms that are able to degrade a chemical of interest and how widespread these organisms are in the site [4]. The substrate (pollutant) can interact with its surrounding environment to change its <b>bioavailability</b>, or availability to organisms that are capable of degrading it; for example, substrate has low bioavailability if it is tightly bound to soil organic matter or trapped inside aggregates [4]. <b>Physiological requirements</b>, or set of conditions required by organisms to carry out bioremediation in the environment, include nutrient availability, optimal pH, and availability of electron acceptors, such as oxygen and nitrate [4]. Also, the environment needs to be habitable for organisms involved in bioremediation [4].<br />
<br />
=='''Brief History'''==<br />
<br />
[[Image:Wasterwater_treatment.png|upright=2.25|thumb|First Water Treatment Facility in Japan, 1934 Image from http://www.sewerhistory.org/grfx/trtmnt/trtmnt3.htm]] <br />
<br />
Microorganisms in the environment have always broken down waste, and humans have always (knowingly or unknowingly) used them in agricultural, domestic, and industrial activities [24]. As the urbanized world shifted to a more industrial system, however, people began to take an active approach in bioremediation. In the late nineteenth century, wastewater treatment plants were formed, but even so, this was not officially called bioremediation .<br />
The project considered the initial spark of the bioremediation movement was the report “Beneficial Stimulation of Bacterial Activity in Groundwater Containing Petroleum Products” by R.L. Raymond et al. in 1975. By testing the relationship between oil presence and bacterial stimulation, Raymond found that adding nutrients to soil hastened the oil removal. This led to the development of in situ bioremediation [24].<br />
<br />
Initial bioremediation projects focused on “pump and treat” (ex situ) methods in soil around gas stations and refinery spills to get oil out of groundwater sources, but soon cleaning up chlorinated hydrocarbons became a primary concern [24]. Chlorinated compounds were commonly used in pesticides, but when people learned it was a possible carcinogen and causing ozone depletion, research into bioremediation took off [24]. This was when anaerobic bacteria started being used, as it was discovered that they dechlorinate compounds much more quickly than do aerobic bacteria, and produce fewer damaging iron compounds that precipitate from the reactions [24].<br />
<br />
=='''Overview of Pollutants'''==<br />
Pollutants found in soils present a variety of different human health risks. Soil pollutants are typically classified as organic and inorganic pollutants. The remediation of some of these pollutants will be discussed in greater depth in the following sections.<br />
Below is a link to website with a list of examples of soil pollutants and their effects on human health:<br />
<br />
[http://www.environmentalpollutioncenters.org/soil/examples/ Summary of health effects of pollutants]<br />
<br />
==='''Organic Pollutants'''===<br />
Industrialization resulted in increased use of organic compounds that build up and persist in the environment [11]. Main sources of organic pollutants are through anthropogenic activities, including use of solvents, pesticides, and fuels [11]. Some of these organic compounds are highly toxic and they are associated with variety of health issues around the world [11].<br />
<br />
Table below lists some groups of contaminants, examples, and their sources.<br />
<br />
[[Image:Pollutants_list.png|center|upright=2.5|thumb|Retrieved from Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172.]]<br />
<br />
While organic pollutants are causing both environmental and health problems, bioremediation offers an effective solution to the pollution [11]. The table below lists some of the organic pollutants and microorganisms that are found to be able to degrade them.<br />
<br />
[[Image:Pollutants_and_organisms.png|center|upright=2.5|thumb|Retrieved from Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9]]<br />
<br />
==='''Inorganic Pollutants'''=== <br />
{| border="1" style="float:right; margin-left: 10px; text-align:center"<br />
|+ Most inorganic pollutants are due to human activities.<br />
!Pollutant<br />
!Source<br />
|-<br />
| [https://en.wikipedia.org/wiki/Arsenic Arsenic] || Pesticides, wood preservatives, biosolids, ore mining and smelting<br />
|- <br />
| [https://en.wikipedia.org/wiki/Cadmium Cadmium] || Paints and pigments, plastic stabilizers, electroplating, phosphate fertilizers<br />
|-<br />
| [https://en.wikipedia.org/wiki/Chromium Chromium] || Tanneries, steel industries, fly ash<br />
|- <br />
| [https://en.wikipedia.org/wiki/Copper Copper] || Pesticides, fertilizers, biosolids, ore mining and smelting<br />
|-<br />
| [https://en.wikipedia.org/wiki/Mercury_%28element%29 Mercury] || Gold and Silver mining, coal combustion<br />
|-<br />
| [https://en.wikipedia.org/wiki/Nickel Nickel] || Effluent, kitchen appliances, surgical instruments, automobile batteries<br />
|-<br />
| [https://en.wikipedia.org/wiki/Lead Lead] || Aerial emission from combustion of leaded fuel, batteries waste, insecticide and herbicides.<br />
|}<br />
<br />
A majority of heavy metal pollutants come from human sources that accumulate over time.<br />
<br />
There are also natural forms of contamination from normal biological processes, which include:<br />
<br />
1. Weathering of minerals over time<br />
<br />
2. [https://en.wikipedia.org/wiki/Erosion Erosion] and [https://en.wikipedia.org/wiki/Volcano volcanic activities]<br />
<br />
3. [https://en.wikipedia.org/wiki/Wildfire Forest fires] and biogenic source<br />
<br />
4. Particles released by vegetation<br />
<br />
Heavy metals can be absorbed by microbes at cellular binding sites. Extracellular polymers of these microbes can complex heavy metals through various mechanisms [21]. These specialized microorganisms can mineralize the organic contaminants to metabolic intermediates, which are used as primary substrates for cell growth. The microbes prevalent in heavily metal-contaminated soil can alter the oxidation state of the heavy metals by immobilizing them [21], allowing them to be easily removed. Bioremediation of heavy metals from microbes is not heavily researched, mostly due to an incomplete understanding of the genetics of the microbes used in metal adsorption. ''[https://microbewiki.kenyon.edu/index.php/Geomicrobiology Geomicrobiology]'' takes a better look at the interactions between microbes and inorganic material.<br />
<br />
=='''Organisms'''==<br />
As stated previously, bioremediation involves various microorganisms that are able to degrade and reduce toxicity of environmental pollutants [12]. Therefore, the interactions of microbes with the environment and pollutants are significant in determining effectiveness of bioremediation [4]. Those microbes can be either naturally present in the site of bioremediation or isolated from other sites and inoculated artificially [12]. Biodegradation often occurs as part of microbial metabolism and in some cases, microbes are able to directly harvest carbon and energy by breaking down pollutants [12]. Sections below go over bacteria and fungi, the commonly used organisms in bioremediation, and archaea, the more recently discovered group of organisms with unique potential in bioremediation.<br />
<br />
==='''Bacteria'''===<br />
Bacteria are widely diverse organisms, and thus make excellent players in biodegradation and bioremediation. There are few universal toxins to bacteria, so there is likely an organism able to break down any given substrate, when provided with the right conditions (anaerobic versus aerobic environment, sufficient electron donors or acceptors, etc.). Below are several specific bacteria species known to participate in bioremediation.<br />
<br />
===='''''[[Pseudomonas putida]]'''====<br />
[[Image:Pseudomonas_putida.png|upright=1|thumb|Pseudomonas putida, Image © http://www.denniskunkel.com/DK/Bacteria/23859D.html]]<br />
<br />
''Pseudomonas putida'' is a gram-negative soil bacterium that is involved in the bioremediation of toluene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===='''''[[Dechloromonas aromatica]]''' ====<br />
''Dechloromonas aromatica'' is a rod-shaped bacterium which can oxidize aromatics including benzoate, chlorobenzoate, and toluene, coupling the reaction with the reduction of oxygen, chlorate, or nitrate. It is the only organism able to oxidize benzene anaerobically. Due to the high propensity of benzene contamination, especially in ground and surface water, ''D. aromatic'' is especially useful for in situ bioremediation of this substance. [13]<br />
<br />
===='''Nitrifiers and Denitrifiers'''==== <br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage process that involves nitrification and denitrification. During nitrification, ammonium is oxidized to nitrite by organisms like <i>Nitrosomonas europaea</i>.Then, nitrite is further oxidized to nitrate by microbes like <i>Nitrobacter hamburgensis</i>.<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like <i>Paracoccus denitrificans </i>[2]. The result is N2 gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
===='''''[[Deinococcus radiodurans]]'''====<br />
''Deinococcus radiodurans'' is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered strain of Deinococcus radiodurans has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7].<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like ''[[Paracoccus denitrificans]]'' [2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
[[Image:Alcanivorax_borkumensis.png|upright=1|thumb|Alcanivorax borkumensis, Image©https://www.biotechnologie.de/BIO/Navigation/EN/Funding/foerderbeispiele,did=44848.html?view=renderPrint [25]]]<br />
<br />
===='''''[[Methylibium petroleiphilum]]'''====<br />
''Methylibium petroleiphilum'' (formally known as PM1 strain) is a bacterium capable of [https://en.wikipedia.org/wiki/Methyl_tert-butyl_ether methyl tert-butyl ether] (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
===='''''[[Alcanivorax borkumensis]]'''====<br />
''Alcanivorax borkumensis'' is a marine rod-shaped bacterium which consumes hydrocarbons, such as the ones found in fuel, and produces carbon dioxide. It grows rapidly in environments damaged by oil, and has been used to aid in cleaning the more than 830,000 gallons of oil from the [https://en.wikipedia.org/wiki/Deepwater_Horizon_oil_spill Deepwater Horizon oil spill] in the Gulf of Mexico [25].<br />
<br />
==='''Fungi (Mycoremediation)'''===<br />
Current bioremediation applications primarily utilize bacteria, with comparatively few attempts to use fungi. Fungi have fundamentally important roles because of their participation in the cycling of elements through decomposition and transformation of organic and inorganic materials. These characteristics can be translated into applications for bioremediation which could break down organic compounds and reduce the risks of metals. In some cases, fungi have an advantage over bacteria not just in metabolic versatility but also their environmental resilience.They are able to oxidize a diverse amount of chemicals and survive in harsh environmental conditions such as low moisture and high concentrations of pollutants. Therefore, fungi are potentially an extremely powerful tool in soil bioremediation and some versatile species such as <b>[https://en.wikipedia.org/wiki/Wood-decay_fungus#White_rot White Rot Fungi]</b> have been a hot topic of research. [16,17]<br />
<br />
===='''Biodegradation Capacities of White rot fungi'''====<br />
Using fungi as potential treatment of contaminants began in 1985 when the white rot species Phanerochaete chrysosporium was discovered to metabolize multiple key environmental pollutants. The most important feature of these fungi is their enzymatic functional ability to metabolize complex chemicals such as lignin. Similar abilities were later discovered in other white rot fungal species. In addition, white rot fungi are highly advantageous because they degrade lignin extracellularly through its hyphal extension. This allows them to access soil contaminants that other organisms are incapable of and maximize surface area for enzymatic interaction. These inexpensive fungi can tolerate extreme environmental conditions, such as pH, temperature, and moisture content. While many microbial organisms that are used for bioremediation require pre-conditioning of the environment for them to survive in, white rot fungi can directly be applied into most systems because they degrade based upon nutrient deprivation. [18]<br />
<br />
[[Image:040504062021.jpg|right|thumb|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x]]<br />
<br />
===='''''[[Phanerochaete chrysosporium]]'''====<br />
<i>P. chrysosporium</i> was the first fungi linked to degradation of organic pollutants. Extensive research has show this it has strong potential for bioremediation in pesticides, PAHs, dioxins, carbon tetrachloride, and many other pollutants. Among fungal systems, <i>P. chrysosporium</i> has become the model for bioremediation. Other notable species of white rot fungi include <i>Pleurotus ostreatus</i> and <i>Trametes versicolor</i>. [18]<br />
<br />
===='''Bioremediation of Hydrocarbon Pollutants'''====<br />
<br />
Hydrocarbons are stored deep underground but are brought up to the surface to be transformed and utilized, primarily as an energy source known as fossil fuels. The majority of pollution currently comes from these byproducts in the form Polycyclic Aromatic Hydrocarbons (PAHs), which are xenobiotic environmental pollutants that form when carbon materials are incompletely combusted. Some of examples of PAHs include burning wood, fossil fuels, and cigarette smoke. [19,20]<br />
Currently, bioremediation is only effective for soils contaminated with low-molecular weight PAHs because of bacterial commercial use. However, fungi are effective at PAH degradation in comparison to bacteria for a few reasons. Firstly, they are capable degrading PAH’s that are high in molecular weight, bacteria in comparison are better at degrading smaller molecules. Secondly, fungi can function well in non-aqueous environments and low oxygen conditions, both are conditions where PAH’s can accumulate. Many fungi have evolved mechanisms that allow the to target specific PAHs. Fungi produce extracellular enzymes that degrade lignin, a process called mineralization the produces carbon dioxide as the end product. [19,20]<br />
<br />
===='''Remediating Metals'''====<br />
<br />
Toxic metals can enter the environment all life cycle stages of metal compound. For example, metal leaching can occur from the mining process till the disposal of metal wastes. However in nature, the mobility of metals comes from the geological processes that can be released into the soil and aquatic environments. The environmental largest risk from metal contamination comes from the relationship between metals and compounds that are inherently of incapable of being degraded by any natural procedures. The best solution to treating contamination is transporting the metals to location where they cannot produce negative environmental effects. Fungi have various ways of interacting with metals, some of the techniques are increasing or decreasing the mobility of metals, sorption, or even cellular uptake. After the metals have been absorbed the fungus, they can chemically altered to be stored or translocated through the hyphae and into various plants that participate in symbiosis. [17]<br />
<br />
===='''Pesticide Degradation'''====<br />
<br />
Pesticide accumulation is an issue of great concern among the public, because they are directly associated with food products and water supplies. There are number of technologies used for pesticide clean-up; however, these technologies are generally expensive and inefficient because they require contaminated soil to be excavated and sent to a separate storage location for processing. Bioremediation offers a potential solution that treats contaminated soil and groundwater without needing excavation. Studies show that White Rot Fungi has high promise for soil bioremediation application; however, most tests have been conducted in the lab rather than in the actual environment. This fungi demonstrates the ability to transform and mineralize specific pesticides in soil. [18]<br />
<br />
===='''Environmental Applications'''====<br />
<br />
Although fungi demonstrate significant biochemical and ecological useful qualities, they are hardly utilized for biotechnological purposes. Instead, bacteria are most commonly used because they usually produce superior results in their numerous advantages ranging from their highly specific biochemical reactions to their capabilities of breaking down pollutants efficiently [17]. Fungi are underused primarily because of the costs that come from providing oxygen to fungi in polluted environments. However, filamentous fungi could be highly valuable in situations where bacteria cannot perform. For example, fungi are useful in situations where contaminants are physically blockaded and bacteria cannot reach or in circumstances of environmental extremes such as high acidity or dryness prevent bacteria from functioning. [17]<br />
<br />
==='''[https://en.wikipedia.org/wiki/Archaea Archaea]'''===<br />
The role of archaea in bioremediation has not been studied as commonly as that of bacteria [10]. Nevertheless, numbers of researchers have shown their ability to degrade various pollutants and scientists began to discover more about their potential in participating in bioremediation. Below lists some important facts regarding archaea’s potential role in bioremediation.<br />
<br />
- Biodegradation by extreme [https://en.wikipedia.org/wiki/Halophile halophilic] archaea was not recognized widely in the past, but scientists have found out that extreme halophilic archaea have greater catabolic diversity than expected [9]<br />
<br />
- Hydrocarbon-contamination is observed in some extreme environments, including hypersaline (high salt concentration), high or low temperature, or extreme pH [10]. Archaea’s adaptation to extreme environment gives them the potential to participate in biodegradation and bioremediation in these environments; in fact, microorganisms naturally adapted to the cold environments are known to be important degraders of hydrocarbons in those environments [10].<br />
<br />
- Extreme halophilic archaea has potential to biodegrade pollutants in hypersaline environment, in which bacteria typically used in bioremediation cannot survive or function properly. [5]<br />
<br />
- Some archaea are known to be resistant to variety of antibiotics, including penicillin, cycloheximide, streptomycin, etc, which gives them great advantage in participating in bioremediation in the presence of antibiotics [5].<br />
<br />
===='''Examples of studies of Archaea involved in bioremediation'''====<br />
<br />
Four extreme halophilic strains of archaea (belonging to genus ''[https://en.wikipedia.org/wiki/Halobacterium Halobacterium]'', ''[https://en.wikipedia.org/wiki/Haloferax Haloferax]'', and ''[https://en.wikipedia.org/wiki/Halococcus Halococcus]'') were studied to evaluate their potential to biodegrade crude oil and hydrocarbons. [5] All four strains could use various kinds of hydrocarbons as their carbon or energy sources [5]. Two strains of Haloferax grew on n-alkanes with different lengths, ranging from C8 to C34, and also benzene, toluene, biphenyl, and naphthalene. The research demonstrated the important fact that archaea have potential to carry out biodegradation at high temperatures, in the range of 40-45 °C [5], which is advantageous because hydrocarbons have higher solubility and bioavailability at these higher temperature [10]. The four strains studied were resistant to six different antibiotics, including penicillin, streptomycin, cycloheximide [5] and this gave them the potential to carry out biodegradation in conditions unfavorable for bacteria. Research suggests other genera of archaea are also capable of biodegrading in hypersaline environments [6]<br />
<br />
''[https://en.wikipedia.org/wiki/Halococcus Archaeglobus] fulgidus'', a [https://en.wikipedia.org/wiki/Hyperthermophile hyperthermophile] which can use sulfate as an electron acceptor, can also break down various aromatic hydrocarbons (Peeples, 2014).<br />
<br />
=='''Microbial Processes'''==<br />
<br />
Microorganisms use a wide range of processes to transform chemicals in their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor. This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. Below, several steps and details of the microorganisms’ actions are described.<br />
<br />
==='''Factors Affecting Rates of Biodegradation'''===<br />
Biodegradation may be influenced by pH, temperature, moisture, carbon sources, soil texture, aerobic versus anaerobic conditions, the number of substituents, and the concentration of the pollutant. It is impossible, however, to make a generalization about the best universal conditions for biodegradation. What’s toxic to some microbes is a nutrient to others, what might be a damaging pH to some is beneficial to others, and so on.<br />
<br />
A greater amount of substituents will cause slower degradation in aerobic environments, but faster degradation in anaerobic ones. Chlorine makes a molecule less degradable due to steric hindrance preventing access to necessary enzymes, therefore molecules with higher chlorination are slower to degrade in aerobic conditions. High concentration of a pollutant generally results in faster rates of degradation. If the concentration drops below a threshold concentration, the enzymes may not detect it and will cease to degrade it [26].<br />
<br />
Soil with small pores, especially clays, may cause biodegradation to take years due to the decrease in bioavailability. Chlorine makes a molecule less degradable due to steric hindrance preventing necessary enzymes from accessing the compound, therefore molecules with higher chlorination are slower to degrade. <br />
<br />
The rate at which a compound is transformed, as well as the curves that describe its transformation, is referred to as kinetics, and is affected by all factors listed above. First order kinetics (exponential decay) often describes biodegradation when the initial substrate concentration is low, while zero-order kinetics (linear biodegradation) is often observed when the substrate concentration is very high. In some cases if the concentration of the chemical falls below a critical threshold concentration, the microbes can no longer transform it and the chemical persists. <br />
<br />
The power rate model depicting the relationship between concentration and rate of degradation (first order decay here) is as follows:<br />
<br />
-dC/dt = kC^n<br />
<br />
C is substrate concentration, t is time, k is a rate constant for the chemical in question, and n is an appropriate parameter. The values of k and n are adjusted until a line is found to match experimental data [23].<br />
<br />
==='''Primary substrate utilization'''===<br />
<b>Primary substrate utilization</b> occurs when a microbe both transforms a substrate and uses it as an energy or carbon source. [15] An electron acceptor is required for these transformations. It can be anaerobic or aerobic, although the presence of oxygen tends to speed up reactions. This form of biodegradation can be used for treating petroleum spills or the runoff of a number of pesticides. The rate of reaction follows the guidelines in the previous section, where a higher concentration leads to a higher rate. [15]<br />
<br />
==='''Cometabolism (Secondary Substrate Utilization)'''===<br />
<b>Cometabolism</b> involves the transformation of a chemical by an organism while the organism uses a different substance as its primary energy or carbon source [14]. This is a technique often used when the substrate by itself is considered non-biodegradable, and can only be transformed with another compound. During the actual reaction degrading the substance, the organism has no net carbon or energy gain, and may even result in a product with no use to the organism or which is toxic to the cell [14]. However, it is often difficult to tell whether microorganisms have a second substrate available during their transformations [23]. Cometabolism occurs in parallel with metabolism, not instead of.<br />
<br />
A key example of cometabolism is fortuitous metabolism in the degradation of trichloroethylene, shown in the diagram below. An organic growth substrate such as propane or butane is required for the enzymatic activity that transforms TCE. [14]<br />
<br />
[[Image:Cometabolism.png|center|upright=3|thumb|Image from Kate Scow lecture, 2016]]<br />
<br />
==='''Reductive and Hydrolytic Dehalogenation'''===<br />
Chloride and other halogens are common components of pesticides and hazardous industrial wastes, and by removing them the toxic chemical can often be remediated [23]. If the halogen is replaced by a hydrogen (RCl -> RH), then it is <b>reductive dehalogenation</b>. If two halogens are replaced simultaneously, then the process is called <b>dihaloelimination</b>, although it still falls under reductive dehalogenation [14]. If the halogen is replaced by OH (RCl -> ROH) then it’s <b>hydrolytic dehalogenation</b>. In both cases, the halogen is released as its inorganic form into the environment [23].<br />
<br />
==='''Acclimation'''===<br />
An <b>acclimation period</b>, also called an <b>adaptation</b> or <b>lag period</b>, occurs when no destruction of a given chemical is observed [23]. It is caused by the microbes transitioning to their altered environment and shifting their metabolism to better suit it [14]. It can last for anywhere from hours (such as aromatic compounds in warm, oxygenated soils) to months (such as halobenzoates in anaerobic sediments) depending on the chemical in question and the environment [23]. Acclimation periods can be affected by temperature, the presence of oxygen, pH, and concentration of the substance. Although they are most often faster in warm, aerated, and fairly dry environments, there are few consistencies between what shortens or lengthens the period, even if the concentration is the same [23]. Insecticides including methyl parathion and azinphosmethyl; herbicides including 2, 4-D, MCPA, Mecoprop, TCA, and amitrole; the quaternary ammonium compound dodecyltrimethylammonium chloride; polycyclic aromatic hydrocarbons including naphthalene and anthracene; and other chemicals such as phenol, chlorobenzene, PCP, diphenyl-methane, and NTA have all been reported to have acclimation periods, and this can be of severe human concern [23]. The continued presence of these toxins extends human, plant, and animal exposure, and if the chemical is in water, it can allow the substance to flow further and impact environments distant to its site of origin before being degraded.<br />
<br />
==='''Detoxification and Activation'''===<br />
<b>Detoxication</b>, sometimes called <b>detoxification</b>, has been referred to as the “most important role of microorganisms in the transformation of pollutants” [23]. The process is the changing of a molecule into something less harmful to a species in question. There are a number of ways a molecule can be transformed, including hydrolysis, hydroxylation, dehalogenation, demethylation, methylation, and ether cleavage [23]. By breaking bonds, or adding or removing groups, the organism reduces its effect on the environment. Furthermore, although sometimes the resulting chemical is simply excreted as waste, the organism may also be able to use this new compound as a carbon source or further modifies it until it is released as CO2 [23].<br />
<br />
There are instances where the initial compound is harmless, and in fact the substance produced by microorganisms, or an intermediate in the degradation process, is a toxin [23]. This process is called activation. For this reason, it is important to test all steps of a reaction when determining how a compound is degrading. The new toxins may also be more or less mobile than its predecessor, so it can either stick around one area for extended periods of time or spread to other areas and increase damage [23]. A prevalent example of this is the dechlorination of TCE, which produces DCE (50 times more hazardous than TCE) and Vinyl Chloride (a known carcinogen) [14]. Commonly used insecticides in the past, like zinophos, trichloronat, and carbofuran, were all found to increase a soil’s toxicity with extended use [23].<br />
<br />
=='''Bioremediation treatment methods'''==<br />
In order for bioremediation to be successful, it requires sufficient proof for the degradation of contaminants. However, determining the effectiveness and completeness to reach sufficient results is one of the major issues. Natural attenuation relies on natural processes to clean up or attenuate pollution in soil and groundwater [27]. This remediation is done without human interaction, and is primarily used as a monitoring technique, to make sure more aggressive cleanup strategies are not needed. [https://en.wikipedia.org/wiki/Abiotic_component Abiotic] and [https://en.wikipedia.org/wiki/Biotic_component biotic] factors play a distinguishing factor of how effective bioremediation is.<br />
<br />
Current monitoring practices determine the disappearance of contaminants and their degradation products to regulatory levels that are monitored by toxicity testing, usually on single organisms or species to ensure there are no induced changes that may result in residual toxicity. The problem with these monitoring techniques is that the assessment of contaminants may result in an inaccurate indicator of residual toxicity[28]. Rather, studying the microbial community response may be a more comprehensive indicator of residual toxicity than a single species. Once sufficient evidence is provided, human intervention may be needed for a more effective cleanup process. <br />
<br />
There are two types of remediation that are done, ex situ: which is done by removing the contaminated soil or water and treating it outside the source, and in situ: which treatment takes place within the contaminated area. There are some treatments methods that can be either ex situ or in situ. Some techniques may deal with the mobilization of pollutants, to move them out of an area, or immobilized to keep them out of an area such as a water table.<br />
<br />
<br />
[[Image:Summary_of_bioremediation_strategies.png|center|upright=3|thumb|A comparative analysis of the different types of bioremediation. It can be used to find which remediation technique may be used in certain circumstances [12]]]<br />
<br />
<br />
[[Image:Biopiling.png|right|upright=1.5|thumb|Contaminated soil is mixed with amendments and piled on top of a liner, while a pipe with a blower controls aeration. [29]]]<br />
==='''Ex-situ'''===<br />
Ex-situ techniques are those that are applied to soil and groundwater which has been removed from the site via excavation or pumping [12]. The methods used include composting, biofilters, and biopiling. Ex-situ is used for smaller projects, primarily because larger excavation of soil is not prefered. The movement of the soil can be more detrimental by destroying the preestablish horizons in the soil.<br />
<br />
[[Image:Composting.png|right|upright=3|thumb|Composting is a very versatile remediation technique that can be used for either: a very broad treatment with many contaminants, or very specific treatment that utilizes particular microbes that target specific contaminants [30]. It can also be used to augment other treatment methods.]]<br />
<br />
===='''Biopiling'''====<br />
Excavated soils are mixed with soil amendments and placed on a treatment area. Biopiles are aerated with the use of perforated pipes and blowers in order to control the progression of biodegradation more efficiently by controlling the supply of oxygen [29], which in turn may affect other factors such as pH. This system is primarily used to remediate systems with oil and hydrocarbon contamination. The remediated soil is placed in a liner to prevent further contamination of the soil, they may also be covered with plastic to control runoff, evaporation, and [https://en.wikipedia.org/wiki/Volatilisation volatilization].<br />
<br />
===='''Composting'''====<br />
Nutrients are added to soil that is mixed to increase aeration and activation of indigenous microorganisms. Composting is done in a separate container, then when composting is complete it is incorporated into the soil. Bioremediation by the utilization of compost relies on the adsorption capabilities of organic matter and the degradation capabilities of microorganisms present[30]. Composting is recognized as as one of the most cost-effective technologies for soil bioremediation and it can be done on large and small scales. The use of composting is a very versatile technique for soil polluted by a wide range of organic pollutants and heavy metals, making it great for easier remediation involving various pollutants. The utilization of organic wastes for soil remediation is also helpful in decreasing the need for their storage and treatment. Organic matter that is generated from composting offers the benefit of improving soil quality and structure. Composting is primarily used for remediation over a longer period of time, as the nutrients for the microbes are released gradually and requrire more time compared to quicker treatments such as biostimulation.<br />
<br />
==='''In-situ'''===<br />
In-situ techniques are applied to soil and groundwater at the site with minimal disturbance[12]. These methods include biostimulation, bioleaching, biosorption, and bioventing. In-situ is preferred because it is often minimally invasive to the soil structure in comparison to ex-situ, but it can be expensive due to specialized equipment.<br />
<br />
===='''Biostimulation'''====<br />
This method involves the addition of nutrients to a polluted site in order to encourage the growth of naturally occurring chemical-degrading microorganisms[31]. Biostimulation is primarily done by the addition of various nutrients that are limited in the soil as well as electron acceptors, such as phosphorus, nitrogen and oxygen, or increasing the amount of available carbon in order to increase the population or activity of naturally occurring microorganisms. Other approaches are to optimize environmental conditions such as aeration, the addition of nutrients, altering pH and temperature control [32]. The primary advantage of biostimulation is that it is done by native microorganisms that are well-suited to the environment, and are already well distributed spatially. The challenge is delivering additives so they are readily available to the subsurface microbes.<br />
<br />
===='''Metal Biosorption'''====<br />
Adsorption of metals and other ions of an aqueous solution by the use of microbes. The biosorption process involves a solid phase and a liquid phase containing a dissolved species to be sorbed [34]. The process continues until equilibrium is established between the amount of solid-bound sorbate species and its portion remaining in the solution. The degree of affinity for the sorbate determines its distribution between the solid and liquid phases.<br />
<br />
Biosorption processes are very important in the environment, and has been utalized for conventional biotreatment processes. Biosorption is primarily aimed at the removal or recovery of organic and inorganic substances from solution [35]. The commercialization of biosorption technologies has been limited so far.<br />
<br />
[[Image:Bioventing.png|right|upright=2.5|thumb|Bioventing is primarily used for injecting air into specific remediation zones, adding oxygen as a readily available electron acceptor where it would otherwise be anaerobic. It can also be reversed to make a more anaerobic environment. Either technique can be applied depending on the remediating microbes would thrive in [36].]]<br />
<br />
===='''Bioventing'''====<br />
Bioventing is an In situ remediation technology that uses indigenous microorganisms to biodegrade organic constituents adsorbed to soils in the unsaturated zone[36]. The availability of oxygen generally controls the rate at which aerobic bioremediation proceeds. Bioventing is the coupling of soil venting and bioremediation. Bioventing can be successfully applied to compounds ranging from gasoline or diesel, to heavier hydrocarbons[36]. The addition of nutrients with the bioventing flow rates can achieve greater contaminant reductions than venting alone.<br />
<br />
==='''Ex-situ or In-situ'''===<br />
Some methods can be used by either in-situ or ex-situ methods. The soil or water can be removed from the contamination source and treated, or treated at the source, the method chosen can be based on many factors such as how expensive the project may be or how much contaminant needs to be treated. These methods include bioaugmentation, land farming and biofiltration.<br />
<br />
===='''Bioaugmentation'''====<br />
Bioaugmentation is the addition of non-native microorganisms that have the ability to degrade the contaminants that are recalcitrant to the indigenous microbiota. Bioaugmentation has been proven successful in cleaning organic pollutant, but still faces many environmental problems, such as the survival of strains introduced to soil[37]. The number of introduced microorganisms usually decreases shortly after soil inoculation. <br />
<br />
Bioaugmentation is ideal for soil:<br />
<br />
1. With low number of microbes that are capable of degrading targeted pollutants<br />
<br />
2. Containing compounds requiring multi stepped remediation.<br />
<br />
Augmentation techniques have a great potential for [https://en.wikipedia.org/wiki/Category:Aromatic_compounds aromatic compound] remediation. The most important step in successful bioaugmentation is selection of proper microbial strains. The success of bioaugmentation strongly depends on the ability of inoculants to survive in contaminated soil, which may vary due to predation and an environment that does provide all the conditions and nutrients that the organism needs to survive. In some cases the environment may be toxic to the added organism.<br />
<br />
===='''Land Farming'''====<br />
Contaminated soil is mixed with amendments such as nutrients, and then they are tilled into the earth, or the contaminated soil is applied into lined beds and periodically turned over or tilled to aerate the waste [38]. The topmost layer is the area of concentration for this method, so it is not ideal for deeper remediation. Land farming differs from composting because it actually incorporates contaminated soil into soil that is uncontaminated [38]. The higher zone of remediation will typically contain primarily lighter hydrocarbons that can be volatilized. The material is periodically tilled for aeration to hasten remediation of any nutrients and allow more oxygen to act as electron acceptors, as well as allowing volatilization to occur. Contaminants are degraded, transformed, and immobilized by microbiological processes and oxidation. Soil conditions are controlled to optimize the rate of contaminant degradation, moisture content, frequency of aeration, and pH are all conditions that may be controlled [38]. <br />
<br />
[[Image:Biofilter.png|right|upright=1.5|thumb|The application of a micro-algal/bacterial biofilter in the primary outflow of soil water [39]]]<br />
<br />
===='''Biofilter'''====<br />
Biofilters are primarily used for the filtration of contaminated groundwater in the soil. Biofilters can be used above soil, where the water will be pumped aboveground for treatment, or a filter can be placed in the soil near an outflow. A micro-algal/bacterial biofilter can be used for the detoxification of copper and cadmium metal wastes [22]. Biofilters have been used in larger industry environments to treat contaminated outflow of water. [https://en.wikipedia.org/wiki/Chromobacterium_violaceum Chromobacterium violaceum], is used to treat water and soil contaminated with silver nanoparticles, reducing its concentration.<br />
<br />
=='''Bioremediation Synopsis'''==<br />
<br />
==='''Advantages'''===<br />
1. Bioremediation that involves natural attenuation or biostimulation is a publicly accepted treatment of polluted soil because it is based upon natural processes. Microbes that metabolize contaminants often increase in population when the contaminant is present and thus rates of biodegradation may increase over time, up to a point. If biodegradation is complete (i.e. mineralization) the products from treatment are harmless; such as carbon dioxide, water, and cellular biomass. [12]<br />
<br />
2. In situ bioremediation can result in complete degradation of pollutants into harmless products on site. This removes the risks involved with transportation for treatment and elimination of contaminated substances. [12]<br />
<br />
3. Bioremediation can be a cheaper alternative to other technologies used for pollution mitigation. [12]<br />
<br />
==='''Disadvantages'''===<br />
1. Only biodegradable compounds are capable of undergoing bioremediation. Not every compound is capable of fully degrading quickly. [12]<br />
<br />
2. The products of biodegradation may potentially be even more persistent or toxic than the original contaminant. [12]<br />
<br />
3. Biological functions are usually extremely specific and require the presence of microbes that are capable of metabolizing the contaminants. In order for the correct microbes to be present, the appropriate environmental conditions, levels of nutrients, and contaminants need to be met. [12]<br />
<br />
4. Scaling up the size of studies from small initial studies to commercial-scale field operations is difficult.[12]<br />
<br />
5. The real environment contains contaminants that are mixed, unevenly distributed, and in different phases (solid, liquid, gas). More research needs to be completed to create technologies that can adapt. [12]<br />
<br />
6. Compared to other treatment technologies, bioremediation often takes more time. [12]<br />
<br />
7. Problems with ensuring adequate contact between the microbes and the contaminant. preferential pathway and soil structure can leave uncertainty in remediation dispersal.[12]<br />
<br />
=='''References'''== <br />
<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdf United States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120. <br />
<br />
5. Al-Mailem, D. M., Sorkhoh, N. A., Al-Awadhi, H., Eliyas, M., & Radwan, S. S. (2010). Biodegradation of crude oil and pure hydrocarbons by extreme halophilic archaea from hypersaline coasts of the Arabian Gulf. Extremophiles, 14(3), 321-328. doi: 10.1007/s00792-010-0312-9<br />
<br />
6. Fairley, D. J., Boyd, D. R., Sharma, N. D., Allen, C. C., Morgan, P., & Larkin, M. J. (2002). Aerobic metabolism of 4-hydroxybenzoic acid in Archaea via an unusual pathway involving an intramolecular migration (NIH shift). Appl Environ Microbiol, 68(12), 6246-6255.<br />
<br />
7. Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008<br />
<br />
8. Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008<br />
<br />
9. Le Borgne, S., Paniagua, D., & Vazquez-Duhalt, R. (2008). Biodegradation of organic pollutants by halophilic bacteria and archaea. J Mol Microbiol Biotechnol, 15(2-3), 74-92. doi: 10.1159/000121323<br />
<br />
10. Margesin, R., & Schinner, F. (2001). Biodegradation and biore<br />
mediation of hydrocarbons in extreme environments. Appl Microbiol Biotechnol, 56(5-6), 650-663.<br />
<br />
11. Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9<br />
<br />
12. Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172. <br />
<br />
13. "Dechloromonas Aromatica RCB." JGI Genome Portal, 16 Feb. 2016. [http://genome.jgi.doe.gov/decar/decar.home.html http://genome.jgi.doe.gov/decar/decar.home.html]<br />
<br />
14. King, R. Barry, John K. Sheldon, and GIlbert M. Long. (1998). Practical Environmental Bioremediation: The Field Guide. 2nd ed. Boca Raton: CRC, 1998.<br />
<br />
15. "Manual, Bioventing Principles and Practices." United States Environmental Protection Agency I (1995)<br />
<br />
16. Gadd, G. M. (Ed.). (2001). Fungi in bioremediation (No. 23). Cambridge University Press<br />
<br />
17. Harms, H., Schlosser, D., & Wick, L. Y. (2011). Untapped potential: exploiting fungi in bioremediation of hazardous chemicals. Nature Reviews Microbiology, 9(3), 177-192<br />
<br />
18. Fragoeiro, S. (2005). Use of fungi in bioremediation of pesticides. Applied Mycology Group Institute of Bioscience and Technology. Cranfield University<br />
<br />
19. Singh, H. (2006). Mycoremediation: fungal bioremediation. John Wiley & Sons. 283-285<br />
<br />
20. Norton, J. M. (2012). Fungi for Bioremediation of Hydrocarbon Pollutants. University of Hawai’i at Hilo. Hohonu, 10, 18-21<br />
<br />
21. Dixit, Ruchita, Emptyyn Wasiullah, Deepti Malaviya, Kuppusamy Pandiyan, Udai Singh, Asha Sahu, Renu Shukla, Bhanu Singh, Jai Rai, Pawan Sharma, Harshad Lade, and Diby Paul. "Bioremediation of Heavy Metals from Soil and Aquatic Environment: An Overview of Principles and Criteria of Fundamental Processes." Sustainability 7.2 (2015): 2189-212. Print.<br />
<br />
22. Bio-filters for Edge-of-Field Water Quality Management. (n.d.). Retrieved February 24, 2016, from [http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html]<br />
<br />
23. Alexander, Martin. (1999). Biodegradation and Bioremediation. San Diego: Academic Print. <br />
<br />
24. Litchfield, Carol. "Thirty Years and Counting: Bioremediation in Its Prime?" BioScience 55.3 (2005): 273.<br />
<br />
25. Biello, David. "Slick Solution: How Microbes Will Clean Up the Deepwater Horizon Oil Spill." Scientific American (n.d.): n. pag. 25 May 2010. <br />
<br />
26. Scow, Kate. “Lectures in Soil Microbiology.” UC Davis, Winter 2016.<br />
<br />
27 CLU-IN | Technologies Remediation About Remediation Technologies Natural Attenuation Overview. (n.d.). Retrieved February 24, 2016, from https://clu-in.org/techfocus/default.focus/sec/Natural_Attenuation/cat/Overview/<br />
<br />
28. Chauhan, Ashok K., and A. Varma. A Textbook of Molecular Biotechnology. New Delhi: I.K. International Pub. House, 2009. Print.<br />
<br />
29. Biopiles. (n.d.). Retrieved March 13, 2016, from [http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html]<br />
<br />
30. Chen, M., Xu, P., Zeng, G., Yang, C., Huang, D., & Zhang, J. (2015). Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: Applications, microbes and future research needs. Biotechnology Advances, 33(6, Part 1), 745–755.<br />
<br />
31. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. Retrieved March 13, 2016, from [http://www.sciencedirect.com/science/article/pii/S0944501309000585 http://www.sciencedirect.com/science/article/pii/S0944501309000585]<br />
<br />
32. Bioremediation, Biostimulation and Bioaugmention: A Review. (n.d.). Retrieved March 13, 2016, from http://pubs.sciepub.com/ijebb/3/1/5/<br />
<br />
33. Sulfur Oxides—Advances in Research and Application: 2013 Edition<br />
<br />
34. Fomina, M., & Gadd, G. M. (2014). Biosorption: current perspectives on concept, definition and application. Bioresource Technology, 160, 3–14. Retrieved February 24, 2016, from [https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application]<br />
<br />
35. Kotrba, Pavel, Martina Mackova, and Tomas Macek. (2011). Microbial Biosorption of Metals. Dordrecht: Springer Science Business Media Print.<br />
<br />
36. Bioventing » Water and Soil Bio-Remediation. (n.d.). Retrieved February 24, 2016, from [http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing]<br />
<br />
37. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. <br />
<br />
38. Land Farming. (n.d.). Retrieved March 13, 2016, from http://www.cpeo.org/techtree/ttdescript/lanfarm.htm<br />
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<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=132746
Bioremediation
2018-03-12T02:49:36Z
<p>Kmscow: /* Metal Bioleaching */</p>
<hr />
<div>{{Curated}}<br />
<br />
Through agriculture, industry, and daily life, harmful chemicals have been released into the earth’s air, soil, and water. Depending on their concentrations, these substances can have destructive consequences on ecosystems, as well as cause severe damage to humans and other organisms nearby. Soil pollution is of special importance because of its impact on surface, groundwater and air contamination and can easily spread and be consumed by humans. <br />
<br />
[[Image:Bioremediation_images.jpeg|upright=3|thumb|Retrieved from Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120.]]<br />
<br />
<b>Biodegradation</b> is the biologically catalyzed modification of an organic chemical's structure. However, this modification can be through different metabolic pathways and does not necessarily mean a reduction in toxicity. Mineralization, one type of biodegradation, is defined as the conversion of an organic substance to its inorganic constituents, rendering the original compound harmless. [23]. Transformation is defined as any metabolically-induced change in the chemical composition of a compound [14].<br />
<br />
<b>Bioremediation</b> refers to the use of microorganisms to degrade contaminants that pose environmental and human risks. Bioremediation processes typically involve the actions of many different microbes acting in parallel or sequence to complete the degradation process. Both in situ (in place) and ex situ (removal and treatment in another place) remediation approaches are used. The versatility of microbes to degrade a vast array of pollutants makes bioremediation a technology that can be applied in different soil conditions [3]. Though it can be inexpensive and in situ approaches can reduce disruptive engineering practices, bioremediation is still not a common practice [1].<br />
<br />
A widely used approach to bioremediation involves stimulating naturally occurring microbial communities, providing them with nutrients and other needs, to break down a contaminant. This is termed <b>biostimulation.</b> Biostimulation can be achieved through changes in pH, moisture, aeration, or additions of electron donors, electron acceptors or nutrients. Another bioremediation approach is termed <b>bioaugmentation</b>, where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously.<br />
<br />
Recent awareness of the dangers of many chemicals used in society has led to research on formulation of products that are more easily degraded in the environment.<br />
<br />
From an ecological point of view, bioremediation depends on the various interactions between three factors: substrate (pollutant), organisms, and environment, as shown in the figure at right [4]. The interactions of these factors affect biodegradability, bioavailability, and physiological requirements, which are important in assessing the feasibility of bioremediation [4]. <b>Biodegradability</b>, or whether a chemical can be degraded or not, is determined by the presence or absence of organisms that are able to degrade a chemical of interest and how widespread these organisms are in the site [4]. The substrate (pollutant) can interact with its surrounding environment to change its <b>bioavailability</b>, or availability to organisms that are capable of degrading it; for example, substrate has low bioavailability if it is tightly bound to soil organic matter or trapped inside aggregates [4]. <b>Physiological requirements</b>, or set of conditions required by organisms to carry out bioremediation in the environment, include nutrient availability, optimal pH, and availability of electron acceptors, such as oxygen and nitrate [4]. Also, the environment needs to be habitable for organisms involved in bioremediation [4].<br />
<br />
=='''Brief History'''==<br />
<br />
[[Image:Wasterwater_treatment.png|upright=2.25|thumb|First Water Treatment Facility in Japan, 1934 Image from http://www.sewerhistory.org/grfx/trtmnt/trtmnt3.htm]] <br />
<br />
Microorganisms in the environment have always broken down waste, and humans have always (knowingly or unknowingly) used them in agricultural, domestic, and industrial activities [24]. As the urbanized world shifted to a more industrial system, however, people began to take an active approach in bioremediation. In the late nineteenth century, wastewater treatment plants were formed, but even so, this was not officially called bioremediation .<br />
The project considered the initial spark of the bioremediation movement was the report “Beneficial Stimulation of Bacterial Activity in Groundwater Containing Petroleum Products” by R.L. Raymond et al. in 1975. By testing the relationship between oil presence and bacterial stimulation, Raymond found that adding nutrients to soil hastened the oil removal. This led to the development of in situ bioremediation [24].<br />
<br />
Initial bioremediation projects focused on “pump and treat” (ex situ) methods in soil around gas stations and refinery spills to get oil out of groundwater sources, but soon cleaning up chlorinated hydrocarbons became a primary concern [24]. Chlorinated compounds were commonly used in pesticides, but when people learned it was a possible carcinogen and causing ozone depletion, research into bioremediation took off [24]. This was when anaerobic bacteria started being used, as it was discovered that they dechlorinate compounds much more quickly than do aerobic bacteria, and produce fewer damaging iron compounds that precipitate from the reactions [24].<br />
<br />
=='''Overview of Pollutants'''==<br />
Pollutants found in soils present a variety of different human health risks. Soil pollutants are typically classified as organic and inorganic pollutants. The remediation of some of these pollutants will be discussed in greater depth in the following sections.<br />
Below is a link to website with a list of examples of soil pollutants and their effects on human health:<br />
<br />
[http://www.environmentalpollutioncenters.org/soil/examples/ Summary of health effects of pollutants]<br />
<br />
==='''Organic Pollutants'''===<br />
Industrialization resulted in increased use of organic compounds that build up and persist in the environment [11]. Main sources of organic pollutants are through anthropogenic activities, including use of solvents, pesticides, and fuels [11]. Some of these organic compounds are highly toxic and they are associated with variety of health issues around the world [11].<br />
<br />
Table below lists some groups of contaminants, examples, and their sources.<br />
<br />
[[Image:Pollutants_list.png|center|upright=2.5|thumb|Retrieved from Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172.]]<br />
<br />
While organic pollutants are causing both environmental and health problems, bioremediation offers an effective solution to the pollution [11]. The table below lists some of the organic pollutants and microorganisms that are found to be able to degrade them.<br />
<br />
[[Image:Pollutants_and_organisms.png|center|upright=2.5|thumb|Retrieved from Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9]]<br />
<br />
==='''Inorganic Pollutants'''=== <br />
{| border="1" style="float:right; margin-left: 10px; text-align:center"<br />
|+ Most inorganic pollutants are due to human activities.<br />
!Pollutant<br />
!Source<br />
|-<br />
| [https://en.wikipedia.org/wiki/Arsenic Arsenic] || Pesticides, wood preservatives, biosolids, ore mining and smelting<br />
|- <br />
| [https://en.wikipedia.org/wiki/Cadmium Cadmium] || Paints and pigments, plastic stabilizers, electroplating, phosphate fertilizers<br />
|-<br />
| [https://en.wikipedia.org/wiki/Chromium Chromium] || Tanneries, steel industries, fly ash<br />
|- <br />
| [https://en.wikipedia.org/wiki/Copper Copper] || Pesticides, fertilizers, biosolids, ore mining and smelting<br />
|-<br />
| [https://en.wikipedia.org/wiki/Mercury_%28element%29 Mercury] || Gold and Silver mining, coal combustion<br />
|-<br />
| [https://en.wikipedia.org/wiki/Nickel Nickel] || Effluent, kitchen appliances, surgical instruments, automobile batteries<br />
|-<br />
| [https://en.wikipedia.org/wiki/Lead Lead] || Aerial emission from combustion of leaded fuel, batteries waste, insecticide and herbicides.<br />
|}<br />
<br />
A majority of heavy metal pollutants come from human sources that accumulate over time.<br />
<br />
There are also natural forms of contamination from normal biological processes, which include:<br />
<br />
1. Weathering of minerals over time<br />
<br />
2. [https://en.wikipedia.org/wiki/Erosion Erosion] and [https://en.wikipedia.org/wiki/Volcano volcanic activities]<br />
<br />
3. [https://en.wikipedia.org/wiki/Wildfire Forest fires] and biogenic source<br />
<br />
4. Particles released by vegetation<br />
<br />
Heavy metals can be absorbed by microbes at cellular binding sites. Extracellular polymers of these microbes can complex heavy metals through various mechanisms [21]. These specialized microorganisms can mineralize the organic contaminants to metabolic intermediates, which are used as primary substrates for cell growth. The microbes prevalent in heavily metal-contaminated soil can alter the oxidation state of the heavy metals by immobilizing them [21], allowing them to be easily removed. Bioremediation of heavy metals from microbes is not heavily researched, mostly due to an incomplete understanding of the genetics of the microbes used in metal adsorption. ''[https://microbewiki.kenyon.edu/index.php/Geomicrobiology Geomicrobiology]'' takes a better look at the interactions between microbes and inorganic material.<br />
<br />
=='''Organisms'''==<br />
As stated previously, bioremediation involves various microorganisms that are able to degrade and reduce toxicity of environmental pollutants [12]. Therefore, the interactions of microbes with the environment and pollutants are significant in determining effectiveness of bioremediation [4]. Those microbes can be either naturally present in the site of bioremediation or isolated from other sites and inoculated artificially [12]. Biodegradation often occurs as part of microbial metabolism and in some cases, microbes are able to directly harvest carbon and energy by breaking down pollutants [12]. Sections below go over bacteria and fungi, the commonly used organisms in bioremediation, and archaea, the more recently discovered group of organisms with unique potential in bioremediation.<br />
<br />
==='''Bacteria'''===<br />
Bacteria are widely diverse organisms, and thus make excellent players in biodegradation and bioremediation. There are few universal toxins to bacteria, so there is likely an organism able to break down any given substrate, when provided with the right conditions (anaerobic versus aerobic environment, sufficient electron donors or acceptors, etc.). Below are several specific bacteria species known to participate in bioremediation.<br />
<br />
===='''''[[Pseudomonas putida]]'''====<br />
[[Image:Pseudomonas_putida.png|upright=1|thumb|Pseudomonas putida, Image © http://www.denniskunkel.com/DK/Bacteria/23859D.html]]<br />
<br />
''Pseudomonas putida'' is a gram-negative soil bacterium that is involved in the bioremediation of toluene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===='''''[[Dechloromonas aromatica]]''' ====<br />
''Dechloromonas aromatica'' is a rod-shaped bacterium which can oxidize aromatics including benzoate, chlorobenzoate, and toluene, coupling the reaction with the reduction of oxygen, chlorate, or nitrate. It is the only organism able to oxidize benzene anaerobically. Due to the high propensity of benzene contamination, especially in ground and surface water, ''D. aromatic'' is especially useful for in situ bioremediation of this substance. [13]<br />
<br />
===='''Nitrifiers and Denitrifiers'''==== <br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage process that involves nitrification and denitrification. During nitrification, ammonium is oxidized to nitrite by organisms like <i>Nitrosomonas europaea</i>.Then, nitrite is further oxidized to nitrate by microbes like <i>Nitrobacter hamburgensis</i>.<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like <i>Paracoccus denitrificans </i>[2]. The result is N2 gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
===='''''[[Deinococcus radiodurans]]'''====<br />
''Deinococcus radiodurans'' is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered strain of Deinococcus radiodurans has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7].<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like ''[[Paracoccus denitrificans]]'' [2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
[[Image:Alcanivorax_borkumensis.png|upright=1|thumb|Alcanivorax borkumensis, Image©https://www.biotechnologie.de/BIO/Navigation/EN/Funding/foerderbeispiele,did=44848.html?view=renderPrint [25]]]<br />
<br />
===='''''[[Methylibium petroleiphilum]]'''====<br />
''Methylibium petroleiphilum'' (formally known as PM1 strain) is a bacterium capable of [https://en.wikipedia.org/wiki/Methyl_tert-butyl_ether methyl tert-butyl ether] (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
===='''''[[Alcanivorax borkumensis]]'''====<br />
''Alcanivorax borkumensis'' is a marine rod-shaped bacterium which consumes hydrocarbons, such as the ones found in fuel, and produces carbon dioxide. It grows rapidly in environments damaged by oil, and has been used to aid in cleaning the more than 830,000 gallons of oil from the [https://en.wikipedia.org/wiki/Deepwater_Horizon_oil_spill Deepwater Horizon oil spill] in the Gulf of Mexico [25].<br />
<br />
==='''Fungi (Mycoremediation)'''===<br />
Current bioremediation applications primarily utilize bacteria, with comparatively few attempts to use fungi. Fungi have fundamentally important roles because of their participation in the cycling of elements through decomposition and transformation of organic and inorganic materials. These characteristics can be translated into applications for bioremediation which could break down organic compounds and reduce the risks of metals. In some cases, fungi have an advantage over bacteria not just in metabolic versatility but also their environmental resilience.They are able to oxidize a diverse amount of chemicals and survive in harsh environmental conditions such as low moisture and high concentrations of pollutants. Therefore, fungi are potentially an extremely powerful tool in soil bioremediation and some versatile species such as <b>[https://en.wikipedia.org/wiki/Wood-decay_fungus#White_rot White Rot Fungi]</b> have been a hot topic of research. [16,17]<br />
<br />
===='''Biodegradation Capacities of White rot fungi'''====<br />
Using fungi as potential treatment of contaminants began in 1985 when the white rot species Phanerochaete chrysosporium was discovered to metabolize multiple key environmental pollutants. The most important feature of these fungi is their enzymatic functional ability to metabolize complex chemicals such as lignin. Similar abilities were later discovered in other white rot fungal species. In addition, white rot fungi are highly advantageous because they degrade lignin extracellularly through its hyphal extension. This allows them to access soil contaminants that other organisms are incapable of and maximize surface area for enzymatic interaction. These inexpensive fungi can tolerate extreme environmental conditions, such as pH, temperature, and moisture content. While many microbial organisms that are used for bioremediation require pre-conditioning of the environment for them to survive in, white rot fungi can directly be applied into most systems because they degrade based upon nutrient deprivation. [18]<br />
<br />
[[Image:040504062021.jpg|right|thumb|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x]]<br />
<br />
===='''''[[Phanerochaete chrysosporium]]'''====<br />
<i>P. chrysosporium</i> was the first fungi linked to degradation of organic pollutants. Extensive research has show this it has strong potential for bioremediation in pesticides, PAHs, dioxins, carbon tetrachloride, and many other pollutants. Among fungal systems, <i>P. chrysosporium</i> has become the model for bioremediation. Other notable species of white rot fungi include <i>Pleurotus ostreatus</i> and <i>Trametes versicolor</i>. [18]<br />
<br />
===='''Bioremediation of Hydrocarbon Pollutants'''====<br />
<br />
Hydrocarbons are stored deep underground but are brought up to the surface to be transformed and utilized, primarily as an energy source known as fossil fuels. The majority of pollution currently comes from these byproducts in the form Polycyclic Aromatic Hydrocarbons (PAHs), which are xenobiotic environmental pollutants that form when carbon materials are incompletely combusted. Some of examples of PAHs include burning wood, fossil fuels, and cigarette smoke. [19,20]<br />
Currently, bioremediation is only effective for soils contaminated with low-molecular weight PAHs because of bacterial commercial use. However, fungi are effective at PAH degradation in comparison to bacteria for a few reasons. Firstly, they are capable degrading PAH’s that are high in molecular weight, bacteria in comparison are better at degrading smaller molecules. Secondly, fungi can function well in non-aqueous environments and low oxygen conditions, both are conditions where PAH’s can accumulate. Many fungi have evolved mechanisms that allow the to target specific PAHs. Fungi produce extracellular enzymes that degrade lignin, a process called mineralization the produces carbon dioxide as the end product. [19,20]<br />
<br />
===='''Remediating Metals'''====<br />
<br />
Toxic metals can enter the environment all life cycle stages of metal compound. For example, metal leaching can occur from the mining process till the disposal of metal wastes. However in nature, the mobility of metals comes from the geological processes that can be released into the soil and aquatic environments. The environmental largest risk from metal contamination comes from the relationship between metals and compounds that are inherently of incapable of being degraded by any natural procedures. The best solution to treating contamination is transporting the metals to location where they cannot produce negative environmental effects. Fungi have various ways of interacting with metals, some of the techniques are increasing or decreasing the mobility of metals, sorption, or even cellular uptake. After the metals have been absorbed the fungus, they can chemically altered to be stored or translocated through the hyphae and into various plants that participate in symbiosis. [17]<br />
<br />
===='''Pesticide Degradation'''====<br />
<br />
Pesticide accumulation is an issue of great concern among the public, because they are directly associated with food products and water supplies. There are number of technologies used for pesticide clean-up; however, these technologies are generally expensive and inefficient because they require contaminated soil to be excavated and sent to a separate storage location for processing. Bioremediation offers a potential solution that treats contaminated soil and groundwater without needing excavation. Studies show that White Rot Fungi has high promise for soil bioremediation application; however, most tests have been conducted in the lab rather than in the actual environment. This fungi demonstrates the ability to transform and mineralize specific pesticides in soil. [18]<br />
<br />
===='''Environmental Applications'''====<br />
<br />
Although fungi demonstrate significant biochemical and ecological useful qualities, they are hardly utilized for biotechnological purposes. Instead, bacteria are most commonly used because they usually produce superior results in their numerous advantages ranging from their highly specific biochemical reactions to their capabilities of breaking down pollutants efficiently [17]. Fungi are underused primarily because of the costs that come from providing oxygen to fungi in polluted environments. However, filamentous fungi could be highly valuable in situations where bacteria cannot perform. For example, fungi are useful in situations where contaminants are physically blockaded and bacteria cannot reach or in circumstances of environmental extremes such as high acidity or dryness prevent bacteria from functioning. [17]<br />
<br />
==='''[https://en.wikipedia.org/wiki/Archaea Archaea]'''===<br />
The role of archaea in bioremediation has not been studied as commonly as that of bacteria [10]. Nevertheless, numbers of researchers have shown their ability to degrade various pollutants and scientists began to discover more about their potential in participating in bioremediation. Below lists some important facts regarding archaea’s potential role in bioremediation.<br />
<br />
- Biodegradation by extreme [https://en.wikipedia.org/wiki/Halophile halophilic] archaea was not recognized widely in the past, but scientists have found out that extreme halophilic archaea have greater catabolic diversity than expected [9]<br />
<br />
- Hydrocarbon-contamination is observed in some extreme environments, including hypersaline (high salt concentration), high or low temperature, or extreme pH [10]. Archaea’s adaptation to extreme environment gives them the potential to participate in biodegradation and bioremediation in these environments; in fact, microorganisms naturally adapted to the cold environments are known to be important degraders of hydrocarbons in those environments [10].<br />
<br />
- Extreme halophilic archaea has potential to biodegrade pollutants in hypersaline environment, in which bacteria typically used in bioremediation cannot survive or function properly. [5]<br />
<br />
- Some archaea are known to be resistant to variety of antibiotics, including penicillin, cycloheximide, streptomycin, etc, which gives them great advantage in participating in bioremediation in the presence of antibiotics [5].<br />
<br />
===='''Examples of studies of Archaea involved in bioremediation'''====<br />
<br />
Four extreme halophilic strains of archaea (belonging to genus ''[https://en.wikipedia.org/wiki/Halobacterium Halobacterium]'', ''[https://en.wikipedia.org/wiki/Haloferax Haloferax]'', and ''[https://en.wikipedia.org/wiki/Halococcus Halococcus]'') were studied to evaluate their potential to biodegrade crude oil and hydrocarbons. [5] All four strains could use various kinds of hydrocarbons as their carbon or energy sources [5]. Two strains of Haloferax grew on n-alkanes with different lengths, ranging from C8 to C34, and also benzene, toluene, biphenyl, and naphthalene. The research demonstrated the important fact that archaea have potential to carry out biodegradation at high temperatures, in the range of 40-45 °C [5], which is advantageous because hydrocarbons have higher solubility and bioavailability at these higher temperature [10]. The four strains studied were resistant to six different antibiotics, including penicillin, streptomycin, cycloheximide [5] and this gave them the potential to carry out biodegradation in conditions unfavorable for bacteria. Research suggests other genera of archaea are also capable of biodegrading in hypersaline environments [6]<br />
<br />
''[https://en.wikipedia.org/wiki/Halococcus Archaeglobus] fulgidus'', a [https://en.wikipedia.org/wiki/Hyperthermophile hyperthermophile] which can use sulfate as an electron acceptor, can also break down various aromatic hydrocarbons (Peeples, 2014).<br />
<br />
=='''Microbial Processes'''==<br />
<br />
Microorganisms use a wide range of processes to transform chemicals in their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor. This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. Below, several steps and details of the microorganisms’ actions are described.<br />
<br />
==='''Factors Affecting Rates of Biodegradation'''===<br />
Biodegradation may be influenced by pH, temperature, moisture, carbon sources, soil texture, aerobic versus anaerobic conditions, the number of substituents, and the concentration of the pollutant. It is impossible, however, to make a generalization about the best universal conditions for biodegradation. What’s toxic to some microbes is a nutrient to others, what might be a damaging pH to some is beneficial to others, and so on.<br />
<br />
A greater amount of substituents will cause slower degradation in aerobic environments, but faster degradation in anaerobic ones. Chlorine makes a molecule less degradable due to steric hindrance preventing access to necessary enzymes, therefore molecules with higher chlorination are slower to degrade in aerobic conditions. High concentration of a pollutant generally results in faster rates of degradation. If the concentration drops below a threshold concentration, the enzymes may not detect it and will cease to degrade it [26].<br />
<br />
Soil with small pores, especially clays, may cause biodegradation to take years due to the decrease in bioavailability. Chlorine makes a molecule less degradable due to steric hindrance preventing necessary enzymes from accessing the compound, therefore molecules with higher chlorination are slower to degrade. <br />
<br />
The rate at which a compound is transformed, as well as the curves that describe its transformation, is referred to as kinetics, and is affected by all factors listed above. First order kinetics (exponential decay) often describes biodegradation when the initial substrate concentration is low, while zero-order kinetics (linear biodegradation) is often observed when the substrate concentration is very high. In some cases if the concentration of the chemical falls below a critical threshold concentration, the microbes can no longer transform it and the chemical persists. <br />
<br />
The power rate model depicting the relationship between concentration and rate of degradation (first order decay here) is as follows:<br />
<br />
-dC/dt = kC^n<br />
<br />
C is substrate concentration, t is time, k is a rate constant for the chemical in question, and n is an appropriate parameter. The values of k and n are adjusted until a line is found to match experimental data [23].<br />
<br />
==='''Primary substrate utilization'''===<br />
<b>Primary substrate utilization</b> occurs when a microbe both transforms a substrate and uses it as an energy or carbon source. [15] An electron acceptor is required for these transformations. It can be anaerobic or aerobic, although the presence of oxygen tends to speed up reactions. This form of biodegradation can be used for treating petroleum spills or the runoff of a number of pesticides. The rate of reaction follows the guidelines in the previous section, where a higher concentration leads to a higher rate. [15]<br />
<br />
==='''Cometabolism (Secondary Substrate Utilization)'''===<br />
<b>Cometabolism</b> involves the transformation of a chemical by an organism while the organism uses a different substance as its primary energy or carbon source [14]. This is a technique often used when the substrate by itself is considered non-biodegradable, and can only be transformed with another compound. During the actual reaction degrading the substance, the organism has no net carbon or energy gain, and may even result in a product with no use to the organism or which is toxic to the cell [14]. However, it is often difficult to tell whether microorganisms have a second substrate available during their transformations [23]. Cometabolism occurs in parallel with metabolism, not instead of.<br />
<br />
A key example of cometabolism is fortuitous metabolism in the degradation of trichloroethylene, shown in the diagram below. An organic growth substrate such as propane or butane is required for the enzymatic activity that transforms TCE. [14]<br />
<br />
[[Image:Cometabolism.png|center|upright=3|thumb|Image from Kate Scow lecture, 2016]]<br />
<br />
==='''Reductive and Hydrolytic Dehalogenation'''===<br />
Chloride and other halogens are common components of pesticides and hazardous industrial wastes, and by removing them the toxic chemical can often be remediated [23]. If the halogen is replaced by a hydrogen (RCl -> RH), then it is <b>reductive dehalogenation</b>. If two halogens are replaced simultaneously, then the process is called <b>dihaloelimination</b>, although it still falls under reductive dehalogenation [14]. If the halogen is replaced by OH (RCl -> ROH) then it’s <b>hydrolytic dehalogenation</b>. In both cases, the halogen is released as its inorganic form into the environment [23].<br />
<br />
==='''Acclimation'''===<br />
An <b>acclimation period</b>, also called an <b>adaptation</b> or <b>lag period</b>, occurs when no destruction of a given chemical is observed [23]. It is caused by the microbes transitioning to their altered environment and shifting their metabolism to better suit it [14]. It can last for anywhere from hours (such as aromatic compounds in warm, oxygenated soils) to months (such as halobenzoates in anaerobic sediments) depending on the chemical in question and the environment [23]. Acclimation periods can be affected by temperature, the presence of oxygen, pH, and concentration of the substance. Although they are most often faster in warm, aerated, and fairly dry environments, there are few consistencies between what shortens or lengthens the period, even if the concentration is the same [23]. Insecticides including methyl parathion and azinphosmethyl; herbicides including 2, 4-D, MCPA, Mecoprop, TCA, and amitrole; the quaternary ammonium compound dodecyltrimethylammonium chloride; polycyclic aromatic hydrocarbons including naphthalene and anthracene; and other chemicals such as phenol, chlorobenzene, PCP, diphenyl-methane, and NTA have all been reported to have acclimation periods, and this can be of severe human concern [23]. The continued presence of these toxins extends human, plant, and animal exposure, and if the chemical is in water, it can allow the substance to flow further and impact environments distant to its site of origin before being degraded.<br />
<br />
==='''Detoxification and Activation'''===<br />
<b>Detoxication</b>, sometimes called <b>detoxification</b>, has been referred to as the “most important role of microorganisms in the transformation of pollutants” [23]. The process is the changing of a molecule into something less harmful to a species in question. There are a number of ways a molecule can be transformed, including hydrolysis, hydroxylation, dehalogenation, demethylation, methylation, and ether cleavage [23]. By breaking bonds, or adding or removing groups, the organism reduces its effect on the environment. Furthermore, although sometimes the resulting chemical is simply excreted as waste, the organism may also be able to use this new compound as a carbon source or further modifies it until it is released as CO2 [23].<br />
<br />
There are instances where the initial compound is harmless, and in fact the substance produced by microorganisms, or an intermediate in the degradation process, is a toxin [23]. This process is called activation. For this reason, it is important to test all steps of a reaction when determining how a compound is degrading. The new toxins may also be more or less mobile than its predecessor, so it can either stick around one area for extended periods of time or spread to other areas and increase damage [23]. A prevalent example of this is the dechlorination of TCE, which produces DCE (50 times more hazardous than TCE) and Vinyl Chloride (a known carcinogen) [14]. Commonly used insecticides in the past, like zinophos, trichloronat, and carbofuran, were all found to increase a soil’s toxicity with extended use [23].<br />
<br />
=='''Bioremediation treatment methods'''==<br />
In order for bioremediation to be successful, it requires sufficient proof for the degradation of contaminants. However, determining the effectiveness and completeness to reach sufficient results is one of the major issues. Natural attenuation relies on natural processes to clean up or attenuate pollution in soil and groundwater [27]. This remediation is done without human interaction, and is primarily used as a monitoring technique, to make sure more aggressive cleanup strategies are not needed. [https://en.wikipedia.org/wiki/Abiotic_component Abiotic] and [https://en.wikipedia.org/wiki/Biotic_component biotic] factors play a distinguishing factor of how effective bioremediation is.<br />
<br />
Current monitoring practices determine the disappearance of contaminants and their degradation products to regulatory levels that are monitored by toxicity testing, usually on single organisms or species to ensure there are no induced changes that may result in residual toxicity. The problem with these monitoring techniques is that the assessment of contaminants may result in an inaccurate indicator of residual toxicity[28]. Rather, studying the microbial community response may be a more comprehensive indicator of residual toxicity than a single species. Once sufficient evidence is provided, human intervention may be needed for a more effective cleanup process. <br />
<br />
There are two types of remediation that are done, ex situ: which is done by removing the contaminated soil or water and treating it outside the source, and in situ: which treatment takes place within the contaminated area. There are some treatments methods that can be either ex situ or in situ. Some techniques may deal with the mobilization of pollutants, to move them out of an area, or immobilized to keep them out of an area such as a water table.<br />
<br />
<br />
[[Image:Summary_of_bioremediation_strategies.png|center|upright=3|thumb|A comparative analysis of the different types of bioremediation. It can be used to find which remediation technique may be used in certain circumstances [12]]]<br />
<br />
<br />
[[Image:Biopiling.png|right|upright=1.5|thumb|Contaminated soil is mixed with amendments and piled on top of a liner, while a pipe with a blower controls aeration. [29]]]<br />
==='''Ex-situ'''===<br />
Ex-situ techniques are those that are applied to soil and groundwater which has been removed from the site via excavation or pumping [12]. The methods used include composting, biofilters, and biopiling. Ex-situ is used for smaller projects, primarily because larger excavation of soil is not prefered. The movement of the soil can be more detrimental by destroying the preestablish horizons in the soil.<br />
<br />
[[Image:Composting.png|right|upright=3|thumb|Composting is a very versatile remediation technique that can be used for either: a very broad treatment with many contaminants, or very specific treatment that utilizes particular microbes that target specific contaminants [30]. It can also be used to augment other treatment methods.]]<br />
<br />
===='''Biopiling'''====<br />
Excavated soils are mixed with soil amendments and placed on a treatment area. Biopiles are aerated with the use of perforated pipes and blowers in order to control the progression of biodegradation more efficiently by controlling the supply of oxygen [29], which in turn may affect other factors such as pH. This system is primarily used to remediate systems with oil and hydrocarbon contamination. The remediated soil is placed in a liner to prevent further contamination of the soil, they may also be covered with plastic to control runoff, evaporation, and [https://en.wikipedia.org/wiki/Volatilisation volatilization].<br />
<br />
===='''Composting'''====<br />
Nutrients are added to soil that is mixed to increase aeration and activation of indigenous microorganisms. Composting is done in a separate container, then when composting is complete it is incorporated into the soil. Bioremediation by the utilization of compost relies on the adsorption capabilities of organic matter and the degradation capabilities of microorganisms present[30]. Composting is recognized as as one of the most cost-effective technologies for soil bioremediation and it can be done on large and small scales. The use of composting is a very versatile technique for soil polluted by a wide range of organic pollutants and heavy metals, making it great for easier remediation involving various pollutants. The utilization of organic wastes for soil remediation is also helpful in decreasing the need for their storage and treatment. Organic matter that is generated from composting offers the benefit of improving soil quality and structure. Composting is primarily used for remediation over a longer period of time, as the nutrients for the microbes are released gradually and requrire more time compared to quicker treatments such as biostimulation.<br />
<br />
==='''In-situ'''===<br />
In-situ techniques are applied to soil and groundwater at the site with minimal disturbance[12]. These methods include biostimulation, bioleaching, biosorption, and bioventing. In-situ is preferred because it is often minimally invasive to the soil structure in comparison to ex-situ, but it can be expensive due to specialized equipment.<br />
<br />
===='''Biostimulation'''====<br />
This method involves the addition of nutrients to a polluted site in order to encourage the growth of naturally occurring chemical-degrading microorganisms[31]. Biostimulation is primarily done by the addition of various nutrients that are limited in the soil as well as electron acceptors, such as phosphorus, nitrogen and oxygen, or increasing the amount of available carbon in order to increase the population or activity of naturally occurring microorganisms. Other approaches are to optimize environmental conditions such as aeration, the addition of nutrients, altering pH and temperature control [32]. The primary advantage of biostimulation is that it is done by native microorganisms that are well-suited to the environment, and are already well distributed spatially. The challenge is delivering additives so they are readily available to the subsurface microbes.<br />
<br />
===='''Metal Biosorption'''====<br />
Adsorption of metals and other ions of an aqueous solution by the use of microbes. The biosorption process involves a solid phase and a liquid phase containing a dissolved species to be sorbed [34]. The process continues until equilibrium is established between the amount of solid-bound sorbate species and its portion remaining in the solution. The degree of affinity for the sorbate determines its distribution between the solid and liquid phases.<br />
<br />
Biosorption processes are very important in the environment, and has been utalized for conventional biotreatment processes. Biosorption is primarily aimed at the removal or recovery of organic and inorganic substances from solution [35]. The commercialization of biosorption technologies has been limited so far.<br />
<br />
[[Image:Bioventing.png|right|upright=2.5|thumb|Bioventing is primarily used for injecting air into specific remediation zones, adding oxygen as a readily available electron acceptor where it would otherwise be anaerobic. It can also be reversed to make a more anaerobic environment. Either technique can be applied depending on the remediating microbes would thrive in [36].]]<br />
<br />
===='''Bioventing'''====<br />
Bioventing is an In situ remediation technology that uses indigenous microorganisms to biodegrade organic constituents adsorbed to soils in the unsaturated zone[36]. The availability of oxygen generally controls the rate at which aerobic bioremediation proceeds. Bioventing is the coupling of soil venting and bioremediation. Bioventing can be successfully applied to compounds ranging from gasoline or diesel, to heavier hydrocarbons[36]. The addition of nutrients with the bioventing flow rates can achieve greater contaminant reductions than venting alone.<br />
<br />
==='''Ex-situ or In-situ'''===<br />
Some methods can be used by either in-situ or ex-situ methods. The soil or water can be removed from the contamination source and treated, or treated at the source, the method chosen can be based on many factors such as how expensive the project may be or how much contaminant needs to be treated. These methods include bioaugmentation, land farming and biofiltration.<br />
<br />
===='''Bioaugmentation'''====<br />
Bioaugmentation is the addition of non-native microorganisms that have the ability to degrade the contaminants that are recalcitrant to the indigenous microbiota. Bioaugmentation has been proven successful in cleaning organic pollutant, but still faces many environmental problems, such as the survival of strains introduced to soil[37]. The number of introduced microorganisms usually decreases shortly after soil inoculation, when the pollutant has been heavily removed. But the introduced species may linger for long periods of time, a wider use of non-natives runs the possible risk of creating a monoculture in the soil.<br />
<br />
Bioaugmentation is ideal for soil:<br />
<br />
1. With low number of microbes that are capable of degrading targeted pollutants<br />
<br />
2. Containing compounds requiring multi stepped remediation.<br />
<br />
Augmentation techniques have a great potential for [https://en.wikipedia.org/wiki/Category:Aromatic_compounds aromatic compound] remediation. The most important step in successful bioaugmentation is selection of proper microbial strains. The success of bioaugmentation strongly depends on the ability of inoculants to survive in contaminated soil, which may vary due to predation and an environment that does not identically mimic the lab it was grown in.<br />
<br />
===='''Land Farming'''====<br />
Contaminated soil is mixed with amendments such as nutrients, and then they are tilled into the earth, or the contaminated soil is applied into lined beds and periodically turned over or tilled to aerate the waste [38]. The topmost layer is the area of concentration for this method, so it is not ideal for deeper remediation. Land farming differs from composting because it actually incorporates contaminated soil into soil that is uncontaminated [38]. The higher zone of remediation will typically contain primarily lighter hydrocarbons that can be volatilized. The material is periodically tilled for aeration to hasten remediation of any nutrients and allow more oxygen to act as electron acceptors, as well as allowing volatilization to occur. Contaminants are degraded, transformed, and immobilized by microbiological processes and oxidation. Soil conditions are controlled to optimize the rate of contaminant degradation, moisture content, frequency of aeration, and pH are all conditions that may be controlled [38]. <br />
<br />
[[Image:Biofilter.png|right|upright=1.5|thumb|The application of a micro-algal/bacterial biofilter in the primary outflow of soil water [39]]]<br />
<br />
===='''Biofilter'''====<br />
Biofilters are primarily used for the filtration of contaminated groundwater in the soil. Biofilters can be used above soil, where the water will be pumped aboveground for treatment, or a filter can be placed in the soil near an outflow. A micro-algal/bacterial biofilter can be used for the detoxification of copper and cadmium metal wastes [22]. Biofilters have been used in larger industry environments to treat contaminated outflow of water. [https://en.wikipedia.org/wiki/Chromobacterium_violaceum Chromobacterium violaceum], is used to treat water and soil contaminated with silver nanoparticles, reducing its concentration.<br />
<br />
=='''Bioremediation Synopsis'''==<br />
<br />
==='''Advantages'''===<br />
1. Bioremediation that involves natural attenuation or biostimulation is a publicly accepted treatment of polluted soil because it is based upon natural processes. Microbes that metabolize contaminants often increase in population when the contaminant is present and thus rates of biodegradation may increase over time, up to a point. If biodegradation is complete (i.e. mineralization) the products from treatment are harmless; such as carbon dioxide, water, and cellular biomass. [12]<br />
<br />
2. In situ bioremediation can result in complete degradation of pollutants into harmless products on site. This removes the risks involved with transportation for treatment and elimination of contaminated substances. [12]<br />
<br />
3. Bioremediation can be a cheaper alternative to other technologies used for pollution mitigation. [12]<br />
<br />
==='''Disadvantages'''===<br />
1. Only biodegradable compounds are capable of undergoing bioremediation. Not every compound is capable of fully degrading quickly. [12]<br />
<br />
2. The products of biodegradation may potentially be even more persistent or toxic than the original contaminant. [12]<br />
<br />
3. Biological functions are usually extremely specific and require the presence of microbes that are capable of metabolizing the contaminants. In order for the correct microbes to be present, the appropriate environmental conditions, levels of nutrients, and contaminants need to be met. [12]<br />
<br />
4. Scaling up the size of studies from small initial studies to commercial-scale field operations is difficult.[12]<br />
<br />
5. The real environment contains contaminants that are mixed, unevenly distributed, and in different phases (solid, liquid, gas). More research needs to be completed to create technologies that can adapt. [12]<br />
<br />
6. Compared to other treatment technologies, bioremediation often takes more time. [12]<br />
<br />
7. Problems with ensuring adequate contact between the microbes and the contaminant. preferential pathway and soil structure can leave uncertainty in remediation dispersal.[12]<br />
<br />
=='''References'''== <br />
<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdf United States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120. <br />
<br />
5. Al-Mailem, D. M., Sorkhoh, N. A., Al-Awadhi, H., Eliyas, M., & Radwan, S. S. (2010). Biodegradation of crude oil and pure hydrocarbons by extreme halophilic archaea from hypersaline coasts of the Arabian Gulf. Extremophiles, 14(3), 321-328. doi: 10.1007/s00792-010-0312-9<br />
<br />
6. Fairley, D. J., Boyd, D. R., Sharma, N. D., Allen, C. C., Morgan, P., & Larkin, M. J. (2002). Aerobic metabolism of 4-hydroxybenzoic acid in Archaea via an unusual pathway involving an intramolecular migration (NIH shift). Appl Environ Microbiol, 68(12), 6246-6255.<br />
<br />
7. Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008<br />
<br />
8. Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008<br />
<br />
9. Le Borgne, S., Paniagua, D., & Vazquez-Duhalt, R. (2008). Biodegradation of organic pollutants by halophilic bacteria and archaea. J Mol Microbiol Biotechnol, 15(2-3), 74-92. doi: 10.1159/000121323<br />
<br />
10. Margesin, R., & Schinner, F. (2001). Biodegradation and biore<br />
mediation of hydrocarbons in extreme environments. Appl Microbiol Biotechnol, 56(5-6), 650-663.<br />
<br />
11. Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9<br />
<br />
12. Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172. <br />
<br />
13. "Dechloromonas Aromatica RCB." JGI Genome Portal, 16 Feb. 2016. [http://genome.jgi.doe.gov/decar/decar.home.html http://genome.jgi.doe.gov/decar/decar.home.html]<br />
<br />
14. King, R. Barry, John K. Sheldon, and GIlbert M. Long. (1998). Practical Environmental Bioremediation: The Field Guide. 2nd ed. Boca Raton: CRC, 1998.<br />
<br />
15. "Manual, Bioventing Principles and Practices." United States Environmental Protection Agency I (1995)<br />
<br />
16. Gadd, G. M. (Ed.). (2001). Fungi in bioremediation (No. 23). Cambridge University Press<br />
<br />
17. Harms, H., Schlosser, D., & Wick, L. Y. (2011). Untapped potential: exploiting fungi in bioremediation of hazardous chemicals. Nature Reviews Microbiology, 9(3), 177-192<br />
<br />
18. Fragoeiro, S. (2005). Use of fungi in bioremediation of pesticides. Applied Mycology Group Institute of Bioscience and Technology. Cranfield University<br />
<br />
19. Singh, H. (2006). Mycoremediation: fungal bioremediation. John Wiley & Sons. 283-285<br />
<br />
20. Norton, J. M. (2012). Fungi for Bioremediation of Hydrocarbon Pollutants. University of Hawai’i at Hilo. Hohonu, 10, 18-21<br />
<br />
21. Dixit, Ruchita, Emptyyn Wasiullah, Deepti Malaviya, Kuppusamy Pandiyan, Udai Singh, Asha Sahu, Renu Shukla, Bhanu Singh, Jai Rai, Pawan Sharma, Harshad Lade, and Diby Paul. "Bioremediation of Heavy Metals from Soil and Aquatic Environment: An Overview of Principles and Criteria of Fundamental Processes." Sustainability 7.2 (2015): 2189-212. Print.<br />
<br />
22. Bio-filters for Edge-of-Field Water Quality Management. (n.d.). Retrieved February 24, 2016, from [http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html]<br />
<br />
23. Alexander, Martin. (1999). Biodegradation and Bioremediation. San Diego: Academic Print. <br />
<br />
24. Litchfield, Carol. "Thirty Years and Counting: Bioremediation in Its Prime?" BioScience 55.3 (2005): 273.<br />
<br />
25. Biello, David. "Slick Solution: How Microbes Will Clean Up the Deepwater Horizon Oil Spill." Scientific American (n.d.): n. pag. 25 May 2010. <br />
<br />
26. Scow, Kate. “Lectures in Soil Microbiology.” UC Davis, Winter 2016.<br />
<br />
27 CLU-IN | Technologies Remediation About Remediation Technologies Natural Attenuation Overview. (n.d.). Retrieved February 24, 2016, from https://clu-in.org/techfocus/default.focus/sec/Natural_Attenuation/cat/Overview/<br />
<br />
28. Chauhan, Ashok K., and A. Varma. A Textbook of Molecular Biotechnology. New Delhi: I.K. International Pub. House, 2009. Print.<br />
<br />
29. Biopiles. (n.d.). Retrieved March 13, 2016, from [http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html]<br />
<br />
30. Chen, M., Xu, P., Zeng, G., Yang, C., Huang, D., & Zhang, J. (2015). Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: Applications, microbes and future research needs. Biotechnology Advances, 33(6, Part 1), 745–755.<br />
<br />
31. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. Retrieved March 13, 2016, from [http://www.sciencedirect.com/science/article/pii/S0944501309000585 http://www.sciencedirect.com/science/article/pii/S0944501309000585]<br />
<br />
32. Bioremediation, Biostimulation and Bioaugmention: A Review. (n.d.). Retrieved March 13, 2016, from http://pubs.sciepub.com/ijebb/3/1/5/<br />
<br />
33. Sulfur Oxides—Advances in Research and Application: 2013 Edition<br />
<br />
34. Fomina, M., & Gadd, G. M. (2014). Biosorption: current perspectives on concept, definition and application. Bioresource Technology, 160, 3–14. Retrieved February 24, 2016, from [https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application]<br />
<br />
35. Kotrba, Pavel, Martina Mackova, and Tomas Macek. (2011). Microbial Biosorption of Metals. Dordrecht: Springer Science Business Media Print.<br />
<br />
36. Bioventing » Water and Soil Bio-Remediation. (n.d.). Retrieved February 24, 2016, from [http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing]<br />
<br />
37. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. <br />
<br />
38. Land Farming. (n.d.). Retrieved March 13, 2016, from http://www.cpeo.org/techtree/ttdescript/lanfarm.htm<br />
<br />
<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=132745
Bioremediation
2018-03-12T02:48:19Z
<p>Kmscow: /* Advantages */</p>
<hr />
<div>{{Curated}}<br />
<br />
Through agriculture, industry, and daily life, harmful chemicals have been released into the earth’s air, soil, and water. Depending on their concentrations, these substances can have destructive consequences on ecosystems, as well as cause severe damage to humans and other organisms nearby. Soil pollution is of special importance because of its impact on surface, groundwater and air contamination and can easily spread and be consumed by humans. <br />
<br />
[[Image:Bioremediation_images.jpeg|upright=3|thumb|Retrieved from Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120.]]<br />
<br />
<b>Biodegradation</b> is the biologically catalyzed modification of an organic chemical's structure. However, this modification can be through different metabolic pathways and does not necessarily mean a reduction in toxicity. Mineralization, one type of biodegradation, is defined as the conversion of an organic substance to its inorganic constituents, rendering the original compound harmless. [23]. Transformation is defined as any metabolically-induced change in the chemical composition of a compound [14].<br />
<br />
<b>Bioremediation</b> refers to the use of microorganisms to degrade contaminants that pose environmental and human risks. Bioremediation processes typically involve the actions of many different microbes acting in parallel or sequence to complete the degradation process. Both in situ (in place) and ex situ (removal and treatment in another place) remediation approaches are used. The versatility of microbes to degrade a vast array of pollutants makes bioremediation a technology that can be applied in different soil conditions [3]. Though it can be inexpensive and in situ approaches can reduce disruptive engineering practices, bioremediation is still not a common practice [1].<br />
<br />
A widely used approach to bioremediation involves stimulating naturally occurring microbial communities, providing them with nutrients and other needs, to break down a contaminant. This is termed <b>biostimulation.</b> Biostimulation can be achieved through changes in pH, moisture, aeration, or additions of electron donors, electron acceptors or nutrients. Another bioremediation approach is termed <b>bioaugmentation</b>, where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously.<br />
<br />
Recent awareness of the dangers of many chemicals used in society has led to research on formulation of products that are more easily degraded in the environment.<br />
<br />
From an ecological point of view, bioremediation depends on the various interactions between three factors: substrate (pollutant), organisms, and environment, as shown in the figure at right [4]. The interactions of these factors affect biodegradability, bioavailability, and physiological requirements, which are important in assessing the feasibility of bioremediation [4]. <b>Biodegradability</b>, or whether a chemical can be degraded or not, is determined by the presence or absence of organisms that are able to degrade a chemical of interest and how widespread these organisms are in the site [4]. The substrate (pollutant) can interact with its surrounding environment to change its <b>bioavailability</b>, or availability to organisms that are capable of degrading it; for example, substrate has low bioavailability if it is tightly bound to soil organic matter or trapped inside aggregates [4]. <b>Physiological requirements</b>, or set of conditions required by organisms to carry out bioremediation in the environment, include nutrient availability, optimal pH, and availability of electron acceptors, such as oxygen and nitrate [4]. Also, the environment needs to be habitable for organisms involved in bioremediation [4].<br />
<br />
=='''Brief History'''==<br />
<br />
[[Image:Wasterwater_treatment.png|upright=2.25|thumb|First Water Treatment Facility in Japan, 1934 Image from http://www.sewerhistory.org/grfx/trtmnt/trtmnt3.htm]] <br />
<br />
Microorganisms in the environment have always broken down waste, and humans have always (knowingly or unknowingly) used them in agricultural, domestic, and industrial activities [24]. As the urbanized world shifted to a more industrial system, however, people began to take an active approach in bioremediation. In the late nineteenth century, wastewater treatment plants were formed, but even so, this was not officially called bioremediation .<br />
The project considered the initial spark of the bioremediation movement was the report “Beneficial Stimulation of Bacterial Activity in Groundwater Containing Petroleum Products” by R.L. Raymond et al. in 1975. By testing the relationship between oil presence and bacterial stimulation, Raymond found that adding nutrients to soil hastened the oil removal. This led to the development of in situ bioremediation [24].<br />
<br />
Initial bioremediation projects focused on “pump and treat” (ex situ) methods in soil around gas stations and refinery spills to get oil out of groundwater sources, but soon cleaning up chlorinated hydrocarbons became a primary concern [24]. Chlorinated compounds were commonly used in pesticides, but when people learned it was a possible carcinogen and causing ozone depletion, research into bioremediation took off [24]. This was when anaerobic bacteria started being used, as it was discovered that they dechlorinate compounds much more quickly than do aerobic bacteria, and produce fewer damaging iron compounds that precipitate from the reactions [24].<br />
<br />
=='''Overview of Pollutants'''==<br />
Pollutants found in soils present a variety of different human health risks. Soil pollutants are typically classified as organic and inorganic pollutants. The remediation of some of these pollutants will be discussed in greater depth in the following sections.<br />
Below is a link to website with a list of examples of soil pollutants and their effects on human health:<br />
<br />
[http://www.environmentalpollutioncenters.org/soil/examples/ Summary of health effects of pollutants]<br />
<br />
==='''Organic Pollutants'''===<br />
Industrialization resulted in increased use of organic compounds that build up and persist in the environment [11]. Main sources of organic pollutants are through anthropogenic activities, including use of solvents, pesticides, and fuels [11]. Some of these organic compounds are highly toxic and they are associated with variety of health issues around the world [11].<br />
<br />
Table below lists some groups of contaminants, examples, and their sources.<br />
<br />
[[Image:Pollutants_list.png|center|upright=2.5|thumb|Retrieved from Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172.]]<br />
<br />
While organic pollutants are causing both environmental and health problems, bioremediation offers an effective solution to the pollution [11]. The table below lists some of the organic pollutants and microorganisms that are found to be able to degrade them.<br />
<br />
[[Image:Pollutants_and_organisms.png|center|upright=2.5|thumb|Retrieved from Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9]]<br />
<br />
==='''Inorganic Pollutants'''=== <br />
{| border="1" style="float:right; margin-left: 10px; text-align:center"<br />
|+ Most inorganic pollutants are due to human activities.<br />
!Pollutant<br />
!Source<br />
|-<br />
| [https://en.wikipedia.org/wiki/Arsenic Arsenic] || Pesticides, wood preservatives, biosolids, ore mining and smelting<br />
|- <br />
| [https://en.wikipedia.org/wiki/Cadmium Cadmium] || Paints and pigments, plastic stabilizers, electroplating, phosphate fertilizers<br />
|-<br />
| [https://en.wikipedia.org/wiki/Chromium Chromium] || Tanneries, steel industries, fly ash<br />
|- <br />
| [https://en.wikipedia.org/wiki/Copper Copper] || Pesticides, fertilizers, biosolids, ore mining and smelting<br />
|-<br />
| [https://en.wikipedia.org/wiki/Mercury_%28element%29 Mercury] || Gold and Silver mining, coal combustion<br />
|-<br />
| [https://en.wikipedia.org/wiki/Nickel Nickel] || Effluent, kitchen appliances, surgical instruments, automobile batteries<br />
|-<br />
| [https://en.wikipedia.org/wiki/Lead Lead] || Aerial emission from combustion of leaded fuel, batteries waste, insecticide and herbicides.<br />
|}<br />
<br />
A majority of heavy metal pollutants come from human sources that accumulate over time.<br />
<br />
There are also natural forms of contamination from normal biological processes, which include:<br />
<br />
1. Weathering of minerals over time<br />
<br />
2. [https://en.wikipedia.org/wiki/Erosion Erosion] and [https://en.wikipedia.org/wiki/Volcano volcanic activities]<br />
<br />
3. [https://en.wikipedia.org/wiki/Wildfire Forest fires] and biogenic source<br />
<br />
4. Particles released by vegetation<br />
<br />
Heavy metals can be absorbed by microbes at cellular binding sites. Extracellular polymers of these microbes can complex heavy metals through various mechanisms [21]. These specialized microorganisms can mineralize the organic contaminants to metabolic intermediates, which are used as primary substrates for cell growth. The microbes prevalent in heavily metal-contaminated soil can alter the oxidation state of the heavy metals by immobilizing them [21], allowing them to be easily removed. Bioremediation of heavy metals from microbes is not heavily researched, mostly due to an incomplete understanding of the genetics of the microbes used in metal adsorption. ''[https://microbewiki.kenyon.edu/index.php/Geomicrobiology Geomicrobiology]'' takes a better look at the interactions between microbes and inorganic material.<br />
<br />
=='''Organisms'''==<br />
As stated previously, bioremediation involves various microorganisms that are able to degrade and reduce toxicity of environmental pollutants [12]. Therefore, the interactions of microbes with the environment and pollutants are significant in determining effectiveness of bioremediation [4]. Those microbes can be either naturally present in the site of bioremediation or isolated from other sites and inoculated artificially [12]. Biodegradation often occurs as part of microbial metabolism and in some cases, microbes are able to directly harvest carbon and energy by breaking down pollutants [12]. Sections below go over bacteria and fungi, the commonly used organisms in bioremediation, and archaea, the more recently discovered group of organisms with unique potential in bioremediation.<br />
<br />
==='''Bacteria'''===<br />
Bacteria are widely diverse organisms, and thus make excellent players in biodegradation and bioremediation. There are few universal toxins to bacteria, so there is likely an organism able to break down any given substrate, when provided with the right conditions (anaerobic versus aerobic environment, sufficient electron donors or acceptors, etc.). Below are several specific bacteria species known to participate in bioremediation.<br />
<br />
===='''''[[Pseudomonas putida]]'''====<br />
[[Image:Pseudomonas_putida.png|upright=1|thumb|Pseudomonas putida, Image © http://www.denniskunkel.com/DK/Bacteria/23859D.html]]<br />
<br />
''Pseudomonas putida'' is a gram-negative soil bacterium that is involved in the bioremediation of toluene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===='''''[[Dechloromonas aromatica]]''' ====<br />
''Dechloromonas aromatica'' is a rod-shaped bacterium which can oxidize aromatics including benzoate, chlorobenzoate, and toluene, coupling the reaction with the reduction of oxygen, chlorate, or nitrate. It is the only organism able to oxidize benzene anaerobically. Due to the high propensity of benzene contamination, especially in ground and surface water, ''D. aromatic'' is especially useful for in situ bioremediation of this substance. [13]<br />
<br />
===='''Nitrifiers and Denitrifiers'''==== <br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage process that involves nitrification and denitrification. During nitrification, ammonium is oxidized to nitrite by organisms like <i>Nitrosomonas europaea</i>.Then, nitrite is further oxidized to nitrate by microbes like <i>Nitrobacter hamburgensis</i>.<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like <i>Paracoccus denitrificans </i>[2]. The result is N2 gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
===='''''[[Deinococcus radiodurans]]'''====<br />
''Deinococcus radiodurans'' is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered strain of Deinococcus radiodurans has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7].<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like ''[[Paracoccus denitrificans]]'' [2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
[[Image:Alcanivorax_borkumensis.png|upright=1|thumb|Alcanivorax borkumensis, Image©https://www.biotechnologie.de/BIO/Navigation/EN/Funding/foerderbeispiele,did=44848.html?view=renderPrint [25]]]<br />
<br />
===='''''[[Methylibium petroleiphilum]]'''====<br />
''Methylibium petroleiphilum'' (formally known as PM1 strain) is a bacterium capable of [https://en.wikipedia.org/wiki/Methyl_tert-butyl_ether methyl tert-butyl ether] (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
===='''''[[Alcanivorax borkumensis]]'''====<br />
''Alcanivorax borkumensis'' is a marine rod-shaped bacterium which consumes hydrocarbons, such as the ones found in fuel, and produces carbon dioxide. It grows rapidly in environments damaged by oil, and has been used to aid in cleaning the more than 830,000 gallons of oil from the [https://en.wikipedia.org/wiki/Deepwater_Horizon_oil_spill Deepwater Horizon oil spill] in the Gulf of Mexico [25].<br />
<br />
==='''Fungi (Mycoremediation)'''===<br />
Current bioremediation applications primarily utilize bacteria, with comparatively few attempts to use fungi. Fungi have fundamentally important roles because of their participation in the cycling of elements through decomposition and transformation of organic and inorganic materials. These characteristics can be translated into applications for bioremediation which could break down organic compounds and reduce the risks of metals. In some cases, fungi have an advantage over bacteria not just in metabolic versatility but also their environmental resilience.They are able to oxidize a diverse amount of chemicals and survive in harsh environmental conditions such as low moisture and high concentrations of pollutants. Therefore, fungi are potentially an extremely powerful tool in soil bioremediation and some versatile species such as <b>[https://en.wikipedia.org/wiki/Wood-decay_fungus#White_rot White Rot Fungi]</b> have been a hot topic of research. [16,17]<br />
<br />
===='''Biodegradation Capacities of White rot fungi'''====<br />
Using fungi as potential treatment of contaminants began in 1985 when the white rot species Phanerochaete chrysosporium was discovered to metabolize multiple key environmental pollutants. The most important feature of these fungi is their enzymatic functional ability to metabolize complex chemicals such as lignin. Similar abilities were later discovered in other white rot fungal species. In addition, white rot fungi are highly advantageous because they degrade lignin extracellularly through its hyphal extension. This allows them to access soil contaminants that other organisms are incapable of and maximize surface area for enzymatic interaction. These inexpensive fungi can tolerate extreme environmental conditions, such as pH, temperature, and moisture content. While many microbial organisms that are used for bioremediation require pre-conditioning of the environment for them to survive in, white rot fungi can directly be applied into most systems because they degrade based upon nutrient deprivation. [18]<br />
<br />
[[Image:040504062021.jpg|right|thumb|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x]]<br />
<br />
===='''''[[Phanerochaete chrysosporium]]'''====<br />
<i>P. chrysosporium</i> was the first fungi linked to degradation of organic pollutants. Extensive research has show this it has strong potential for bioremediation in pesticides, PAHs, dioxins, carbon tetrachloride, and many other pollutants. Among fungal systems, <i>P. chrysosporium</i> has become the model for bioremediation. Other notable species of white rot fungi include <i>Pleurotus ostreatus</i> and <i>Trametes versicolor</i>. [18]<br />
<br />
===='''Bioremediation of Hydrocarbon Pollutants'''====<br />
<br />
Hydrocarbons are stored deep underground but are brought up to the surface to be transformed and utilized, primarily as an energy source known as fossil fuels. The majority of pollution currently comes from these byproducts in the form Polycyclic Aromatic Hydrocarbons (PAHs), which are xenobiotic environmental pollutants that form when carbon materials are incompletely combusted. Some of examples of PAHs include burning wood, fossil fuels, and cigarette smoke. [19,20]<br />
Currently, bioremediation is only effective for soils contaminated with low-molecular weight PAHs because of bacterial commercial use. However, fungi are effective at PAH degradation in comparison to bacteria for a few reasons. Firstly, they are capable degrading PAH’s that are high in molecular weight, bacteria in comparison are better at degrading smaller molecules. Secondly, fungi can function well in non-aqueous environments and low oxygen conditions, both are conditions where PAH’s can accumulate. Many fungi have evolved mechanisms that allow the to target specific PAHs. Fungi produce extracellular enzymes that degrade lignin, a process called mineralization the produces carbon dioxide as the end product. [19,20]<br />
<br />
===='''Remediating Metals'''====<br />
<br />
Toxic metals can enter the environment all life cycle stages of metal compound. For example, metal leaching can occur from the mining process till the disposal of metal wastes. However in nature, the mobility of metals comes from the geological processes that can be released into the soil and aquatic environments. The environmental largest risk from metal contamination comes from the relationship between metals and compounds that are inherently of incapable of being degraded by any natural procedures. The best solution to treating contamination is transporting the metals to location where they cannot produce negative environmental effects. Fungi have various ways of interacting with metals, some of the techniques are increasing or decreasing the mobility of metals, sorption, or even cellular uptake. After the metals have been absorbed the fungus, they can chemically altered to be stored or translocated through the hyphae and into various plants that participate in symbiosis. [17]<br />
<br />
===='''Pesticide Degradation'''====<br />
<br />
Pesticide accumulation is an issue of great concern among the public, because they are directly associated with food products and water supplies. There are number of technologies used for pesticide clean-up; however, these technologies are generally expensive and inefficient because they require contaminated soil to be excavated and sent to a separate storage location for processing. Bioremediation offers a potential solution that treats contaminated soil and groundwater without needing excavation. Studies show that White Rot Fungi has high promise for soil bioremediation application; however, most tests have been conducted in the lab rather than in the actual environment. This fungi demonstrates the ability to transform and mineralize specific pesticides in soil. [18]<br />
<br />
===='''Environmental Applications'''====<br />
<br />
Although fungi demonstrate significant biochemical and ecological useful qualities, they are hardly utilized for biotechnological purposes. Instead, bacteria are most commonly used because they usually produce superior results in their numerous advantages ranging from their highly specific biochemical reactions to their capabilities of breaking down pollutants efficiently [17]. Fungi are underused primarily because of the costs that come from providing oxygen to fungi in polluted environments. However, filamentous fungi could be highly valuable in situations where bacteria cannot perform. For example, fungi are useful in situations where contaminants are physically blockaded and bacteria cannot reach or in circumstances of environmental extremes such as high acidity or dryness prevent bacteria from functioning. [17]<br />
<br />
==='''[https://en.wikipedia.org/wiki/Archaea Archaea]'''===<br />
The role of archaea in bioremediation has not been studied as commonly as that of bacteria [10]. Nevertheless, numbers of researchers have shown their ability to degrade various pollutants and scientists began to discover more about their potential in participating in bioremediation. Below lists some important facts regarding archaea’s potential role in bioremediation.<br />
<br />
- Biodegradation by extreme [https://en.wikipedia.org/wiki/Halophile halophilic] archaea was not recognized widely in the past, but scientists have found out that extreme halophilic archaea have greater catabolic diversity than expected [9]<br />
<br />
- Hydrocarbon-contamination is observed in some extreme environments, including hypersaline (high salt concentration), high or low temperature, or extreme pH [10]. Archaea’s adaptation to extreme environment gives them the potential to participate in biodegradation and bioremediation in these environments; in fact, microorganisms naturally adapted to the cold environments are known to be important degraders of hydrocarbons in those environments [10].<br />
<br />
- Extreme halophilic archaea has potential to biodegrade pollutants in hypersaline environment, in which bacteria typically used in bioremediation cannot survive or function properly. [5]<br />
<br />
- Some archaea are known to be resistant to variety of antibiotics, including penicillin, cycloheximide, streptomycin, etc, which gives them great advantage in participating in bioremediation in the presence of antibiotics [5].<br />
<br />
===='''Examples of studies of Archaea involved in bioremediation'''====<br />
<br />
Four extreme halophilic strains of archaea (belonging to genus ''[https://en.wikipedia.org/wiki/Halobacterium Halobacterium]'', ''[https://en.wikipedia.org/wiki/Haloferax Haloferax]'', and ''[https://en.wikipedia.org/wiki/Halococcus Halococcus]'') were studied to evaluate their potential to biodegrade crude oil and hydrocarbons. [5] All four strains could use various kinds of hydrocarbons as their carbon or energy sources [5]. Two strains of Haloferax grew on n-alkanes with different lengths, ranging from C8 to C34, and also benzene, toluene, biphenyl, and naphthalene. The research demonstrated the important fact that archaea have potential to carry out biodegradation at high temperatures, in the range of 40-45 °C [5], which is advantageous because hydrocarbons have higher solubility and bioavailability at these higher temperature [10]. The four strains studied were resistant to six different antibiotics, including penicillin, streptomycin, cycloheximide [5] and this gave them the potential to carry out biodegradation in conditions unfavorable for bacteria. Research suggests other genera of archaea are also capable of biodegrading in hypersaline environments [6]<br />
<br />
''[https://en.wikipedia.org/wiki/Halococcus Archaeglobus] fulgidus'', a [https://en.wikipedia.org/wiki/Hyperthermophile hyperthermophile] which can use sulfate as an electron acceptor, can also break down various aromatic hydrocarbons (Peeples, 2014).<br />
<br />
=='''Microbial Processes'''==<br />
<br />
Microorganisms use a wide range of processes to transform chemicals in their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor. This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. Below, several steps and details of the microorganisms’ actions are described.<br />
<br />
==='''Factors Affecting Rates of Biodegradation'''===<br />
Biodegradation may be influenced by pH, temperature, moisture, carbon sources, soil texture, aerobic versus anaerobic conditions, the number of substituents, and the concentration of the pollutant. It is impossible, however, to make a generalization about the best universal conditions for biodegradation. What’s toxic to some microbes is a nutrient to others, what might be a damaging pH to some is beneficial to others, and so on.<br />
<br />
A greater amount of substituents will cause slower degradation in aerobic environments, but faster degradation in anaerobic ones. Chlorine makes a molecule less degradable due to steric hindrance preventing access to necessary enzymes, therefore molecules with higher chlorination are slower to degrade in aerobic conditions. High concentration of a pollutant generally results in faster rates of degradation. If the concentration drops below a threshold concentration, the enzymes may not detect it and will cease to degrade it [26].<br />
<br />
Soil with small pores, especially clays, may cause biodegradation to take years due to the decrease in bioavailability. Chlorine makes a molecule less degradable due to steric hindrance preventing necessary enzymes from accessing the compound, therefore molecules with higher chlorination are slower to degrade. <br />
<br />
The rate at which a compound is transformed, as well as the curves that describe its transformation, is referred to as kinetics, and is affected by all factors listed above. First order kinetics (exponential decay) often describes biodegradation when the initial substrate concentration is low, while zero-order kinetics (linear biodegradation) is often observed when the substrate concentration is very high. In some cases if the concentration of the chemical falls below a critical threshold concentration, the microbes can no longer transform it and the chemical persists. <br />
<br />
The power rate model depicting the relationship between concentration and rate of degradation (first order decay here) is as follows:<br />
<br />
-dC/dt = kC^n<br />
<br />
C is substrate concentration, t is time, k is a rate constant for the chemical in question, and n is an appropriate parameter. The values of k and n are adjusted until a line is found to match experimental data [23].<br />
<br />
==='''Primary substrate utilization'''===<br />
<b>Primary substrate utilization</b> occurs when a microbe both transforms a substrate and uses it as an energy or carbon source. [15] An electron acceptor is required for these transformations. It can be anaerobic or aerobic, although the presence of oxygen tends to speed up reactions. This form of biodegradation can be used for treating petroleum spills or the runoff of a number of pesticides. The rate of reaction follows the guidelines in the previous section, where a higher concentration leads to a higher rate. [15]<br />
<br />
==='''Cometabolism (Secondary Substrate Utilization)'''===<br />
<b>Cometabolism</b> involves the transformation of a chemical by an organism while the organism uses a different substance as its primary energy or carbon source [14]. This is a technique often used when the substrate by itself is considered non-biodegradable, and can only be transformed with another compound. During the actual reaction degrading the substance, the organism has no net carbon or energy gain, and may even result in a product with no use to the organism or which is toxic to the cell [14]. However, it is often difficult to tell whether microorganisms have a second substrate available during their transformations [23]. Cometabolism occurs in parallel with metabolism, not instead of.<br />
<br />
A key example of cometabolism is fortuitous metabolism in the degradation of trichloroethylene, shown in the diagram below. An organic growth substrate such as propane or butane is required for the enzymatic activity that transforms TCE. [14]<br />
<br />
[[Image:Cometabolism.png|center|upright=3|thumb|Image from Kate Scow lecture, 2016]]<br />
<br />
==='''Reductive and Hydrolytic Dehalogenation'''===<br />
Chloride and other halogens are common components of pesticides and hazardous industrial wastes, and by removing them the toxic chemical can often be remediated [23]. If the halogen is replaced by a hydrogen (RCl -> RH), then it is <b>reductive dehalogenation</b>. If two halogens are replaced simultaneously, then the process is called <b>dihaloelimination</b>, although it still falls under reductive dehalogenation [14]. If the halogen is replaced by OH (RCl -> ROH) then it’s <b>hydrolytic dehalogenation</b>. In both cases, the halogen is released as its inorganic form into the environment [23].<br />
<br />
==='''Acclimation'''===<br />
An <b>acclimation period</b>, also called an <b>adaptation</b> or <b>lag period</b>, occurs when no destruction of a given chemical is observed [23]. It is caused by the microbes transitioning to their altered environment and shifting their metabolism to better suit it [14]. It can last for anywhere from hours (such as aromatic compounds in warm, oxygenated soils) to months (such as halobenzoates in anaerobic sediments) depending on the chemical in question and the environment [23]. Acclimation periods can be affected by temperature, the presence of oxygen, pH, and concentration of the substance. Although they are most often faster in warm, aerated, and fairly dry environments, there are few consistencies between what shortens or lengthens the period, even if the concentration is the same [23]. Insecticides including methyl parathion and azinphosmethyl; herbicides including 2, 4-D, MCPA, Mecoprop, TCA, and amitrole; the quaternary ammonium compound dodecyltrimethylammonium chloride; polycyclic aromatic hydrocarbons including naphthalene and anthracene; and other chemicals such as phenol, chlorobenzene, PCP, diphenyl-methane, and NTA have all been reported to have acclimation periods, and this can be of severe human concern [23]. The continued presence of these toxins extends human, plant, and animal exposure, and if the chemical is in water, it can allow the substance to flow further and impact environments distant to its site of origin before being degraded.<br />
<br />
==='''Detoxification and Activation'''===<br />
<b>Detoxication</b>, sometimes called <b>detoxification</b>, has been referred to as the “most important role of microorganisms in the transformation of pollutants” [23]. The process is the changing of a molecule into something less harmful to a species in question. There are a number of ways a molecule can be transformed, including hydrolysis, hydroxylation, dehalogenation, demethylation, methylation, and ether cleavage [23]. By breaking bonds, or adding or removing groups, the organism reduces its effect on the environment. Furthermore, although sometimes the resulting chemical is simply excreted as waste, the organism may also be able to use this new compound as a carbon source or further modifies it until it is released as CO2 [23].<br />
<br />
There are instances where the initial compound is harmless, and in fact the substance produced by microorganisms, or an intermediate in the degradation process, is a toxin [23]. This process is called activation. For this reason, it is important to test all steps of a reaction when determining how a compound is degrading. The new toxins may also be more or less mobile than its predecessor, so it can either stick around one area for extended periods of time or spread to other areas and increase damage [23]. A prevalent example of this is the dechlorination of TCE, which produces DCE (50 times more hazardous than TCE) and Vinyl Chloride (a known carcinogen) [14]. Commonly used insecticides in the past, like zinophos, trichloronat, and carbofuran, were all found to increase a soil’s toxicity with extended use [23].<br />
<br />
=='''Bioremediation treatment methods'''==<br />
In order for bioremediation to be successful, it requires sufficient proof for the degradation of contaminants. However, determining the effectiveness and completeness to reach sufficient results is one of the major issues. Natural attenuation relies on natural processes to clean up or attenuate pollution in soil and groundwater [27]. This remediation is done without human interaction, and is primarily used as a monitoring technique, to make sure more aggressive cleanup strategies are not needed. [https://en.wikipedia.org/wiki/Abiotic_component Abiotic] and [https://en.wikipedia.org/wiki/Biotic_component biotic] factors play a distinguishing factor of how effective bioremediation is.<br />
<br />
Current monitoring practices determine the disappearance of contaminants and their degradation products to regulatory levels that are monitored by toxicity testing, usually on single organisms or species to ensure there are no induced changes that may result in residual toxicity. The problem with these monitoring techniques is that the assessment of contaminants may result in an inaccurate indicator of residual toxicity[28]. Rather, studying the microbial community response may be a more comprehensive indicator of residual toxicity than a single species. Once sufficient evidence is provided, human intervention may be needed for a more effective cleanup process. <br />
<br />
There are two types of remediation that are done, ex situ: which is done by removing the contaminated soil or water and treating it outside the source, and in situ: which treatment takes place within the contaminated area. There are some treatments methods that can be either ex situ or in situ. Some techniques may deal with the mobilization of pollutants, to move them out of an area, or immobilized to keep them out of an area such as a water table.<br />
<br />
<br />
[[Image:Summary_of_bioremediation_strategies.png|center|upright=3|thumb|A comparative analysis of the different types of bioremediation. It can be used to find which remediation technique may be used in certain circumstances [12]]]<br />
<br />
<br />
[[Image:Biopiling.png|right|upright=1.5|thumb|Contaminated soil is mixed with amendments and piled on top of a liner, while a pipe with a blower controls aeration. [29]]]<br />
==='''Ex-situ'''===<br />
Ex-situ techniques are those that are applied to soil and groundwater which has been removed from the site via excavation or pumping [12]. The methods used include composting, biofilters, and biopiling. Ex-situ is used for smaller projects, primarily because larger excavation of soil is not prefered. The movement of the soil can be more detrimental by destroying the preestablish horizons in the soil.<br />
<br />
[[Image:Composting.png|right|upright=3|thumb|Composting is a very versatile remediation technique that can be used for either: a very broad treatment with many contaminants, or very specific treatment that utilizes particular microbes that target specific contaminants [30]. It can also be used to augment other treatment methods.]]<br />
<br />
===='''Biopiling'''====<br />
Excavated soils are mixed with soil amendments and placed on a treatment area. Biopiles are aerated with the use of perforated pipes and blowers in order to control the progression of biodegradation more efficiently by controlling the supply of oxygen [29], which in turn may affect other factors such as pH. This system is primarily used to remediate systems with oil and hydrocarbon contamination. The remediated soil is placed in a liner to prevent further contamination of the soil, they may also be covered with plastic to control runoff, evaporation, and [https://en.wikipedia.org/wiki/Volatilisation volatilization].<br />
<br />
===='''Composting'''====<br />
Nutrients are added to soil that is mixed to increase aeration and activation of indigenous microorganisms. Composting is done in a separate container, then when composting is complete it is incorporated into the soil. Bioremediation by the utilization of compost relies on the adsorption capabilities of organic matter and the degradation capabilities of microorganisms present[30]. Composting is recognized as as one of the most cost-effective technologies for soil bioremediation and it can be done on large and small scales. The use of composting is a very versatile technique for soil polluted by a wide range of organic pollutants and heavy metals, making it great for easier remediation involving various pollutants. The utilization of organic wastes for soil remediation is also helpful in decreasing the need for their storage and treatment. Organic matter that is generated from composting offers the benefit of improving soil quality and structure. Composting is primarily used for remediation over a longer period of time, as the nutrients for the microbes are released gradually and requrire more time compared to quicker treatments such as biostimulation.<br />
<br />
==='''In-situ'''===<br />
In-situ techniques are applied to soil and groundwater at the site with minimal disturbance[12]. These methods include biostimulation, bioleaching, biosorption, and bioventing. In-situ is preferred because it is often minimally invasive to the soil structure in comparison to ex-situ, but it can be expensive due to specialized equipment.<br />
<br />
===='''Biostimulation'''====<br />
This method involves the addition of nutrients to a polluted site in order to encourage the growth of naturally occurring chemical-degrading microorganisms[31]. Biostimulation is primarily done by the addition of various nutrients that are limited in the soil as well as electron acceptors, such as phosphorus, nitrogen and oxygen, or increasing the amount of available carbon in order to increase the population or activity of naturally occurring microorganisms. Other approaches are to optimize environmental conditions such as aeration, the addition of nutrients, altering pH and temperature control [32]. The primary advantage of biostimulation is that it is done by native microorganisms that are well-suited to the environment, and are already well distributed spatially. The challenge is delivering additives so they are readily available to the subsurface microbes.<br />
<br />
===='''Metal Bioleaching'''====<br />
Metal bioleaching is the extraction of metals from soils utilizing a biological source such as microbes. This technique was first developed to extract minerals from ores. Specific microorganisms like Thiobacillus ferrooxidans and T. thiooxidans promote the metals’ solubilization. Several species of fungi are used for bioleaching. These remediation fungi can also produced in a lab. Two prevalent fungal strains ([https://microbewiki.kenyon.edu/index.php/Aspergillus_niger Aspergillus Niger], [https://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium Simplicissimum]) are capable of mobilizing metals such as copper, tin, aluminium, nickel, palladium, and zinc[33], which will make them much easier to remove from the soil.<br />
<br />
===='''Metal Biosorption'''====<br />
Adsorption of metals and other ions of an aqueous solution by the use of microbes. The biosorption process involves a solid phase and a liquid phase containing a dissolved species to be sorbed [34]. The process continues until equilibrium is established between the amount of solid-bound sorbate species and its portion remaining in the solution. The degree of affinity for the sorbate determines its distribution between the solid and liquid phases.<br />
<br />
Biosorption processes are very important in the environment, and has been utalized for conventional biotreatment processes. Biosorption is primarily aimed at the removal or recovery of organic and inorganic substances from solution [35]. The commercialization of biosorption technologies has been limited so far.<br />
<br />
[[Image:Bioventing.png|right|upright=2.5|thumb|Bioventing is primarily used for injecting air into specific remediation zones, adding oxygen as a readily available electron acceptor where it would otherwise be anaerobic. It can also be reversed to make a more anaerobic environment. Either technique can be applied depending on the remediating microbes would thrive in [36].]]<br />
<br />
===='''Bioventing'''====<br />
Bioventing is an In situ remediation technology that uses indigenous microorganisms to biodegrade organic constituents adsorbed to soils in the unsaturated zone[36]. The availability of oxygen generally controls the rate at which aerobic bioremediation proceeds. Bioventing is the coupling of soil venting and bioremediation. Bioventing can be successfully applied to compounds ranging from gasoline or diesel, to heavier hydrocarbons[36]. The addition of nutrients with the bioventing flow rates can achieve greater contaminant reductions than venting alone.<br />
<br />
==='''Ex-situ or In-situ'''===<br />
Some methods can be used by either in-situ or ex-situ methods. The soil or water can be removed from the contamination source and treated, or treated at the source, the method chosen can be based on many factors such as how expensive the project may be or how much contaminant needs to be treated. These methods include bioaugmentation, land farming and biofiltration.<br />
<br />
===='''Bioaugmentation'''====<br />
Bioaugmentation is the addition of non-native microorganisms that have the ability to degrade the contaminants that are recalcitrant to the indigenous microbiota. Bioaugmentation has been proven successful in cleaning organic pollutant, but still faces many environmental problems, such as the survival of strains introduced to soil[37]. The number of introduced microorganisms usually decreases shortly after soil inoculation, when the pollutant has been heavily removed. But the introduced species may linger for long periods of time, a wider use of non-natives runs the possible risk of creating a monoculture in the soil.<br />
<br />
Bioaugmentation is ideal for soil:<br />
<br />
1. With low number of microbes that are capable of degrading targeted pollutants<br />
<br />
2. Containing compounds requiring multi stepped remediation.<br />
<br />
Augmentation techniques have a great potential for [https://en.wikipedia.org/wiki/Category:Aromatic_compounds aromatic compound] remediation. The most important step in successful bioaugmentation is selection of proper microbial strains. The success of bioaugmentation strongly depends on the ability of inoculants to survive in contaminated soil, which may vary due to predation and an environment that does not identically mimic the lab it was grown in.<br />
<br />
===='''Land Farming'''====<br />
Contaminated soil is mixed with amendments such as nutrients, and then they are tilled into the earth, or the contaminated soil is applied into lined beds and periodically turned over or tilled to aerate the waste [38]. The topmost layer is the area of concentration for this method, so it is not ideal for deeper remediation. Land farming differs from composting because it actually incorporates contaminated soil into soil that is uncontaminated [38]. The higher zone of remediation will typically contain primarily lighter hydrocarbons that can be volatilized. The material is periodically tilled for aeration to hasten remediation of any nutrients and allow more oxygen to act as electron acceptors, as well as allowing volatilization to occur. Contaminants are degraded, transformed, and immobilized by microbiological processes and oxidation. Soil conditions are controlled to optimize the rate of contaminant degradation, moisture content, frequency of aeration, and pH are all conditions that may be controlled [38]. <br />
<br />
[[Image:Biofilter.png|right|upright=1.5|thumb|The application of a micro-algal/bacterial biofilter in the primary outflow of soil water [39]]]<br />
<br />
===='''Biofilter'''====<br />
Biofilters are primarily used for the filtration of contaminated groundwater in the soil. Biofilters can be used above soil, where the water will be pumped aboveground for treatment, or a filter can be placed in the soil near an outflow. A micro-algal/bacterial biofilter can be used for the detoxification of copper and cadmium metal wastes [22]. Biofilters have been used in larger industry environments to treat contaminated outflow of water. [https://en.wikipedia.org/wiki/Chromobacterium_violaceum Chromobacterium violaceum], is used to treat water and soil contaminated with silver nanoparticles, reducing its concentration.<br />
<br />
=='''Bioremediation Synopsis'''==<br />
<br />
==='''Advantages'''===<br />
1. Bioremediation that involves natural attenuation or biostimulation is a publicly accepted treatment of polluted soil because it is based upon natural processes. Microbes that metabolize contaminants often increase in population when the contaminant is present and thus rates of biodegradation may increase over time, up to a point. If biodegradation is complete (i.e. mineralization) the products from treatment are harmless; such as carbon dioxide, water, and cellular biomass. [12]<br />
<br />
2. In situ bioremediation can result in complete degradation of pollutants into harmless products on site. This removes the risks involved with transportation for treatment and elimination of contaminated substances. [12]<br />
<br />
3. Bioremediation can be a cheaper alternative to other technologies used for pollution mitigation. [12]<br />
<br />
==='''Disadvantages'''===<br />
1. Only biodegradable compounds are capable of undergoing bioremediation. Not every compound is capable of fully degrading quickly. [12]<br />
<br />
2. The products of biodegradation may potentially be even more persistent or toxic than the original contaminant. [12]<br />
<br />
3. Biological functions are usually extremely specific and require the presence of microbes that are capable of metabolizing the contaminants. In order for the correct microbes to be present, the appropriate environmental conditions, levels of nutrients, and contaminants need to be met. [12]<br />
<br />
4. Scaling up the size of studies from small initial studies to commercial-scale field operations is difficult.[12]<br />
<br />
5. The real environment contains contaminants that are mixed, unevenly distributed, and in different phases (solid, liquid, gas). More research needs to be completed to create technologies that can adapt. [12]<br />
<br />
6. Compared to other treatment technologies, bioremediation often takes more time. [12]<br />
<br />
7. Problems with ensuring adequate contact between the microbes and the contaminant. preferential pathway and soil structure can leave uncertainty in remediation dispersal.[12]<br />
<br />
=='''References'''== <br />
<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdf United States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120. <br />
<br />
5. Al-Mailem, D. M., Sorkhoh, N. A., Al-Awadhi, H., Eliyas, M., & Radwan, S. S. (2010). Biodegradation of crude oil and pure hydrocarbons by extreme halophilic archaea from hypersaline coasts of the Arabian Gulf. Extremophiles, 14(3), 321-328. doi: 10.1007/s00792-010-0312-9<br />
<br />
6. Fairley, D. J., Boyd, D. R., Sharma, N. D., Allen, C. C., Morgan, P., & Larkin, M. J. (2002). Aerobic metabolism of 4-hydroxybenzoic acid in Archaea via an unusual pathway involving an intramolecular migration (NIH shift). Appl Environ Microbiol, 68(12), 6246-6255.<br />
<br />
7. Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008<br />
<br />
8. Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008<br />
<br />
9. Le Borgne, S., Paniagua, D., & Vazquez-Duhalt, R. (2008). Biodegradation of organic pollutants by halophilic bacteria and archaea. J Mol Microbiol Biotechnol, 15(2-3), 74-92. doi: 10.1159/000121323<br />
<br />
10. Margesin, R., & Schinner, F. (2001). Biodegradation and biore<br />
mediation of hydrocarbons in extreme environments. Appl Microbiol Biotechnol, 56(5-6), 650-663.<br />
<br />
11. Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9<br />
<br />
12. Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172. <br />
<br />
13. "Dechloromonas Aromatica RCB." JGI Genome Portal, 16 Feb. 2016. [http://genome.jgi.doe.gov/decar/decar.home.html http://genome.jgi.doe.gov/decar/decar.home.html]<br />
<br />
14. King, R. Barry, John K. Sheldon, and GIlbert M. Long. (1998). Practical Environmental Bioremediation: The Field Guide. 2nd ed. Boca Raton: CRC, 1998.<br />
<br />
15. "Manual, Bioventing Principles and Practices." United States Environmental Protection Agency I (1995)<br />
<br />
16. Gadd, G. M. (Ed.). (2001). Fungi in bioremediation (No. 23). Cambridge University Press<br />
<br />
17. Harms, H., Schlosser, D., & Wick, L. Y. (2011). Untapped potential: exploiting fungi in bioremediation of hazardous chemicals. Nature Reviews Microbiology, 9(3), 177-192<br />
<br />
18. Fragoeiro, S. (2005). Use of fungi in bioremediation of pesticides. Applied Mycology Group Institute of Bioscience and Technology. Cranfield University<br />
<br />
19. Singh, H. (2006). Mycoremediation: fungal bioremediation. John Wiley & Sons. 283-285<br />
<br />
20. Norton, J. M. (2012). Fungi for Bioremediation of Hydrocarbon Pollutants. University of Hawai’i at Hilo. Hohonu, 10, 18-21<br />
<br />
21. Dixit, Ruchita, Emptyyn Wasiullah, Deepti Malaviya, Kuppusamy Pandiyan, Udai Singh, Asha Sahu, Renu Shukla, Bhanu Singh, Jai Rai, Pawan Sharma, Harshad Lade, and Diby Paul. "Bioremediation of Heavy Metals from Soil and Aquatic Environment: An Overview of Principles and Criteria of Fundamental Processes." Sustainability 7.2 (2015): 2189-212. Print.<br />
<br />
22. Bio-filters for Edge-of-Field Water Quality Management. (n.d.). Retrieved February 24, 2016, from [http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html]<br />
<br />
23. Alexander, Martin. (1999). Biodegradation and Bioremediation. San Diego: Academic Print. <br />
<br />
24. Litchfield, Carol. "Thirty Years and Counting: Bioremediation in Its Prime?" BioScience 55.3 (2005): 273.<br />
<br />
25. Biello, David. "Slick Solution: How Microbes Will Clean Up the Deepwater Horizon Oil Spill." Scientific American (n.d.): n. pag. 25 May 2010. <br />
<br />
26. Scow, Kate. “Lectures in Soil Microbiology.” UC Davis, Winter 2016.<br />
<br />
27 CLU-IN | Technologies Remediation About Remediation Technologies Natural Attenuation Overview. (n.d.). Retrieved February 24, 2016, from https://clu-in.org/techfocus/default.focus/sec/Natural_Attenuation/cat/Overview/<br />
<br />
28. Chauhan, Ashok K., and A. Varma. A Textbook of Molecular Biotechnology. New Delhi: I.K. International Pub. House, 2009. Print.<br />
<br />
29. Biopiles. (n.d.). Retrieved March 13, 2016, from [http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html]<br />
<br />
30. Chen, M., Xu, P., Zeng, G., Yang, C., Huang, D., & Zhang, J. (2015). Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: Applications, microbes and future research needs. Biotechnology Advances, 33(6, Part 1), 745–755.<br />
<br />
31. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. Retrieved March 13, 2016, from [http://www.sciencedirect.com/science/article/pii/S0944501309000585 http://www.sciencedirect.com/science/article/pii/S0944501309000585]<br />
<br />
32. Bioremediation, Biostimulation and Bioaugmention: A Review. (n.d.). Retrieved March 13, 2016, from http://pubs.sciepub.com/ijebb/3/1/5/<br />
<br />
33. Sulfur Oxides—Advances in Research and Application: 2013 Edition<br />
<br />
34. Fomina, M., & Gadd, G. M. (2014). Biosorption: current perspectives on concept, definition and application. Bioresource Technology, 160, 3–14. Retrieved February 24, 2016, from [https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application]<br />
<br />
35. Kotrba, Pavel, Martina Mackova, and Tomas Macek. (2011). Microbial Biosorption of Metals. Dordrecht: Springer Science Business Media Print.<br />
<br />
36. Bioventing » Water and Soil Bio-Remediation. (n.d.). Retrieved February 24, 2016, from [http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing]<br />
<br />
37. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. <br />
<br />
38. Land Farming. (n.d.). Retrieved March 13, 2016, from http://www.cpeo.org/techtree/ttdescript/lanfarm.htm<br />
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<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Central_Metabolism_(Flooded_soils)&diff=132732
Central Metabolism (Flooded soils)
2018-02-09T07:26:37Z
<p>Kmscow: /* Flooded to Unflooded Conditions */</p>
<hr />
<div>{{Curated}}<br />
[[Image:FloodedSoil.png|600px|thumb|right|Comparison of water levels in three environments: unsaturated soil, saturated soil, and flooded soil. [http://www.floodsite.net/juniorfloodsite/html/en/student/thingstoknow/hydrology/waterstorage2.html Source]]] <br />
[[Image:Peatland.jpg|thumb|500px|right|A peatland, a type of flooded environment with a layer of organic matter, in Australia. Peatlands produce a high amount of methane emissions. [http://photography.nationalgeographic.com/photography/photo-of-the-day/peatland-australia-essick/ Source]]] <br />
<br />
Flooded soils are a condition in which an area of soil is oversaturated with water, often due to natural occurrence or with intended purpose for agricultural reasons. Perpetually flooded soils can be found in wetlands, swamps and marshes; temporary flooded soils can be an effect of season weather or agricultural practices. As water levels fluctuate, and soils alternate between flooded and unflooded states, the chemical makeup of the [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] will continuously change. A soil’s water content directly influences both inorganic and microbial reactions that affect the soil’s redox potential (E<sub>h</sub>), acidity, alkalinity, and salinity.<ref name="Campos">Dassonville, F., & Renault, P. (2002). Interactions between microbial processes and geochemical transformations under anaerobic conditions: A review. Agronomie, 22(1), 51-68. Retrieved from http://www.agronomy-journal.org/articles/agro/abs/2002/01/05/05.html. </ref><br />
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One of the most important effects of flooded soils is that the presence of oxygen is limited in such an environment, and any remaining oxygen is quickly used up via aerobic respiration. As a result, other compounds are used as electron acceptors in energy acquisition reactions; the microorganisms that specialize in conducting these other reactions are able to flourish and affect nutrient cycling in the ecosystem. <br />
<br />
Microbial transformations of elements in anaerobic soils play a worldwide role in biogeochemical cycling of nutrients and in greenhouse gas emissions. Changes in the oxidation state of terminal electron acceptors may result in nutrient loss from the system via volatilization or leaching. Anaerobic microbial processes including denitrification, methanogenesis, and methanotrophy are responsible for releasing greenhouse gases (N<sub>2</sub>O, CH<sub>4</sub>, CO<sub>2</sub>) into the atmosphere. <ref>United States Environmental Protection Agency. (n.d.). Overview of Greenhouse Gases. Retrieved March 13, 2016, from http://www3.epa.gov/climatechange/ghgemissions/gases/ch4.html .</ref><br />
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<br />
==Key Microbial Processes==<br />
<br />
===Microbial Respiration: [http://en.wikipedia.org/wiki/Redox Oxidation/Reduction Reactions]===<br />
[[Image:RedoxReaction.jpg|300px|thumb|left|General process of a paired reduction and oxidation. The transfer of electrons from molecule A to B is shown. [https://online.science.psu.edu/biol011_sandbox_7239/node/7381 Source]]] <br />
[[Image:Succession1.JPG|300px|thumb|right|Redox potentials of various couples. In soil, the order of succession begins with oxygen and generally ends with carbon dioxide. <ref>Schüring, J., Schulz, H. D., & Fischer, W. R. (Eds.). (2000). Redox: Fundamentals, processes, and applications. New York City, NY: Springer.</ref>]] <br />
<br />
In order to obtain energy, many microbes make use of the process of respiration through an oxidation-reduction (redox) reaction. Respiration is a catabolic reaction that produces ATP in which either organic or inorganic compounds act as primary electron donors, and exogenous compounds act as the terminal electron acceptors. In a redox reaction, one molecule (the reducing agent) loses electrons and another molecule (the oxidizing agent) accepts electrons. Electron donors such as glucose, methanol, and [https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH] are energy sources that can be thought of as “giving up” their electrons, while another molecule is in need to receive said electrons. For example, in aerobic respiration, energy rich compounds like glucose (the reducing agent) are oxidized to carbon dioxide, with oxygen (the oxidizing agent) acting as a terminal electron acceptor and being reduced to water. In addition to oxygen, microorganisms use a large variety of electron acceptors. <br />
<br />
Depending on the type of electron acceptors used by microorganisms, microbes can be placed into a variety of classifications. Strict aerobes can only use oxygen as a terminal electron acceptor. Obligate anaerobes cannot use oxygen and are actually inhibited or poisoned by oxygen. Facultative anaerobes are flexible in electron acceptor usage; as a result of this they can make use of other redox reactions to maintain a supply of energy as oxygen levels decrease.<br />
<br />
Oxygen gas (O<sub>2</sub>) is one of the most favorable electron acceptors, but it is typically not available in flooded soils. Instead, facultative and strict anaerobic microbes utilize other oxidizing agents (electron acceptors) to carry out respiration. The amount of energy that can be obtained through respiration varies between compounds and microbes and will make use of these compounds in order of the decreasing redox potential, thus leading to a succession of acceptors.<br />
<br />
====Redox Potential (E<sub>h</sub>)====<br />
Redox potential is the tendency for a reaction, specifically the movement and transfer of electrons, to occur spontaneously and is reported as E<sub>h</sub> in mV. These measurements have been experimentally determined through aqueous solutions containing electrodes, one being the cathode (electron donator) and one being the anode (electron receiver). <ref>Redox Chemistry Primer. (n.d.). Retrieved March 12, 2016, from http://www.kgs.ku.edu/Hydro/GWtutor/Plume_Busters/remediate_refs/redox_chemistry.htm .</ref><br />
<br />
This voltage shows how likely the electrons will be moved in a solution. Redox potential is assigned individually to half-reactions (a single instance of oxidation or reduction), e.g. the E<sub>h</sub> of the reduction of O<sub>2</sub> to H<sub>2</sub>O will be different from that of the opposite oxidation of H<sub>2</sub>O to O<sub>2</sub>. Redox potential is also reported as standard reduction potential E<sub>o</sub>. Reactions with a higher redox potential yield more net energy for the organism performing them, and this results in higher growth rates (in terms of population).<br />
<br />
===The Electron Tower===<br />
[[Image:RedoxTower.jpg|300px|thumb|right|A tower showing common redox pairs. The greater the "distance" between a donor and acceptor, the greater the energy released. From ''Brock Biology of Microorganisms''.]] <br />
Microbes will successively use the highest energy yielding electron acceptors available in the order indicated on the electron tower, which is a ranking of common redox reactions by the amount of energy that can be obtained from them. Compounds are listed in redox pairs (oxidized form and reduced form) The greater the difference in electrical potential between the reactants and products of a reaction, the greater the release of energy that is crucial for microbial growth. <ref>Madigan, M. T., Martinko, J. M., & Parker, J. (2003). Brock biology of microorganisms (10th ed.). Upper Saddle River, NJ: Prentice Hall/Pearson Education. </ref><br />
<br />
O<sub>2</sub>, the lowest oxidizing agent on the tower, yields the most energy when reduced in a redox reaction with a specific electron donor and will be the first electron acceptor depleted when commonly available. In flooded soils, the amount of oxygen in the system will be very small. When the soil’s microbial population exhausts its remaining O<sub>2</sub>, it will begin using other available electron acceptors which provide the next highest amount of energy. Competition generally limits the use of weaker electron acceptors; for example, iron reducers (using Fe<sup>3+</sup>) may exist in the soil but will be dominated by the presence of denitrifiers, who will growth faster with access to their stronger electron acceptor (NO<sub>3</sub><sup>-</sup>). Overall, this process of succession will continue as each electron acceptor supply is used.<br />
<br />
===Succession of Electron Acceptors=== <br />
The main succession of electron acceptor usage in flooded soils is as follows:<br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobes and aerobes)<br />
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Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by denitrifiers) <br />
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Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by manganese reducing bacteria)<br />
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Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by iron reducing bacteria)<br />
<br />
Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
<br />
Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by methanogens)<br />
<br />
====[[Nitrogen Cycle|Nitrate Reduction]]====<br />
After O<sub>2</sub>, nitrate (NO<sub>3</sub><sup>-</sup>) is one of the strongest electron acceptors as is represented in the electron tower. It can be obtained from transformations of other compounds containing nitrogen, such as ammonium (NH<sub>4</sub><sup>+</sup>) and nitrite (NO<sub>2</sub><sup>-</sup>). Denitrification reduces NO<sub>3</sub><sup>-</sup> to nitrogen gas (N<sub>2</sub>) or various nitrogen oxides and is performed by facultative anaerobic microorganisms. Oxygen depletion is important for the nitrogen cycle as a whole, since if it were constantly present NO<sub>3</sub><sup>-</sup> would be used at a much slower rate and contaminate soils through accumulation. <ref name="Sylvia">Silvia, D.M., et al. 2005. Principles and Applications of Soil Microbiology. 2nd ed. Pearson Prentice Hall, New Jersey. </ref><br />
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====Manganese Reduction====<br />
The next most energy-releasing electron acceptor after NO<sub>3</sub><sup>-</sup> is manganese (IV) oxide (MnO<sub>2</sub>) which is is reduced to Mn<sup>2+</sup> ions. In this form, manganese is very insoluble in water and forms masses in soils. Mn<sup>2+</sup> is generally oxidized to this form in soils with a pH between 5 and 8, (as the rate increases with basicity). Many microorganisms that conduct this process are also capable of iron reduction, described below. <ref name="Sylvia" /> <br />
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====Iron Reduction====<br />
[[Image:pipe.jpg|100px|thumb|left|Corroded water main. [http://coloradogeologicalsurvey.org/geologic-hazards/corrosive-soils/corrosive-soil-damage/ Source] ]] <br />
The utilization of ferric iron ions (Fe<sup>3+</sup>), at approximately 120 mV, occurs when ions are released from metal deposits or minerals in the soil. Ferrous iron (Fe<sup>2+</sup>) product causes soil gleying, (a process described in a later section) when it accumulates. The source of the iron is also of relevance; whereas iron reduction in phosphate minerals can release phosphate for other organisms, it can also lead to corrosion of steel where iron reducers are present. Some ''Pseudomonas'' species can release pseudobactin, an iron-binding compound that limits its availability to other bacteria. <ref name="Sylvia" /><br />
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====Sulfate Reduction====<br />
Sulfate reduction begins occurring at 0 mV, and the dissimilatory reduction results in hydrogen sulfide (H<sub>2</sub>S) being released. However, H<sub>2</sub>S is prone to reaction with Fe<sup>2+</sub> to form iron sulfide (FeS). As a result, it often reacts before it reaches the surface of the soil, unable to disperse into the air. <ref name="Sylvia" /> Sulfate reduction has several documented consequences, ranging from corrosion of underground iron pipes due to FeS formation and blackening of soil caused by liberation of organic matter. Hydrogen sulfide is known as “swamp gas”, due to its emergence from one form of soil flooding, and has an odor comparable to rotting eggs. It can accumulate in many bodies of water and the air above them; due to its flammability and toxicity, this is very dangerous. <ref>Occupational Safety & Health Administration. (n.d.). Safety and Health Topics | Hydrogen Sulfide. Retrieved February 23, 2016, from https://www.osha.gov/SLTC/hydrogensulfide/index.html .</ref><br />
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====Methanogenesis (by Carbon Dioxide Reduction)====<br />
The process of using carbon dioxide (CO<sub>2</sub>) as a terminal electron acceptor results in the formation of methane (CH<sub>4</sub>) and is known as methanogenesis. In soil, methanogenesis occurs almost exclusively in a flooded condition due to its reduction potential being so low (below 100 mV). The use of CO<sub>2</sub> in this fashion yields much less energy than the reactions of previous electron acceptors, so this process has lower growth rates in turn. Organisms who perform methanogenesis are known as [[methanogens]] and are a group of anaerobic Archaea. CH<sub>4</sub> can also be produced as a result of acetate (CH<sub>3</sub>COOH) fermentation, which is also performed by methanogens. <ref name="Sylvia" /><br />
<br />
===Fermentation in Flooded Soils (Non-Respiratory)===<br />
Fermentation is a different form of metabolism from respiration that occurs in the absence of a suitable terminal electron acceptor. Cells convert NADH and pyruvate from the glycolysis of sugars into NAD+ and other compounds, depending on the species that is fermenting. The various products of fermentation, including alcohols, lactic acid, and acetate are released into the surrounding soil and then become available for use by other anaerobic organisms. Additionally, fermentation generally reduces soil pH, which will encourage dissolution of minerals and their subsequent access by bacteria. <ref name="Richardson">Richardson, J. L., & Vepraskas, M. J. (2001). Wetland soils: Genesis, hydrology, landscapes, and classification. Boca Raton, FL: Lewis. </ref><br />
<br />
==Microorganisms Involved==<br />
As available oxygen declines, organisms that thrive under anoxic conditions proliferate using alternative electron acceptors. The order in which available electron acceptors are consumed can generally be predicted by the electron tower and associated energy yields of electron pairs. Changes in redox conditions of flooded soils over time reflects the successive availability of terminal electron acceptors from the electron tower, and will govern which microbes will thrive through being able to use them.<br />
<br />
Some microbes below are able to oxidize the reduced form of their corresponding substance.<ref>Liesack, W. (2000). Microbiology of flooded rice paddies. FEMS Microbiology Reviews, 24(5), 625-645. </ref><br />
[[Image:Processes.jpg|500px|thumb|right|Summary of reducing conditions in flooded soils. [http://www.des.ucdavis.edu/faculty/rejmankova/ESP155_Soils-2004.pdf Source]]]<br />
<br />
<br />
{| width="800" border="1"<br />
|----- bgcolor ="grey"<br />
| width="200" height="25" | '''Process'''<br />
| width="1000" | '''Example Genera of Common Bacteria Involved'''<br />
|-<br />
| Aerobic Respiration<br />
| Aerobes and facultative anaerobes such as ''Staphylococcus'', ''[https://en.wikipedia.org/wiki/Nocardia Nocardia]'', ''[[Pseudomonas]]''<br />
|-<br />
| Denitrification<br />
| Facultative anaerobes such as ''[[Agrobacterium]]'', ''[[Alcaligenes]]'', ''[[Bacillus]]'', ''Paracoccus'', ''Micrococcus''<br />
|-<br />
| Manganese Reduction<br />
| ''[[Bacillus]]'', ''[[Geobacter]]'', ''[[Pseudomonas]]'', ''Shewanella''<br />
|-<br />
| Iron Reduction<br />
| ''[[Desulfovibrio]]'', ''[[Pseudomonas]]'', ''Geothrix'', ''Shewanella'', ''Thiobacillus''<br />
|-<br />
| Sulfate Reduction<br />
| Generally obligate anaerobes such as ''[[Desulfobacter]]'', ''[[Desulfococcus]]'', ''[[Desulfosarcina]]'', ''Desulfosporosinus''<br />
|-<br />
| Methanogenesis<br />
| [[Methanogens]] such as ''Methanobacterium'' and [https://en.wikipedia.org/wiki/Archaea Archaea] (different from bacteria)<br />
|}<br />
[[Image:PseudomonasImage.jpg|300px|thumb|left|The ''Pseudomonas'' genus has a wide variety of metabolic capabilities among its species. [https://elmundodelavida.wordpress.com/category/ciencia/ Source]]]<br />
[[Image:Probes.gif|400px|thumb|center|[https://en.wikipedia.org/wiki/Hybridization_probe DNA and RNA probes] are used for identifying bacteria in samples. [http://tle.westone.wa.gov.au/content/file/969144ed-0d3b-fa04-2e88-8b23de2a630c/1/human_bio_science_3b.zip/content/005_dna/page_17.htm Source]]]<br />
<br />
==Effects of Flooding on Soil Environment==<br />
<br />
===Mobility of Minerals and Gasses===<br />
[[Image:Aggregation.jpg|200px|thumb|right|A) unaffected soil and B) soil incubated anaerobically. Flooding caused mobilization of organic matter and disaggregation, resulting in the larger grains (decreased stability). [https://dl.sciencesocieties.org/publications/sssaj/abstracts/73/2/550 Source]]]<br />
Water also acts as a solvent for ions and soluble compounds, thus increasing the mobility and availability of metal ions, nutrients, and minerals. As a result of these physical effects in flooded soils, microbial respiration will have improved access to water-soluble compounds such as nitrate, perchlorate, manganese/ferric iron, sulfate, and carbon dioxide to act as electron acceptors. <br />
<br />
The diffusion of oxygen is over 10000 times slower in water than it is in air at standard temperature and pressure, resulting in the replenishing rate being much slower in flooded soils. Carbon dioxide is also decreased but to a lesser degree due to it being far more soluble than oxygen. <ref>Greenway H, William A, Timothy DC. (2006). Conditions leading to high CO2 (>5 kPa) in waterlogged-flooded soils and possible effects on root growth and metabolism. Annals of Botany, 98, 9–32. Retrieved March 10, 2016 from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3291891/ .</ref><br />
<br />
===Flooded Soil Aggregate Structure===<br />
Though some degree of moisture is important for aggregate formation and microbial activity, flooded soils exhibit decreased aggregate stability compared to unsaturated soils. Oxygen depletion and subsequent use of various elements for redox contributes to this decreased aggregation. Organic carbon is also made more soluble (like metals and minerals) under reducing conditions. The decreased stability of the soil is unlikely to recover due to drainage or volatilization of chemicals, removing them from the local environment. Since areas such as marshlands and rice fields are perpetually flooded, their soil’s aggregate stability rarely improves. <ref>De-Campos, A. B., Mamedov, A. I., & Huang, C. (2009). Short-Term Reducing Conditions Decrease Soil Aggregation. Soil Science Society of America Journal, 73(2), 550. Retrieved February 23, 2016, from https://dl.sciencesocieties.org/publications/sssaj/abstracts/73/2/550 .</ref><br />
<br />
===Soil Gradients===<br />
[[Image:Column.jpg|200px|thumb|left|A Winogradsky column. [http://beautyinscience.com/Biology.html Source] ]] <br />
The progression of electron acceptor utilization occurs at different rates in different layers of soil. A process like methanogenesis will occur earlier several feet underground than at the surface due to decreased access to other compounds. This will result in gradients at various depths of soil. These gradients will differ by pH, color, chemical prevalence, and microbial population. <br />
<br />
Since the soil is a more closed system (with less mobility of chemicals) than the surface, air, or bodies of water, gradients can be observed with a similar closed system: a Winogradsky column. This column, consisting of a sealed column of soil with provided organic material (such as an egg), allows for simulation of an anaerobic soil environment. <ref>Scientific American. (2013, September 19). Soil Science: Make a Winogradsky Column. Retrieved from http://www.scientificamerican.com/article/bring-science-home-soil-column/ </ref><br />
<br />
===Variation of pH===<br />
pH has a major influence over the dissolution and sorption of several important toxins and nutrients in the soil. Low pH values increase the solubility of free aluminum (Al<sup>3+</sup>) and iron (Fe<sup>3+</sup> and Fe<sup>2+</sup>) ions which can be toxic in high concentrations, while also reducing the availability of phosphorus.<br />
<br />
When soil is initially saturated with water, the pH drops due to the accumulation of carbonic acid formed from trapped carbon dioxide produced from respiration. Fermentation also contributes to pH decreasing through the production of organic acids. This is quickly followed by an increase of pH as hydrogen cations are consumed in microbially-driven redox reactions. The soil then will gradually approach and stabilize near a neutral pH, with pH increasing in acidic soil and decreasing in basic soil due to products such as carbonate forming a buffer. <ref>Kirk, G. J. (2004). The biogeochemistry of submerged soils. Chichester: Wiley. </ref><br />
<br />
===Soil Gleying===<br />
[[Image:gleyed.jpg|200px|thumb|right|Gray colors produced in gleyed soil. [http://wetland-delineation.rutgers.edu/87-wetland-delineation-manual/wetland-delineation-manual-part3.html Source] ]] <br />
<br />
Gleying is a phenomenon in which waterlogged soils are discolored by the color changes due to reduction of ferric iron into ferrous iron. Although ferric iron exists as an insoluble form in flooded soils, more ferrous iron can accumulate by the reduction of ferric iron over time. This results in a greenish, blue, grey soil color. In general Fe<sup>3+</sup> -reducing fermentative bacteria can be readily isolated from gleyed soils. The black color of soils/solution is frequently observed in flooded soil. This may result from the formation of iron sulfides (FeS) and pyrite (FeS2). <ref>Wenk, H., & Bulakh, A. G. (2004). Minerals: Their constitution and origin. Cambridge: Cambridge University Press. </ref><br />
<br />
===Plant Nutrient Availability===<br />
Flooded soils can have a direct impact on plants by preventing efficient gas exchange between the plant roots and the soil. These conditions also change the types of microbes that are active and what they produce. Flooded soils cause anaerobic conditions which forces many microbes to use less favorable electron acceptors. These less favorable acceptors could have also served as nutrition for the plants; this creates competition between the plants and the microbes in certain flooded soils. By using different electron acceptors the microbes will release different products causing a chemical change in the soil that can be toxic. <ref>Minamikawa, K., & Sakai, N. (2005). The effect of water management based on soil redox potential on methane emission from two kinds of paddy soils in Japan. Agriculture, Ecosystems & Environment, 107(4), 397-407. Retrieved from http://www.sciencedirect.com/science/article/pii/S0167880904002208 .</ref><br />
<br />
===Flooded to Unflooded Conditions===<br />
When waterlogged soils drain, oxygen diffuses into soil pores. The soil’s Eh increases and aerobic activity kicks in. At higher Eh zones ( > 500 mV), undecomposed soil organic matter is rapidly used as an electron donor by aerobes. With oxygen, many of the reduced products of anaerobic respiration can now be used as electron donors by lithotrophs. Manganese is oxidized back to MnO2 which gives some aerated soils a black color, and ferrous iron is oxidized by an iron-oxidizing bacteria, resulting in the formation of ferric oxides or ferric hydroxide minerals that give the soil a red, yellow, or brownish texture. <ref name="Richardson" /><br />
<br />
==Environmental Issues==<br />
<br />
Flooded soils are dynamic ecosystems that play an important role in biogeochemical cycling and in the production of greenhouse gases. Methane (CH<sub>4</sub><sup>+</sup>) and nitrous oxide (N<sub>2</sub>O) are produced as byproducts of anaerobic metabolism in the low-redox zones characteristic of flooded soils, where oxygen is lacking. Carbon dioxide (CO<sub>2</sub>), which receives widespread attention as a greenhouse gas and potential source of global warming, may also be produced at the interface of anaerobic-aerobic zones through the consumption of methane gas. However, it should be noted that from a global standpoint methane and nitrous oxide on a per molecule basis have the potential to contribute 25x and 300x more to global warming over the next century than carbon dioxide, respectively. Thus the conversion of methane gas to carbon dioxide essentially reduces the greenhouse gas effect by 25x per molecule per 100 years. Although the number areas classified as wetlands has decreased in past years, the effect of flooded soils to the global climate is clear.<ref>Schlesinger, W. H., & Bernhardt, E. S. (2013). Biogeochemistry: An analysis of global change (3rd ed.). San Diego, CA: Academic Press. </ref><br />
<br />
===Methane Production; Methanogenesis===<br />
[[Image:Methane.jpg|thumb|300px|A natural source of methane gas]]<br />
Methane production occurs exclusively in anaerobic conditions by a group of Archaea known as methanogens. These microbes are obligatory, and require extremely low redox conditions in the range of -100mV. If oxygen is introduced into the system, methanogenesis ceases; thus, the process of methanogenesis depends on saturated soil conditions.<ref name="Sylvia" /> <br />
<br />
Methanogenesis can occur via one of two pathways: either by 1) CO<sub>2</sub> reduction or by 2) acetate fermentation.<br />
<br />
1) CO<sub>2</sub> + H<sub>2</sub> --> CH<sub>4</sub><sup>+</sup> (CO<sub>2</sub> reduction)<br />
<br />
and <br />
<br />
2) CH<sub>3</sub>COOH --> CH<sub>4</sub><sup>+</sup> + CO<sub>2</sub> (acetate fermentation)<br />
<br />
Both acetate and hydrogen are byproducts of anaerobic fermentation. <br />
<br />
Because the process of methanogenesis is “fed” byproducts produced from a complex series of degradation processes which are themselves “fed” complex organic matter, rates of methane production are highly sensitive to changes in temperature. Methanogenesis has a Q10 value in the range of 30-40, which is substantially higher than most biochemical process.<br />
<br />
Despite the clear effect of increasing temperatures on the rate of methanogenesis, the actual impact of global warming on methane production rates in wetlands and permafrost regions is highly unpredictable. Because methanogenesis requires anoxic conditions, any drying of flooded soil environments would both decrease methane production and increase methane oxidation, reducing overall methane emissions. Alternatively, warmer climates could increase growing seasons, which would increase methane emissions.<ref name="Sylvia" /><br />
<br />
===CO<sub>2</sub> Production via Methane Consumption: Methanotrophy===<br />
Some of the methane produced via methanogenesis in flooded soils may be consumed and oxidized to CO<sub>2</sub> at the interface of the anaerobic-aerobic zones. This process occurs primarily by a group of bacteria known as methanotrophs. These microbes can be found in surface layers of wetland soils and unsaturated upland soils, and may be exposed to very high concentrations of methane gas, sometimes amounting to 10% or more of the dissolved gases. Methane is thought to be the only source of C and energy for these bacteria.<br />
<br />
Methanotrophy occurs in the following reaction:<br />
<br />
CH<sub>4</sub><sup>+</sup> + 2O<sub>2</sub> --> CO<sub>2</sub> + 2H<sub>2</sub>O<br />
<br />
Methane is similar in size and shape to ammonium; and there is some evidence that nitrifiers (ammonium oxidizers) can also oxidize methane. Because they are molecularly similar, NH<sup>4</sup><sup>+</sup> competes at the enzyme’s active site, inhibiting methane oxidation. As a result, methanotrophy is generally inhibited by the addition of fertilizer or excess nitrogen in the system, when ammonium levels are high. <br />
<br />
Alternatively, if nitrogen is extremely limiting the addition of nitrogen will stimulate methanotrophy and actually increase methane consumption. So although it is generally expected that adding N-fertilizer will decrease CH<sub>4</sub><sup>+</sup> consumption and lead to increased global warming potential, sometime the opposite effect may occur.<ref name="Sylvia" /><br />
<br />
===Nitrous Oxide; Denitrification===<br />
Denitrification is an anaerobic process in which nitrate serves as the terminal electron acceptor, and generally some source of organic carbon is the electron donor (also H<sub>2</sub> may serve as a donor). <br />
<br />
In this process, nitrate is oxidized to nitric oxide, then nitrous oxide, and then fully oxidized to dinitrogen:<br />
<br />
NO<sub>2</sub><sup>-</sup> --> NO --> N<sub>2</sub>O --> N<sub>2</sub><br />
<br />
However, under certain conditions the full oxidation of NO<sub>3</sub><sup>-</sup> to N<sub>2</sub> does not occur and nitrous oxide (N<sub>2</sub>O) is produced.<br />
<br />
Microbes responsible include both organotrophs and lithotrophs, and this process occurs primarily by facultative anaerobes. <br />
<br />
Although a low redox potential is important for denitrification to occur (oxygen must not be present or it will “out-compete” nitrate as a terminal electron acceptor), redox requirements are not so low that this process cannot occur within anaerobic microsites of soil aggregates. <br />
<br />
Factors affecting nitrous oxide production include oxygen, pH, and the ratio of nitrate to available C. Although denitrification rates decrease with increasing oxygen, the proportion of N evolved as nitrous oxide actually increases with increasing oxygen. Low pH generally inhibits the reduction of N<sub>2</sub>O to N<sub>2</sub>; thus at low pH, N<sub>2</sub>O will likely dominate. However, highly acidic soils have low N availability and low nitrification and denitrification rates. Thus, the highest rate of nitrous oxide production from denitrification occurs in moist soils that cycle N rapidly.<ref name="Sylvia" /><br />
<br />
==Current Research==<br />
Current research topics on the issue of flooded soils are heavily focused on greenhouse gas emissions produced as a result of the low redox conditions characteristic of these ecosystems. Other research topics may address impacts to plant growth, and chemical, physical, and biological aspects of flooded soils. <br />
<br />
Many agricultural studies focus on rice paddies. Bacteria that oxidized acetate and reduced iron were identified and studied in flooded rice paddy soil through RNA probing.<ref>Hori, T., Müller, A., Igarashi, Y., Conrad, R., & Friedrich, M. W. (2009). Identification of iron-reducing microorganisms in anoxic rice paddy soil by 13C-acetate probing. The ISME Journal ISME J, 4(2), 267-278. from http://www.nature.com/ismej/journal/v4/n2/full/ismej2009100a.html </ref> Another study observed factors affecting delivery of nitrogen to plants by microbial populations in flooded soils and found that the addition of sludge to soil facilitated nitrogen formation more than the addition of straw compost.<ref>El-Sharkawi, H. M. (2012). Effect of Nitrogen Sources on Microbial Biomass Nitrogen under Different Soil Types. ISRN Soil Science, 2012, 1-7. from http://www.citationmachine.net/bibliographies/77289062?new=true </ref> The effect of oxygen concentration on rates of reactions involving nitrogen, including nitrification and mineralization, in paddy soils was also studied.<ref>Yang, Y., Zhang, J., & Cai, Z. (2015). Nitrification activities and N mineralization in paddy soils are insensitive to oxygen concentration. Acta Agriculturae Scandinavica, Section B — Soil & Plant Science, 66(3), 272-281. from http://www.tandfonline.com/doi/full/10.1080/09064710.2015.1093653 </ref><br />
<br />
A review article was published in 2012, focusing on soil-plant interactions, including redox reactions’ effects on plant function, in wetlands.<ref>Pezeshki, S. R., & Delaune, R. D. (2012). Soil Oxidation-Reduction in Wetlands and Its Impact on Plant Functioning. Biology, 1(3), 196-221. from http://www.mdpi.com/2079-7737/1/2/196 </ref><br />
<br />
[[Carbon cycle | Long-term retention of carbon in soil organic matter]] is an issue in frequently harvested soils. One study looked at various treatments of rice paddies and found that a combination of rice straw and inorganic fertilizer aided sequestration and led to “a higher grain yield”.<ref> Bhattacharyya, P., Roy, K., Neogi, S., Adhya, T., Rao, K., & Manna, M. (2012). Effects of rice straw and nitrogen fertilization on greenhouse gas emissions and carbon storage in tropical flooded soil planted with rice. Soil and Tillage Research, 124, 119-130. from http://www.sciencedirect.com/science/article/pii/S0167198712001195 </ref><br />
<br />
A recent study discussed the fate of metals such as cadmium, nickel, and aluminum in impacted creeks in Kenya, Tanzania, and Mozambique.<ref>Kamau, J. N., Kuschk, P., Machiwa, J., Macia, A., Mothes, S., Mwangi, S., . . . Kappelmeyer, U. (2015). Investigating the distribution and fate of Al, Cd, Cr, Cu, Mn, Ni, Pb and Zn in sewage-impacted mangrove-fringed creeks of Kenya, Tanzania and Mozambique. J Soils Sediments Journal of Soils and Sediments, 15(12), 2453-2465. Retrieved from http://link.springer.com/article/10.1007/s11368-015-1214-3 </ref><br />
<br />
Many other studies focus on the degradation of ground contaminants such as pesticides so that their results can be used in [[bioremediation]].<ref>Levén, L., Nyberg, K., & Schnürer, A. (2012). Conversion of phenols during anaerobic digestion of organic solid waste – A review of important microorganisms and impact of temperature. Journal of Environmental Management, 95. Retrieved from http://www.sciencedirect.com/science/article/pii/S0301479710003531 </ref> The fate of cycloxaprid, an agricultural insecticide, was observed in anaerobic conditions (including flooded soils). Radioisotopic tracing showed that various soil types had different effects on the chemical.<ref>Liu, X., Xu, X., Li, C., Zhang, H., Fu, Q., Shao, X., . . . Li, Z. (2016). Assessment of the environmental fate of cycloxaprid in flooded and anaerobic soils by radioisotopic tracing. Science of The Total Environment, 543, 116-122. Retrieved from http://www.sciencedirect.com/science/article/pii/S0048969715310007 </ref><br />
<br />
Lastly, there is always the topic of greenhouse gas emissions. Arctic, temperate, and tropical regions were recently studied for measurements of greenhouse gas emissions and its relation to temperature.<ref>Turetsky, M. R., Kotowska, A., Bubier, J., Dise, N. B., Crill, P., Hornibrook, E. R., . . . Wilmking, M. (2014). A synthesis of methane emissions from 71 northern, temperate, and subtropical wetlands. Glob Change Biol Global Change Biology, 20(7), 2183-2197. Retrieved from http://onlinelibrary.wiley.com/doi/10.1111/gcb.12580/pdf </ref> Another group of researchers found a correlation between anaerobic methane oxidation in freshwater wetlands and reduced methane emissions.<ref>Segarra, K. E., Schubotz, F., Samarkin, V., Yoshinaga, M. Y., Hinrichs, K., & Joye, S. B. (2015). High rates of anaerobic methane oxidation in freshwater wetlands reduce potential atmospheric methane emissions. Nature Communications Nat Comms, 6, 7477. Retrieved from http://www.nature.com/ncomms/2015/150630/ncomms8477/full/ncomms8477.html </ref><br />
<br />
==References==<br />
<references /><br />
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Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]<br />
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<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Central_Metabolism_(Flooded_soils)&diff=132731
Central Metabolism (Flooded soils)
2018-02-09T07:24:47Z
<p>Kmscow: /* Soil Gleying */</p>
<hr />
<div>{{Curated}}<br />
[[Image:FloodedSoil.png|600px|thumb|right|Comparison of water levels in three environments: unsaturated soil, saturated soil, and flooded soil. [http://www.floodsite.net/juniorfloodsite/html/en/student/thingstoknow/hydrology/waterstorage2.html Source]]] <br />
[[Image:Peatland.jpg|thumb|500px|right|A peatland, a type of flooded environment with a layer of organic matter, in Australia. Peatlands produce a high amount of methane emissions. [http://photography.nationalgeographic.com/photography/photo-of-the-day/peatland-australia-essick/ Source]]] <br />
<br />
Flooded soils are a condition in which an area of soil is oversaturated with water, often due to natural occurrence or with intended purpose for agricultural reasons. Perpetually flooded soils can be found in wetlands, swamps and marshes; temporary flooded soils can be an effect of season weather or agricultural practices. As water levels fluctuate, and soils alternate between flooded and unflooded states, the chemical makeup of the [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] will continuously change. A soil’s water content directly influences both inorganic and microbial reactions that affect the soil’s redox potential (E<sub>h</sub>), acidity, alkalinity, and salinity.<ref name="Campos">Dassonville, F., & Renault, P. (2002). Interactions between microbial processes and geochemical transformations under anaerobic conditions: A review. Agronomie, 22(1), 51-68. Retrieved from http://www.agronomy-journal.org/articles/agro/abs/2002/01/05/05.html. </ref><br />
<br />
One of the most important effects of flooded soils is that the presence of oxygen is limited in such an environment, and any remaining oxygen is quickly used up via aerobic respiration. As a result, other compounds are used as electron acceptors in energy acquisition reactions; the microorganisms that specialize in conducting these other reactions are able to flourish and affect nutrient cycling in the ecosystem. <br />
<br />
Microbial transformations of elements in anaerobic soils play a worldwide role in biogeochemical cycling of nutrients and in greenhouse gas emissions. Changes in the oxidation state of terminal electron acceptors may result in nutrient loss from the system via volatilization or leaching. Anaerobic microbial processes including denitrification, methanogenesis, and methanotrophy are responsible for releasing greenhouse gases (N<sub>2</sub>O, CH<sub>4</sub>, CO<sub>2</sub>) into the atmosphere. <ref>United States Environmental Protection Agency. (n.d.). Overview of Greenhouse Gases. Retrieved March 13, 2016, from http://www3.epa.gov/climatechange/ghgemissions/gases/ch4.html .</ref><br />
<br />
<br />
==Key Microbial Processes==<br />
<br />
===Microbial Respiration: [http://en.wikipedia.org/wiki/Redox Oxidation/Reduction Reactions]===<br />
[[Image:RedoxReaction.jpg|300px|thumb|left|General process of a paired reduction and oxidation. The transfer of electrons from molecule A to B is shown. [https://online.science.psu.edu/biol011_sandbox_7239/node/7381 Source]]] <br />
[[Image:Succession1.JPG|300px|thumb|right|Redox potentials of various couples. In soil, the order of succession begins with oxygen and generally ends with carbon dioxide. <ref>Schüring, J., Schulz, H. D., & Fischer, W. R. (Eds.). (2000). Redox: Fundamentals, processes, and applications. New York City, NY: Springer.</ref>]] <br />
<br />
In order to obtain energy, many microbes make use of the process of respiration through an oxidation-reduction (redox) reaction. Respiration is a catabolic reaction that produces ATP in which either organic or inorganic compounds act as primary electron donors, and exogenous compounds act as the terminal electron acceptors. In a redox reaction, one molecule (the reducing agent) loses electrons and another molecule (the oxidizing agent) accepts electrons. Electron donors such as glucose, methanol, and [https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH] are energy sources that can be thought of as “giving up” their electrons, while another molecule is in need to receive said electrons. For example, in aerobic respiration, energy rich compounds like glucose (the reducing agent) are oxidized to carbon dioxide, with oxygen (the oxidizing agent) acting as a terminal electron acceptor and being reduced to water. In addition to oxygen, microorganisms use a large variety of electron acceptors. <br />
<br />
Depending on the type of electron acceptors used by microorganisms, microbes can be placed into a variety of classifications. Strict aerobes can only use oxygen as a terminal electron acceptor. Obligate anaerobes cannot use oxygen and are actually inhibited or poisoned by oxygen. Facultative anaerobes are flexible in electron acceptor usage; as a result of this they can make use of other redox reactions to maintain a supply of energy as oxygen levels decrease.<br />
<br />
Oxygen gas (O<sub>2</sub>) is one of the most favorable electron acceptors, but it is typically not available in flooded soils. Instead, facultative and strict anaerobic microbes utilize other oxidizing agents (electron acceptors) to carry out respiration. The amount of energy that can be obtained through respiration varies between compounds and microbes and will make use of these compounds in order of the decreasing redox potential, thus leading to a succession of acceptors.<br />
<br />
====Redox Potential (E<sub>h</sub>)====<br />
Redox potential is the tendency for a reaction, specifically the movement and transfer of electrons, to occur spontaneously and is reported as E<sub>h</sub> in mV. These measurements have been experimentally determined through aqueous solutions containing electrodes, one being the cathode (electron donator) and one being the anode (electron receiver). <ref>Redox Chemistry Primer. (n.d.). Retrieved March 12, 2016, from http://www.kgs.ku.edu/Hydro/GWtutor/Plume_Busters/remediate_refs/redox_chemistry.htm .</ref><br />
<br />
This voltage shows how likely the electrons will be moved in a solution. Redox potential is assigned individually to half-reactions (a single instance of oxidation or reduction), e.g. the E<sub>h</sub> of the reduction of O<sub>2</sub> to H<sub>2</sub>O will be different from that of the opposite oxidation of H<sub>2</sub>O to O<sub>2</sub>. Redox potential is also reported as standard reduction potential E<sub>o</sub>. Reactions with a higher redox potential yield more net energy for the organism performing them, and this results in higher growth rates (in terms of population).<br />
<br />
===The Electron Tower===<br />
[[Image:RedoxTower.jpg|300px|thumb|right|A tower showing common redox pairs. The greater the "distance" between a donor and acceptor, the greater the energy released. From ''Brock Biology of Microorganisms''.]] <br />
Microbes will successively use the highest energy yielding electron acceptors available in the order indicated on the electron tower, which is a ranking of common redox reactions by the amount of energy that can be obtained from them. Compounds are listed in redox pairs (oxidized form and reduced form) The greater the difference in electrical potential between the reactants and products of a reaction, the greater the release of energy that is crucial for microbial growth. <ref>Madigan, M. T., Martinko, J. M., & Parker, J. (2003). Brock biology of microorganisms (10th ed.). Upper Saddle River, NJ: Prentice Hall/Pearson Education. </ref><br />
<br />
O<sub>2</sub>, the lowest oxidizing agent on the tower, yields the most energy when reduced in a redox reaction with a specific electron donor and will be the first electron acceptor depleted when commonly available. In flooded soils, the amount of oxygen in the system will be very small. When the soil’s microbial population exhausts its remaining O<sub>2</sub>, it will begin using other available electron acceptors which provide the next highest amount of energy. Competition generally limits the use of weaker electron acceptors; for example, iron reducers (using Fe<sup>3+</sup>) may exist in the soil but will be dominated by the presence of denitrifiers, who will growth faster with access to their stronger electron acceptor (NO<sub>3</sub><sup>-</sup>). Overall, this process of succession will continue as each electron acceptor supply is used.<br />
<br />
===Succession of Electron Acceptors=== <br />
The main succession of electron acceptor usage in flooded soils is as follows:<br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobes and aerobes)<br />
<br />
Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by denitrifiers) <br />
<br />
Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by manganese reducing bacteria)<br />
<br />
Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by iron reducing bacteria)<br />
<br />
Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
<br />
Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by methanogens)<br />
<br />
====[[Nitrogen Cycle|Nitrate Reduction]]====<br />
After O<sub>2</sub>, nitrate (NO<sub>3</sub><sup>-</sup>) is one of the strongest electron acceptors as is represented in the electron tower. It can be obtained from transformations of other compounds containing nitrogen, such as ammonium (NH<sub>4</sub><sup>+</sup>) and nitrite (NO<sub>2</sub><sup>-</sup>). Denitrification reduces NO<sub>3</sub><sup>-</sup> to nitrogen gas (N<sub>2</sub>) or various nitrogen oxides and is performed by facultative anaerobic microorganisms. Oxygen depletion is important for the nitrogen cycle as a whole, since if it were constantly present NO<sub>3</sub><sup>-</sup> would be used at a much slower rate and contaminate soils through accumulation. <ref name="Sylvia">Silvia, D.M., et al. 2005. Principles and Applications of Soil Microbiology. 2nd ed. Pearson Prentice Hall, New Jersey. </ref><br />
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====Manganese Reduction====<br />
The next most energy-releasing electron acceptor after NO<sub>3</sub><sup>-</sup> is manganese (IV) oxide (MnO<sub>2</sub>) which is is reduced to Mn<sup>2+</sup> ions. In this form, manganese is very insoluble in water and forms masses in soils. Mn<sup>2+</sup> is generally oxidized to this form in soils with a pH between 5 and 8, (as the rate increases with basicity). Many microorganisms that conduct this process are also capable of iron reduction, described below. <ref name="Sylvia" /> <br />
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====Iron Reduction====<br />
[[Image:pipe.jpg|100px|thumb|left|Corroded water main. [http://coloradogeologicalsurvey.org/geologic-hazards/corrosive-soils/corrosive-soil-damage/ Source] ]] <br />
The utilization of ferric iron ions (Fe<sup>3+</sup>), at approximately 120 mV, occurs when ions are released from metal deposits or minerals in the soil. Ferrous iron (Fe<sup>2+</sup>) product causes soil gleying, (a process described in a later section) when it accumulates. The source of the iron is also of relevance; whereas iron reduction in phosphate minerals can release phosphate for other organisms, it can also lead to corrosion of steel where iron reducers are present. Some ''Pseudomonas'' species can release pseudobactin, an iron-binding compound that limits its availability to other bacteria. <ref name="Sylvia" /><br />
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====Sulfate Reduction====<br />
Sulfate reduction begins occurring at 0 mV, and the dissimilatory reduction results in hydrogen sulfide (H<sub>2</sub>S) being released. However, H<sub>2</sub>S is prone to reaction with Fe<sup>2+</sub> to form iron sulfide (FeS). As a result, it often reacts before it reaches the surface of the soil, unable to disperse into the air. <ref name="Sylvia" /> Sulfate reduction has several documented consequences, ranging from corrosion of underground iron pipes due to FeS formation and blackening of soil caused by liberation of organic matter. Hydrogen sulfide is known as “swamp gas”, due to its emergence from one form of soil flooding, and has an odor comparable to rotting eggs. It can accumulate in many bodies of water and the air above them; due to its flammability and toxicity, this is very dangerous. <ref>Occupational Safety & Health Administration. (n.d.). Safety and Health Topics | Hydrogen Sulfide. Retrieved February 23, 2016, from https://www.osha.gov/SLTC/hydrogensulfide/index.html .</ref><br />
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====Methanogenesis (by Carbon Dioxide Reduction)====<br />
The process of using carbon dioxide (CO<sub>2</sub>) as a terminal electron acceptor results in the formation of methane (CH<sub>4</sub>) and is known as methanogenesis. In soil, methanogenesis occurs almost exclusively in a flooded condition due to its reduction potential being so low (below 100 mV). The use of CO<sub>2</sub> in this fashion yields much less energy than the reactions of previous electron acceptors, so this process has lower growth rates in turn. Organisms who perform methanogenesis are known as [[methanogens]] and are a group of anaerobic Archaea. CH<sub>4</sub> can also be produced as a result of acetate (CH<sub>3</sub>COOH) fermentation, which is also performed by methanogens. <ref name="Sylvia" /><br />
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===Fermentation in Flooded Soils (Non-Respiratory)===<br />
Fermentation is a different form of metabolism from respiration that occurs in the absence of a suitable terminal electron acceptor. Cells convert NADH and pyruvate from the glycolysis of sugars into NAD+ and other compounds, depending on the species that is fermenting. The various products of fermentation, including alcohols, lactic acid, and acetate are released into the surrounding soil and then become available for use by other anaerobic organisms. Additionally, fermentation generally reduces soil pH, which will encourage dissolution of minerals and their subsequent access by bacteria. <ref name="Richardson">Richardson, J. L., & Vepraskas, M. J. (2001). Wetland soils: Genesis, hydrology, landscapes, and classification. Boca Raton, FL: Lewis. </ref><br />
<br />
==Microorganisms Involved==<br />
As available oxygen declines, organisms that thrive under anoxic conditions proliferate using alternative electron acceptors. The order in which available electron acceptors are consumed can generally be predicted by the electron tower and associated energy yields of electron pairs. Changes in redox conditions of flooded soils over time reflects the successive availability of terminal electron acceptors from the electron tower, and will govern which microbes will thrive through being able to use them.<br />
<br />
Some microbes below are able to oxidize the reduced form of their corresponding substance.<ref>Liesack, W. (2000). Microbiology of flooded rice paddies. FEMS Microbiology Reviews, 24(5), 625-645. </ref><br />
[[Image:Processes.jpg|500px|thumb|right|Summary of reducing conditions in flooded soils. [http://www.des.ucdavis.edu/faculty/rejmankova/ESP155_Soils-2004.pdf Source]]]<br />
<br />
<br />
{| width="800" border="1"<br />
|----- bgcolor ="grey"<br />
| width="200" height="25" | '''Process'''<br />
| width="1000" | '''Example Genera of Common Bacteria Involved'''<br />
|-<br />
| Aerobic Respiration<br />
| Aerobes and facultative anaerobes such as ''Staphylococcus'', ''[https://en.wikipedia.org/wiki/Nocardia Nocardia]'', ''[[Pseudomonas]]''<br />
|-<br />
| Denitrification<br />
| Facultative anaerobes such as ''[[Agrobacterium]]'', ''[[Alcaligenes]]'', ''[[Bacillus]]'', ''Paracoccus'', ''Micrococcus''<br />
|-<br />
| Manganese Reduction<br />
| ''[[Bacillus]]'', ''[[Geobacter]]'', ''[[Pseudomonas]]'', ''Shewanella''<br />
|-<br />
| Iron Reduction<br />
| ''[[Desulfovibrio]]'', ''[[Pseudomonas]]'', ''Geothrix'', ''Shewanella'', ''Thiobacillus''<br />
|-<br />
| Sulfate Reduction<br />
| Generally obligate anaerobes such as ''[[Desulfobacter]]'', ''[[Desulfococcus]]'', ''[[Desulfosarcina]]'', ''Desulfosporosinus''<br />
|-<br />
| Methanogenesis<br />
| [[Methanogens]] such as ''Methanobacterium'' and [https://en.wikipedia.org/wiki/Archaea Archaea] (different from bacteria)<br />
|}<br />
[[Image:PseudomonasImage.jpg|300px|thumb|left|The ''Pseudomonas'' genus has a wide variety of metabolic capabilities among its species. [https://elmundodelavida.wordpress.com/category/ciencia/ Source]]]<br />
[[Image:Probes.gif|400px|thumb|center|[https://en.wikipedia.org/wiki/Hybridization_probe DNA and RNA probes] are used for identifying bacteria in samples. [http://tle.westone.wa.gov.au/content/file/969144ed-0d3b-fa04-2e88-8b23de2a630c/1/human_bio_science_3b.zip/content/005_dna/page_17.htm Source]]]<br />
<br />
==Effects of Flooding on Soil Environment==<br />
<br />
===Mobility of Minerals and Gasses===<br />
[[Image:Aggregation.jpg|200px|thumb|right|A) unaffected soil and B) soil incubated anaerobically. Flooding caused mobilization of organic matter and disaggregation, resulting in the larger grains (decreased stability). [https://dl.sciencesocieties.org/publications/sssaj/abstracts/73/2/550 Source]]]<br />
Water also acts as a solvent for ions and soluble compounds, thus increasing the mobility and availability of metal ions, nutrients, and minerals. As a result of these physical effects in flooded soils, microbial respiration will have improved access to water-soluble compounds such as nitrate, perchlorate, manganese/ferric iron, sulfate, and carbon dioxide to act as electron acceptors. <br />
<br />
The diffusion of oxygen is over 10000 times slower in water than it is in air at standard temperature and pressure, resulting in the replenishing rate being much slower in flooded soils. Carbon dioxide is also decreased but to a lesser degree due to it being far more soluble than oxygen. <ref>Greenway H, William A, Timothy DC. (2006). Conditions leading to high CO2 (>5 kPa) in waterlogged-flooded soils and possible effects on root growth and metabolism. Annals of Botany, 98, 9–32. Retrieved March 10, 2016 from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3291891/ .</ref><br />
<br />
===Flooded Soil Aggregate Structure===<br />
Though some degree of moisture is important for aggregate formation and microbial activity, flooded soils exhibit decreased aggregate stability compared to unsaturated soils. Oxygen depletion and subsequent use of various elements for redox contributes to this decreased aggregation. Organic carbon is also made more soluble (like metals and minerals) under reducing conditions. The decreased stability of the soil is unlikely to recover due to drainage or volatilization of chemicals, removing them from the local environment. Since areas such as marshlands and rice fields are perpetually flooded, their soil’s aggregate stability rarely improves. <ref>De-Campos, A. B., Mamedov, A. I., & Huang, C. (2009). Short-Term Reducing Conditions Decrease Soil Aggregation. Soil Science Society of America Journal, 73(2), 550. Retrieved February 23, 2016, from https://dl.sciencesocieties.org/publications/sssaj/abstracts/73/2/550 .</ref><br />
<br />
===Soil Gradients===<br />
[[Image:Column.jpg|200px|thumb|left|A Winogradsky column. [http://beautyinscience.com/Biology.html Source] ]] <br />
The progression of electron acceptor utilization occurs at different rates in different layers of soil. A process like methanogenesis will occur earlier several feet underground than at the surface due to decreased access to other compounds. This will result in gradients at various depths of soil. These gradients will differ by pH, color, chemical prevalence, and microbial population. <br />
<br />
Since the soil is a more closed system (with less mobility of chemicals) than the surface, air, or bodies of water, gradients can be observed with a similar closed system: a Winogradsky column. This column, consisting of a sealed column of soil with provided organic material (such as an egg), allows for simulation of an anaerobic soil environment. <ref>Scientific American. (2013, September 19). Soil Science: Make a Winogradsky Column. Retrieved from http://www.scientificamerican.com/article/bring-science-home-soil-column/ </ref><br />
<br />
===Variation of pH===<br />
pH has a major influence over the dissolution and sorption of several important toxins and nutrients in the soil. Low pH values increase the solubility of free aluminum (Al<sup>3+</sup>) and iron (Fe<sup>3+</sup> and Fe<sup>2+</sup>) ions which can be toxic in high concentrations, while also reducing the availability of phosphorus.<br />
<br />
When soil is initially saturated with water, the pH drops due to the accumulation of carbonic acid formed from trapped carbon dioxide produced from respiration. Fermentation also contributes to pH decreasing through the production of organic acids. This is quickly followed by an increase of pH as hydrogen cations are consumed in microbially-driven redox reactions. The soil then will gradually approach and stabilize near a neutral pH, with pH increasing in acidic soil and decreasing in basic soil due to products such as carbonate forming a buffer. <ref>Kirk, G. J. (2004). The biogeochemistry of submerged soils. Chichester: Wiley. </ref><br />
<br />
===Soil Gleying===<br />
[[Image:gleyed.jpg|200px|thumb|right|Gray colors produced in gleyed soil. [http://wetland-delineation.rutgers.edu/87-wetland-delineation-manual/wetland-delineation-manual-part3.html Source] ]] <br />
<br />
Gleying is a phenomenon in which waterlogged soils are discolored by the color changes due to reduction of ferric iron into ferrous iron. Although ferric iron exists as an insoluble form in flooded soils, more ferrous iron can accumulate by the reduction of ferric iron over time. This results in a greenish, blue, grey soil color. In general Fe<sup>3+</sup> -reducing fermentative bacteria can be readily isolated from gleyed soils. The black color of soils/solution is frequently observed in flooded soil. This may result from the formation of iron sulfides (FeS) and pyrite (FeS2). <ref>Wenk, H., & Bulakh, A. G. (2004). Minerals: Their constitution and origin. Cambridge: Cambridge University Press. </ref><br />
<br />
===Plant Nutrient Availability===<br />
Flooded soils can have a direct impact on plants by preventing efficient gas exchange between the plant roots and the soil. These conditions also change the types of microbes that are active and what they produce. Flooded soils cause anaerobic conditions which forces many microbes to use less favorable electron acceptors. These less favorable acceptors could have also served as nutrition for the plants; this creates competition between the plants and the microbes in certain flooded soils. By using different electron acceptors the microbes will release different products causing a chemical change in the soil that can be toxic. <ref>Minamikawa, K., & Sakai, N. (2005). The effect of water management based on soil redox potential on methane emission from two kinds of paddy soils in Japan. Agriculture, Ecosystems & Environment, 107(4), 397-407. Retrieved from http://www.sciencedirect.com/science/article/pii/S0167880904002208 .</ref><br />
<br />
===Flooded to Unflooded Conditions===<br />
When waterlogged soils drain, oxygen diffuses into soil pores. The soil’s Eh increases and aerobic activity kicks in ceasing the production of anaerobic products. At higher Eh zones ( > 500 mV), undecomposed soil organic matter is used as an electron donor by aerobes and converted to water and CO2. Many of the anaerobic redox reactions are also reversed as with oxygen available as an electron acceptor many of the reduced products of anaerobic respiration can now be used as electron donors by lithotrophs. Manganese is oxidized back to MnO2 which gives some aerated soils a black color, and ferrous iron is oxidized by an iron-oxidizing bacteria, resulting in the formation of ferric oxides or ferric hydroxide minerals that give the soil a red, yellow, or brownish texture. <ref name="Richardson" /><br />
<br />
<br />
==Environmental Issues==<br />
<br />
Flooded soils are dynamic ecosystems that play an important role in biogeochemical cycling and in the production of greenhouse gases. Methane (CH<sub>4</sub><sup>+</sup>) and nitrous oxide (N<sub>2</sub>O) are produced as byproducts of anaerobic metabolism in the low-redox zones characteristic of flooded soils, where oxygen is lacking. Carbon dioxide (CO<sub>2</sub>), which receives widespread attention as a greenhouse gas and potential source of global warming, may also be produced at the interface of anaerobic-aerobic zones through the consumption of methane gas. However, it should be noted that from a global standpoint methane and nitrous oxide on a per molecule basis have the potential to contribute 25x and 300x more to global warming over the next century than carbon dioxide, respectively. Thus the conversion of methane gas to carbon dioxide essentially reduces the greenhouse gas effect by 25x per molecule per 100 years. Although the number areas classified as wetlands has decreased in past years, the effect of flooded soils to the global climate is clear.<ref>Schlesinger, W. H., & Bernhardt, E. S. (2013). Biogeochemistry: An analysis of global change (3rd ed.). San Diego, CA: Academic Press. </ref><br />
<br />
===Methane Production; Methanogenesis===<br />
[[Image:Methane.jpg|thumb|300px|A natural source of methane gas]]<br />
Methane production occurs exclusively in anaerobic conditions by a group of Archaea known as methanogens. These microbes are obligatory, and require extremely low redox conditions in the range of -100mV. If oxygen is introduced into the system, methanogenesis ceases; thus, the process of methanogenesis depends on saturated soil conditions.<ref name="Sylvia" /> <br />
<br />
Methanogenesis can occur via one of two pathways: either by 1) CO<sub>2</sub> reduction or by 2) acetate fermentation.<br />
<br />
1) CO<sub>2</sub> + H<sub>2</sub> --> CH<sub>4</sub><sup>+</sup> (CO<sub>2</sub> reduction)<br />
<br />
and <br />
<br />
2) CH<sub>3</sub>COOH --> CH<sub>4</sub><sup>+</sup> + CO<sub>2</sub> (acetate fermentation)<br />
<br />
Both acetate and hydrogen are byproducts of anaerobic fermentation. <br />
<br />
Because the process of methanogenesis is “fed” byproducts produced from a complex series of degradation processes which are themselves “fed” complex organic matter, rates of methane production are highly sensitive to changes in temperature. Methanogenesis has a Q10 value in the range of 30-40, which is substantially higher than most biochemical process.<br />
<br />
Despite the clear effect of increasing temperatures on the rate of methanogenesis, the actual impact of global warming on methane production rates in wetlands and permafrost regions is highly unpredictable. Because methanogenesis requires anoxic conditions, any drying of flooded soil environments would both decrease methane production and increase methane oxidation, reducing overall methane emissions. Alternatively, warmer climates could increase growing seasons, which would increase methane emissions.<ref name="Sylvia" /><br />
<br />
===CO<sub>2</sub> Production via Methane Consumption: Methanotrophy===<br />
Some of the methane produced via methanogenesis in flooded soils may be consumed and oxidized to CO<sub>2</sub> at the interface of the anaerobic-aerobic zones. This process occurs primarily by a group of bacteria known as methanotrophs. These microbes can be found in surface layers of wetland soils and unsaturated upland soils, and may be exposed to very high concentrations of methane gas, sometimes amounting to 10% or more of the dissolved gases. Methane is thought to be the only source of C and energy for these bacteria.<br />
<br />
Methanotrophy occurs in the following reaction:<br />
<br />
CH<sub>4</sub><sup>+</sup> + 2O<sub>2</sub> --> CO<sub>2</sub> + 2H<sub>2</sub>O<br />
<br />
Methane is similar in size and shape to ammonium; and there is some evidence that nitrifiers (ammonium oxidizers) can also oxidize methane. Because they are molecularly similar, NH<sup>4</sup><sup>+</sup> competes at the enzyme’s active site, inhibiting methane oxidation. As a result, methanotrophy is generally inhibited by the addition of fertilizer or excess nitrogen in the system, when ammonium levels are high. <br />
<br />
Alternatively, if nitrogen is extremely limiting the addition of nitrogen will stimulate methanotrophy and actually increase methane consumption. So although it is generally expected that adding N-fertilizer will decrease CH<sub>4</sub><sup>+</sup> consumption and lead to increased global warming potential, sometime the opposite effect may occur.<ref name="Sylvia" /><br />
<br />
===Nitrous Oxide; Denitrification===<br />
Denitrification is an anaerobic process in which nitrate serves as the terminal electron acceptor, and generally some source of organic carbon is the electron donor (also H<sub>2</sub> may serve as a donor). <br />
<br />
In this process, nitrate is oxidized to nitric oxide, then nitrous oxide, and then fully oxidized to dinitrogen:<br />
<br />
NO<sub>2</sub><sup>-</sup> --> NO --> N<sub>2</sub>O --> N<sub>2</sub><br />
<br />
However, under certain conditions the full oxidation of NO<sub>3</sub><sup>-</sup> to N<sub>2</sub> does not occur and nitrous oxide (N<sub>2</sub>O) is produced.<br />
<br />
Microbes responsible include both organotrophs and lithotrophs, and this process occurs primarily by facultative anaerobes. <br />
<br />
Although a low redox potential is important for denitrification to occur (oxygen must not be present or it will “out-compete” nitrate as a terminal electron acceptor), redox requirements are not so low that this process cannot occur within anaerobic microsites of soil aggregates. <br />
<br />
Factors affecting nitrous oxide production include oxygen, pH, and the ratio of nitrate to available C. Although denitrification rates decrease with increasing oxygen, the proportion of N evolved as nitrous oxide actually increases with increasing oxygen. Low pH generally inhibits the reduction of N<sub>2</sub>O to N<sub>2</sub>; thus at low pH, N<sub>2</sub>O will likely dominate. However, highly acidic soils have low N availability and low nitrification and denitrification rates. Thus, the highest rate of nitrous oxide production from denitrification occurs in moist soils that cycle N rapidly.<ref name="Sylvia" /><br />
<br />
==Current Research==<br />
Current research topics on the issue of flooded soils are heavily focused on greenhouse gas emissions produced as a result of the low redox conditions characteristic of these ecosystems. Other research topics may address impacts to plant growth, and chemical, physical, and biological aspects of flooded soils. <br />
<br />
Many agricultural studies focus on rice paddies. Bacteria that oxidized acetate and reduced iron were identified and studied in flooded rice paddy soil through RNA probing.<ref>Hori, T., Müller, A., Igarashi, Y., Conrad, R., & Friedrich, M. W. (2009). Identification of iron-reducing microorganisms in anoxic rice paddy soil by 13C-acetate probing. The ISME Journal ISME J, 4(2), 267-278. from http://www.nature.com/ismej/journal/v4/n2/full/ismej2009100a.html </ref> Another study observed factors affecting delivery of nitrogen to plants by microbial populations in flooded soils and found that the addition of sludge to soil facilitated nitrogen formation more than the addition of straw compost.<ref>El-Sharkawi, H. M. (2012). Effect of Nitrogen Sources on Microbial Biomass Nitrogen under Different Soil Types. ISRN Soil Science, 2012, 1-7. from http://www.citationmachine.net/bibliographies/77289062?new=true </ref> The effect of oxygen concentration on rates of reactions involving nitrogen, including nitrification and mineralization, in paddy soils was also studied.<ref>Yang, Y., Zhang, J., & Cai, Z. (2015). Nitrification activities and N mineralization in paddy soils are insensitive to oxygen concentration. Acta Agriculturae Scandinavica, Section B — Soil & Plant Science, 66(3), 272-281. from http://www.tandfonline.com/doi/full/10.1080/09064710.2015.1093653 </ref><br />
<br />
A review article was published in 2012, focusing on soil-plant interactions, including redox reactions’ effects on plant function, in wetlands.<ref>Pezeshki, S. R., & Delaune, R. D. (2012). Soil Oxidation-Reduction in Wetlands and Its Impact on Plant Functioning. Biology, 1(3), 196-221. from http://www.mdpi.com/2079-7737/1/2/196 </ref><br />
<br />
[[Carbon cycle | Long-term retention of carbon in soil organic matter]] is an issue in frequently harvested soils. One study looked at various treatments of rice paddies and found that a combination of rice straw and inorganic fertilizer aided sequestration and led to “a higher grain yield”.<ref> Bhattacharyya, P., Roy, K., Neogi, S., Adhya, T., Rao, K., & Manna, M. (2012). Effects of rice straw and nitrogen fertilization on greenhouse gas emissions and carbon storage in tropical flooded soil planted with rice. Soil and Tillage Research, 124, 119-130. from http://www.sciencedirect.com/science/article/pii/S0167198712001195 </ref><br />
<br />
A recent study discussed the fate of metals such as cadmium, nickel, and aluminum in impacted creeks in Kenya, Tanzania, and Mozambique.<ref>Kamau, J. N., Kuschk, P., Machiwa, J., Macia, A., Mothes, S., Mwangi, S., . . . Kappelmeyer, U. (2015). Investigating the distribution and fate of Al, Cd, Cr, Cu, Mn, Ni, Pb and Zn in sewage-impacted mangrove-fringed creeks of Kenya, Tanzania and Mozambique. J Soils Sediments Journal of Soils and Sediments, 15(12), 2453-2465. Retrieved from http://link.springer.com/article/10.1007/s11368-015-1214-3 </ref><br />
<br />
Many other studies focus on the degradation of ground contaminants such as pesticides so that their results can be used in [[bioremediation]].<ref>Levén, L., Nyberg, K., & Schnürer, A. (2012). Conversion of phenols during anaerobic digestion of organic solid waste – A review of important microorganisms and impact of temperature. Journal of Environmental Management, 95. Retrieved from http://www.sciencedirect.com/science/article/pii/S0301479710003531 </ref> The fate of cycloxaprid, an agricultural insecticide, was observed in anaerobic conditions (including flooded soils). Radioisotopic tracing showed that various soil types had different effects on the chemical.<ref>Liu, X., Xu, X., Li, C., Zhang, H., Fu, Q., Shao, X., . . . Li, Z. (2016). Assessment of the environmental fate of cycloxaprid in flooded and anaerobic soils by radioisotopic tracing. Science of The Total Environment, 543, 116-122. Retrieved from http://www.sciencedirect.com/science/article/pii/S0048969715310007 </ref><br />
<br />
Lastly, there is always the topic of greenhouse gas emissions. Arctic, temperate, and tropical regions were recently studied for measurements of greenhouse gas emissions and its relation to temperature.<ref>Turetsky, M. R., Kotowska, A., Bubier, J., Dise, N. B., Crill, P., Hornibrook, E. R., . . . Wilmking, M. (2014). A synthesis of methane emissions from 71 northern, temperate, and subtropical wetlands. Glob Change Biol Global Change Biology, 20(7), 2183-2197. Retrieved from http://onlinelibrary.wiley.com/doi/10.1111/gcb.12580/pdf </ref> Another group of researchers found a correlation between anaerobic methane oxidation in freshwater wetlands and reduced methane emissions.<ref>Segarra, K. E., Schubotz, F., Samarkin, V., Yoshinaga, M. Y., Hinrichs, K., & Joye, S. B. (2015). High rates of anaerobic methane oxidation in freshwater wetlands reduce potential atmospheric methane emissions. Nature Communications Nat Comms, 6, 7477. Retrieved from http://www.nature.com/ncomms/2015/150630/ncomms8477/full/ncomms8477.html </ref><br />
<br />
==References==<br />
<references /><br />
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Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]<br />
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<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Central_Metabolism_(Flooded_soils)&diff=132730
Central Metabolism (Flooded soils)
2018-02-09T07:23:45Z
<p>Kmscow: /* Flooded Soil Aggregate Structure */</p>
<hr />
<div>{{Curated}}<br />
[[Image:FloodedSoil.png|600px|thumb|right|Comparison of water levels in three environments: unsaturated soil, saturated soil, and flooded soil. [http://www.floodsite.net/juniorfloodsite/html/en/student/thingstoknow/hydrology/waterstorage2.html Source]]] <br />
[[Image:Peatland.jpg|thumb|500px|right|A peatland, a type of flooded environment with a layer of organic matter, in Australia. Peatlands produce a high amount of methane emissions. [http://photography.nationalgeographic.com/photography/photo-of-the-day/peatland-australia-essick/ Source]]] <br />
<br />
Flooded soils are a condition in which an area of soil is oversaturated with water, often due to natural occurrence or with intended purpose for agricultural reasons. Perpetually flooded soils can be found in wetlands, swamps and marshes; temporary flooded soils can be an effect of season weather or agricultural practices. As water levels fluctuate, and soils alternate between flooded and unflooded states, the chemical makeup of the [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] will continuously change. A soil’s water content directly influences both inorganic and microbial reactions that affect the soil’s redox potential (E<sub>h</sub>), acidity, alkalinity, and salinity.<ref name="Campos">Dassonville, F., & Renault, P. (2002). Interactions between microbial processes and geochemical transformations under anaerobic conditions: A review. Agronomie, 22(1), 51-68. Retrieved from http://www.agronomy-journal.org/articles/agro/abs/2002/01/05/05.html. </ref><br />
<br />
One of the most important effects of flooded soils is that the presence of oxygen is limited in such an environment, and any remaining oxygen is quickly used up via aerobic respiration. As a result, other compounds are used as electron acceptors in energy acquisition reactions; the microorganisms that specialize in conducting these other reactions are able to flourish and affect nutrient cycling in the ecosystem. <br />
<br />
Microbial transformations of elements in anaerobic soils play a worldwide role in biogeochemical cycling of nutrients and in greenhouse gas emissions. Changes in the oxidation state of terminal electron acceptors may result in nutrient loss from the system via volatilization or leaching. Anaerobic microbial processes including denitrification, methanogenesis, and methanotrophy are responsible for releasing greenhouse gases (N<sub>2</sub>O, CH<sub>4</sub>, CO<sub>2</sub>) into the atmosphere. <ref>United States Environmental Protection Agency. (n.d.). Overview of Greenhouse Gases. Retrieved March 13, 2016, from http://www3.epa.gov/climatechange/ghgemissions/gases/ch4.html .</ref><br />
<br />
<br />
==Key Microbial Processes==<br />
<br />
===Microbial Respiration: [http://en.wikipedia.org/wiki/Redox Oxidation/Reduction Reactions]===<br />
[[Image:RedoxReaction.jpg|300px|thumb|left|General process of a paired reduction and oxidation. The transfer of electrons from molecule A to B is shown. [https://online.science.psu.edu/biol011_sandbox_7239/node/7381 Source]]] <br />
[[Image:Succession1.JPG|300px|thumb|right|Redox potentials of various couples. In soil, the order of succession begins with oxygen and generally ends with carbon dioxide. <ref>Schüring, J., Schulz, H. D., & Fischer, W. R. (Eds.). (2000). Redox: Fundamentals, processes, and applications. New York City, NY: Springer.</ref>]] <br />
<br />
In order to obtain energy, many microbes make use of the process of respiration through an oxidation-reduction (redox) reaction. Respiration is a catabolic reaction that produces ATP in which either organic or inorganic compounds act as primary electron donors, and exogenous compounds act as the terminal electron acceptors. In a redox reaction, one molecule (the reducing agent) loses electrons and another molecule (the oxidizing agent) accepts electrons. Electron donors such as glucose, methanol, and [https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH] are energy sources that can be thought of as “giving up” their electrons, while another molecule is in need to receive said electrons. For example, in aerobic respiration, energy rich compounds like glucose (the reducing agent) are oxidized to carbon dioxide, with oxygen (the oxidizing agent) acting as a terminal electron acceptor and being reduced to water. In addition to oxygen, microorganisms use a large variety of electron acceptors. <br />
<br />
Depending on the type of electron acceptors used by microorganisms, microbes can be placed into a variety of classifications. Strict aerobes can only use oxygen as a terminal electron acceptor. Obligate anaerobes cannot use oxygen and are actually inhibited or poisoned by oxygen. Facultative anaerobes are flexible in electron acceptor usage; as a result of this they can make use of other redox reactions to maintain a supply of energy as oxygen levels decrease.<br />
<br />
Oxygen gas (O<sub>2</sub>) is one of the most favorable electron acceptors, but it is typically not available in flooded soils. Instead, facultative and strict anaerobic microbes utilize other oxidizing agents (electron acceptors) to carry out respiration. The amount of energy that can be obtained through respiration varies between compounds and microbes and will make use of these compounds in order of the decreasing redox potential, thus leading to a succession of acceptors.<br />
<br />
====Redox Potential (E<sub>h</sub>)====<br />
Redox potential is the tendency for a reaction, specifically the movement and transfer of electrons, to occur spontaneously and is reported as E<sub>h</sub> in mV. These measurements have been experimentally determined through aqueous solutions containing electrodes, one being the cathode (electron donator) and one being the anode (electron receiver). <ref>Redox Chemistry Primer. (n.d.). Retrieved March 12, 2016, from http://www.kgs.ku.edu/Hydro/GWtutor/Plume_Busters/remediate_refs/redox_chemistry.htm .</ref><br />
<br />
This voltage shows how likely the electrons will be moved in a solution. Redox potential is assigned individually to half-reactions (a single instance of oxidation or reduction), e.g. the E<sub>h</sub> of the reduction of O<sub>2</sub> to H<sub>2</sub>O will be different from that of the opposite oxidation of H<sub>2</sub>O to O<sub>2</sub>. Redox potential is also reported as standard reduction potential E<sub>o</sub>. Reactions with a higher redox potential yield more net energy for the organism performing them, and this results in higher growth rates (in terms of population).<br />
<br />
===The Electron Tower===<br />
[[Image:RedoxTower.jpg|300px|thumb|right|A tower showing common redox pairs. The greater the "distance" between a donor and acceptor, the greater the energy released. From ''Brock Biology of Microorganisms''.]] <br />
Microbes will successively use the highest energy yielding electron acceptors available in the order indicated on the electron tower, which is a ranking of common redox reactions by the amount of energy that can be obtained from them. Compounds are listed in redox pairs (oxidized form and reduced form) The greater the difference in electrical potential between the reactants and products of a reaction, the greater the release of energy that is crucial for microbial growth. <ref>Madigan, M. T., Martinko, J. M., & Parker, J. (2003). Brock biology of microorganisms (10th ed.). Upper Saddle River, NJ: Prentice Hall/Pearson Education. </ref><br />
<br />
O<sub>2</sub>, the lowest oxidizing agent on the tower, yields the most energy when reduced in a redox reaction with a specific electron donor and will be the first electron acceptor depleted when commonly available. In flooded soils, the amount of oxygen in the system will be very small. When the soil’s microbial population exhausts its remaining O<sub>2</sub>, it will begin using other available electron acceptors which provide the next highest amount of energy. Competition generally limits the use of weaker electron acceptors; for example, iron reducers (using Fe<sup>3+</sup>) may exist in the soil but will be dominated by the presence of denitrifiers, who will growth faster with access to their stronger electron acceptor (NO<sub>3</sub><sup>-</sup>). Overall, this process of succession will continue as each electron acceptor supply is used.<br />
<br />
===Succession of Electron Acceptors=== <br />
The main succession of electron acceptor usage in flooded soils is as follows:<br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobes and aerobes)<br />
<br />
Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by denitrifiers) <br />
<br />
Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by manganese reducing bacteria)<br />
<br />
Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by iron reducing bacteria)<br />
<br />
Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
<br />
Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by methanogens)<br />
<br />
====[[Nitrogen Cycle|Nitrate Reduction]]====<br />
After O<sub>2</sub>, nitrate (NO<sub>3</sub><sup>-</sup>) is one of the strongest electron acceptors as is represented in the electron tower. It can be obtained from transformations of other compounds containing nitrogen, such as ammonium (NH<sub>4</sub><sup>+</sup>) and nitrite (NO<sub>2</sub><sup>-</sup>). Denitrification reduces NO<sub>3</sub><sup>-</sup> to nitrogen gas (N<sub>2</sub>) or various nitrogen oxides and is performed by facultative anaerobic microorganisms. Oxygen depletion is important for the nitrogen cycle as a whole, since if it were constantly present NO<sub>3</sub><sup>-</sup> would be used at a much slower rate and contaminate soils through accumulation. <ref name="Sylvia">Silvia, D.M., et al. 2005. Principles and Applications of Soil Microbiology. 2nd ed. Pearson Prentice Hall, New Jersey. </ref><br />
<br />
====Manganese Reduction====<br />
The next most energy-releasing electron acceptor after NO<sub>3</sub><sup>-</sup> is manganese (IV) oxide (MnO<sub>2</sub>) which is is reduced to Mn<sup>2+</sup> ions. In this form, manganese is very insoluble in water and forms masses in soils. Mn<sup>2+</sup> is generally oxidized to this form in soils with a pH between 5 and 8, (as the rate increases with basicity). Many microorganisms that conduct this process are also capable of iron reduction, described below. <ref name="Sylvia" /> <br />
<br />
====Iron Reduction====<br />
[[Image:pipe.jpg|100px|thumb|left|Corroded water main. [http://coloradogeologicalsurvey.org/geologic-hazards/corrosive-soils/corrosive-soil-damage/ Source] ]] <br />
The utilization of ferric iron ions (Fe<sup>3+</sup>), at approximately 120 mV, occurs when ions are released from metal deposits or minerals in the soil. Ferrous iron (Fe<sup>2+</sup>) product causes soil gleying, (a process described in a later section) when it accumulates. The source of the iron is also of relevance; whereas iron reduction in phosphate minerals can release phosphate for other organisms, it can also lead to corrosion of steel where iron reducers are present. Some ''Pseudomonas'' species can release pseudobactin, an iron-binding compound that limits its availability to other bacteria. <ref name="Sylvia" /><br />
<br />
====Sulfate Reduction====<br />
Sulfate reduction begins occurring at 0 mV, and the dissimilatory reduction results in hydrogen sulfide (H<sub>2</sub>S) being released. However, H<sub>2</sub>S is prone to reaction with Fe<sup>2+</sub> to form iron sulfide (FeS). As a result, it often reacts before it reaches the surface of the soil, unable to disperse into the air. <ref name="Sylvia" /> Sulfate reduction has several documented consequences, ranging from corrosion of underground iron pipes due to FeS formation and blackening of soil caused by liberation of organic matter. Hydrogen sulfide is known as “swamp gas”, due to its emergence from one form of soil flooding, and has an odor comparable to rotting eggs. It can accumulate in many bodies of water and the air above them; due to its flammability and toxicity, this is very dangerous. <ref>Occupational Safety & Health Administration. (n.d.). Safety and Health Topics | Hydrogen Sulfide. Retrieved February 23, 2016, from https://www.osha.gov/SLTC/hydrogensulfide/index.html .</ref><br />
<br />
====Methanogenesis (by Carbon Dioxide Reduction)====<br />
The process of using carbon dioxide (CO<sub>2</sub>) as a terminal electron acceptor results in the formation of methane (CH<sub>4</sub>) and is known as methanogenesis. In soil, methanogenesis occurs almost exclusively in a flooded condition due to its reduction potential being so low (below 100 mV). The use of CO<sub>2</sub> in this fashion yields much less energy than the reactions of previous electron acceptors, so this process has lower growth rates in turn. Organisms who perform methanogenesis are known as [[methanogens]] and are a group of anaerobic Archaea. CH<sub>4</sub> can also be produced as a result of acetate (CH<sub>3</sub>COOH) fermentation, which is also performed by methanogens. <ref name="Sylvia" /><br />
<br />
===Fermentation in Flooded Soils (Non-Respiratory)===<br />
Fermentation is a different form of metabolism from respiration that occurs in the absence of a suitable terminal electron acceptor. Cells convert NADH and pyruvate from the glycolysis of sugars into NAD+ and other compounds, depending on the species that is fermenting. The various products of fermentation, including alcohols, lactic acid, and acetate are released into the surrounding soil and then become available for use by other anaerobic organisms. Additionally, fermentation generally reduces soil pH, which will encourage dissolution of minerals and their subsequent access by bacteria. <ref name="Richardson">Richardson, J. L., & Vepraskas, M. J. (2001). Wetland soils: Genesis, hydrology, landscapes, and classification. Boca Raton, FL: Lewis. </ref><br />
<br />
==Microorganisms Involved==<br />
As available oxygen declines, organisms that thrive under anoxic conditions proliferate using alternative electron acceptors. The order in which available electron acceptors are consumed can generally be predicted by the electron tower and associated energy yields of electron pairs. Changes in redox conditions of flooded soils over time reflects the successive availability of terminal electron acceptors from the electron tower, and will govern which microbes will thrive through being able to use them.<br />
<br />
Some microbes below are able to oxidize the reduced form of their corresponding substance.<ref>Liesack, W. (2000). Microbiology of flooded rice paddies. FEMS Microbiology Reviews, 24(5), 625-645. </ref><br />
[[Image:Processes.jpg|500px|thumb|right|Summary of reducing conditions in flooded soils. [http://www.des.ucdavis.edu/faculty/rejmankova/ESP155_Soils-2004.pdf Source]]]<br />
<br />
<br />
{| width="800" border="1"<br />
|----- bgcolor ="grey"<br />
| width="200" height="25" | '''Process'''<br />
| width="1000" | '''Example Genera of Common Bacteria Involved'''<br />
|-<br />
| Aerobic Respiration<br />
| Aerobes and facultative anaerobes such as ''Staphylococcus'', ''[https://en.wikipedia.org/wiki/Nocardia Nocardia]'', ''[[Pseudomonas]]''<br />
|-<br />
| Denitrification<br />
| Facultative anaerobes such as ''[[Agrobacterium]]'', ''[[Alcaligenes]]'', ''[[Bacillus]]'', ''Paracoccus'', ''Micrococcus''<br />
|-<br />
| Manganese Reduction<br />
| ''[[Bacillus]]'', ''[[Geobacter]]'', ''[[Pseudomonas]]'', ''Shewanella''<br />
|-<br />
| Iron Reduction<br />
| ''[[Desulfovibrio]]'', ''[[Pseudomonas]]'', ''Geothrix'', ''Shewanella'', ''Thiobacillus''<br />
|-<br />
| Sulfate Reduction<br />
| Generally obligate anaerobes such as ''[[Desulfobacter]]'', ''[[Desulfococcus]]'', ''[[Desulfosarcina]]'', ''Desulfosporosinus''<br />
|-<br />
| Methanogenesis<br />
| [[Methanogens]] such as ''Methanobacterium'' and [https://en.wikipedia.org/wiki/Archaea Archaea] (different from bacteria)<br />
|}<br />
[[Image:PseudomonasImage.jpg|300px|thumb|left|The ''Pseudomonas'' genus has a wide variety of metabolic capabilities among its species. [https://elmundodelavida.wordpress.com/category/ciencia/ Source]]]<br />
[[Image:Probes.gif|400px|thumb|center|[https://en.wikipedia.org/wiki/Hybridization_probe DNA and RNA probes] are used for identifying bacteria in samples. [http://tle.westone.wa.gov.au/content/file/969144ed-0d3b-fa04-2e88-8b23de2a630c/1/human_bio_science_3b.zip/content/005_dna/page_17.htm Source]]]<br />
<br />
==Effects of Flooding on Soil Environment==<br />
<br />
===Mobility of Minerals and Gasses===<br />
[[Image:Aggregation.jpg|200px|thumb|right|A) unaffected soil and B) soil incubated anaerobically. Flooding caused mobilization of organic matter and disaggregation, resulting in the larger grains (decreased stability). [https://dl.sciencesocieties.org/publications/sssaj/abstracts/73/2/550 Source]]]<br />
Water also acts as a solvent for ions and soluble compounds, thus increasing the mobility and availability of metal ions, nutrients, and minerals. As a result of these physical effects in flooded soils, microbial respiration will have improved access to water-soluble compounds such as nitrate, perchlorate, manganese/ferric iron, sulfate, and carbon dioxide to act as electron acceptors. <br />
<br />
The diffusion of oxygen is over 10000 times slower in water than it is in air at standard temperature and pressure, resulting in the replenishing rate being much slower in flooded soils. Carbon dioxide is also decreased but to a lesser degree due to it being far more soluble than oxygen. <ref>Greenway H, William A, Timothy DC. (2006). Conditions leading to high CO2 (>5 kPa) in waterlogged-flooded soils and possible effects on root growth and metabolism. Annals of Botany, 98, 9–32. Retrieved March 10, 2016 from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3291891/ .</ref><br />
<br />
===Flooded Soil Aggregate Structure===<br />
Though some degree of moisture is important for aggregate formation and microbial activity, flooded soils exhibit decreased aggregate stability compared to unsaturated soils. Oxygen depletion and subsequent use of various elements for redox contributes to this decreased aggregation. Organic carbon is also made more soluble (like metals and minerals) under reducing conditions. The decreased stability of the soil is unlikely to recover due to drainage or volatilization of chemicals, removing them from the local environment. Since areas such as marshlands and rice fields are perpetually flooded, their soil’s aggregate stability rarely improves. <ref>De-Campos, A. B., Mamedov, A. I., & Huang, C. (2009). Short-Term Reducing Conditions Decrease Soil Aggregation. Soil Science Society of America Journal, 73(2), 550. Retrieved February 23, 2016, from https://dl.sciencesocieties.org/publications/sssaj/abstracts/73/2/550 .</ref><br />
<br />
===Soil Gradients===<br />
[[Image:Column.jpg|200px|thumb|left|A Winogradsky column. [http://beautyinscience.com/Biology.html Source] ]] <br />
The progression of electron acceptor utilization occurs at different rates in different layers of soil. A process like methanogenesis will occur earlier several feet underground than at the surface due to decreased access to other compounds. This will result in gradients at various depths of soil. These gradients will differ by pH, color, chemical prevalence, and microbial population. <br />
<br />
Since the soil is a more closed system (with less mobility of chemicals) than the surface, air, or bodies of water, gradients can be observed with a similar closed system: a Winogradsky column. This column, consisting of a sealed column of soil with provided organic material (such as an egg), allows for simulation of an anaerobic soil environment. <ref>Scientific American. (2013, September 19). Soil Science: Make a Winogradsky Column. Retrieved from http://www.scientificamerican.com/article/bring-science-home-soil-column/ </ref><br />
<br />
===Variation of pH===<br />
pH has a major influence over the dissolution and sorption of several important toxins and nutrients in the soil. Low pH values increase the solubility of free aluminum (Al<sup>3+</sup>) and iron (Fe<sup>3+</sup> and Fe<sup>2+</sup>) ions which can be toxic in high concentrations, while also reducing the availability of phosphorus.<br />
<br />
When soil is initially saturated with water, the pH drops due to the accumulation of carbonic acid formed from trapped carbon dioxide produced from respiration. Fermentation also contributes to pH decreasing through the production of organic acids. This is quickly followed by an increase of pH as hydrogen cations are consumed in microbially-driven redox reactions. The soil then will gradually approach and stabilize near a neutral pH, with pH increasing in acidic soil and decreasing in basic soil due to products such as carbonate forming a buffer. <ref>Kirk, G. J. (2004). The biogeochemistry of submerged soils. Chichester: Wiley. </ref><br />
<br />
===Soil Gleying===<br />
[[Image:gleyed.jpg|200px|thumb|right|Gray colors produced in gleyed soil. [http://wetland-delineation.rutgers.edu/87-wetland-delineation-manual/wetland-delineation-manual-part3.html Source] ]] <br />
<br />
Gleying is a phenomenon in which waterlogged soils are discolored by accumulation of iron oxide (FeO) due to reduction of ferric iron into ferrous iron. Although ferric iron exists as an insoluble form in flooded soils, more ferrous iron can accumulate by the reduction of ferric iron over time. This results in a greenish, blue, grey soil color. In general Fe<sup>3+</sup> -reducing fermentative bacteria can be readily isolated from gleyed soils. The black color of soils/solution is frequently observed in flooded soil. This may result from the formation of iron sulfides (FeS) and pyrite (FeS2). <ref>Wenk, H., & Bulakh, A. G. (2004). Minerals: Their constitution and origin. Cambridge: Cambridge University Press. </ref><br />
<br />
===Plant Nutrient Availability===<br />
Flooded soils can have a direct impact on plants by preventing efficient gas exchange between the plant roots and the soil. These conditions also change the types of microbes that are active and what they produce. Flooded soils cause anaerobic conditions which forces many microbes to use less favorable electron acceptors. These less favorable acceptors could have also served as nutrition for the plants; this creates competition between the plants and the microbes in certain flooded soils. By using different electron acceptors the microbes will release different products causing a chemical change in the soil that can be toxic. <ref>Minamikawa, K., & Sakai, N. (2005). The effect of water management based on soil redox potential on methane emission from two kinds of paddy soils in Japan. Agriculture, Ecosystems & Environment, 107(4), 397-407. Retrieved from http://www.sciencedirect.com/science/article/pii/S0167880904002208 .</ref><br />
<br />
===Flooded to Unflooded Conditions===<br />
When waterlogged soils drain, oxygen diffuses into soil pores. The soil’s Eh increases and aerobic activity kicks in ceasing the production of anaerobic products. At higher Eh zones ( > 500 mV), undecomposed soil organic matter is used as an electron donor by aerobes and converted to water and CO2. Many of the anaerobic redox reactions are also reversed as with oxygen available as an electron acceptor many of the reduced products of anaerobic respiration can now be used as electron donors by lithotrophs. Manganese is oxidized back to MnO2 which gives some aerated soils a black color, and ferrous iron is oxidized by an iron-oxidizing bacteria, resulting in the formation of ferric oxides or ferric hydroxide minerals that give the soil a red, yellow, or brownish texture. <ref name="Richardson" /><br />
<br />
<br />
==Environmental Issues==<br />
<br />
Flooded soils are dynamic ecosystems that play an important role in biogeochemical cycling and in the production of greenhouse gases. Methane (CH<sub>4</sub><sup>+</sup>) and nitrous oxide (N<sub>2</sub>O) are produced as byproducts of anaerobic metabolism in the low-redox zones characteristic of flooded soils, where oxygen is lacking. Carbon dioxide (CO<sub>2</sub>), which receives widespread attention as a greenhouse gas and potential source of global warming, may also be produced at the interface of anaerobic-aerobic zones through the consumption of methane gas. However, it should be noted that from a global standpoint methane and nitrous oxide on a per molecule basis have the potential to contribute 25x and 300x more to global warming over the next century than carbon dioxide, respectively. Thus the conversion of methane gas to carbon dioxide essentially reduces the greenhouse gas effect by 25x per molecule per 100 years. Although the number areas classified as wetlands has decreased in past years, the effect of flooded soils to the global climate is clear.<ref>Schlesinger, W. H., & Bernhardt, E. S. (2013). Biogeochemistry: An analysis of global change (3rd ed.). San Diego, CA: Academic Press. </ref><br />
<br />
===Methane Production; Methanogenesis===<br />
[[Image:Methane.jpg|thumb|300px|A natural source of methane gas]]<br />
Methane production occurs exclusively in anaerobic conditions by a group of Archaea known as methanogens. These microbes are obligatory, and require extremely low redox conditions in the range of -100mV. If oxygen is introduced into the system, methanogenesis ceases; thus, the process of methanogenesis depends on saturated soil conditions.<ref name="Sylvia" /> <br />
<br />
Methanogenesis can occur via one of two pathways: either by 1) CO<sub>2</sub> reduction or by 2) acetate fermentation.<br />
<br />
1) CO<sub>2</sub> + H<sub>2</sub> --> CH<sub>4</sub><sup>+</sup> (CO<sub>2</sub> reduction)<br />
<br />
and <br />
<br />
2) CH<sub>3</sub>COOH --> CH<sub>4</sub><sup>+</sup> + CO<sub>2</sub> (acetate fermentation)<br />
<br />
Both acetate and hydrogen are byproducts of anaerobic fermentation. <br />
<br />
Because the process of methanogenesis is “fed” byproducts produced from a complex series of degradation processes which are themselves “fed” complex organic matter, rates of methane production are highly sensitive to changes in temperature. Methanogenesis has a Q10 value in the range of 30-40, which is substantially higher than most biochemical process.<br />
<br />
Despite the clear effect of increasing temperatures on the rate of methanogenesis, the actual impact of global warming on methane production rates in wetlands and permafrost regions is highly unpredictable. Because methanogenesis requires anoxic conditions, any drying of flooded soil environments would both decrease methane production and increase methane oxidation, reducing overall methane emissions. Alternatively, warmer climates could increase growing seasons, which would increase methane emissions.<ref name="Sylvia" /><br />
<br />
===CO<sub>2</sub> Production via Methane Consumption: Methanotrophy===<br />
Some of the methane produced via methanogenesis in flooded soils may be consumed and oxidized to CO<sub>2</sub> at the interface of the anaerobic-aerobic zones. This process occurs primarily by a group of bacteria known as methanotrophs. These microbes can be found in surface layers of wetland soils and unsaturated upland soils, and may be exposed to very high concentrations of methane gas, sometimes amounting to 10% or more of the dissolved gases. Methane is thought to be the only source of C and energy for these bacteria.<br />
<br />
Methanotrophy occurs in the following reaction:<br />
<br />
CH<sub>4</sub><sup>+</sup> + 2O<sub>2</sub> --> CO<sub>2</sub> + 2H<sub>2</sub>O<br />
<br />
Methane is similar in size and shape to ammonium; and there is some evidence that nitrifiers (ammonium oxidizers) can also oxidize methane. Because they are molecularly similar, NH<sup>4</sup><sup>+</sup> competes at the enzyme’s active site, inhibiting methane oxidation. As a result, methanotrophy is generally inhibited by the addition of fertilizer or excess nitrogen in the system, when ammonium levels are high. <br />
<br />
Alternatively, if nitrogen is extremely limiting the addition of nitrogen will stimulate methanotrophy and actually increase methane consumption. So although it is generally expected that adding N-fertilizer will decrease CH<sub>4</sub><sup>+</sup> consumption and lead to increased global warming potential, sometime the opposite effect may occur.<ref name="Sylvia" /><br />
<br />
===Nitrous Oxide; Denitrification===<br />
Denitrification is an anaerobic process in which nitrate serves as the terminal electron acceptor, and generally some source of organic carbon is the electron donor (also H<sub>2</sub> may serve as a donor). <br />
<br />
In this process, nitrate is oxidized to nitric oxide, then nitrous oxide, and then fully oxidized to dinitrogen:<br />
<br />
NO<sub>2</sub><sup>-</sup> --> NO --> N<sub>2</sub>O --> N<sub>2</sub><br />
<br />
However, under certain conditions the full oxidation of NO<sub>3</sub><sup>-</sup> to N<sub>2</sub> does not occur and nitrous oxide (N<sub>2</sub>O) is produced.<br />
<br />
Microbes responsible include both organotrophs and lithotrophs, and this process occurs primarily by facultative anaerobes. <br />
<br />
Although a low redox potential is important for denitrification to occur (oxygen must not be present or it will “out-compete” nitrate as a terminal electron acceptor), redox requirements are not so low that this process cannot occur within anaerobic microsites of soil aggregates. <br />
<br />
Factors affecting nitrous oxide production include oxygen, pH, and the ratio of nitrate to available C. Although denitrification rates decrease with increasing oxygen, the proportion of N evolved as nitrous oxide actually increases with increasing oxygen. Low pH generally inhibits the reduction of N<sub>2</sub>O to N<sub>2</sub>; thus at low pH, N<sub>2</sub>O will likely dominate. However, highly acidic soils have low N availability and low nitrification and denitrification rates. Thus, the highest rate of nitrous oxide production from denitrification occurs in moist soils that cycle N rapidly.<ref name="Sylvia" /><br />
<br />
==Current Research==<br />
Current research topics on the issue of flooded soils are heavily focused on greenhouse gas emissions produced as a result of the low redox conditions characteristic of these ecosystems. Other research topics may address impacts to plant growth, and chemical, physical, and biological aspects of flooded soils. <br />
<br />
Many agricultural studies focus on rice paddies. Bacteria that oxidized acetate and reduced iron were identified and studied in flooded rice paddy soil through RNA probing.<ref>Hori, T., Müller, A., Igarashi, Y., Conrad, R., & Friedrich, M. W. (2009). Identification of iron-reducing microorganisms in anoxic rice paddy soil by 13C-acetate probing. The ISME Journal ISME J, 4(2), 267-278. from http://www.nature.com/ismej/journal/v4/n2/full/ismej2009100a.html </ref> Another study observed factors affecting delivery of nitrogen to plants by microbial populations in flooded soils and found that the addition of sludge to soil facilitated nitrogen formation more than the addition of straw compost.<ref>El-Sharkawi, H. M. (2012). Effect of Nitrogen Sources on Microbial Biomass Nitrogen under Different Soil Types. ISRN Soil Science, 2012, 1-7. from http://www.citationmachine.net/bibliographies/77289062?new=true </ref> The effect of oxygen concentration on rates of reactions involving nitrogen, including nitrification and mineralization, in paddy soils was also studied.<ref>Yang, Y., Zhang, J., & Cai, Z. (2015). Nitrification activities and N mineralization in paddy soils are insensitive to oxygen concentration. Acta Agriculturae Scandinavica, Section B — Soil & Plant Science, 66(3), 272-281. from http://www.tandfonline.com/doi/full/10.1080/09064710.2015.1093653 </ref><br />
<br />
A review article was published in 2012, focusing on soil-plant interactions, including redox reactions’ effects on plant function, in wetlands.<ref>Pezeshki, S. R., & Delaune, R. D. (2012). Soil Oxidation-Reduction in Wetlands and Its Impact on Plant Functioning. Biology, 1(3), 196-221. from http://www.mdpi.com/2079-7737/1/2/196 </ref><br />
<br />
[[Carbon cycle | Long-term retention of carbon in soil organic matter]] is an issue in frequently harvested soils. One study looked at various treatments of rice paddies and found that a combination of rice straw and inorganic fertilizer aided sequestration and led to “a higher grain yield”.<ref> Bhattacharyya, P., Roy, K., Neogi, S., Adhya, T., Rao, K., & Manna, M. (2012). Effects of rice straw and nitrogen fertilization on greenhouse gas emissions and carbon storage in tropical flooded soil planted with rice. Soil and Tillage Research, 124, 119-130. from http://www.sciencedirect.com/science/article/pii/S0167198712001195 </ref><br />
<br />
A recent study discussed the fate of metals such as cadmium, nickel, and aluminum in impacted creeks in Kenya, Tanzania, and Mozambique.<ref>Kamau, J. N., Kuschk, P., Machiwa, J., Macia, A., Mothes, S., Mwangi, S., . . . Kappelmeyer, U. (2015). Investigating the distribution and fate of Al, Cd, Cr, Cu, Mn, Ni, Pb and Zn in sewage-impacted mangrove-fringed creeks of Kenya, Tanzania and Mozambique. J Soils Sediments Journal of Soils and Sediments, 15(12), 2453-2465. Retrieved from http://link.springer.com/article/10.1007/s11368-015-1214-3 </ref><br />
<br />
Many other studies focus on the degradation of ground contaminants such as pesticides so that their results can be used in [[bioremediation]].<ref>Levén, L., Nyberg, K., & Schnürer, A. (2012). Conversion of phenols during anaerobic digestion of organic solid waste – A review of important microorganisms and impact of temperature. Journal of Environmental Management, 95. Retrieved from http://www.sciencedirect.com/science/article/pii/S0301479710003531 </ref> The fate of cycloxaprid, an agricultural insecticide, was observed in anaerobic conditions (including flooded soils). Radioisotopic tracing showed that various soil types had different effects on the chemical.<ref>Liu, X., Xu, X., Li, C., Zhang, H., Fu, Q., Shao, X., . . . Li, Z. (2016). Assessment of the environmental fate of cycloxaprid in flooded and anaerobic soils by radioisotopic tracing. Science of The Total Environment, 543, 116-122. Retrieved from http://www.sciencedirect.com/science/article/pii/S0048969715310007 </ref><br />
<br />
Lastly, there is always the topic of greenhouse gas emissions. Arctic, temperate, and tropical regions were recently studied for measurements of greenhouse gas emissions and its relation to temperature.<ref>Turetsky, M. R., Kotowska, A., Bubier, J., Dise, N. B., Crill, P., Hornibrook, E. R., . . . Wilmking, M. (2014). A synthesis of methane emissions from 71 northern, temperate, and subtropical wetlands. Glob Change Biol Global Change Biology, 20(7), 2183-2197. Retrieved from http://onlinelibrary.wiley.com/doi/10.1111/gcb.12580/pdf </ref> Another group of researchers found a correlation between anaerobic methane oxidation in freshwater wetlands and reduced methane emissions.<ref>Segarra, K. E., Schubotz, F., Samarkin, V., Yoshinaga, M. Y., Hinrichs, K., & Joye, S. B. (2015). High rates of anaerobic methane oxidation in freshwater wetlands reduce potential atmospheric methane emissions. Nature Communications Nat Comms, 6, 7477. Retrieved from http://www.nature.com/ncomms/2015/150630/ncomms8477/full/ncomms8477.html </ref><br />
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==References==<br />
<references /><br />
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Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]<br />
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<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Central_Metabolism_(Flooded_soils)&diff=132729
Central Metabolism (Flooded soils)
2018-02-09T07:22:40Z
<p>Kmscow: /* Mobility of Minerals and Gasses */</p>
<hr />
<div>{{Curated}}<br />
[[Image:FloodedSoil.png|600px|thumb|right|Comparison of water levels in three environments: unsaturated soil, saturated soil, and flooded soil. [http://www.floodsite.net/juniorfloodsite/html/en/student/thingstoknow/hydrology/waterstorage2.html Source]]] <br />
[[Image:Peatland.jpg|thumb|500px|right|A peatland, a type of flooded environment with a layer of organic matter, in Australia. Peatlands produce a high amount of methane emissions. [http://photography.nationalgeographic.com/photography/photo-of-the-day/peatland-australia-essick/ Source]]] <br />
<br />
Flooded soils are a condition in which an area of soil is oversaturated with water, often due to natural occurrence or with intended purpose for agricultural reasons. Perpetually flooded soils can be found in wetlands, swamps and marshes; temporary flooded soils can be an effect of season weather or agricultural practices. As water levels fluctuate, and soils alternate between flooded and unflooded states, the chemical makeup of the [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] will continuously change. A soil’s water content directly influences both inorganic and microbial reactions that affect the soil’s redox potential (E<sub>h</sub>), acidity, alkalinity, and salinity.<ref name="Campos">Dassonville, F., & Renault, P. (2002). Interactions between microbial processes and geochemical transformations under anaerobic conditions: A review. Agronomie, 22(1), 51-68. Retrieved from http://www.agronomy-journal.org/articles/agro/abs/2002/01/05/05.html. </ref><br />
<br />
One of the most important effects of flooded soils is that the presence of oxygen is limited in such an environment, and any remaining oxygen is quickly used up via aerobic respiration. As a result, other compounds are used as electron acceptors in energy acquisition reactions; the microorganisms that specialize in conducting these other reactions are able to flourish and affect nutrient cycling in the ecosystem. <br />
<br />
Microbial transformations of elements in anaerobic soils play a worldwide role in biogeochemical cycling of nutrients and in greenhouse gas emissions. Changes in the oxidation state of terminal electron acceptors may result in nutrient loss from the system via volatilization or leaching. Anaerobic microbial processes including denitrification, methanogenesis, and methanotrophy are responsible for releasing greenhouse gases (N<sub>2</sub>O, CH<sub>4</sub>, CO<sub>2</sub>) into the atmosphere. <ref>United States Environmental Protection Agency. (n.d.). Overview of Greenhouse Gases. Retrieved March 13, 2016, from http://www3.epa.gov/climatechange/ghgemissions/gases/ch4.html .</ref><br />
<br />
<br />
==Key Microbial Processes==<br />
<br />
===Microbial Respiration: [http://en.wikipedia.org/wiki/Redox Oxidation/Reduction Reactions]===<br />
[[Image:RedoxReaction.jpg|300px|thumb|left|General process of a paired reduction and oxidation. The transfer of electrons from molecule A to B is shown. [https://online.science.psu.edu/biol011_sandbox_7239/node/7381 Source]]] <br />
[[Image:Succession1.JPG|300px|thumb|right|Redox potentials of various couples. In soil, the order of succession begins with oxygen and generally ends with carbon dioxide. <ref>Schüring, J., Schulz, H. D., & Fischer, W. R. (Eds.). (2000). Redox: Fundamentals, processes, and applications. New York City, NY: Springer.</ref>]] <br />
<br />
In order to obtain energy, many microbes make use of the process of respiration through an oxidation-reduction (redox) reaction. Respiration is a catabolic reaction that produces ATP in which either organic or inorganic compounds act as primary electron donors, and exogenous compounds act as the terminal electron acceptors. In a redox reaction, one molecule (the reducing agent) loses electrons and another molecule (the oxidizing agent) accepts electrons. Electron donors such as glucose, methanol, and [https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH] are energy sources that can be thought of as “giving up” their electrons, while another molecule is in need to receive said electrons. For example, in aerobic respiration, energy rich compounds like glucose (the reducing agent) are oxidized to carbon dioxide, with oxygen (the oxidizing agent) acting as a terminal electron acceptor and being reduced to water. In addition to oxygen, microorganisms use a large variety of electron acceptors. <br />
<br />
Depending on the type of electron acceptors used by microorganisms, microbes can be placed into a variety of classifications. Strict aerobes can only use oxygen as a terminal electron acceptor. Obligate anaerobes cannot use oxygen and are actually inhibited or poisoned by oxygen. Facultative anaerobes are flexible in electron acceptor usage; as a result of this they can make use of other redox reactions to maintain a supply of energy as oxygen levels decrease.<br />
<br />
Oxygen gas (O<sub>2</sub>) is one of the most favorable electron acceptors, but it is typically not available in flooded soils. Instead, facultative and strict anaerobic microbes utilize other oxidizing agents (electron acceptors) to carry out respiration. The amount of energy that can be obtained through respiration varies between compounds and microbes and will make use of these compounds in order of the decreasing redox potential, thus leading to a succession of acceptors.<br />
<br />
====Redox Potential (E<sub>h</sub>)====<br />
Redox potential is the tendency for a reaction, specifically the movement and transfer of electrons, to occur spontaneously and is reported as E<sub>h</sub> in mV. These measurements have been experimentally determined through aqueous solutions containing electrodes, one being the cathode (electron donator) and one being the anode (electron receiver). <ref>Redox Chemistry Primer. (n.d.). Retrieved March 12, 2016, from http://www.kgs.ku.edu/Hydro/GWtutor/Plume_Busters/remediate_refs/redox_chemistry.htm .</ref><br />
<br />
This voltage shows how likely the electrons will be moved in a solution. Redox potential is assigned individually to half-reactions (a single instance of oxidation or reduction), e.g. the E<sub>h</sub> of the reduction of O<sub>2</sub> to H<sub>2</sub>O will be different from that of the opposite oxidation of H<sub>2</sub>O to O<sub>2</sub>. Redox potential is also reported as standard reduction potential E<sub>o</sub>. Reactions with a higher redox potential yield more net energy for the organism performing them, and this results in higher growth rates (in terms of population).<br />
<br />
===The Electron Tower===<br />
[[Image:RedoxTower.jpg|300px|thumb|right|A tower showing common redox pairs. The greater the "distance" between a donor and acceptor, the greater the energy released. From ''Brock Biology of Microorganisms''.]] <br />
Microbes will successively use the highest energy yielding electron acceptors available in the order indicated on the electron tower, which is a ranking of common redox reactions by the amount of energy that can be obtained from them. Compounds are listed in redox pairs (oxidized form and reduced form) The greater the difference in electrical potential between the reactants and products of a reaction, the greater the release of energy that is crucial for microbial growth. <ref>Madigan, M. T., Martinko, J. M., & Parker, J. (2003). Brock biology of microorganisms (10th ed.). Upper Saddle River, NJ: Prentice Hall/Pearson Education. </ref><br />
<br />
O<sub>2</sub>, the lowest oxidizing agent on the tower, yields the most energy when reduced in a redox reaction with a specific electron donor and will be the first electron acceptor depleted when commonly available. In flooded soils, the amount of oxygen in the system will be very small. When the soil’s microbial population exhausts its remaining O<sub>2</sub>, it will begin using other available electron acceptors which provide the next highest amount of energy. Competition generally limits the use of weaker electron acceptors; for example, iron reducers (using Fe<sup>3+</sup>) may exist in the soil but will be dominated by the presence of denitrifiers, who will growth faster with access to their stronger electron acceptor (NO<sub>3</sub><sup>-</sup>). Overall, this process of succession will continue as each electron acceptor supply is used.<br />
<br />
===Succession of Electron Acceptors=== <br />
The main succession of electron acceptor usage in flooded soils is as follows:<br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobes and aerobes)<br />
<br />
Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by denitrifiers) <br />
<br />
Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by manganese reducing bacteria)<br />
<br />
Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by iron reducing bacteria)<br />
<br />
Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
<br />
Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by methanogens)<br />
<br />
====[[Nitrogen Cycle|Nitrate Reduction]]====<br />
After O<sub>2</sub>, nitrate (NO<sub>3</sub><sup>-</sup>) is one of the strongest electron acceptors as is represented in the electron tower. It can be obtained from transformations of other compounds containing nitrogen, such as ammonium (NH<sub>4</sub><sup>+</sup>) and nitrite (NO<sub>2</sub><sup>-</sup>). Denitrification reduces NO<sub>3</sub><sup>-</sup> to nitrogen gas (N<sub>2</sub>) or various nitrogen oxides and is performed by facultative anaerobic microorganisms. Oxygen depletion is important for the nitrogen cycle as a whole, since if it were constantly present NO<sub>3</sub><sup>-</sup> would be used at a much slower rate and contaminate soils through accumulation. <ref name="Sylvia">Silvia, D.M., et al. 2005. Principles and Applications of Soil Microbiology. 2nd ed. Pearson Prentice Hall, New Jersey. </ref><br />
<br />
====Manganese Reduction====<br />
The next most energy-releasing electron acceptor after NO<sub>3</sub><sup>-</sup> is manganese (IV) oxide (MnO<sub>2</sub>) which is is reduced to Mn<sup>2+</sup> ions. In this form, manganese is very insoluble in water and forms masses in soils. Mn<sup>2+</sup> is generally oxidized to this form in soils with a pH between 5 and 8, (as the rate increases with basicity). Many microorganisms that conduct this process are also capable of iron reduction, described below. <ref name="Sylvia" /> <br />
<br />
====Iron Reduction====<br />
[[Image:pipe.jpg|100px|thumb|left|Corroded water main. [http://coloradogeologicalsurvey.org/geologic-hazards/corrosive-soils/corrosive-soil-damage/ Source] ]] <br />
The utilization of ferric iron ions (Fe<sup>3+</sup>), at approximately 120 mV, occurs when ions are released from metal deposits or minerals in the soil. Ferrous iron (Fe<sup>2+</sup>) product causes soil gleying, (a process described in a later section) when it accumulates. The source of the iron is also of relevance; whereas iron reduction in phosphate minerals can release phosphate for other organisms, it can also lead to corrosion of steel where iron reducers are present. Some ''Pseudomonas'' species can release pseudobactin, an iron-binding compound that limits its availability to other bacteria. <ref name="Sylvia" /><br />
<br />
====Sulfate Reduction====<br />
Sulfate reduction begins occurring at 0 mV, and the dissimilatory reduction results in hydrogen sulfide (H<sub>2</sub>S) being released. However, H<sub>2</sub>S is prone to reaction with Fe<sup>2+</sub> to form iron sulfide (FeS). As a result, it often reacts before it reaches the surface of the soil, unable to disperse into the air. <ref name="Sylvia" /> Sulfate reduction has several documented consequences, ranging from corrosion of underground iron pipes due to FeS formation and blackening of soil caused by liberation of organic matter. Hydrogen sulfide is known as “swamp gas”, due to its emergence from one form of soil flooding, and has an odor comparable to rotting eggs. It can accumulate in many bodies of water and the air above them; due to its flammability and toxicity, this is very dangerous. <ref>Occupational Safety & Health Administration. (n.d.). Safety and Health Topics | Hydrogen Sulfide. Retrieved February 23, 2016, from https://www.osha.gov/SLTC/hydrogensulfide/index.html .</ref><br />
<br />
====Methanogenesis (by Carbon Dioxide Reduction)====<br />
The process of using carbon dioxide (CO<sub>2</sub>) as a terminal electron acceptor results in the formation of methane (CH<sub>4</sub>) and is known as methanogenesis. In soil, methanogenesis occurs almost exclusively in a flooded condition due to its reduction potential being so low (below 100 mV). The use of CO<sub>2</sub> in this fashion yields much less energy than the reactions of previous electron acceptors, so this process has lower growth rates in turn. Organisms who perform methanogenesis are known as [[methanogens]] and are a group of anaerobic Archaea. CH<sub>4</sub> can also be produced as a result of acetate (CH<sub>3</sub>COOH) fermentation, which is also performed by methanogens. <ref name="Sylvia" /><br />
<br />
===Fermentation in Flooded Soils (Non-Respiratory)===<br />
Fermentation is a different form of metabolism from respiration that occurs in the absence of a suitable terminal electron acceptor. Cells convert NADH and pyruvate from the glycolysis of sugars into NAD+ and other compounds, depending on the species that is fermenting. The various products of fermentation, including alcohols, lactic acid, and acetate are released into the surrounding soil and then become available for use by other anaerobic organisms. Additionally, fermentation generally reduces soil pH, which will encourage dissolution of minerals and their subsequent access by bacteria. <ref name="Richardson">Richardson, J. L., & Vepraskas, M. J. (2001). Wetland soils: Genesis, hydrology, landscapes, and classification. Boca Raton, FL: Lewis. </ref><br />
<br />
==Microorganisms Involved==<br />
As available oxygen declines, organisms that thrive under anoxic conditions proliferate using alternative electron acceptors. The order in which available electron acceptors are consumed can generally be predicted by the electron tower and associated energy yields of electron pairs. Changes in redox conditions of flooded soils over time reflects the successive availability of terminal electron acceptors from the electron tower, and will govern which microbes will thrive through being able to use them.<br />
<br />
Some microbes below are able to oxidize the reduced form of their corresponding substance.<ref>Liesack, W. (2000). Microbiology of flooded rice paddies. FEMS Microbiology Reviews, 24(5), 625-645. </ref><br />
[[Image:Processes.jpg|500px|thumb|right|Summary of reducing conditions in flooded soils. [http://www.des.ucdavis.edu/faculty/rejmankova/ESP155_Soils-2004.pdf Source]]]<br />
<br />
<br />
{| width="800" border="1"<br />
|----- bgcolor ="grey"<br />
| width="200" height="25" | '''Process'''<br />
| width="1000" | '''Example Genera of Common Bacteria Involved'''<br />
|-<br />
| Aerobic Respiration<br />
| Aerobes and facultative anaerobes such as ''Staphylococcus'', ''[https://en.wikipedia.org/wiki/Nocardia Nocardia]'', ''[[Pseudomonas]]''<br />
|-<br />
| Denitrification<br />
| Facultative anaerobes such as ''[[Agrobacterium]]'', ''[[Alcaligenes]]'', ''[[Bacillus]]'', ''Paracoccus'', ''Micrococcus''<br />
|-<br />
| Manganese Reduction<br />
| ''[[Bacillus]]'', ''[[Geobacter]]'', ''[[Pseudomonas]]'', ''Shewanella''<br />
|-<br />
| Iron Reduction<br />
| ''[[Desulfovibrio]]'', ''[[Pseudomonas]]'', ''Geothrix'', ''Shewanella'', ''Thiobacillus''<br />
|-<br />
| Sulfate Reduction<br />
| Generally obligate anaerobes such as ''[[Desulfobacter]]'', ''[[Desulfococcus]]'', ''[[Desulfosarcina]]'', ''Desulfosporosinus''<br />
|-<br />
| Methanogenesis<br />
| [[Methanogens]] such as ''Methanobacterium'' and [https://en.wikipedia.org/wiki/Archaea Archaea] (different from bacteria)<br />
|}<br />
[[Image:PseudomonasImage.jpg|300px|thumb|left|The ''Pseudomonas'' genus has a wide variety of metabolic capabilities among its species. [https://elmundodelavida.wordpress.com/category/ciencia/ Source]]]<br />
[[Image:Probes.gif|400px|thumb|center|[https://en.wikipedia.org/wiki/Hybridization_probe DNA and RNA probes] are used for identifying bacteria in samples. [http://tle.westone.wa.gov.au/content/file/969144ed-0d3b-fa04-2e88-8b23de2a630c/1/human_bio_science_3b.zip/content/005_dna/page_17.htm Source]]]<br />
<br />
==Effects of Flooding on Soil Environment==<br />
<br />
===Mobility of Minerals and Gasses===<br />
[[Image:Aggregation.jpg|200px|thumb|right|A) unaffected soil and B) soil incubated anaerobically. Flooding caused mobilization of organic matter and disaggregation, resulting in the larger grains (decreased stability). [https://dl.sciencesocieties.org/publications/sssaj/abstracts/73/2/550 Source]]]<br />
Water also acts as a solvent for ions and soluble compounds, thus increasing the mobility and availability of metal ions, nutrients, and minerals. As a result of these physical effects in flooded soils, microbial respiration will have improved access to water-soluble compounds such as nitrate, perchlorate, manganese/ferric iron, sulfate, and carbon dioxide to act as electron acceptors. <br />
<br />
The diffusion of oxygen is over 10000 times slower in water than it is in air at standard temperature and pressure, resulting in the replenishing rate being much slower in flooded soils. Carbon dioxide is also decreased but to a lesser degree due to it being far more soluble than oxygen. <ref>Greenway H, William A, Timothy DC. (2006). Conditions leading to high CO2 (>5 kPa) in waterlogged-flooded soils and possible effects on root growth and metabolism. Annals of Botany, 98, 9–32. Retrieved March 10, 2016 from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3291891/ .</ref><br />
<br />
===Flooded Soil Aggregate Structure===<br />
Though some degree of moisture is important for aggregate formation and microbial activity, flooded soils exhibit decreased aggregate stability. Oxygen depletion and subsequent use of various elements for redox contributes to this decreased aggregation. Organic carbon is also made more soluble (like metals and minerals) under reducing conditions. The decreased stability of the soil is unlikely to recover due to drainage or volatilization of chemicals, removing them from the local environment. Since areas such as marshlands and rice fields are perpetually flooded, their soil’s aggregate stability rarely improves. <ref>De-Campos, A. B., Mamedov, A. I., & Huang, C. (2009). Short-Term Reducing Conditions Decrease Soil Aggregation. Soil Science Society of America Journal, 73(2), 550. Retrieved February 23, 2016, from https://dl.sciencesocieties.org/publications/sssaj/abstracts/73/2/550 .</ref><br />
<br />
===Soil Gradients===<br />
[[Image:Column.jpg|200px|thumb|left|A Winogradsky column. [http://beautyinscience.com/Biology.html Source] ]] <br />
The progression of electron acceptor utilization occurs at different rates in different layers of soil. A process like methanogenesis will occur earlier several feet underground than at the surface due to decreased access to other compounds. This will result in gradients at various depths of soil. These gradients will differ by pH, color, chemical prevalence, and microbial population. <br />
<br />
Since the soil is a more closed system (with less mobility of chemicals) than the surface, air, or bodies of water, gradients can be observed with a similar closed system: a Winogradsky column. This column, consisting of a sealed column of soil with provided organic material (such as an egg), allows for simulation of an anaerobic soil environment. <ref>Scientific American. (2013, September 19). Soil Science: Make a Winogradsky Column. Retrieved from http://www.scientificamerican.com/article/bring-science-home-soil-column/ </ref><br />
<br />
===Variation of pH===<br />
pH has a major influence over the dissolution and sorption of several important toxins and nutrients in the soil. Low pH values increase the solubility of free aluminum (Al<sup>3+</sup>) and iron (Fe<sup>3+</sup> and Fe<sup>2+</sup>) ions which can be toxic in high concentrations, while also reducing the availability of phosphorus.<br />
<br />
When soil is initially saturated with water, the pH drops due to the accumulation of carbonic acid formed from trapped carbon dioxide produced from respiration. Fermentation also contributes to pH decreasing through the production of organic acids. This is quickly followed by an increase of pH as hydrogen cations are consumed in microbially-driven redox reactions. The soil then will gradually approach and stabilize near a neutral pH, with pH increasing in acidic soil and decreasing in basic soil due to products such as carbonate forming a buffer. <ref>Kirk, G. J. (2004). The biogeochemistry of submerged soils. Chichester: Wiley. </ref><br />
<br />
===Soil Gleying===<br />
[[Image:gleyed.jpg|200px|thumb|right|Gray colors produced in gleyed soil. [http://wetland-delineation.rutgers.edu/87-wetland-delineation-manual/wetland-delineation-manual-part3.html Source] ]] <br />
<br />
Gleying is a phenomenon in which waterlogged soils are discolored by accumulation of iron oxide (FeO) due to reduction of ferric iron into ferrous iron. Although ferric iron exists as an insoluble form in flooded soils, more ferrous iron can accumulate by the reduction of ferric iron over time. This results in a greenish, blue, grey soil color. In general Fe<sup>3+</sup> -reducing fermentative bacteria can be readily isolated from gleyed soils. The black color of soils/solution is frequently observed in flooded soil. This may result from the formation of iron sulfides (FeS) and pyrite (FeS2). <ref>Wenk, H., & Bulakh, A. G. (2004). Minerals: Their constitution and origin. Cambridge: Cambridge University Press. </ref><br />
<br />
===Plant Nutrient Availability===<br />
Flooded soils can have a direct impact on plants by preventing efficient gas exchange between the plant roots and the soil. These conditions also change the types of microbes that are active and what they produce. Flooded soils cause anaerobic conditions which forces many microbes to use less favorable electron acceptors. These less favorable acceptors could have also served as nutrition for the plants; this creates competition between the plants and the microbes in certain flooded soils. By using different electron acceptors the microbes will release different products causing a chemical change in the soil that can be toxic. <ref>Minamikawa, K., & Sakai, N. (2005). The effect of water management based on soil redox potential on methane emission from two kinds of paddy soils in Japan. Agriculture, Ecosystems & Environment, 107(4), 397-407. Retrieved from http://www.sciencedirect.com/science/article/pii/S0167880904002208 .</ref><br />
<br />
===Flooded to Unflooded Conditions===<br />
When waterlogged soils drain, oxygen diffuses into soil pores. The soil’s Eh increases and aerobic activity kicks in ceasing the production of anaerobic products. At higher Eh zones ( > 500 mV), undecomposed soil organic matter is used as an electron donor by aerobes and converted to water and CO2. Many of the anaerobic redox reactions are also reversed as with oxygen available as an electron acceptor many of the reduced products of anaerobic respiration can now be used as electron donors by lithotrophs. Manganese is oxidized back to MnO2 which gives some aerated soils a black color, and ferrous iron is oxidized by an iron-oxidizing bacteria, resulting in the formation of ferric oxides or ferric hydroxide minerals that give the soil a red, yellow, or brownish texture. <ref name="Richardson" /><br />
<br />
<br />
==Environmental Issues==<br />
<br />
Flooded soils are dynamic ecosystems that play an important role in biogeochemical cycling and in the production of greenhouse gases. Methane (CH<sub>4</sub><sup>+</sup>) and nitrous oxide (N<sub>2</sub>O) are produced as byproducts of anaerobic metabolism in the low-redox zones characteristic of flooded soils, where oxygen is lacking. Carbon dioxide (CO<sub>2</sub>), which receives widespread attention as a greenhouse gas and potential source of global warming, may also be produced at the interface of anaerobic-aerobic zones through the consumption of methane gas. However, it should be noted that from a global standpoint methane and nitrous oxide on a per molecule basis have the potential to contribute 25x and 300x more to global warming over the next century than carbon dioxide, respectively. Thus the conversion of methane gas to carbon dioxide essentially reduces the greenhouse gas effect by 25x per molecule per 100 years. Although the number areas classified as wetlands has decreased in past years, the effect of flooded soils to the global climate is clear.<ref>Schlesinger, W. H., & Bernhardt, E. S. (2013). Biogeochemistry: An analysis of global change (3rd ed.). San Diego, CA: Academic Press. </ref><br />
<br />
===Methane Production; Methanogenesis===<br />
[[Image:Methane.jpg|thumb|300px|A natural source of methane gas]]<br />
Methane production occurs exclusively in anaerobic conditions by a group of Archaea known as methanogens. These microbes are obligatory, and require extremely low redox conditions in the range of -100mV. If oxygen is introduced into the system, methanogenesis ceases; thus, the process of methanogenesis depends on saturated soil conditions.<ref name="Sylvia" /> <br />
<br />
Methanogenesis can occur via one of two pathways: either by 1) CO<sub>2</sub> reduction or by 2) acetate fermentation.<br />
<br />
1) CO<sub>2</sub> + H<sub>2</sub> --> CH<sub>4</sub><sup>+</sup> (CO<sub>2</sub> reduction)<br />
<br />
and <br />
<br />
2) CH<sub>3</sub>COOH --> CH<sub>4</sub><sup>+</sup> + CO<sub>2</sub> (acetate fermentation)<br />
<br />
Both acetate and hydrogen are byproducts of anaerobic fermentation. <br />
<br />
Because the process of methanogenesis is “fed” byproducts produced from a complex series of degradation processes which are themselves “fed” complex organic matter, rates of methane production are highly sensitive to changes in temperature. Methanogenesis has a Q10 value in the range of 30-40, which is substantially higher than most biochemical process.<br />
<br />
Despite the clear effect of increasing temperatures on the rate of methanogenesis, the actual impact of global warming on methane production rates in wetlands and permafrost regions is highly unpredictable. Because methanogenesis requires anoxic conditions, any drying of flooded soil environments would both decrease methane production and increase methane oxidation, reducing overall methane emissions. Alternatively, warmer climates could increase growing seasons, which would increase methane emissions.<ref name="Sylvia" /><br />
<br />
===CO<sub>2</sub> Production via Methane Consumption: Methanotrophy===<br />
Some of the methane produced via methanogenesis in flooded soils may be consumed and oxidized to CO<sub>2</sub> at the interface of the anaerobic-aerobic zones. This process occurs primarily by a group of bacteria known as methanotrophs. These microbes can be found in surface layers of wetland soils and unsaturated upland soils, and may be exposed to very high concentrations of methane gas, sometimes amounting to 10% or more of the dissolved gases. Methane is thought to be the only source of C and energy for these bacteria.<br />
<br />
Methanotrophy occurs in the following reaction:<br />
<br />
CH<sub>4</sub><sup>+</sup> + 2O<sub>2</sub> --> CO<sub>2</sub> + 2H<sub>2</sub>O<br />
<br />
Methane is similar in size and shape to ammonium; and there is some evidence that nitrifiers (ammonium oxidizers) can also oxidize methane. Because they are molecularly similar, NH<sup>4</sup><sup>+</sup> competes at the enzyme’s active site, inhibiting methane oxidation. As a result, methanotrophy is generally inhibited by the addition of fertilizer or excess nitrogen in the system, when ammonium levels are high. <br />
<br />
Alternatively, if nitrogen is extremely limiting the addition of nitrogen will stimulate methanotrophy and actually increase methane consumption. So although it is generally expected that adding N-fertilizer will decrease CH<sub>4</sub><sup>+</sup> consumption and lead to increased global warming potential, sometime the opposite effect may occur.<ref name="Sylvia" /><br />
<br />
===Nitrous Oxide; Denitrification===<br />
Denitrification is an anaerobic process in which nitrate serves as the terminal electron acceptor, and generally some source of organic carbon is the electron donor (also H<sub>2</sub> may serve as a donor). <br />
<br />
In this process, nitrate is oxidized to nitric oxide, then nitrous oxide, and then fully oxidized to dinitrogen:<br />
<br />
NO<sub>2</sub><sup>-</sup> --> NO --> N<sub>2</sub>O --> N<sub>2</sub><br />
<br />
However, under certain conditions the full oxidation of NO<sub>3</sub><sup>-</sup> to N<sub>2</sub> does not occur and nitrous oxide (N<sub>2</sub>O) is produced.<br />
<br />
Microbes responsible include both organotrophs and lithotrophs, and this process occurs primarily by facultative anaerobes. <br />
<br />
Although a low redox potential is important for denitrification to occur (oxygen must not be present or it will “out-compete” nitrate as a terminal electron acceptor), redox requirements are not so low that this process cannot occur within anaerobic microsites of soil aggregates. <br />
<br />
Factors affecting nitrous oxide production include oxygen, pH, and the ratio of nitrate to available C. Although denitrification rates decrease with increasing oxygen, the proportion of N evolved as nitrous oxide actually increases with increasing oxygen. Low pH generally inhibits the reduction of N<sub>2</sub>O to N<sub>2</sub>; thus at low pH, N<sub>2</sub>O will likely dominate. However, highly acidic soils have low N availability and low nitrification and denitrification rates. Thus, the highest rate of nitrous oxide production from denitrification occurs in moist soils that cycle N rapidly.<ref name="Sylvia" /><br />
<br />
==Current Research==<br />
Current research topics on the issue of flooded soils are heavily focused on greenhouse gas emissions produced as a result of the low redox conditions characteristic of these ecosystems. Other research topics may address impacts to plant growth, and chemical, physical, and biological aspects of flooded soils. <br />
<br />
Many agricultural studies focus on rice paddies. Bacteria that oxidized acetate and reduced iron were identified and studied in flooded rice paddy soil through RNA probing.<ref>Hori, T., Müller, A., Igarashi, Y., Conrad, R., & Friedrich, M. W. (2009). Identification of iron-reducing microorganisms in anoxic rice paddy soil by 13C-acetate probing. The ISME Journal ISME J, 4(2), 267-278. from http://www.nature.com/ismej/journal/v4/n2/full/ismej2009100a.html </ref> Another study observed factors affecting delivery of nitrogen to plants by microbial populations in flooded soils and found that the addition of sludge to soil facilitated nitrogen formation more than the addition of straw compost.<ref>El-Sharkawi, H. M. (2012). Effect of Nitrogen Sources on Microbial Biomass Nitrogen under Different Soil Types. ISRN Soil Science, 2012, 1-7. from http://www.citationmachine.net/bibliographies/77289062?new=true </ref> The effect of oxygen concentration on rates of reactions involving nitrogen, including nitrification and mineralization, in paddy soils was also studied.<ref>Yang, Y., Zhang, J., & Cai, Z. (2015). Nitrification activities and N mineralization in paddy soils are insensitive to oxygen concentration. Acta Agriculturae Scandinavica, Section B — Soil & Plant Science, 66(3), 272-281. from http://www.tandfonline.com/doi/full/10.1080/09064710.2015.1093653 </ref><br />
<br />
A review article was published in 2012, focusing on soil-plant interactions, including redox reactions’ effects on plant function, in wetlands.<ref>Pezeshki, S. R., & Delaune, R. D. (2012). Soil Oxidation-Reduction in Wetlands and Its Impact on Plant Functioning. Biology, 1(3), 196-221. from http://www.mdpi.com/2079-7737/1/2/196 </ref><br />
<br />
[[Carbon cycle | Long-term retention of carbon in soil organic matter]] is an issue in frequently harvested soils. One study looked at various treatments of rice paddies and found that a combination of rice straw and inorganic fertilizer aided sequestration and led to “a higher grain yield”.<ref> Bhattacharyya, P., Roy, K., Neogi, S., Adhya, T., Rao, K., & Manna, M. (2012). Effects of rice straw and nitrogen fertilization on greenhouse gas emissions and carbon storage in tropical flooded soil planted with rice. Soil and Tillage Research, 124, 119-130. from http://www.sciencedirect.com/science/article/pii/S0167198712001195 </ref><br />
<br />
A recent study discussed the fate of metals such as cadmium, nickel, and aluminum in impacted creeks in Kenya, Tanzania, and Mozambique.<ref>Kamau, J. N., Kuschk, P., Machiwa, J., Macia, A., Mothes, S., Mwangi, S., . . . Kappelmeyer, U. (2015). Investigating the distribution and fate of Al, Cd, Cr, Cu, Mn, Ni, Pb and Zn in sewage-impacted mangrove-fringed creeks of Kenya, Tanzania and Mozambique. J Soils Sediments Journal of Soils and Sediments, 15(12), 2453-2465. Retrieved from http://link.springer.com/article/10.1007/s11368-015-1214-3 </ref><br />
<br />
Many other studies focus on the degradation of ground contaminants such as pesticides so that their results can be used in [[bioremediation]].<ref>Levén, L., Nyberg, K., & Schnürer, A. (2012). Conversion of phenols during anaerobic digestion of organic solid waste – A review of important microorganisms and impact of temperature. Journal of Environmental Management, 95. Retrieved from http://www.sciencedirect.com/science/article/pii/S0301479710003531 </ref> The fate of cycloxaprid, an agricultural insecticide, was observed in anaerobic conditions (including flooded soils). Radioisotopic tracing showed that various soil types had different effects on the chemical.<ref>Liu, X., Xu, X., Li, C., Zhang, H., Fu, Q., Shao, X., . . . Li, Z. (2016). Assessment of the environmental fate of cycloxaprid in flooded and anaerobic soils by radioisotopic tracing. Science of The Total Environment, 543, 116-122. Retrieved from http://www.sciencedirect.com/science/article/pii/S0048969715310007 </ref><br />
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Lastly, there is always the topic of greenhouse gas emissions. Arctic, temperate, and tropical regions were recently studied for measurements of greenhouse gas emissions and its relation to temperature.<ref>Turetsky, M. R., Kotowska, A., Bubier, J., Dise, N. B., Crill, P., Hornibrook, E. R., . . . Wilmking, M. (2014). A synthesis of methane emissions from 71 northern, temperate, and subtropical wetlands. Glob Change Biol Global Change Biology, 20(7), 2183-2197. Retrieved from http://onlinelibrary.wiley.com/doi/10.1111/gcb.12580/pdf </ref> Another group of researchers found a correlation between anaerobic methane oxidation in freshwater wetlands and reduced methane emissions.<ref>Segarra, K. E., Schubotz, F., Samarkin, V., Yoshinaga, M. Y., Hinrichs, K., & Joye, S. B. (2015). High rates of anaerobic methane oxidation in freshwater wetlands reduce potential atmospheric methane emissions. Nature Communications Nat Comms, 6, 7477. Retrieved from http://www.nature.com/ncomms/2015/150630/ncomms8477/full/ncomms8477.html </ref><br />
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==References==<br />
<references /><br />
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Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]<br />
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<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Central_Metabolism_(Flooded_soils)&diff=132728
Central Metabolism (Flooded soils)
2018-02-09T07:21:39Z
<p>Kmscow: /* Microorganisms Involved */</p>
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<div>{{Curated}}<br />
[[Image:FloodedSoil.png|600px|thumb|right|Comparison of water levels in three environments: unsaturated soil, saturated soil, and flooded soil. [http://www.floodsite.net/juniorfloodsite/html/en/student/thingstoknow/hydrology/waterstorage2.html Source]]] <br />
[[Image:Peatland.jpg|thumb|500px|right|A peatland, a type of flooded environment with a layer of organic matter, in Australia. Peatlands produce a high amount of methane emissions. [http://photography.nationalgeographic.com/photography/photo-of-the-day/peatland-australia-essick/ Source]]] <br />
<br />
Flooded soils are a condition in which an area of soil is oversaturated with water, often due to natural occurrence or with intended purpose for agricultural reasons. Perpetually flooded soils can be found in wetlands, swamps and marshes; temporary flooded soils can be an effect of season weather or agricultural practices. As water levels fluctuate, and soils alternate between flooded and unflooded states, the chemical makeup of the [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] will continuously change. A soil’s water content directly influences both inorganic and microbial reactions that affect the soil’s redox potential (E<sub>h</sub>), acidity, alkalinity, and salinity.<ref name="Campos">Dassonville, F., & Renault, P. (2002). Interactions between microbial processes and geochemical transformations under anaerobic conditions: A review. Agronomie, 22(1), 51-68. Retrieved from http://www.agronomy-journal.org/articles/agro/abs/2002/01/05/05.html. </ref><br />
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One of the most important effects of flooded soils is that the presence of oxygen is limited in such an environment, and any remaining oxygen is quickly used up via aerobic respiration. As a result, other compounds are used as electron acceptors in energy acquisition reactions; the microorganisms that specialize in conducting these other reactions are able to flourish and affect nutrient cycling in the ecosystem. <br />
<br />
Microbial transformations of elements in anaerobic soils play a worldwide role in biogeochemical cycling of nutrients and in greenhouse gas emissions. Changes in the oxidation state of terminal electron acceptors may result in nutrient loss from the system via volatilization or leaching. Anaerobic microbial processes including denitrification, methanogenesis, and methanotrophy are responsible for releasing greenhouse gases (N<sub>2</sub>O, CH<sub>4</sub>, CO<sub>2</sub>) into the atmosphere. <ref>United States Environmental Protection Agency. (n.d.). Overview of Greenhouse Gases. Retrieved March 13, 2016, from http://www3.epa.gov/climatechange/ghgemissions/gases/ch4.html .</ref><br />
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<br />
==Key Microbial Processes==<br />
<br />
===Microbial Respiration: [http://en.wikipedia.org/wiki/Redox Oxidation/Reduction Reactions]===<br />
[[Image:RedoxReaction.jpg|300px|thumb|left|General process of a paired reduction and oxidation. The transfer of electrons from molecule A to B is shown. [https://online.science.psu.edu/biol011_sandbox_7239/node/7381 Source]]] <br />
[[Image:Succession1.JPG|300px|thumb|right|Redox potentials of various couples. In soil, the order of succession begins with oxygen and generally ends with carbon dioxide. <ref>Schüring, J., Schulz, H. D., & Fischer, W. R. (Eds.). (2000). Redox: Fundamentals, processes, and applications. New York City, NY: Springer.</ref>]] <br />
<br />
In order to obtain energy, many microbes make use of the process of respiration through an oxidation-reduction (redox) reaction. Respiration is a catabolic reaction that produces ATP in which either organic or inorganic compounds act as primary electron donors, and exogenous compounds act as the terminal electron acceptors. In a redox reaction, one molecule (the reducing agent) loses electrons and another molecule (the oxidizing agent) accepts electrons. Electron donors such as glucose, methanol, and [https://en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide NADH] are energy sources that can be thought of as “giving up” their electrons, while another molecule is in need to receive said electrons. For example, in aerobic respiration, energy rich compounds like glucose (the reducing agent) are oxidized to carbon dioxide, with oxygen (the oxidizing agent) acting as a terminal electron acceptor and being reduced to water. In addition to oxygen, microorganisms use a large variety of electron acceptors. <br />
<br />
Depending on the type of electron acceptors used by microorganisms, microbes can be placed into a variety of classifications. Strict aerobes can only use oxygen as a terminal electron acceptor. Obligate anaerobes cannot use oxygen and are actually inhibited or poisoned by oxygen. Facultative anaerobes are flexible in electron acceptor usage; as a result of this they can make use of other redox reactions to maintain a supply of energy as oxygen levels decrease.<br />
<br />
Oxygen gas (O<sub>2</sub>) is one of the most favorable electron acceptors, but it is typically not available in flooded soils. Instead, facultative and strict anaerobic microbes utilize other oxidizing agents (electron acceptors) to carry out respiration. The amount of energy that can be obtained through respiration varies between compounds and microbes and will make use of these compounds in order of the decreasing redox potential, thus leading to a succession of acceptors.<br />
<br />
====Redox Potential (E<sub>h</sub>)====<br />
Redox potential is the tendency for a reaction, specifically the movement and transfer of electrons, to occur spontaneously and is reported as E<sub>h</sub> in mV. These measurements have been experimentally determined through aqueous solutions containing electrodes, one being the cathode (electron donator) and one being the anode (electron receiver). <ref>Redox Chemistry Primer. (n.d.). Retrieved March 12, 2016, from http://www.kgs.ku.edu/Hydro/GWtutor/Plume_Busters/remediate_refs/redox_chemistry.htm .</ref><br />
<br />
This voltage shows how likely the electrons will be moved in a solution. Redox potential is assigned individually to half-reactions (a single instance of oxidation or reduction), e.g. the E<sub>h</sub> of the reduction of O<sub>2</sub> to H<sub>2</sub>O will be different from that of the opposite oxidation of H<sub>2</sub>O to O<sub>2</sub>. Redox potential is also reported as standard reduction potential E<sub>o</sub>. Reactions with a higher redox potential yield more net energy for the organism performing them, and this results in higher growth rates (in terms of population).<br />
<br />
===The Electron Tower===<br />
[[Image:RedoxTower.jpg|300px|thumb|right|A tower showing common redox pairs. The greater the "distance" between a donor and acceptor, the greater the energy released. From ''Brock Biology of Microorganisms''.]] <br />
Microbes will successively use the highest energy yielding electron acceptors available in the order indicated on the electron tower, which is a ranking of common redox reactions by the amount of energy that can be obtained from them. Compounds are listed in redox pairs (oxidized form and reduced form) The greater the difference in electrical potential between the reactants and products of a reaction, the greater the release of energy that is crucial for microbial growth. <ref>Madigan, M. T., Martinko, J. M., & Parker, J. (2003). Brock biology of microorganisms (10th ed.). Upper Saddle River, NJ: Prentice Hall/Pearson Education. </ref><br />
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O<sub>2</sub>, the lowest oxidizing agent on the tower, yields the most energy when reduced in a redox reaction with a specific electron donor and will be the first electron acceptor depleted when commonly available. In flooded soils, the amount of oxygen in the system will be very small. When the soil’s microbial population exhausts its remaining O<sub>2</sub>, it will begin using other available electron acceptors which provide the next highest amount of energy. Competition generally limits the use of weaker electron acceptors; for example, iron reducers (using Fe<sup>3+</sup>) may exist in the soil but will be dominated by the presence of denitrifiers, who will growth faster with access to their stronger electron acceptor (NO<sub>3</sub><sup>-</sup>). Overall, this process of succession will continue as each electron acceptor supply is used.<br />
<br />
===Succession of Electron Acceptors=== <br />
The main succession of electron acceptor usage in flooded soils is as follows:<br />
<br />
Aerobic respiration: ½ O<sub>2</sub> + 2e<sup>-</sup> + 2H<sup>+</sup> -> H<sub>2</sub>O (by facultative anaerobes and aerobes)<br />
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Denitrification: 2NO<sub>3</sub><sup>-</sup> + 12 H<sup>+</sup> +10e<sup>-</sup> -> N<sub>2</sub>+6H<sub>2</sub>O (by denitrifiers) <br />
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Manganese reduction: MnO<sub>2</sub> + 4H<sup>+</sup> + 2e<sup>-</sup> ->Mn<sup>2+</sup> + 2H<sub>2</sub>O (by manganese reducing bacteria)<br />
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Iron reduction: Fe(OH)<sub>3</sub> + 3 H<sup>+</sup> + 2e<sup>-</sup> -> Fe<sup>2+</sup> + 2H<sub>2</sub>O (by iron reducing bacteria)<br />
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Sulfate reduction: SO<sub>4</sub><sup>2-</sup> + 10H<sup>+</sup> +8e<sup>-</sup> -> H<sub>2</sub>S + 4H<sub>2</sub>O (by sulfate reducing bacteria)<br />
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Methane production: CO<sub>2</sub> + 8 H<sup>+</sup> + 8e<sup>-</sup> -> CH<sub>4</sub> +2 H<sub>2</sub>O (by methanogens)<br />
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====[[Nitrogen Cycle|Nitrate Reduction]]====<br />
After O<sub>2</sub>, nitrate (NO<sub>3</sub><sup>-</sup>) is one of the strongest electron acceptors as is represented in the electron tower. It can be obtained from transformations of other compounds containing nitrogen, such as ammonium (NH<sub>4</sub><sup>+</sup>) and nitrite (NO<sub>2</sub><sup>-</sup>). Denitrification reduces NO<sub>3</sub><sup>-</sup> to nitrogen gas (N<sub>2</sub>) or various nitrogen oxides and is performed by facultative anaerobic microorganisms. Oxygen depletion is important for the nitrogen cycle as a whole, since if it were constantly present NO<sub>3</sub><sup>-</sup> would be used at a much slower rate and contaminate soils through accumulation. <ref name="Sylvia">Silvia, D.M., et al. 2005. Principles and Applications of Soil Microbiology. 2nd ed. Pearson Prentice Hall, New Jersey. </ref><br />
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====Manganese Reduction====<br />
The next most energy-releasing electron acceptor after NO<sub>3</sub><sup>-</sup> is manganese (IV) oxide (MnO<sub>2</sub>) which is is reduced to Mn<sup>2+</sup> ions. In this form, manganese is very insoluble in water and forms masses in soils. Mn<sup>2+</sup> is generally oxidized to this form in soils with a pH between 5 and 8, (as the rate increases with basicity). Many microorganisms that conduct this process are also capable of iron reduction, described below. <ref name="Sylvia" /> <br />
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====Iron Reduction====<br />
[[Image:pipe.jpg|100px|thumb|left|Corroded water main. [http://coloradogeologicalsurvey.org/geologic-hazards/corrosive-soils/corrosive-soil-damage/ Source] ]] <br />
The utilization of ferric iron ions (Fe<sup>3+</sup>), at approximately 120 mV, occurs when ions are released from metal deposits or minerals in the soil. Ferrous iron (Fe<sup>2+</sup>) product causes soil gleying, (a process described in a later section) when it accumulates. The source of the iron is also of relevance; whereas iron reduction in phosphate minerals can release phosphate for other organisms, it can also lead to corrosion of steel where iron reducers are present. Some ''Pseudomonas'' species can release pseudobactin, an iron-binding compound that limits its availability to other bacteria. <ref name="Sylvia" /><br />
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====Sulfate Reduction====<br />
Sulfate reduction begins occurring at 0 mV, and the dissimilatory reduction results in hydrogen sulfide (H<sub>2</sub>S) being released. However, H<sub>2</sub>S is prone to reaction with Fe<sup>2+</sub> to form iron sulfide (FeS). As a result, it often reacts before it reaches the surface of the soil, unable to disperse into the air. <ref name="Sylvia" /> Sulfate reduction has several documented consequences, ranging from corrosion of underground iron pipes due to FeS formation and blackening of soil caused by liberation of organic matter. Hydrogen sulfide is known as “swamp gas”, due to its emergence from one form of soil flooding, and has an odor comparable to rotting eggs. It can accumulate in many bodies of water and the air above them; due to its flammability and toxicity, this is very dangerous. <ref>Occupational Safety & Health Administration. (n.d.). Safety and Health Topics | Hydrogen Sulfide. Retrieved February 23, 2016, from https://www.osha.gov/SLTC/hydrogensulfide/index.html .</ref><br />
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====Methanogenesis (by Carbon Dioxide Reduction)====<br />
The process of using carbon dioxide (CO<sub>2</sub>) as a terminal electron acceptor results in the formation of methane (CH<sub>4</sub>) and is known as methanogenesis. In soil, methanogenesis occurs almost exclusively in a flooded condition due to its reduction potential being so low (below 100 mV). The use of CO<sub>2</sub> in this fashion yields much less energy than the reactions of previous electron acceptors, so this process has lower growth rates in turn. Organisms who perform methanogenesis are known as [[methanogens]] and are a group of anaerobic Archaea. CH<sub>4</sub> can also be produced as a result of acetate (CH<sub>3</sub>COOH) fermentation, which is also performed by methanogens. <ref name="Sylvia" /><br />
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===Fermentation in Flooded Soils (Non-Respiratory)===<br />
Fermentation is a different form of metabolism from respiration that occurs in the absence of a suitable terminal electron acceptor. Cells convert NADH and pyruvate from the glycolysis of sugars into NAD+ and other compounds, depending on the species that is fermenting. The various products of fermentation, including alcohols, lactic acid, and acetate are released into the surrounding soil and then become available for use by other anaerobic organisms. Additionally, fermentation generally reduces soil pH, which will encourage dissolution of minerals and their subsequent access by bacteria. <ref name="Richardson">Richardson, J. L., & Vepraskas, M. J. (2001). Wetland soils: Genesis, hydrology, landscapes, and classification. Boca Raton, FL: Lewis. </ref><br />
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==Microorganisms Involved==<br />
As available oxygen declines, organisms that thrive under anoxic conditions proliferate using alternative electron acceptors. The order in which available electron acceptors are consumed can generally be predicted by the electron tower and associated energy yields of electron pairs. Changes in redox conditions of flooded soils over time reflects the successive availability of terminal electron acceptors from the electron tower, and will govern which microbes will thrive through being able to use them.<br />
<br />
Some microbes below are able to oxidize the reduced form of their corresponding substance.<ref>Liesack, W. (2000). Microbiology of flooded rice paddies. FEMS Microbiology Reviews, 24(5), 625-645. </ref><br />
[[Image:Processes.jpg|500px|thumb|right|Summary of reducing conditions in flooded soils. [http://www.des.ucdavis.edu/faculty/rejmankova/ESP155_Soils-2004.pdf Source]]]<br />
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<br />
{| width="800" border="1"<br />
|----- bgcolor ="grey"<br />
| width="200" height="25" | '''Process'''<br />
| width="1000" | '''Example Genera of Common Bacteria Involved'''<br />
|-<br />
| Aerobic Respiration<br />
| Aerobes and facultative anaerobes such as ''Staphylococcus'', ''[https://en.wikipedia.org/wiki/Nocardia Nocardia]'', ''[[Pseudomonas]]''<br />
|-<br />
| Denitrification<br />
| Facultative anaerobes such as ''[[Agrobacterium]]'', ''[[Alcaligenes]]'', ''[[Bacillus]]'', ''Paracoccus'', ''Micrococcus''<br />
|-<br />
| Manganese Reduction<br />
| ''[[Bacillus]]'', ''[[Geobacter]]'', ''[[Pseudomonas]]'', ''Shewanella''<br />
|-<br />
| Iron Reduction<br />
| ''[[Desulfovibrio]]'', ''[[Pseudomonas]]'', ''Geothrix'', ''Shewanella'', ''Thiobacillus''<br />
|-<br />
| Sulfate Reduction<br />
| Generally obligate anaerobes such as ''[[Desulfobacter]]'', ''[[Desulfococcus]]'', ''[[Desulfosarcina]]'', ''Desulfosporosinus''<br />
|-<br />
| Methanogenesis<br />
| [[Methanogens]] such as ''Methanobacterium'' and [https://en.wikipedia.org/wiki/Archaea Archaea] (different from bacteria)<br />
|}<br />
[[Image:PseudomonasImage.jpg|300px|thumb|left|The ''Pseudomonas'' genus has a wide variety of metabolic capabilities among its species. [https://elmundodelavida.wordpress.com/category/ciencia/ Source]]]<br />
[[Image:Probes.gif|400px|thumb|center|[https://en.wikipedia.org/wiki/Hybridization_probe DNA and RNA probes] are used for identifying bacteria in samples. [http://tle.westone.wa.gov.au/content/file/969144ed-0d3b-fa04-2e88-8b23de2a630c/1/human_bio_science_3b.zip/content/005_dna/page_17.htm Source]]]<br />
<br />
==Effects of Flooding on Soil Environment==<br />
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===Mobility of Minerals and Gasses===<br />
[[Image:Aggregation.jpg|200px|thumb|right|A) unaffected soil and B) soil incubated anaerobically. Flooding caused mobilization of organic matter and disaggregation, resulting in the larger grains (decreased stability). [https://dl.sciencesocieties.org/publications/sssaj/abstracts/73/2/550 Source]]]<br />
Water also acts as a solvent for ions and soluble compounds, thus increasing the mobility and availability of metal ions, nutrients, and minerals. As a result of these physical effects in flooded soils, microbial respiration will have improved access to water-soluble compounds such as nitrate, perchlorate, manganese/ferric iron, sulfate, and carbon dioxide to act as electron acceptors. <br />
<br />
The diffusion of oxygen is over 10000 times slower in water than it is in air at standard temperature and pressure, resulting in the replenishing rate being much slower rate than microbial respiration. Carbon dioxide is also decreased but to a lesser degree due to it being far more soluble than oxygen. <ref>Greenway H, William A, Timothy DC. (2006). Conditions leading to high CO2 (>5 kPa) in waterlogged-flooded soils and possible effects on root growth and metabolism. Annals of Botany, 98, 9–32. Retrieved March 10, 2016 from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3291891/ .</ref><br />
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===Flooded Soil Aggregate Structure===<br />
Though some degree of moisture is important for aggregate formation and microbial activity, flooded soils exhibit decreased aggregate stability. Oxygen depletion and subsequent use of various elements for redox contributes to this decreased aggregation. Organic carbon is also made more soluble (like metals and minerals) under reducing conditions. The decreased stability of the soil is unlikely to recover due to drainage or volatilization of chemicals, removing them from the local environment. Since areas such as marshlands and rice fields are perpetually flooded, their soil’s aggregate stability rarely improves. <ref>De-Campos, A. B., Mamedov, A. I., & Huang, C. (2009). Short-Term Reducing Conditions Decrease Soil Aggregation. Soil Science Society of America Journal, 73(2), 550. Retrieved February 23, 2016, from https://dl.sciencesocieties.org/publications/sssaj/abstracts/73/2/550 .</ref><br />
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===Soil Gradients===<br />
[[Image:Column.jpg|200px|thumb|left|A Winogradsky column. [http://beautyinscience.com/Biology.html Source] ]] <br />
The progression of electron acceptor utilization occurs at different rates in different layers of soil. A process like methanogenesis will occur earlier several feet underground than at the surface due to decreased access to other compounds. This will result in gradients at various depths of soil. These gradients will differ by pH, color, chemical prevalence, and microbial population. <br />
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Since the soil is a more closed system (with less mobility of chemicals) than the surface, air, or bodies of water, gradients can be observed with a similar closed system: a Winogradsky column. This column, consisting of a sealed column of soil with provided organic material (such as an egg), allows for simulation of an anaerobic soil environment. <ref>Scientific American. (2013, September 19). Soil Science: Make a Winogradsky Column. Retrieved from http://www.scientificamerican.com/article/bring-science-home-soil-column/ </ref><br />
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===Variation of pH===<br />
pH has a major influence over the dissolution and sorption of several important toxins and nutrients in the soil. Low pH values increase the solubility of free aluminum (Al<sup>3+</sup>) and iron (Fe<sup>3+</sup> and Fe<sup>2+</sup>) ions which can be toxic in high concentrations, while also reducing the availability of phosphorus.<br />
<br />
When soil is initially saturated with water, the pH drops due to the accumulation of carbonic acid formed from trapped carbon dioxide produced from respiration. Fermentation also contributes to pH decreasing through the production of organic acids. This is quickly followed by an increase of pH as hydrogen cations are consumed in microbially-driven redox reactions. The soil then will gradually approach and stabilize near a neutral pH, with pH increasing in acidic soil and decreasing in basic soil due to products such as carbonate forming a buffer. <ref>Kirk, G. J. (2004). The biogeochemistry of submerged soils. Chichester: Wiley. </ref><br />
<br />
===Soil Gleying===<br />
[[Image:gleyed.jpg|200px|thumb|right|Gray colors produced in gleyed soil. [http://wetland-delineation.rutgers.edu/87-wetland-delineation-manual/wetland-delineation-manual-part3.html Source] ]] <br />
<br />
Gleying is a phenomenon in which waterlogged soils are discolored by accumulation of iron oxide (FeO) due to reduction of ferric iron into ferrous iron. Although ferric iron exists as an insoluble form in flooded soils, more ferrous iron can accumulate by the reduction of ferric iron over time. This results in a greenish, blue, grey soil color. In general Fe<sup>3+</sup> -reducing fermentative bacteria can be readily isolated from gleyed soils. The black color of soils/solution is frequently observed in flooded soil. This may result from the formation of iron sulfides (FeS) and pyrite (FeS2). <ref>Wenk, H., & Bulakh, A. G. (2004). Minerals: Their constitution and origin. Cambridge: Cambridge University Press. </ref><br />
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===Plant Nutrient Availability===<br />
Flooded soils can have a direct impact on plants by preventing efficient gas exchange between the plant roots and the soil. These conditions also change the types of microbes that are active and what they produce. Flooded soils cause anaerobic conditions which forces many microbes to use less favorable electron acceptors. These less favorable acceptors could have also served as nutrition for the plants; this creates competition between the plants and the microbes in certain flooded soils. By using different electron acceptors the microbes will release different products causing a chemical change in the soil that can be toxic. <ref>Minamikawa, K., & Sakai, N. (2005). The effect of water management based on soil redox potential on methane emission from two kinds of paddy soils in Japan. Agriculture, Ecosystems & Environment, 107(4), 397-407. Retrieved from http://www.sciencedirect.com/science/article/pii/S0167880904002208 .</ref><br />
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===Flooded to Unflooded Conditions===<br />
When waterlogged soils drain, oxygen diffuses into soil pores. The soil’s Eh increases and aerobic activity kicks in ceasing the production of anaerobic products. At higher Eh zones ( > 500 mV), undecomposed soil organic matter is used as an electron donor by aerobes and converted to water and CO2. Many of the anaerobic redox reactions are also reversed as with oxygen available as an electron acceptor many of the reduced products of anaerobic respiration can now be used as electron donors by lithotrophs. Manganese is oxidized back to MnO2 which gives some aerated soils a black color, and ferrous iron is oxidized by an iron-oxidizing bacteria, resulting in the formation of ferric oxides or ferric hydroxide minerals that give the soil a red, yellow, or brownish texture. <ref name="Richardson" /><br />
<br />
<br />
==Environmental Issues==<br />
<br />
Flooded soils are dynamic ecosystems that play an important role in biogeochemical cycling and in the production of greenhouse gases. Methane (CH<sub>4</sub><sup>+</sup>) and nitrous oxide (N<sub>2</sub>O) are produced as byproducts of anaerobic metabolism in the low-redox zones characteristic of flooded soils, where oxygen is lacking. Carbon dioxide (CO<sub>2</sub>), which receives widespread attention as a greenhouse gas and potential source of global warming, may also be produced at the interface of anaerobic-aerobic zones through the consumption of methane gas. However, it should be noted that from a global standpoint methane and nitrous oxide on a per molecule basis have the potential to contribute 25x and 300x more to global warming over the next century than carbon dioxide, respectively. Thus the conversion of methane gas to carbon dioxide essentially reduces the greenhouse gas effect by 25x per molecule per 100 years. Although the number areas classified as wetlands has decreased in past years, the effect of flooded soils to the global climate is clear.<ref>Schlesinger, W. H., & Bernhardt, E. S. (2013). Biogeochemistry: An analysis of global change (3rd ed.). San Diego, CA: Academic Press. </ref><br />
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===Methane Production; Methanogenesis===<br />
[[Image:Methane.jpg|thumb|300px|A natural source of methane gas]]<br />
Methane production occurs exclusively in anaerobic conditions by a group of Archaea known as methanogens. These microbes are obligatory, and require extremely low redox conditions in the range of -100mV. If oxygen is introduced into the system, methanogenesis ceases; thus, the process of methanogenesis depends on saturated soil conditions.<ref name="Sylvia" /> <br />
<br />
Methanogenesis can occur via one of two pathways: either by 1) CO<sub>2</sub> reduction or by 2) acetate fermentation.<br />
<br />
1) CO<sub>2</sub> + H<sub>2</sub> --> CH<sub>4</sub><sup>+</sup> (CO<sub>2</sub> reduction)<br />
<br />
and <br />
<br />
2) CH<sub>3</sub>COOH --> CH<sub>4</sub><sup>+</sup> + CO<sub>2</sub> (acetate fermentation)<br />
<br />
Both acetate and hydrogen are byproducts of anaerobic fermentation. <br />
<br />
Because the process of methanogenesis is “fed” byproducts produced from a complex series of degradation processes which are themselves “fed” complex organic matter, rates of methane production are highly sensitive to changes in temperature. Methanogenesis has a Q10 value in the range of 30-40, which is substantially higher than most biochemical process.<br />
<br />
Despite the clear effect of increasing temperatures on the rate of methanogenesis, the actual impact of global warming on methane production rates in wetlands and permafrost regions is highly unpredictable. Because methanogenesis requires anoxic conditions, any drying of flooded soil environments would both decrease methane production and increase methane oxidation, reducing overall methane emissions. Alternatively, warmer climates could increase growing seasons, which would increase methane emissions.<ref name="Sylvia" /><br />
<br />
===CO<sub>2</sub> Production via Methane Consumption: Methanotrophy===<br />
Some of the methane produced via methanogenesis in flooded soils may be consumed and oxidized to CO<sub>2</sub> at the interface of the anaerobic-aerobic zones. This process occurs primarily by a group of bacteria known as methanotrophs. These microbes can be found in surface layers of wetland soils and unsaturated upland soils, and may be exposed to very high concentrations of methane gas, sometimes amounting to 10% or more of the dissolved gases. Methane is thought to be the only source of C and energy for these bacteria.<br />
<br />
Methanotrophy occurs in the following reaction:<br />
<br />
CH<sub>4</sub><sup>+</sup> + 2O<sub>2</sub> --> CO<sub>2</sub> + 2H<sub>2</sub>O<br />
<br />
Methane is similar in size and shape to ammonium; and there is some evidence that nitrifiers (ammonium oxidizers) can also oxidize methane. Because they are molecularly similar, NH<sup>4</sup><sup>+</sup> competes at the enzyme’s active site, inhibiting methane oxidation. As a result, methanotrophy is generally inhibited by the addition of fertilizer or excess nitrogen in the system, when ammonium levels are high. <br />
<br />
Alternatively, if nitrogen is extremely limiting the addition of nitrogen will stimulate methanotrophy and actually increase methane consumption. So although it is generally expected that adding N-fertilizer will decrease CH<sub>4</sub><sup>+</sup> consumption and lead to increased global warming potential, sometime the opposite effect may occur.<ref name="Sylvia" /><br />
<br />
===Nitrous Oxide; Denitrification===<br />
Denitrification is an anaerobic process in which nitrate serves as the terminal electron acceptor, and generally some source of organic carbon is the electron donor (also H<sub>2</sub> may serve as a donor). <br />
<br />
In this process, nitrate is oxidized to nitric oxide, then nitrous oxide, and then fully oxidized to dinitrogen:<br />
<br />
NO<sub>2</sub><sup>-</sup> --> NO --> N<sub>2</sub>O --> N<sub>2</sub><br />
<br />
However, under certain conditions the full oxidation of NO<sub>3</sub><sup>-</sup> to N<sub>2</sub> does not occur and nitrous oxide (N<sub>2</sub>O) is produced.<br />
<br />
Microbes responsible include both organotrophs and lithotrophs, and this process occurs primarily by facultative anaerobes. <br />
<br />
Although a low redox potential is important for denitrification to occur (oxygen must not be present or it will “out-compete” nitrate as a terminal electron acceptor), redox requirements are not so low that this process cannot occur within anaerobic microsites of soil aggregates. <br />
<br />
Factors affecting nitrous oxide production include oxygen, pH, and the ratio of nitrate to available C. Although denitrification rates decrease with increasing oxygen, the proportion of N evolved as nitrous oxide actually increases with increasing oxygen. Low pH generally inhibits the reduction of N<sub>2</sub>O to N<sub>2</sub>; thus at low pH, N<sub>2</sub>O will likely dominate. However, highly acidic soils have low N availability and low nitrification and denitrification rates. Thus, the highest rate of nitrous oxide production from denitrification occurs in moist soils that cycle N rapidly.<ref name="Sylvia" /><br />
<br />
==Current Research==<br />
Current research topics on the issue of flooded soils are heavily focused on greenhouse gas emissions produced as a result of the low redox conditions characteristic of these ecosystems. Other research topics may address impacts to plant growth, and chemical, physical, and biological aspects of flooded soils. <br />
<br />
Many agricultural studies focus on rice paddies. Bacteria that oxidized acetate and reduced iron were identified and studied in flooded rice paddy soil through RNA probing.<ref>Hori, T., Müller, A., Igarashi, Y., Conrad, R., & Friedrich, M. W. (2009). Identification of iron-reducing microorganisms in anoxic rice paddy soil by 13C-acetate probing. The ISME Journal ISME J, 4(2), 267-278. from http://www.nature.com/ismej/journal/v4/n2/full/ismej2009100a.html </ref> Another study observed factors affecting delivery of nitrogen to plants by microbial populations in flooded soils and found that the addition of sludge to soil facilitated nitrogen formation more than the addition of straw compost.<ref>El-Sharkawi, H. M. (2012). Effect of Nitrogen Sources on Microbial Biomass Nitrogen under Different Soil Types. ISRN Soil Science, 2012, 1-7. from http://www.citationmachine.net/bibliographies/77289062?new=true </ref> The effect of oxygen concentration on rates of reactions involving nitrogen, including nitrification and mineralization, in paddy soils was also studied.<ref>Yang, Y., Zhang, J., & Cai, Z. (2015). Nitrification activities and N mineralization in paddy soils are insensitive to oxygen concentration. Acta Agriculturae Scandinavica, Section B — Soil & Plant Science, 66(3), 272-281. from http://www.tandfonline.com/doi/full/10.1080/09064710.2015.1093653 </ref><br />
<br />
A review article was published in 2012, focusing on soil-plant interactions, including redox reactions’ effects on plant function, in wetlands.<ref>Pezeshki, S. R., & Delaune, R. D. (2012). Soil Oxidation-Reduction in Wetlands and Its Impact on Plant Functioning. Biology, 1(3), 196-221. from http://www.mdpi.com/2079-7737/1/2/196 </ref><br />
<br />
[[Carbon cycle | Long-term retention of carbon in soil organic matter]] is an issue in frequently harvested soils. One study looked at various treatments of rice paddies and found that a combination of rice straw and inorganic fertilizer aided sequestration and led to “a higher grain yield”.<ref> Bhattacharyya, P., Roy, K., Neogi, S., Adhya, T., Rao, K., & Manna, M. (2012). Effects of rice straw and nitrogen fertilization on greenhouse gas emissions and carbon storage in tropical flooded soil planted with rice. Soil and Tillage Research, 124, 119-130. from http://www.sciencedirect.com/science/article/pii/S0167198712001195 </ref><br />
<br />
A recent study discussed the fate of metals such as cadmium, nickel, and aluminum in impacted creeks in Kenya, Tanzania, and Mozambique.<ref>Kamau, J. N., Kuschk, P., Machiwa, J., Macia, A., Mothes, S., Mwangi, S., . . . Kappelmeyer, U. (2015). Investigating the distribution and fate of Al, Cd, Cr, Cu, Mn, Ni, Pb and Zn in sewage-impacted mangrove-fringed creeks of Kenya, Tanzania and Mozambique. J Soils Sediments Journal of Soils and Sediments, 15(12), 2453-2465. Retrieved from http://link.springer.com/article/10.1007/s11368-015-1214-3 </ref><br />
<br />
Many other studies focus on the degradation of ground contaminants such as pesticides so that their results can be used in [[bioremediation]].<ref>Levén, L., Nyberg, K., & Schnürer, A. (2012). Conversion of phenols during anaerobic digestion of organic solid waste – A review of important microorganisms and impact of temperature. Journal of Environmental Management, 95. Retrieved from http://www.sciencedirect.com/science/article/pii/S0301479710003531 </ref> The fate of cycloxaprid, an agricultural insecticide, was observed in anaerobic conditions (including flooded soils). Radioisotopic tracing showed that various soil types had different effects on the chemical.<ref>Liu, X., Xu, X., Li, C., Zhang, H., Fu, Q., Shao, X., . . . Li, Z. (2016). Assessment of the environmental fate of cycloxaprid in flooded and anaerobic soils by radioisotopic tracing. Science of The Total Environment, 543, 116-122. Retrieved from http://www.sciencedirect.com/science/article/pii/S0048969715310007 </ref><br />
<br />
Lastly, there is always the topic of greenhouse gas emissions. Arctic, temperate, and tropical regions were recently studied for measurements of greenhouse gas emissions and its relation to temperature.<ref>Turetsky, M. R., Kotowska, A., Bubier, J., Dise, N. B., Crill, P., Hornibrook, E. R., . . . Wilmking, M. (2014). A synthesis of methane emissions from 71 northern, temperate, and subtropical wetlands. Glob Change Biol Global Change Biology, 20(7), 2183-2197. Retrieved from http://onlinelibrary.wiley.com/doi/10.1111/gcb.12580/pdf </ref> Another group of researchers found a correlation between anaerobic methane oxidation in freshwater wetlands and reduced methane emissions.<ref>Segarra, K. E., Schubotz, F., Samarkin, V., Yoshinaga, M. Y., Hinrichs, K., & Joye, S. B. (2015). High rates of anaerobic methane oxidation in freshwater wetlands reduce potential atmospheric methane emissions. Nature Communications Nat Comms, 6, 7477. Retrieved from http://www.nature.com/ncomms/2015/150630/ncomms8477/full/ncomms8477.html </ref><br />
<br />
==References==<br />
<references /><br />
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Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]<br />
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<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Introduction_to_Organisms&diff=132727
Introduction to Organisms
2018-01-08T06:05:24Z
<p>Kmscow: /* Amoebas */</p>
<hr />
<div>{{Uncurated}}<br />
==Introduction== <br />
The soil ecosystem in an important environment that allows both plants and animals to survive, grow and reproduce. The significance of the soil as an ecosystem is at times overlooked despite its major contributions to the environment. The [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] is a complex and varied microbial habitat.[1] The plants and organisms inhabiting the soil contribute to its thriving diversity. Soil life is diverse in morphology, metabolism, size, and many other characteristics. Soil is a heterogeneous environment with various zones of rhizosphere, aggregates, organic matter and animal residues.[31] Given each zone is a small component of the larger soil ecosystem, rhizosphere accounts for only 5 to 7 percent of the soil environments but contains over “70 percent of the bacterial- and fungal-feeding nematodes.”[31] <br />
<br />
Since soil microbial diversity is immense, with all three domains of life: Archaea, Bacteria and Eukarya represented in the soil environment, it is not possible to discuss each microbial species (many of which have not even been described!). Only a few representative groups of each domain will be discussed to provide examples of the roles these organisms play in soil.<br />
<br />
==Soil Food Web and Microbial Interactions== <br />
<br />
To survive in a soil environment, an organism must be able to adapt to a constantly changing environment and to interactions with other organisms. One type of interaction shown in (Figure 2.1) is predation. Other common interactions in the soil environment are: <br />
<br />
:[[Image:soil_foodweb72.jpg|frame|center|Figure 2.1 Soil Food Web. From[http://www.exploringnature.org/graphics/foodwebs/soil_foodweb72.jpg]]]<br />
<br />
<br />
'''I. Commensalism:''' Organism (A) benefits from the presence of Organism (B) while (B) is unaffected by the presence of (A).[32]<br />
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'''II. Mutualism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) and becomes a necessary association for each other’s survival. [32] [33]<br />
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'''III. Synergism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) but the relationship is not necessary for survival.[33]<br />
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'''IV. Competition:''' Depending on the organisms this interaction benefits organisms who can readily adapt to the environment and overcome any obstacles needed to survive, grow and reproduce.[33]<br />
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'''V. Amensalism:''' An interaction in which Organisms (A) and (B) develop a partnership where (B) is unaffected by (A) but organism (A) is negatively affected by (B).[34]<br />
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'''VI. Parasitism:''' Organism (A) benefits from Organism (B) but Organism (B) does not benefit positively from Organism (A). <br />
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'''VII. Predation:''' “An interaction between organisms in which one benefits and one is harmed based on the ingestion of the smaller sized organism, the prey, by the larger organism, the predator.”[33]<br />
<br />
<br />
<br />
The soil food web consists of microbes, fauna (micro and macro) and plant roots, who play multiple essential roles in soil ecosystem. The interactions between members of the soil food web result not only in chemical processes such as nutrient cycling and biodegradation of pollutants, but also in creation of soil structure, e.g. of aggregates.[35].<br />
<br />
In (Figure 2.1), all three domains, Archaea, Bacteria, and Eukarya, are represented in the soil food web. Thel food web is not only dependent on living creatures but also on decaying organic matter and plant roots. Dead and living matter in the soil environment, including plant roots, contribute to the maintenance of the food web.<br />
<br />
==3 Domains==<br />
[[Image:Big_Tree_Bold_Letters_white.png|frame|center|Figure 3.1 Phylogenetic Tree of the 3 Domains. From[http://phylogenomics.blogspot.com/2014_02_01_archive.html]]]<br />
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===Carl Woese and Phylogeny===<br />
<br />
[[Image:Carlwoese1_0565_b.jpg|frame|center|Figure 3.2 Carl Woese. From[http://ofbacteriaandmen.blogspot.com/2013/01/the-new-biology-of-carl-woese.html]]] <br />
<br />
Carl Woese (Figure 3.2) was an American microbiologist famous for pioneering the technique of phylogenetic taxonomy through use of a 16S (for prokaryotic) and 18S (for eukaryotic) ribosomal RNA, also known as small subunit ribosomal RNA [46]. This refined Linnaean classification, taking out the guesswork classification by using a gene that was present in every living organism- the small subunit ribosomal RNA. This method of classification is comprehensive because all organisms possess this form of genetic material. Ssu rRNA is sequenced because the genes are highly conserved. Due to their functional constancy, some have variable regions to differentiate organisms, and are easy to sequence. This technique also elucidated the tree of life, which shows the three domains of microbial lineage diversity: Bacteria, Archaea, and Eukarya. DNA can be compared using a sample database that allows identification of unknown organisms to a species level.<br />
<br />
===Domain Bacteria===<br />
<br />
====Introduction to Bacteria==== <br />
Bacteria are single celled prokaryotic organisms that lack membrane bound organelles. They are involved in many important processes within the soil such as decomposition, [https://microbewiki.kenyon.edu/index.php/Bioremediation bioremediation], symbiosis and biological transformation of nutrients. They are present in all terrestrial soil environments.[1] Soil is a heterogenous environment that varies in moisture content, temperature, oxygen requirements, carbon source and many other bacterial growth conditions. Those wide ranging growth factors account for the enormous diversity in soil bacteria populations. One gram of soil can contain between 26,000 to 52,000 different bacterial species.[13] In the entire microbial world, only about 1 percent of bacterial species can be cultured under laboratory conditions which leaves an immense number of bacterial species yet to be described. [14]<br />
<br />
Classification based on phenotypic characteristics, such as cellular morphology, metabolism, gram staining, oxygen requirements, carbon source and other traits, was used more readily before modern DNA sequencing. But, phenotypic classification is still used and Bergey’s Manual of Systematic Bacteriology is the most widely used source for determining species based on characteristic species traits.<br />
<br />
Traditional species definitions are not as useful in bacteria. OTUs, or operational taxonomic units, based on DNA sequencing similarity, are more applicable to bacteria. Typically, those bacteria with 97 percent similar DNA sequence are classified within the same OTU.[15] The 16S small subunit ribosomal RNA is used to substantiate phylogenetic relationships between different bacterial groups.<br />
<br />
====Morphology====<br />
<br />
Bacterial cells measure approximately 1μm wide and 1-5μm long.[12] They are smaller than eukaryotic microbes.Due to their small size, bacteria can more easily adapt to changing soil environments than larger eukaryotes.[1] Most bacteria are singled celled, but actinomycetes grow in branching filaments. There are many different bacterial cell shapes. The most common are bacilli (rods), cocci (spheres), spirilla (spirals) and actinomycete (filaments).<br />
[[Image:bacteria_sizes.jpg|frame|center|Figure 3.3 Common cell shapes cocci, bacillus, and spirilla and relative sizes. From[http://www.ppdictionary.com/gnbac.htm]]]<br />
<br />
'''Flagella''' - There are many different types and different arrangement of flagella. Movement in soil environments is dependent on soil moisture content. Though movement in soil is limited, flagellar function is important to allow bacteria to find more favorable microsites.[1]<br />
<br />
'''Cell membrane''' - The cell membrane encloses the cytoplasm. It is semi-permeable phospholipid bilayer that regulates transport of nutrients into the cell and waste products out of the cell.<br />
<br />
'''Cell wall''' - Most bacteria have a rigid cell wall surrounding the cell membrane which protects the cell from osmotic lysis. The cell wall is made of a crosslinked polysaccharide, called peptidoglycan, that is found only in bacteria.[1] The cell wall gives the cell shape and structure, but it is porous enough to permit small water soluble molecules to flow through to the cell membrane surface.[1]<br />
<br />
*'''Gram positive''' bacteria have a thick cell wall made of several layers of peptidoglycan. The cell wall is the outermost structure, as they do not have an outer membrane. The thick cell wall structure make gram positive bacteria more resilient to osmotic shock. Gram positive bacteria can tolerate 5 to 10 times more turgor pressure than gram Gram negative bacteria.[1] Teichoic acids in the cell wall may also help to bind to cationic nutrients in soil surroundings.[1] <br />
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*'''Gram negative''' bacteria have a thin cell wall surrounded by an outer membrane made of phospholipids and lipopolysaccharides. Polysaccharides of the outer membrane interact with surrounding cations and are involved in attachment of bacteria to soil particles. [1] Periplasm is a gel like substance that occupies the space between the outer membrane and the cell wall of gram negative bacteria.[1] The outer membrane and periplasmic space is thought to provide protection from environmental toxins.[1] Proteins within the periplasm are thought to begin the process of catalyzing hydrolysis of organic and toxic substances.[1] <br />
<br />
[[Image:gramposnegmembrane.jpg|frame|center| Figure 3.4 Illustration of Gram positive and Gram negative cell wall structures. From[http://micro.digitalproteus.com/morphology2.php]]]<br />
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'''Endospores''' are made by ''Bacillus'' and ''Clostridium'' in response to environmental stress.[1] Endospores are extremely resistant structures that can withstand extreme temperatures up to 150℃.[12] They can also withstand extreme pressure, desiccation, radiation, pH and chemicals.[12] The endospore protects the bacterial DNA until environmental conditions are more favorable and germination can proceed. Soil is the most common habitat for endospore forming bacteria.[12]<br />
<br />
'''Extracellular polymers''' - Many bacteria secrete a slime layer or capsule made of polysaccharides or glycoproteins.[1] The outer polysaccharide coating of bacteria helps in attachment to surfaces and the formation of biofilms.[1] Bacterial capsule secretions play a big role in soil aggregation and soil structure.[1] When the carbon to nitrogen ratio within soils is high, microbes secrete the excess carbon as extracellular polysaccharides.[1]<br />
<br />
====Reproduction==== <br />
Most bacteria reproduce by binary fission.[12] The bacterial cell expands to twice the original cell size, duplicates the bacterial DNA and pinches off, producing two daughter cells. Each resultant daughter cell is a clone of the parent cell. Prokaryotic Archaea also reproduce by binary fission.<br />
<br />
*'''Spore formation:''' Actinomycetes are a large group of filamentous bacteria, primarily found in soil.[1] Actinomycetes are morphologically similar to fungi. Actinomycetes form long filaments called hyphae. Unlike most bacteria, the majority of actinomycetes reproduce using asexual spores called conidia.[1] Though they share many characteristic with fungi, actinomycetes are still prokaryotes. They are smaller than fungi and the cell wall contains peptidoglycan.[1] Actinomycetes break down a wide variety of organic compounds and play an important role in organic matter decomposition. [1] ''Streptomyces'', a subgroup within actinomycetes, produce geosmin, which gives soil the characteristic earthy smell.[12]<br />
<br />
====Metabolism==== <br />
<br />
Along with archaea, bacteria are the most metabolically diverse and employ many different nutritional strategies.[1]<br />
*Heterotrophs - Most bacteria are heterotrophic, obtaining carbon from preformed organic substances. [1] <br />
*Autotrophs - Carbon dioxide serves as the main source of carbon. Some cyanobacteria, nitrifying and sulfur-oxidizing bacteria are autotrophs.[1]<br />
*Organotrophs - Most bacteria obtain electrons from organic substances.[1]<br />
*Lithotrophs - Some cyanobacteria, nitrifying bacteria and sulfur-oxidizing bacteria obtain electrons from inorganic substances.[1]<br />
*Phototrophs - Cyanobacteria use light as the main source of metabolic energy.[1]<br />
*Chemotrophs - All other nonphotosynthetic bacteria do not rely on light for metabolic energy.[1]<br />
<br />
====Contributions to Biogeochemical Cycling==== <br />
<br />
Bacteria play a significant role in the cycling of a wide range of elements.<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Carbon_cycle '''Carbon Cycle:'''] <br />
<br />
*'''Carbon Assimilation''' is the process of fixing carbon dioxide into organic forms. Carbon fixation is performed by autotrophic bacteria, such as cyanobacteria.[1] Chemoautotrophic nitrifying bacteria, such as ''Nitrobacter, Nitrosospira'' and ''Nitrosomonas'', also fix carbon.[1] Sulfur oxidizing bacteria, such as ''Thiobacillus'', fix carbon as well.<br />
<br />
*'''Carbon Mineralization''' results from microbial decomposition of organic carbon compounds into inorganic forms. As the organic carbon substances, like plant matter, are decomposed, inorganic carbon dioxide is produced. Most bacteria are heterotrophs that perform carbon mineralization. When microorganisms die, they are decomposed by successive microbial generations. Peptidoglycan, the main component of bacterial cell walls, is utilized as a polysaccharide substrate by other heterotrophic soil microbes.[1]<br />
<br />
*'''Methanogenesis''' - Methanogenic bacteria produce methane from the reduction of carbon dioxide. They are all strict anaerobes that use carbon dioxide for the carbon source.[1] They can all use hydrogen as a source of energy and electron donor. [1]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle '''Nitrogen cycle:''']<br />
<br />
*'''Nitrogen fixation:''' ''Azotobacter'' is a free living nitrogen fixing bacteria.[1] ''Rhizobium'' lives in a mutualistic relationship with plants by fixing nitrogen within root the nodules of legumes.[1] ''Anabaena'' and ''Nostoc'' have specialized heterocyte structures where nitrogen fixation occurs.[1] <br />
<br />
*'''Nitrification:''' Nitrifying bacteria, such as ''Nitrobacter, Nitrosospira,'' and ''Nitrosomonas'', oxidize ammonium to nitrate.[1] <br />
<br />
*'''Denitrification:''' ''Alcaligenes, Flavobacterium'', and ''Pseudomonas'' are common soil denitrifying bacteria.[1]<br />
<br />
===Domain Archaea===<br />
<br />
====Introduction to Archaea====<br />
<br />
Vladimir Vernadsky decided, in 1926, that only two domains of life existed on Earth, Bacteria and Eukarya.[37] About 50 years later in 1977, Carl Woese and George Fox theorized that part of the bacterial domain possed multiple dissimilarities from bacteria and recognized it to be another domain of life, now called Archaea.[38] Woese and Fox’s theory regarding the differences of archaea were confirmed in 1990’s through the use of 16S rRNA and 18S rRNA.[38] <br />
<br />
Despite the strongly held belief, in the 1990s, that archaea only inhabited extreme environments, recent discoveries have suggested their presence in abundant numbers all throughout the Earth. It is suggested that Archaea play notable roles in maintaining nutrient cycles.[37] Various methods of research, such as cultivation, culture-independent techniques and isotope-based methods, have facilitated the study of domain Archaea in carbon and nitrogen cycling. [37]<br />
<br />
The use of genomic and biochemical data has permitted the study of archaeal structure.[37] Use of these research methods has shown that domain archaea and domain bacteria differ in cell wall characteristics yet, share various ways to transfer genetic information by replication and transcription from their common ancestor, Eukarya.[37] As of 2012, 116 genera of Archaea have been observed which consists of 450 species. Most of the archaeal species in these genera remains uncultivated, known only through its gene sequences and molecular surveys.[37]<br />
<br />
====Morphology==== <br />
Archaea are characterized by various cell sizes. They are most commonly found to be small organisms ranging from “0.1 to 15 μ diameter and up to 200 μ long.”[38] The shape of many archaea are similar to bacteria, including bacillus, cocci, spirilla and “plate-like forms.” [38] Their cell membranes have ether linked lipids with no periplasmic space, similar to gram-positive bacteria, and contain no intracellular organelles.[39]<br />
<br />
'''Flagella:''' Most motile archaea inhabit a motor rotary system that allows it to move its flagella through the chemical gradient similar to bacteria.[39] Despite its similarity in function and source of energy required for motility, the flagella of both archaea and bacteria differ in structure.[39] Archaeal flagella gets the energy for its movement by ATP and is composed of dependent filaments that rotate singularly. [40] Archaeal flagella are known to be thinner than bacteria flagellin.[40] Since, the archaeal common ancestor is not bacteria but eukarya, convergent evolution is a plausible explanations for the differences between bacterial and archaeal flagellin. [40]<br />
<br />
'''Membranes:''' Archaea have a cell membrane that protects the cytoplasm and the nucleic acids from the environment. The archaeal cell membrane has a lipid bilayer with glycol-ether lipids that are more stable than ester linkages and help some archaea that live in extreme environments to withstand such conditions.[39] Most archaeal species are surrounded by a cell wall which protects the cell membrane and maintains the archaeal structure.[41]<br />
<br />
====Reproduction====<br />
Archaeal organisms reproduce by binary fission since they do not have nucleases thus, the DNA chromosome in a Archaeal organism replicate, separate and create two daughter cells.[43] The process of binary fission can be seen in Figure (3.5) process begins the parent cell duplicating the DNA. The DNA material then goes to the sides of the cell where an invagination to the cell occurs allowing the cell to become two individual cells. Binary fission is a very fast reproduction process, that allows archaeal organisms to grow at an exponential rate.[44]<br />
<br />
[[Image:WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg|frame|center|Figure 3.5 Illustration of binary fission. From[https://d2jmvrsizmvf4x.cloudfront.net/WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg]]]<br />
<br />
====Metabolism==== <br />
Archaea share similar metabolic characteristics to bacteria. The metabolic pathways taken by all archaea shown in the (Figure 3.6) demonstrates the great diversity and variation amongst archaea. [38] The kinds of archaea that are seen in the environment and the metabolic pathways taken by some can be summarized in the image. <br />
<br />
*Photoautotrophs: use light as an energy source and carbon dioxide as the carbon source with the help of the Calvin Cycle.[38]<br />
*Chemoautotrophs: use inorganic chemicals as their energy source and carbon dioxide as carbon source. <br />
*Chemoheterotrophs: take organic chemicals as energy source and organic chemicals as carbon source. The pathways taken by chemoheterotrophs varies from respiration by the Krebs Cycle to fermentation. [38]<br />
*Photoheterotrophs: use light as their energy source and organic chemicals as their carbon source. <br />
<br />
Most archaea inhabiting in the soil environment are major contributors to the biogeochemical cycles.<br />
<br />
[[Image:2000px-Troph_flowchart.svg.png|thumbnail|center|Figure 3.6 Flowchart showing different metabolic pathways. From[https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Troph_flowchart.svg/2000px-Troph_flowchart.svg.png]]]<br />
<br />
====Contributions to the Cycle====<br />
Archaea play a significant role in the nutrient cycles that take place in the ecosystem as they account for about 1-5% of all the prokaryotes present in the soil environment.[42]<br />
<br />
'''Carbon Cycle:''' Archaea have an important role in the carbon cycle that takes place specifically in methane production, carbon mineralization and carbon assimilation all of all of which contribute to the soil’s carbon sink.[42] The carbon dense soil helps to make the soil organic matter rich and helps to form extracellular polymers which creates stable aggregates. For some microbes, an electron acceptor is need to carry out metabolic functions. [42] More info on [https://microbewiki.kenyon.edu/index.php/Carbon_cycle Carbon Cycle].<br />
<br />
*'''Carbon Assimilation:''' Involves the transformation of inorganic carbon into organic carbon compounds. This process is commonly done by autotrophic phyla ''Crenarchaeota, Thaumarchaeota'', and ''Euryarchaeota'' that use carbon dioxide/ bicarbonate converting it to organic compounds.[42] Of the autotrophic lineages observed in carbon assimilation the ''Thaumarchaeota'' are strict autotrophs, the ''Euryarchaeota'' and ''Crenarchaeota'' are facultative autotrophs and the ''Halobacteriales'' and ''Thermococcales'' are obligate heterotrophs.[42] <br />
<br />
*'''Carbon Mineralization:''' The process that converts organic carbon into the oxidized inorganic carbon, carbon dioxide is commonly done by both aerobes and anaerobes.[42] The heterotrophic microbes that use organic compounds as energy to oxidize the carbon source include, methanogens and methane-oxidizing archaea belonging to the phyla ''Euryarchaetota'', and ''Crenarchaeota''.[42] <br />
<br />
*'''Methanogenesis:''' production of methane, a major greenhouse gas in the Earth’s atmosphere is commonly done by archaea upon reducing an oxidized compound.[42] The phyla ''Euryarchaeota'' is the only phyla that consists of archaea that produce methane all of which form five class: ''Methanopyri, Methanococci, Methanobacteria, Methanomicrobia'' and ''Thermoplasmata''.[42] Methanogens are commonly found in anaerobic and aerobic conditions such as bodies of water, aerated soils and oxygenated waters.[42]<br />
<br />
'''Nitrogen Cycle :''' Archaea play a pivotal role in the Nitrogen cycle and help create nitrogenous products for the plants and microbes. More info on [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle Nitrogen cycle].<br />
<br />
*'''Nitrogen Fixation:''' Fixing nitrogen from the environment and converting it to organic nitrogen in the soil or to inorganic nitrogenous form since both organic and inorganic products are in short supply in the biosphere and are fixed by many archaeal organisms.[42] N2 fixation by the environment is usually done by three major archaeal classes ''Methanobactera, Methanococci'' and ''Methanomicrobia''.[42] <br />
<br />
*'''Nitrification:''' Converting the ammonia (NH4+) in the soil to nitrite (NO2-) produces nitrate (NO3-) as an intermediate. [42] The transformation of ammonia to first nitrate then to nitrite is a two step process that is done by different microbes. [42] Most common organisms involved in nitrification include ammonia-oxidizing archaea which are lithotrophic organisms mostly, of the ''Thaumarchaeota'' phylum from the archaea domain. <br />
<br />
*'''Denitrification :''' The conversion of atmospheric N2 using the electron acceptor NO3- or NO2- creating the formation of nitric oxide, nitrous oxide and/or N2.[42] The formation of the end product N2 may not always be produced but other intermediates NO and N2O, greenhouse gases may be produced.[42] Of the archaeal organisms that have been studied in denitrification process is done by ''Pyrobaculum aerophilum'' which accepts both NO3- and NO2- as an electron acceptor producing a variety of products NO2-, NO, N20 and N2.[42]<br />
<br />
===Domain Eukarya===<br />
<br />
====Fungi====<br />
<br />
=====Introduction=====<br />
<br />
'''Introduction'''<br />
<br />
Fungi comes from the ancient Greek word “sphongos” meaning sponge in reference to the mushroom cap [47]. Fungi have the general characteristics of being eukaryotic, heterotrophic, external absorbers of nutrients, containing a hyphal thallus, reproducing via spore, and being pleomorphic (producing several forms). Fungi are generally organoheterotrophs that can survive in low pH and stay active at low moisture content[46]. Fungi reside in the domain Eukarya with an estimated species of 1.5 million, and less than five percent of them have ever been described. The general phyla included within Kingdom Fungi include Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, Chytridiomycota, and Microsporidia [48].<br />
<br />
[[Image:magical-kingdom-620.jpg|frame|center|Figure 3.7 Fungi phyla hierarchy. From.[http://www.motherjones.com/environment/2009/11/fungi-family-tree]]]<br />
<br />
=====Morphology=====<br />
<br />
'''Morphology''' <br />
<br />
Fungi can be either unicellular (yeasts) or multicellular. All multicellular fungi are made up of small, filamentous particles called hyphae. Some hyphae have cross walls called septa, while others do not- this is a large basis of fungal identification. Fungal cells generally have multiple nuclei. Fungal cell walls are generally composed of chitin, a long carbohydrate polymer that adds rigidity and structural support to fungi [49]. <br />
<br />
=====Reproduction=====<br />
<br />
'''Reproduction'''<br />
<br />
Fungal reproduction can occur either sexually or asexually.<br />
<br />
'''Sexual reproduction''' can occur by homothallic or heterothallic mycelia.<br />
<br />
'''Asexual reproduction''' can occur by fragmentation, budding, or by producing spores (the most common method). <br />
<br />
*'''Spores:''' spores come in many different forms. One of the most well known are conidiospores, which are unicellular or multicellular spores that get released from the tip of the hyphae. <br />
<br />
'''Perfect fungi''' are those that can reproduce both sexually and asexually while imperfect fungi are those that can only reproduce asexually.<br />
<br />
*Sexual reproduction always includes the stages plasmogamy (fusion of two haploid cells), karyogamy (creation of a diploid zygote), and meiosis (gametes are created).<br />
<br />
=====Metabolism=====<br />
<br />
'''Metabolism'''<br />
<br />
Many different fungi display a myriad of metabolisms. There are primary metabolites that that help the fungi function properly, and secondary metabolites that are generally bioactive that are not the most pertinent to fungal growth (they can live without these). Secondary metabolites play a large role in chemistry today and can be manufactured into commonly used products such as new drugs. In general fungi are heterotrophic through release of extracellular enzymes into the neighboring environment to break complex molecules down into smaller ones. The materials are then absorbed and metabolized [50]. Fungi are sessile organisms that overcome their little to no movement through apical growth at the hyphal tip. Fungi are noted to grow almost everywhere on the Earth.<br />
<br />
=====Relevance to soil===== <br />
<br />
'''Relevance to soil'''<br />
<br />
Fungi include some of the most abundant biomass of microorganisms in numerous soils. They play an important role as decomposers within the soil food web through conversion of difficult to digest organic material into forms many other organisms can use [51]. Their hyphae can bind soil particles together and create aggregates that increase soil water holding capacity. They perform important functions from water dynamics to nutrient cycling and disease suppression. Soil fungi can be categorized into three different groups based on their actions: <br />
<br />
*decomposers: that convert dead organic material into fungal biomass<br />
<br />
*mutualists: which colonize plant roots and help solubilize phosphorous and bring soil nutrients<br />
<br />
*pathogens/ parasites: which help control diseases in soil via trapping organisms such as nematodes [51]. <br />
<br />
Fungi are seen common in intensively managed agricultural soils due to tillage disrupting hyphae. Fungi also play a very important role in the [https://microbewiki.kenyon.edu/index.php/Rhizosphere_Interactions rhizosphere], the region of soil that is greatly influenced by the plant root system. This area of soil which is concentrated in plant roots and fungal hyphae is known to support greater microbial activity.<br />
<br />
=====Protozoans=====<br />
<br />
'''Protozoans'''<br />
<br />
In general, Protozoans range from 5 to 500 µm in diameter, making them significantly larger than bacteria [21]. They are abundantly located near the surface of the soil (15cm deep) where roots are plentiful [21]. Many protozoans have two life cycles. One is their active form where they are motile and feed on prey. The other is the cyst form where they produce a thick coating to protect them from the environment and can go dormant for years. The protozoa are divided into 4 major categories: the ciliates, the flagellates, the heliozoans, and the amoebas [10]. <br />
<br />
======Ciliates======<br />
<br />
'''Cilliates:'''<br />
This group, within protozoans, is fairly diverse. A common feature shared amongst all of its members is the presence of at least one cilia at any stage of its development [10]. The cilia is used for movement and other things such as predation (tentacles). For movement, they use the massive amounts of tiny cilia to create wave like currents to propel the cell forwards. Most ciliates also have toxicysts which are used to capture prey [10]. Some ciliates even have a symbiotic relationship with algae living inside of them [10]. The algae use the CO2 produced by ciliates and turn it into O2 that can then be reused by the ciliates [10]. They are found in a wide array of habitats ranging from freshwater and soil to the rumen of Animals [22]. They are present in almost anywhere that contains water [23]. They are unicellular heterotrophs so they feed on bacteria and algae in their environment. Ciliates are one of the top predators in the microbial food web and are hypothesized to have been a major predatory group before animals evolved [23]. The large size of ciliates and their rigid cell structure make them less common in unsaturated soils than other types of protozoa.<br />
<br />
[[Image:2spiro.jpg|frame|center|Figure 3.8 Microscope image of ciliated protists. From[http://www.microscopy-uk.org.uk/mag/smallimag/2spiro.jpg]]]<br />
<br />
======Flagellates======<br />
<br />
'''Flagellates''' are one of the most commonly known protists and very commonly found in soils. They are unicellular organisms that may be solitary, colonial, free living, or parasitic [24]. The hallmark feature of protists is that at some point in their life cycle, they possess a flagella. A flagellum is a long hair like structure that is used for locomotion, sensation, and sometimes predation [24]. The flagellum makes waves by whiplike lashing movements which propels the cell forwards. Flagellates also have a protective coating in the form of a thin pellicle to protect them from the environment [24]. <br />
<br />
[[Image:9703607_orig.jpg|frame|center|Figure 3.9 Illustration of flaggelates during different life cycle stages. From[http://diagnosticparasitology.weebly.com/uploads/3/9/5/4/3954522/9703607_orig.jpg]]]<br />
<br />
<br />
*'''Euglenids:'''<br />
<br />
Euglenids are found in freshwater and soil, as long as there are organic materials. Euglenid cells do not contain cell walls or other rigid membranes [26]. This gives the cell tremendous flexibility and allows it to change its shape to easily navigate through muddy terrain. Euglenids have two flagella, one which creates locomotion and movement for the cell [26]. The other flagellum does not protrude from the cell and is contained in the cell body [26].<br />
<br />
======Amoebas======<br />
<br />
'''Amoebas'''<br />
<br />
Amoebae are single celled eukaryotes present in many different types of environments and common in soil. They are scattered throughout a variety of eukaryotic lineages and therefore are not monophyletic [27]. Amoebae range in size from 5 micrometers to 3 mm and don’t have a defined shape, commonly recognized for being polymorphic. They are motile through the use of pseudopodia, which stretch and pull the cell along with it. The pseudopodia are also used for feeding. They are able to sense prey that can be engulfed and engulf them via phagocytosis. The amoeba’s main prey consists of bacteria, algae, and other protozoa [28]. The prey is moved around within the cell via food vacuoles, a feature of amoebae [28]. Another key characteristic of amoebae are the large contractile vacuoles inside the cell. The purpose of the contractile vacuole is to osmoregulate by pumping excess water out of the cell. In times of stress, amoebae have an encysted form that helps them get through the tough times. This form is useful when there is low nutrient availability to limit energy consumption. There are two main forms an amoeba can be characterized as. They can either be testate or nontestate. Testate amoeba produce shells, or “tests”, that help identify their species since each species has a unique shell.<br />
<br />
[[Image:Amoeba_(PSF).png|frame|center|Figure 3.10 Amoeba morphology. From[https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Amoeba_(PSF).png/230px-Amoeba_(PSF).png]]]<br />
<br />
=====Slime Molds=====<br />
<br />
'''Slime molds''' were once classified as fungi, but have now been placed in their own phylogenetic groups. Slime molds are single cells that can live independently, but aggregate to form multicellular reproductive structures when necessary [29]. The fruiting body releases spores which germinate into new cells. Slime molds feed off of bacteria and are most commonly found in forests. They feed off of decaying vegetation as well so they can be seen on rotting logs and leaves.<br />
<br />
[[Image:28-30-cellslimemoldlife-l.jpg|frame|center|Figure 3.11 Illustration of slime mold life cycle. From[https://lichencolony.files.wordpress.com/2006/06/28-30-cellslimemoldlife-l.jpg]]]<br />
<br />
==Current Research== <br />
<br />
'''Bacteria:''' To showcase the great diversity of soil bacterial environments, cyanobacteria have been studied in both desert and polar regions. Cyanobacteria can survive in extreme conditions likely because of their long evolutionary past.[16] Dr. Patzelt and his colleagues studied the diverse cyanobacteria residing in the Atacama desert, one of the driest parts of the world. The diverse taxa found in the Atacama desert can withstand prolonged periods of extreme desiccation.[16] The cyanobacteria dominate the soil crusts, affecting soil stability, soil structure and soil fertility.[16] Cyanobacteria inhabiting the Antarctic and Arctic regions, show similar adaptations to extreme environments as the cyanobacteria found in the desert. The polar cyanobacteria are particularly adapted to high altitudes.[17] They can withstand high ultraviolet radiation, desiccation, and repeated freeze-thaw cycles.[17] The autotrophic cyanobacteria supports heterotrophic microbes, providing an important ecosystem service in an environment with low microbial activity.[17]<br />
<br />
'''Archaea:''' In 150 soil samples acquired from North and South America, about 150,000 species were observed.[45] Of these, over 2,500 were identified as archaea based on their ssu rRNA.[45] The archaeal species were further analyzed to understand their role in the soil environment. Of the archaeal groups, ''Crenarchaeota'' and ''Euryarchaeota'' were found.[45] Bates stated that, “Across the non-experimental soils examined the soil C:N ratio was the single best predictor of archaeal relative abundances” due to their influences in the nutrient cycles.[45]<br />
<br />
'''Fungi:''' Fungi have been in the public eye for a while now due to the many different types of secondary metabolites they produce. Some produce bioactive compounds that can inhibit growth of protozoa, bacteria, parasites, insects, and even other fungi. A large area of investigation is the uses of these chemicals for human interests in use from medicine to plant and animal toxins [52].<br />
<br />
'''Protozoa:''' It’s known that Protozoa stimulate plant growth in different ways. It’s suspected that the Protozoa take part in the microbial loop which is responsible for the nutrient production for plants [19]. However, new developments have shown that the Protozoa themselves are responsible for the nitrogen mineralization and that other bacteria have no effect on the plant’s nitrogen sources [19].<br />
<br />
==References==<br />
<br />
1. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). Principles and Applications of Soil Microbiology. New Jersey: Pearson Education Inc.<br />
<br />
2. Ingham, Elaine R. Ingham R. "Chapter 4: SOIL FUNGI." Soil Biology. Natural Resources Conservation Service Illinois, n.d. Web. 9 Feb. 2016<br />
<br />
3. Reid, Greg, and Percy Wong. "SOIL BACTERIA AND FUNGI - NEW SOUTH WALES." Soil Bacteria and Fungi. New South Wales Department of Primary Industries, 2005. Web. 11 Feb. 2016.<br />
<br />
4. "Fungi." Microbiology Online. Microbiology Society, n.d. Web. 11 Feb. 2016.<br />
<br />
5. Tortora, G.J., Funke, B.R., Case, C.L. (2012). “Microbiology an Introduction.” 11th ed. Pearson Benjamin Cummings, San Francisco.<br />
<br />
6. Rizzo, D. “Intro to Fungi.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
7. Rizzo, D. “Ascomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
8. Rizzo, D. “Basidiomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
9. Pegg G.F., Brady B.L. “Verticillium Wilts.” New York, CABI Publishing 2002. Google Books. Web. 11 Feb. 2016. http://books.google.com<br />
<br />
10. Hebert, Paul. "What Is a Protist / What Are Protozoa? - Encyclopedia of Life." Encyclopedia of Life. N.p., n.d. Web. 11 Feb. 2016.http://eol.org/info/456<br />
<br />
11. "MicrobeWorld." Protista. N.p., n.d. Web. 11 Feb. 2016. http://www.microbeworld.org/types-of-microbes/protista<br />
<br />
12. Madigan, M.T., Martinko, J.M. (2006). Brock Biology of Microorganisms. New Jersey: Pearson Prentice Hall.<br />
<br />
13. Roesch, L.F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H.; Camargo, F. A. O.; Farmerie, W. G.; Triplett, E. W.(2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1(4).283-290. <br />
<br />
14. Amann, R.I, Ludwig, W., Schleifer, K.H.(1995).Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology and Molecular Biology Reviews. 59(1). 143-169. <br />
<br />
15. Geers, D., Cohan, F.M., Lawrence J.G., Spratt, B.G., Coenye, T. Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005). Opinion: Re-evaluating prokaryotic species. Nature Reviews Microbiology. 3(9). 733-739.<br />
<br />
16. Patzelt, D.J., Hodac, L., Friedl, T., Pietrasiak, N., Johansen, J.R. (2014). Biodiversity of soil cyanobacteria in the hyper-arid Atacama Desert, Chile. Journal of phycology. 50(4). 698-710. <br />
<br />
17. Makhalanyane, T. P., Valverde, A., Velázquez, D., Gunnigle, E., Van Goethem, M. W., Quesada, A., & Cowan, D. A. (2015). Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats. Biodiversity and Conservation, 24(4), 819-840.<br />
<br />
18. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist>.<br />
<br />
19. Ekelund, Flemming; Saj, Stephane; Vestergård, Mette; Bertaux, Joanne; Mikola, Juha. (2009). “The “soil microbial loop” is not always needed to explain protozoan stimulation of plants”. Soil Biology & Biochemistry. Vol. 41 Issue 11, p2336-2342, 7p.<br />
<br />
20. Bonkowski, Michael. "Protozoa and Plant Growth: The Microbial Loop in Soil Revisited." New Phytologist New Phytol 162.3 (2004): 617-31. Web.<br />
<br />
21. Hoorman, James. "The Role of Soil Protozoa and Nematodes." Fact Sheet (n.d.): n. pag. Ohio State University, 2011. Web.<br />
<br />
22. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist<br />
<br />
23. Lynn, Denis H(Apr 2012) Ciliophora. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001966.pub3]<br />
<br />
24. "flagellate". Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc., 2016. Web. 23 Feb. 2016 <http://www.britannica.com/science/flagellate>.<br />
<br />
25. "Mastigophora." World of Microbiology and Immunology. 2003. Encyclopedia.com. 23 Feb. 2016<http://www.encyclopedia.com>.<br />
<br />
26. “Plant Life." : Euglenoids. N.p., n.d. Web. 23 Feb. 2016. <http://lifeofplant.blogspot.com/2011/04/euglenoids.html><br />
<br />
27. Parales, R.E. and Martin, M. (2015) Microbial Diversity Laboratory Manual, MIC 105L, Winter 2015. Department of Microbiology and Molecular Genetics, College of Biological Sciences, The University of California, Davis.<br />
<br />
28. Arnold, Paul. "What Does an Amoeba Eat? Plus Other Ameoba Info and Questions." Bright Hub. N.p., n.d. Web. 04 Mar. 2016.<br />
<br />
29. "MicrobeWorld." Slime Molds. N.p., n.d. Web. 24 Feb. 2016. <http://www.microbeworld.org/types-of-microbes/protista/slime-molds><br />
<br />
30. Leeuwenhoek., A. V. (2009, November 18). One gram of soil: A microbial biochemical gene library. Retrieved March 13, 2016, from http://www.ncbi.nlm.nih.gov/pubmed/19921459 <br />
<br />
31. Coleman, D. C., Crossley, D. A. & Hendrix, P. F. "Soil food webs: Detritivory and microbiology in soils," in Fundamentals of Soil Ecology, 2nd ed. (Elsevier, 2004) 236-241.<br />
<br />
32. Welcome to Agriinfo.in. (n.d.). Retrieved February 21, 2016, from http://agriinfo.in/?page=topic&superid=5&topicid=172 <br />
<br />
33. Gouthro, T., & Rice, D. (1987, December 15). Interaction Terminology. Retrieved February 21, 2016, from http://www.rpi.edu/dept/chem-eng/Biotech-Environ/MixCul/ecodefn.htm <br />
<br />
34. AMENSALISM. (n.d.). Retrieved February 21, 2016, from https://biostuds.wikispaces.com/AMENSALISM <br />
<br />
35. Natural Resources Conservation Service. (n.d.). Retrieved March 10, 2016, from <br />
http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053865 <br />
<br />
36. Ecological Linkages Between Aboveground and Belowground Biota. (n.d.). Retrieved March 10, 2016, from http://science.sciencemag.org/content/304/5677/1629 <br />
<br />
37. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf<br />
<br />
38. Kingdom Archaea. (n.d.). Retrieved March 10, 2016, from http://plantphys.info/organismal/lechtml/archaea.shtml <br />
<br />
39. What are Archaea? - Encyclopedia of Life. (n.d.). Retrieved March 10, 2016, from http://eol.org/info/457 <br />
<br />
40. Flagellum. (n.d.). Retrieved March 10, 2016, from http://www.newworldencyclopedia.org/entry/Flagellum#Archaeal_flagellum <br />
<br />
41. Archaea: Morphology. (n.d.). Retrieved March 10, 2016, from http://www.ucmp.berkeley.edu/archaea/archaeamm.html <br />
<br />
42. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf <br />
<br />
43. Archaea. (n.d.). Retrieved March 10, 2016, from http://www.eoearth.org/view/article/150172/ <br />
<br />
44. Binary Fission: Cell Division & Reproduction of Prokaryotes. (n.d.). Retrieved March 10, 2016, from http://www.scienceprofonline.com/microbi <br />
<br />
45. Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2010, November 18). Examining the global distribution of dominant archaeal populations in soil. Retrieved February 21, 2016, from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105767/<br />
<br />
46. Scow, K. M. "Lecture 1 Part 1." Lecture, Davis.<br />
<br />
47. Rizzo, D. "Lecture 1." Lecture, Davis.<br />
<br />
48. Rizzo, D. "Lecture 3." Lecture, Davis.<br />
<br />
49. C.J. Alexopoulos & C. W. Mims, Introductory Mycology 3rd edition. 1979. Wiley NY. Web accessed Mar 8, 2016 from http://www.ucmp.berkeley.edu/fungi/fungimm.html<br />
<br />
50. Rizzo, D. "Lecture 2." Lecture, Davis.<br />
<br />
51. Ingham, E. “Chapter 4: Soil Fungi” (2016) Oregon State University. Retrieved Feb. 20, 2016, from http://extension.illinois.edu/soil/SoilBiology/fungi.htm<br />
<br />
52. Keller, N., Turner, G., Bennett, J. “Fungal Secondary Metabolism- from Biochemistry to Genomics.” 2005 Nature Reviews Microbiology p/ 937 to 947.</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Introduction_to_Organisms&diff=132726
Introduction to Organisms
2018-01-08T06:03:56Z
<p>Kmscow: /* Flagellates */</p>
<hr />
<div>{{Uncurated}}<br />
==Introduction== <br />
The soil ecosystem in an important environment that allows both plants and animals to survive, grow and reproduce. The significance of the soil as an ecosystem is at times overlooked despite its major contributions to the environment. The [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] is a complex and varied microbial habitat.[1] The plants and organisms inhabiting the soil contribute to its thriving diversity. Soil life is diverse in morphology, metabolism, size, and many other characteristics. Soil is a heterogeneous environment with various zones of rhizosphere, aggregates, organic matter and animal residues.[31] Given each zone is a small component of the larger soil ecosystem, rhizosphere accounts for only 5 to 7 percent of the soil environments but contains over “70 percent of the bacterial- and fungal-feeding nematodes.”[31] <br />
<br />
Since soil microbial diversity is immense, with all three domains of life: Archaea, Bacteria and Eukarya represented in the soil environment, it is not possible to discuss each microbial species (many of which have not even been described!). Only a few representative groups of each domain will be discussed to provide examples of the roles these organisms play in soil.<br />
<br />
==Soil Food Web and Microbial Interactions== <br />
<br />
To survive in a soil environment, an organism must be able to adapt to a constantly changing environment and to interactions with other organisms. One type of interaction shown in (Figure 2.1) is predation. Other common interactions in the soil environment are: <br />
<br />
:[[Image:soil_foodweb72.jpg|frame|center|Figure 2.1 Soil Food Web. From[http://www.exploringnature.org/graphics/foodwebs/soil_foodweb72.jpg]]]<br />
<br />
<br />
'''I. Commensalism:''' Organism (A) benefits from the presence of Organism (B) while (B) is unaffected by the presence of (A).[32]<br />
<br />
'''II. Mutualism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) and becomes a necessary association for each other’s survival. [32] [33]<br />
<br />
'''III. Synergism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) but the relationship is not necessary for survival.[33]<br />
<br />
'''IV. Competition:''' Depending on the organisms this interaction benefits organisms who can readily adapt to the environment and overcome any obstacles needed to survive, grow and reproduce.[33]<br />
<br />
'''V. Amensalism:''' An interaction in which Organisms (A) and (B) develop a partnership where (B) is unaffected by (A) but organism (A) is negatively affected by (B).[34]<br />
<br />
'''VI. Parasitism:''' Organism (A) benefits from Organism (B) but Organism (B) does not benefit positively from Organism (A). <br />
<br />
'''VII. Predation:''' “An interaction between organisms in which one benefits and one is harmed based on the ingestion of the smaller sized organism, the prey, by the larger organism, the predator.”[33]<br />
<br />
<br />
<br />
The soil food web consists of microbes, fauna (micro and macro) and plant roots, who play multiple essential roles in soil ecosystem. The interactions between members of the soil food web result not only in chemical processes such as nutrient cycling and biodegradation of pollutants, but also in creation of soil structure, e.g. of aggregates.[35].<br />
<br />
In (Figure 2.1), all three domains, Archaea, Bacteria, and Eukarya, are represented in the soil food web. Thel food web is not only dependent on living creatures but also on decaying organic matter and plant roots. Dead and living matter in the soil environment, including plant roots, contribute to the maintenance of the food web.<br />
<br />
==3 Domains==<br />
[[Image:Big_Tree_Bold_Letters_white.png|frame|center|Figure 3.1 Phylogenetic Tree of the 3 Domains. From[http://phylogenomics.blogspot.com/2014_02_01_archive.html]]]<br />
<br />
===Carl Woese and Phylogeny===<br />
<br />
[[Image:Carlwoese1_0565_b.jpg|frame|center|Figure 3.2 Carl Woese. From[http://ofbacteriaandmen.blogspot.com/2013/01/the-new-biology-of-carl-woese.html]]] <br />
<br />
Carl Woese (Figure 3.2) was an American microbiologist famous for pioneering the technique of phylogenetic taxonomy through use of a 16S (for prokaryotic) and 18S (for eukaryotic) ribosomal RNA, also known as small subunit ribosomal RNA [46]. This refined Linnaean classification, taking out the guesswork classification by using a gene that was present in every living organism- the small subunit ribosomal RNA. This method of classification is comprehensive because all organisms possess this form of genetic material. Ssu rRNA is sequenced because the genes are highly conserved. Due to their functional constancy, some have variable regions to differentiate organisms, and are easy to sequence. This technique also elucidated the tree of life, which shows the three domains of microbial lineage diversity: Bacteria, Archaea, and Eukarya. DNA can be compared using a sample database that allows identification of unknown organisms to a species level.<br />
<br />
===Domain Bacteria===<br />
<br />
====Introduction to Bacteria==== <br />
Bacteria are single celled prokaryotic organisms that lack membrane bound organelles. They are involved in many important processes within the soil such as decomposition, [https://microbewiki.kenyon.edu/index.php/Bioremediation bioremediation], symbiosis and biological transformation of nutrients. They are present in all terrestrial soil environments.[1] Soil is a heterogenous environment that varies in moisture content, temperature, oxygen requirements, carbon source and many other bacterial growth conditions. Those wide ranging growth factors account for the enormous diversity in soil bacteria populations. One gram of soil can contain between 26,000 to 52,000 different bacterial species.[13] In the entire microbial world, only about 1 percent of bacterial species can be cultured under laboratory conditions which leaves an immense number of bacterial species yet to be described. [14]<br />
<br />
Classification based on phenotypic characteristics, such as cellular morphology, metabolism, gram staining, oxygen requirements, carbon source and other traits, was used more readily before modern DNA sequencing. But, phenotypic classification is still used and Bergey’s Manual of Systematic Bacteriology is the most widely used source for determining species based on characteristic species traits.<br />
<br />
Traditional species definitions are not as useful in bacteria. OTUs, or operational taxonomic units, based on DNA sequencing similarity, are more applicable to bacteria. Typically, those bacteria with 97 percent similar DNA sequence are classified within the same OTU.[15] The 16S small subunit ribosomal RNA is used to substantiate phylogenetic relationships between different bacterial groups.<br />
<br />
====Morphology====<br />
<br />
Bacterial cells measure approximately 1μm wide and 1-5μm long.[12] They are smaller than eukaryotic microbes.Due to their small size, bacteria can more easily adapt to changing soil environments than larger eukaryotes.[1] Most bacteria are singled celled, but actinomycetes grow in branching filaments. There are many different bacterial cell shapes. The most common are bacilli (rods), cocci (spheres), spirilla (spirals) and actinomycete (filaments).<br />
[[Image:bacteria_sizes.jpg|frame|center|Figure 3.3 Common cell shapes cocci, bacillus, and spirilla and relative sizes. From[http://www.ppdictionary.com/gnbac.htm]]]<br />
<br />
'''Flagella''' - There are many different types and different arrangement of flagella. Movement in soil environments is dependent on soil moisture content. Though movement in soil is limited, flagellar function is important to allow bacteria to find more favorable microsites.[1]<br />
<br />
'''Cell membrane''' - The cell membrane encloses the cytoplasm. It is semi-permeable phospholipid bilayer that regulates transport of nutrients into the cell and waste products out of the cell.<br />
<br />
'''Cell wall''' - Most bacteria have a rigid cell wall surrounding the cell membrane which protects the cell from osmotic lysis. The cell wall is made of a crosslinked polysaccharide, called peptidoglycan, that is found only in bacteria.[1] The cell wall gives the cell shape and structure, but it is porous enough to permit small water soluble molecules to flow through to the cell membrane surface.[1]<br />
<br />
*'''Gram positive''' bacteria have a thick cell wall made of several layers of peptidoglycan. The cell wall is the outermost structure, as they do not have an outer membrane. The thick cell wall structure make gram positive bacteria more resilient to osmotic shock. Gram positive bacteria can tolerate 5 to 10 times more turgor pressure than gram Gram negative bacteria.[1] Teichoic acids in the cell wall may also help to bind to cationic nutrients in soil surroundings.[1] <br />
<br />
*'''Gram negative''' bacteria have a thin cell wall surrounded by an outer membrane made of phospholipids and lipopolysaccharides. Polysaccharides of the outer membrane interact with surrounding cations and are involved in attachment of bacteria to soil particles. [1] Periplasm is a gel like substance that occupies the space between the outer membrane and the cell wall of gram negative bacteria.[1] The outer membrane and periplasmic space is thought to provide protection from environmental toxins.[1] Proteins within the periplasm are thought to begin the process of catalyzing hydrolysis of organic and toxic substances.[1] <br />
<br />
[[Image:gramposnegmembrane.jpg|frame|center| Figure 3.4 Illustration of Gram positive and Gram negative cell wall structures. From[http://micro.digitalproteus.com/morphology2.php]]]<br />
<br />
'''Endospores''' are made by ''Bacillus'' and ''Clostridium'' in response to environmental stress.[1] Endospores are extremely resistant structures that can withstand extreme temperatures up to 150℃.[12] They can also withstand extreme pressure, desiccation, radiation, pH and chemicals.[12] The endospore protects the bacterial DNA until environmental conditions are more favorable and germination can proceed. Soil is the most common habitat for endospore forming bacteria.[12]<br />
<br />
'''Extracellular polymers''' - Many bacteria secrete a slime layer or capsule made of polysaccharides or glycoproteins.[1] The outer polysaccharide coating of bacteria helps in attachment to surfaces and the formation of biofilms.[1] Bacterial capsule secretions play a big role in soil aggregation and soil structure.[1] When the carbon to nitrogen ratio within soils is high, microbes secrete the excess carbon as extracellular polysaccharides.[1]<br />
<br />
====Reproduction==== <br />
Most bacteria reproduce by binary fission.[12] The bacterial cell expands to twice the original cell size, duplicates the bacterial DNA and pinches off, producing two daughter cells. Each resultant daughter cell is a clone of the parent cell. Prokaryotic Archaea also reproduce by binary fission.<br />
<br />
*'''Spore formation:''' Actinomycetes are a large group of filamentous bacteria, primarily found in soil.[1] Actinomycetes are morphologically similar to fungi. Actinomycetes form long filaments called hyphae. Unlike most bacteria, the majority of actinomycetes reproduce using asexual spores called conidia.[1] Though they share many characteristic with fungi, actinomycetes are still prokaryotes. They are smaller than fungi and the cell wall contains peptidoglycan.[1] Actinomycetes break down a wide variety of organic compounds and play an important role in organic matter decomposition. [1] ''Streptomyces'', a subgroup within actinomycetes, produce geosmin, which gives soil the characteristic earthy smell.[12]<br />
<br />
====Metabolism==== <br />
<br />
Along with archaea, bacteria are the most metabolically diverse and employ many different nutritional strategies.[1]<br />
*Heterotrophs - Most bacteria are heterotrophic, obtaining carbon from preformed organic substances. [1] <br />
*Autotrophs - Carbon dioxide serves as the main source of carbon. Some cyanobacteria, nitrifying and sulfur-oxidizing bacteria are autotrophs.[1]<br />
*Organotrophs - Most bacteria obtain electrons from organic substances.[1]<br />
*Lithotrophs - Some cyanobacteria, nitrifying bacteria and sulfur-oxidizing bacteria obtain electrons from inorganic substances.[1]<br />
*Phototrophs - Cyanobacteria use light as the main source of metabolic energy.[1]<br />
*Chemotrophs - All other nonphotosynthetic bacteria do not rely on light for metabolic energy.[1]<br />
<br />
====Contributions to Biogeochemical Cycling==== <br />
<br />
Bacteria play a significant role in the cycling of a wide range of elements.<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Carbon_cycle '''Carbon Cycle:'''] <br />
<br />
*'''Carbon Assimilation''' is the process of fixing carbon dioxide into organic forms. Carbon fixation is performed by autotrophic bacteria, such as cyanobacteria.[1] Chemoautotrophic nitrifying bacteria, such as ''Nitrobacter, Nitrosospira'' and ''Nitrosomonas'', also fix carbon.[1] Sulfur oxidizing bacteria, such as ''Thiobacillus'', fix carbon as well.<br />
<br />
*'''Carbon Mineralization''' results from microbial decomposition of organic carbon compounds into inorganic forms. As the organic carbon substances, like plant matter, are decomposed, inorganic carbon dioxide is produced. Most bacteria are heterotrophs that perform carbon mineralization. When microorganisms die, they are decomposed by successive microbial generations. Peptidoglycan, the main component of bacterial cell walls, is utilized as a polysaccharide substrate by other heterotrophic soil microbes.[1]<br />
<br />
*'''Methanogenesis''' - Methanogenic bacteria produce methane from the reduction of carbon dioxide. They are all strict anaerobes that use carbon dioxide for the carbon source.[1] They can all use hydrogen as a source of energy and electron donor. [1]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle '''Nitrogen cycle:''']<br />
<br />
*'''Nitrogen fixation:''' ''Azotobacter'' is a free living nitrogen fixing bacteria.[1] ''Rhizobium'' lives in a mutualistic relationship with plants by fixing nitrogen within root the nodules of legumes.[1] ''Anabaena'' and ''Nostoc'' have specialized heterocyte structures where nitrogen fixation occurs.[1] <br />
<br />
*'''Nitrification:''' Nitrifying bacteria, such as ''Nitrobacter, Nitrosospira,'' and ''Nitrosomonas'', oxidize ammonium to nitrate.[1] <br />
<br />
*'''Denitrification:''' ''Alcaligenes, Flavobacterium'', and ''Pseudomonas'' are common soil denitrifying bacteria.[1]<br />
<br />
===Domain Archaea===<br />
<br />
====Introduction to Archaea====<br />
<br />
Vladimir Vernadsky decided, in 1926, that only two domains of life existed on Earth, Bacteria and Eukarya.[37] About 50 years later in 1977, Carl Woese and George Fox theorized that part of the bacterial domain possed multiple dissimilarities from bacteria and recognized it to be another domain of life, now called Archaea.[38] Woese and Fox’s theory regarding the differences of archaea were confirmed in 1990’s through the use of 16S rRNA and 18S rRNA.[38] <br />
<br />
Despite the strongly held belief, in the 1990s, that archaea only inhabited extreme environments, recent discoveries have suggested their presence in abundant numbers all throughout the Earth. It is suggested that Archaea play notable roles in maintaining nutrient cycles.[37] Various methods of research, such as cultivation, culture-independent techniques and isotope-based methods, have facilitated the study of domain Archaea in carbon and nitrogen cycling. [37]<br />
<br />
The use of genomic and biochemical data has permitted the study of archaeal structure.[37] Use of these research methods has shown that domain archaea and domain bacteria differ in cell wall characteristics yet, share various ways to transfer genetic information by replication and transcription from their common ancestor, Eukarya.[37] As of 2012, 116 genera of Archaea have been observed which consists of 450 species. Most of the archaeal species in these genera remains uncultivated, known only through its gene sequences and molecular surveys.[37]<br />
<br />
====Morphology==== <br />
Archaea are characterized by various cell sizes. They are most commonly found to be small organisms ranging from “0.1 to 15 μ diameter and up to 200 μ long.”[38] The shape of many archaea are similar to bacteria, including bacillus, cocci, spirilla and “plate-like forms.” [38] Their cell membranes have ether linked lipids with no periplasmic space, similar to gram-positive bacteria, and contain no intracellular organelles.[39]<br />
<br />
'''Flagella:''' Most motile archaea inhabit a motor rotary system that allows it to move its flagella through the chemical gradient similar to bacteria.[39] Despite its similarity in function and source of energy required for motility, the flagella of both archaea and bacteria differ in structure.[39] Archaeal flagella gets the energy for its movement by ATP and is composed of dependent filaments that rotate singularly. [40] Archaeal flagella are known to be thinner than bacteria flagellin.[40] Since, the archaeal common ancestor is not bacteria but eukarya, convergent evolution is a plausible explanations for the differences between bacterial and archaeal flagellin. [40]<br />
<br />
'''Membranes:''' Archaea have a cell membrane that protects the cytoplasm and the nucleic acids from the environment. The archaeal cell membrane has a lipid bilayer with glycol-ether lipids that are more stable than ester linkages and help some archaea that live in extreme environments to withstand such conditions.[39] Most archaeal species are surrounded by a cell wall which protects the cell membrane and maintains the archaeal structure.[41]<br />
<br />
====Reproduction====<br />
Archaeal organisms reproduce by binary fission since they do not have nucleases thus, the DNA chromosome in a Archaeal organism replicate, separate and create two daughter cells.[43] The process of binary fission can be seen in Figure (3.5) process begins the parent cell duplicating the DNA. The DNA material then goes to the sides of the cell where an invagination to the cell occurs allowing the cell to become two individual cells. Binary fission is a very fast reproduction process, that allows archaeal organisms to grow at an exponential rate.[44]<br />
<br />
[[Image:WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg|frame|center|Figure 3.5 Illustration of binary fission. From[https://d2jmvrsizmvf4x.cloudfront.net/WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg]]]<br />
<br />
====Metabolism==== <br />
Archaea share similar metabolic characteristics to bacteria. The metabolic pathways taken by all archaea shown in the (Figure 3.6) demonstrates the great diversity and variation amongst archaea. [38] The kinds of archaea that are seen in the environment and the metabolic pathways taken by some can be summarized in the image. <br />
<br />
*Photoautotrophs: use light as an energy source and carbon dioxide as the carbon source with the help of the Calvin Cycle.[38]<br />
*Chemoautotrophs: use inorganic chemicals as their energy source and carbon dioxide as carbon source. <br />
*Chemoheterotrophs: take organic chemicals as energy source and organic chemicals as carbon source. The pathways taken by chemoheterotrophs varies from respiration by the Krebs Cycle to fermentation. [38]<br />
*Photoheterotrophs: use light as their energy source and organic chemicals as their carbon source. <br />
<br />
Most archaea inhabiting in the soil environment are major contributors to the biogeochemical cycles.<br />
<br />
[[Image:2000px-Troph_flowchart.svg.png|thumbnail|center|Figure 3.6 Flowchart showing different metabolic pathways. From[https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Troph_flowchart.svg/2000px-Troph_flowchart.svg.png]]]<br />
<br />
====Contributions to the Cycle====<br />
Archaea play a significant role in the nutrient cycles that take place in the ecosystem as they account for about 1-5% of all the prokaryotes present in the soil environment.[42]<br />
<br />
'''Carbon Cycle:''' Archaea have an important role in the carbon cycle that takes place specifically in methane production, carbon mineralization and carbon assimilation all of all of which contribute to the soil’s carbon sink.[42] The carbon dense soil helps to make the soil organic matter rich and helps to form extracellular polymers which creates stable aggregates. For some microbes, an electron acceptor is need to carry out metabolic functions. [42] More info on [https://microbewiki.kenyon.edu/index.php/Carbon_cycle Carbon Cycle].<br />
<br />
*'''Carbon Assimilation:''' Involves the transformation of inorganic carbon into organic carbon compounds. This process is commonly done by autotrophic phyla ''Crenarchaeota, Thaumarchaeota'', and ''Euryarchaeota'' that use carbon dioxide/ bicarbonate converting it to organic compounds.[42] Of the autotrophic lineages observed in carbon assimilation the ''Thaumarchaeota'' are strict autotrophs, the ''Euryarchaeota'' and ''Crenarchaeota'' are facultative autotrophs and the ''Halobacteriales'' and ''Thermococcales'' are obligate heterotrophs.[42] <br />
<br />
*'''Carbon Mineralization:''' The process that converts organic carbon into the oxidized inorganic carbon, carbon dioxide is commonly done by both aerobes and anaerobes.[42] The heterotrophic microbes that use organic compounds as energy to oxidize the carbon source include, methanogens and methane-oxidizing archaea belonging to the phyla ''Euryarchaetota'', and ''Crenarchaeota''.[42] <br />
<br />
*'''Methanogenesis:''' production of methane, a major greenhouse gas in the Earth’s atmosphere is commonly done by archaea upon reducing an oxidized compound.[42] The phyla ''Euryarchaeota'' is the only phyla that consists of archaea that produce methane all of which form five class: ''Methanopyri, Methanococci, Methanobacteria, Methanomicrobia'' and ''Thermoplasmata''.[42] Methanogens are commonly found in anaerobic and aerobic conditions such as bodies of water, aerated soils and oxygenated waters.[42]<br />
<br />
'''Nitrogen Cycle :''' Archaea play a pivotal role in the Nitrogen cycle and help create nitrogenous products for the plants and microbes. More info on [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle Nitrogen cycle].<br />
<br />
*'''Nitrogen Fixation:''' Fixing nitrogen from the environment and converting it to organic nitrogen in the soil or to inorganic nitrogenous form since both organic and inorganic products are in short supply in the biosphere and are fixed by many archaeal organisms.[42] N2 fixation by the environment is usually done by three major archaeal classes ''Methanobactera, Methanococci'' and ''Methanomicrobia''.[42] <br />
<br />
*'''Nitrification:''' Converting the ammonia (NH4+) in the soil to nitrite (NO2-) produces nitrate (NO3-) as an intermediate. [42] The transformation of ammonia to first nitrate then to nitrite is a two step process that is done by different microbes. [42] Most common organisms involved in nitrification include ammonia-oxidizing archaea which are lithotrophic organisms mostly, of the ''Thaumarchaeota'' phylum from the archaea domain. <br />
<br />
*'''Denitrification :''' The conversion of atmospheric N2 using the electron acceptor NO3- or NO2- creating the formation of nitric oxide, nitrous oxide and/or N2.[42] The formation of the end product N2 may not always be produced but other intermediates NO and N2O, greenhouse gases may be produced.[42] Of the archaeal organisms that have been studied in denitrification process is done by ''Pyrobaculum aerophilum'' which accepts both NO3- and NO2- as an electron acceptor producing a variety of products NO2-, NO, N20 and N2.[42]<br />
<br />
===Domain Eukarya===<br />
<br />
====Fungi====<br />
<br />
=====Introduction=====<br />
<br />
'''Introduction'''<br />
<br />
Fungi comes from the ancient Greek word “sphongos” meaning sponge in reference to the mushroom cap [47]. Fungi have the general characteristics of being eukaryotic, heterotrophic, external absorbers of nutrients, containing a hyphal thallus, reproducing via spore, and being pleomorphic (producing several forms). Fungi are generally organoheterotrophs that can survive in low pH and stay active at low moisture content[46]. Fungi reside in the domain Eukarya with an estimated species of 1.5 million, and less than five percent of them have ever been described. The general phyla included within Kingdom Fungi include Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, Chytridiomycota, and Microsporidia [48].<br />
<br />
[[Image:magical-kingdom-620.jpg|frame|center|Figure 3.7 Fungi phyla hierarchy. From.[http://www.motherjones.com/environment/2009/11/fungi-family-tree]]]<br />
<br />
=====Morphology=====<br />
<br />
'''Morphology''' <br />
<br />
Fungi can be either unicellular (yeasts) or multicellular. All multicellular fungi are made up of small, filamentous particles called hyphae. Some hyphae have cross walls called septa, while others do not- this is a large basis of fungal identification. Fungal cells generally have multiple nuclei. Fungal cell walls are generally composed of chitin, a long carbohydrate polymer that adds rigidity and structural support to fungi [49]. <br />
<br />
=====Reproduction=====<br />
<br />
'''Reproduction'''<br />
<br />
Fungal reproduction can occur either sexually or asexually.<br />
<br />
'''Sexual reproduction''' can occur by homothallic or heterothallic mycelia.<br />
<br />
'''Asexual reproduction''' can occur by fragmentation, budding, or by producing spores (the most common method). <br />
<br />
*'''Spores:''' spores come in many different forms. One of the most well known are conidiospores, which are unicellular or multicellular spores that get released from the tip of the hyphae. <br />
<br />
'''Perfect fungi''' are those that can reproduce both sexually and asexually while imperfect fungi are those that can only reproduce asexually.<br />
<br />
*Sexual reproduction always includes the stages plasmogamy (fusion of two haploid cells), karyogamy (creation of a diploid zygote), and meiosis (gametes are created).<br />
<br />
=====Metabolism=====<br />
<br />
'''Metabolism'''<br />
<br />
Many different fungi display a myriad of metabolisms. There are primary metabolites that that help the fungi function properly, and secondary metabolites that are generally bioactive that are not the most pertinent to fungal growth (they can live without these). Secondary metabolites play a large role in chemistry today and can be manufactured into commonly used products such as new drugs. In general fungi are heterotrophic through release of extracellular enzymes into the neighboring environment to break complex molecules down into smaller ones. The materials are then absorbed and metabolized [50]. Fungi are sessile organisms that overcome their little to no movement through apical growth at the hyphal tip. Fungi are noted to grow almost everywhere on the Earth.<br />
<br />
=====Relevance to soil===== <br />
<br />
'''Relevance to soil'''<br />
<br />
Fungi include some of the most abundant biomass of microorganisms in numerous soils. They play an important role as decomposers within the soil food web through conversion of difficult to digest organic material into forms many other organisms can use [51]. Their hyphae can bind soil particles together and create aggregates that increase soil water holding capacity. They perform important functions from water dynamics to nutrient cycling and disease suppression. Soil fungi can be categorized into three different groups based on their actions: <br />
<br />
*decomposers: that convert dead organic material into fungal biomass<br />
<br />
*mutualists: which colonize plant roots and help solubilize phosphorous and bring soil nutrients<br />
<br />
*pathogens/ parasites: which help control diseases in soil via trapping organisms such as nematodes [51]. <br />
<br />
Fungi are seen common in intensively managed agricultural soils due to tillage disrupting hyphae. Fungi also play a very important role in the [https://microbewiki.kenyon.edu/index.php/Rhizosphere_Interactions rhizosphere], the region of soil that is greatly influenced by the plant root system. This area of soil which is concentrated in plant roots and fungal hyphae is known to support greater microbial activity.<br />
<br />
=====Protozoans=====<br />
<br />
'''Protozoans'''<br />
<br />
In general, Protozoans range from 5 to 500 µm in diameter, making them significantly larger than bacteria [21]. They are abundantly located near the surface of the soil (15cm deep) where roots are plentiful [21]. Many protozoans have two life cycles. One is their active form where they are motile and feed on prey. The other is the cyst form where they produce a thick coating to protect them from the environment and can go dormant for years. The protozoa are divided into 4 major categories: the ciliates, the flagellates, the heliozoans, and the amoebas [10]. <br />
<br />
======Ciliates======<br />
<br />
'''Cilliates:'''<br />
This group, within protozoans, is fairly diverse. A common feature shared amongst all of its members is the presence of at least one cilia at any stage of its development [10]. The cilia is used for movement and other things such as predation (tentacles). For movement, they use the massive amounts of tiny cilia to create wave like currents to propel the cell forwards. Most ciliates also have toxicysts which are used to capture prey [10]. Some ciliates even have a symbiotic relationship with algae living inside of them [10]. The algae use the CO2 produced by ciliates and turn it into O2 that can then be reused by the ciliates [10]. They are found in a wide array of habitats ranging from freshwater and soil to the rumen of Animals [22]. They are present in almost anywhere that contains water [23]. They are unicellular heterotrophs so they feed on bacteria and algae in their environment. Ciliates are one of the top predators in the microbial food web and are hypothesized to have been a major predatory group before animals evolved [23]. The large size of ciliates and their rigid cell structure make them less common in unsaturated soils than other types of protozoa.<br />
<br />
[[Image:2spiro.jpg|frame|center|Figure 3.8 Microscope image of ciliated protists. From[http://www.microscopy-uk.org.uk/mag/smallimag/2spiro.jpg]]]<br />
<br />
======Flagellates======<br />
<br />
'''Flagellates''' are one of the most commonly known protists and very commonly found in soils. They are unicellular organisms that may be solitary, colonial, free living, or parasitic [24]. The hallmark feature of protists is that at some point in their life cycle, they possess a flagella. A flagellum is a long hair like structure that is used for locomotion, sensation, and sometimes predation [24]. The flagellum makes waves by whiplike lashing movements which propels the cell forwards. Flagellates also have a protective coating in the form of a thin pellicle to protect them from the environment [24]. <br />
<br />
[[Image:9703607_orig.jpg|frame|center|Figure 3.9 Illustration of flaggelates during different life cycle stages. From[http://diagnosticparasitology.weebly.com/uploads/3/9/5/4/3954522/9703607_orig.jpg]]]<br />
<br />
<br />
*'''Euglenids:'''<br />
<br />
Euglenids are found in freshwater and soil, as long as there are organic materials. Euglenid cells do not contain cell walls or other rigid membranes [26]. This gives the cell tremendous flexibility and allows it to change its shape to easily navigate through muddy terrain. Euglenids have two flagella, one which creates locomotion and movement for the cell [26]. The other flagellum does not protrude from the cell and is contained in the cell body [26].<br />
<br />
======Amoebas======<br />
<br />
'''Amoebas'''<br />
<br />
Amoebae are single celled eukaryotes present in many different types of environments. They are scattered throughout a variety of eukaryotic lineages and therefore are not monophyletic [27]. Amoebae range in size from 5 micrometers to 3 mm and don’t have a defined shape, commonly recognized for being polymorphic. They are motile through the use of pseudopodia, which stretch and pull the cell along with it. The pseudopodia are also used for feeding. They are able to sense prey that can be engulfed and engulf them via phagocytosis. The amoeba’s main prey consists of bacteria, algae, and other protozoa [28]. The prey is moved around within the cell via food vacuoles, a feature of amoebae [28]. Another key characteristic of amoebae are the large contractile vacuoles inside the cell. The purpose of the contractile vacuole is to osmoregulate by pumping excess water out of the cell. In times of turmoil, amoebae have an encysted form that helps them get through the tough times. This form is useful when there is low nutrient availability to limit energy consumption. There are two main forms an amoeba can be characterized as. They can either be testate or nontestate. Testate amoeba produce shells, or “tests”, that help identify their species since each species has a unique shell.<br />
<br />
[[Image:Amoeba_(PSF).png|frame|center|Figure 3.10 Amoeba morphology. From[https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Amoeba_(PSF).png/230px-Amoeba_(PSF).png]]]<br />
<br />
=====Slime Molds=====<br />
<br />
'''Slime molds''' were once classified as fungi, but have now been placed in their own phylogenetic groups. Slime molds are single cells that can live independently, but aggregate to form multicellular reproductive structures when necessary [29]. The fruiting body releases spores which germinate into new cells. Slime molds feed off of bacteria and are most commonly found in forests. They feed off of decaying vegetation as well so they can be seen on rotting logs and leaves.<br />
<br />
[[Image:28-30-cellslimemoldlife-l.jpg|frame|center|Figure 3.11 Illustration of slime mold life cycle. From[https://lichencolony.files.wordpress.com/2006/06/28-30-cellslimemoldlife-l.jpg]]]<br />
<br />
==Current Research== <br />
<br />
'''Bacteria:''' To showcase the great diversity of soil bacterial environments, cyanobacteria have been studied in both desert and polar regions. Cyanobacteria can survive in extreme conditions likely because of their long evolutionary past.[16] Dr. Patzelt and his colleagues studied the diverse cyanobacteria residing in the Atacama desert, one of the driest parts of the world. The diverse taxa found in the Atacama desert can withstand prolonged periods of extreme desiccation.[16] The cyanobacteria dominate the soil crusts, affecting soil stability, soil structure and soil fertility.[16] Cyanobacteria inhabiting the Antarctic and Arctic regions, show similar adaptations to extreme environments as the cyanobacteria found in the desert. The polar cyanobacteria are particularly adapted to high altitudes.[17] They can withstand high ultraviolet radiation, desiccation, and repeated freeze-thaw cycles.[17] The autotrophic cyanobacteria supports heterotrophic microbes, providing an important ecosystem service in an environment with low microbial activity.[17]<br />
<br />
'''Archaea:''' In 150 soil samples acquired from North and South America, about 150,000 species were observed.[45] Of these, over 2,500 were identified as archaea based on their ssu rRNA.[45] The archaeal species were further analyzed to understand their role in the soil environment. Of the archaeal groups, ''Crenarchaeota'' and ''Euryarchaeota'' were found.[45] Bates stated that, “Across the non-experimental soils examined the soil C:N ratio was the single best predictor of archaeal relative abundances” due to their influences in the nutrient cycles.[45]<br />
<br />
'''Fungi:''' Fungi have been in the public eye for a while now due to the many different types of secondary metabolites they produce. Some produce bioactive compounds that can inhibit growth of protozoa, bacteria, parasites, insects, and even other fungi. A large area of investigation is the uses of these chemicals for human interests in use from medicine to plant and animal toxins [52].<br />
<br />
'''Protozoa:''' It’s known that Protozoa stimulate plant growth in different ways. It’s suspected that the Protozoa take part in the microbial loop which is responsible for the nutrient production for plants [19]. However, new developments have shown that the Protozoa themselves are responsible for the nitrogen mineralization and that other bacteria have no effect on the plant’s nitrogen sources [19].<br />
<br />
==References==<br />
<br />
1. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). Principles and Applications of Soil Microbiology. New Jersey: Pearson Education Inc.<br />
<br />
2. Ingham, Elaine R. Ingham R. "Chapter 4: SOIL FUNGI." Soil Biology. Natural Resources Conservation Service Illinois, n.d. Web. 9 Feb. 2016<br />
<br />
3. Reid, Greg, and Percy Wong. "SOIL BACTERIA AND FUNGI - NEW SOUTH WALES." Soil Bacteria and Fungi. New South Wales Department of Primary Industries, 2005. Web. 11 Feb. 2016.<br />
<br />
4. "Fungi." Microbiology Online. Microbiology Society, n.d. Web. 11 Feb. 2016.<br />
<br />
5. Tortora, G.J., Funke, B.R., Case, C.L. (2012). “Microbiology an Introduction.” 11th ed. Pearson Benjamin Cummings, San Francisco.<br />
<br />
6. Rizzo, D. “Intro to Fungi.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
7. Rizzo, D. “Ascomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
8. Rizzo, D. “Basidiomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
9. Pegg G.F., Brady B.L. “Verticillium Wilts.” New York, CABI Publishing 2002. Google Books. Web. 11 Feb. 2016. http://books.google.com<br />
<br />
10. Hebert, Paul. "What Is a Protist / What Are Protozoa? - Encyclopedia of Life." Encyclopedia of Life. N.p., n.d. Web. 11 Feb. 2016.http://eol.org/info/456<br />
<br />
11. "MicrobeWorld." Protista. N.p., n.d. Web. 11 Feb. 2016. http://www.microbeworld.org/types-of-microbes/protista<br />
<br />
12. Madigan, M.T., Martinko, J.M. (2006). Brock Biology of Microorganisms. New Jersey: Pearson Prentice Hall.<br />
<br />
13. Roesch, L.F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H.; Camargo, F. A. O.; Farmerie, W. G.; Triplett, E. W.(2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1(4).283-290. <br />
<br />
14. Amann, R.I, Ludwig, W., Schleifer, K.H.(1995).Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology and Molecular Biology Reviews. 59(1). 143-169. <br />
<br />
15. Geers, D., Cohan, F.M., Lawrence J.G., Spratt, B.G., Coenye, T. Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005). Opinion: Re-evaluating prokaryotic species. Nature Reviews Microbiology. 3(9). 733-739.<br />
<br />
16. Patzelt, D.J., Hodac, L., Friedl, T., Pietrasiak, N., Johansen, J.R. (2014). Biodiversity of soil cyanobacteria in the hyper-arid Atacama Desert, Chile. Journal of phycology. 50(4). 698-710. <br />
<br />
17. Makhalanyane, T. P., Valverde, A., Velázquez, D., Gunnigle, E., Van Goethem, M. W., Quesada, A., & Cowan, D. A. (2015). Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats. Biodiversity and Conservation, 24(4), 819-840.<br />
<br />
18. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist>.<br />
<br />
19. Ekelund, Flemming; Saj, Stephane; Vestergård, Mette; Bertaux, Joanne; Mikola, Juha. (2009). “The “soil microbial loop” is not always needed to explain protozoan stimulation of plants”. Soil Biology & Biochemistry. Vol. 41 Issue 11, p2336-2342, 7p.<br />
<br />
20. Bonkowski, Michael. "Protozoa and Plant Growth: The Microbial Loop in Soil Revisited." New Phytologist New Phytol 162.3 (2004): 617-31. Web.<br />
<br />
21. Hoorman, James. "The Role of Soil Protozoa and Nematodes." Fact Sheet (n.d.): n. pag. Ohio State University, 2011. Web.<br />
<br />
22. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist<br />
<br />
23. Lynn, Denis H(Apr 2012) Ciliophora. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001966.pub3]<br />
<br />
24. "flagellate". Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc., 2016. Web. 23 Feb. 2016 <http://www.britannica.com/science/flagellate>.<br />
<br />
25. "Mastigophora." World of Microbiology and Immunology. 2003. Encyclopedia.com. 23 Feb. 2016<http://www.encyclopedia.com>.<br />
<br />
26. “Plant Life." : Euglenoids. N.p., n.d. Web. 23 Feb. 2016. <http://lifeofplant.blogspot.com/2011/04/euglenoids.html><br />
<br />
27. Parales, R.E. and Martin, M. (2015) Microbial Diversity Laboratory Manual, MIC 105L, Winter 2015. Department of Microbiology and Molecular Genetics, College of Biological Sciences, The University of California, Davis.<br />
<br />
28. Arnold, Paul. "What Does an Amoeba Eat? Plus Other Ameoba Info and Questions." Bright Hub. N.p., n.d. Web. 04 Mar. 2016.<br />
<br />
29. "MicrobeWorld." Slime Molds. N.p., n.d. Web. 24 Feb. 2016. <http://www.microbeworld.org/types-of-microbes/protista/slime-molds><br />
<br />
30. Leeuwenhoek., A. V. (2009, November 18). One gram of soil: A microbial biochemical gene library. Retrieved March 13, 2016, from http://www.ncbi.nlm.nih.gov/pubmed/19921459 <br />
<br />
31. Coleman, D. C., Crossley, D. A. & Hendrix, P. F. "Soil food webs: Detritivory and microbiology in soils," in Fundamentals of Soil Ecology, 2nd ed. (Elsevier, 2004) 236-241.<br />
<br />
32. Welcome to Agriinfo.in. (n.d.). Retrieved February 21, 2016, from http://agriinfo.in/?page=topic&superid=5&topicid=172 <br />
<br />
33. Gouthro, T., & Rice, D. (1987, December 15). Interaction Terminology. Retrieved February 21, 2016, from http://www.rpi.edu/dept/chem-eng/Biotech-Environ/MixCul/ecodefn.htm <br />
<br />
34. AMENSALISM. (n.d.). Retrieved February 21, 2016, from https://biostuds.wikispaces.com/AMENSALISM <br />
<br />
35. Natural Resources Conservation Service. (n.d.). Retrieved March 10, 2016, from <br />
http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053865 <br />
<br />
36. Ecological Linkages Between Aboveground and Belowground Biota. (n.d.). Retrieved March 10, 2016, from http://science.sciencemag.org/content/304/5677/1629 <br />
<br />
37. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf<br />
<br />
38. Kingdom Archaea. (n.d.). Retrieved March 10, 2016, from http://plantphys.info/organismal/lechtml/archaea.shtml <br />
<br />
39. What are Archaea? - Encyclopedia of Life. (n.d.). Retrieved March 10, 2016, from http://eol.org/info/457 <br />
<br />
40. Flagellum. (n.d.). Retrieved March 10, 2016, from http://www.newworldencyclopedia.org/entry/Flagellum#Archaeal_flagellum <br />
<br />
41. Archaea: Morphology. (n.d.). Retrieved March 10, 2016, from http://www.ucmp.berkeley.edu/archaea/archaeamm.html <br />
<br />
42. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf <br />
<br />
43. Archaea. (n.d.). Retrieved March 10, 2016, from http://www.eoearth.org/view/article/150172/ <br />
<br />
44. Binary Fission: Cell Division & Reproduction of Prokaryotes. (n.d.). Retrieved March 10, 2016, from http://www.scienceprofonline.com/microbi <br />
<br />
45. Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2010, November 18). Examining the global distribution of dominant archaeal populations in soil. Retrieved February 21, 2016, from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105767/<br />
<br />
46. Scow, K. M. "Lecture 1 Part 1." Lecture, Davis.<br />
<br />
47. Rizzo, D. "Lecture 1." Lecture, Davis.<br />
<br />
48. Rizzo, D. "Lecture 3." Lecture, Davis.<br />
<br />
49. C.J. Alexopoulos & C. W. Mims, Introductory Mycology 3rd edition. 1979. Wiley NY. Web accessed Mar 8, 2016 from http://www.ucmp.berkeley.edu/fungi/fungimm.html<br />
<br />
50. Rizzo, D. "Lecture 2." Lecture, Davis.<br />
<br />
51. Ingham, E. “Chapter 4: Soil Fungi” (2016) Oregon State University. Retrieved Feb. 20, 2016, from http://extension.illinois.edu/soil/SoilBiology/fungi.htm<br />
<br />
52. Keller, N., Turner, G., Bennett, J. “Fungal Secondary Metabolism- from Biochemistry to Genomics.” 2005 Nature Reviews Microbiology p/ 937 to 947.</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Introduction_to_Organisms&diff=132725
Introduction to Organisms
2018-01-08T06:01:32Z
<p>Kmscow: /* Ciliates */</p>
<hr />
<div>{{Uncurated}}<br />
==Introduction== <br />
The soil ecosystem in an important environment that allows both plants and animals to survive, grow and reproduce. The significance of the soil as an ecosystem is at times overlooked despite its major contributions to the environment. The [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] is a complex and varied microbial habitat.[1] The plants and organisms inhabiting the soil contribute to its thriving diversity. Soil life is diverse in morphology, metabolism, size, and many other characteristics. Soil is a heterogeneous environment with various zones of rhizosphere, aggregates, organic matter and animal residues.[31] Given each zone is a small component of the larger soil ecosystem, rhizosphere accounts for only 5 to 7 percent of the soil environments but contains over “70 percent of the bacterial- and fungal-feeding nematodes.”[31] <br />
<br />
Since soil microbial diversity is immense, with all three domains of life: Archaea, Bacteria and Eukarya represented in the soil environment, it is not possible to discuss each microbial species (many of which have not even been described!). Only a few representative groups of each domain will be discussed to provide examples of the roles these organisms play in soil.<br />
<br />
==Soil Food Web and Microbial Interactions== <br />
<br />
To survive in a soil environment, an organism must be able to adapt to a constantly changing environment and to interactions with other organisms. One type of interaction shown in (Figure 2.1) is predation. Other common interactions in the soil environment are: <br />
<br />
:[[Image:soil_foodweb72.jpg|frame|center|Figure 2.1 Soil Food Web. From[http://www.exploringnature.org/graphics/foodwebs/soil_foodweb72.jpg]]]<br />
<br />
<br />
'''I. Commensalism:''' Organism (A) benefits from the presence of Organism (B) while (B) is unaffected by the presence of (A).[32]<br />
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'''II. Mutualism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) and becomes a necessary association for each other’s survival. [32] [33]<br />
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'''III. Synergism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) but the relationship is not necessary for survival.[33]<br />
<br />
'''IV. Competition:''' Depending on the organisms this interaction benefits organisms who can readily adapt to the environment and overcome any obstacles needed to survive, grow and reproduce.[33]<br />
<br />
'''V. Amensalism:''' An interaction in which Organisms (A) and (B) develop a partnership where (B) is unaffected by (A) but organism (A) is negatively affected by (B).[34]<br />
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'''VI. Parasitism:''' Organism (A) benefits from Organism (B) but Organism (B) does not benefit positively from Organism (A). <br />
<br />
'''VII. Predation:''' “An interaction between organisms in which one benefits and one is harmed based on the ingestion of the smaller sized organism, the prey, by the larger organism, the predator.”[33]<br />
<br />
<br />
<br />
The soil food web consists of microbes, fauna (micro and macro) and plant roots, who play multiple essential roles in soil ecosystem. The interactions between members of the soil food web result not only in chemical processes such as nutrient cycling and biodegradation of pollutants, but also in creation of soil structure, e.g. of aggregates.[35].<br />
<br />
In (Figure 2.1), all three domains, Archaea, Bacteria, and Eukarya, are represented in the soil food web. Thel food web is not only dependent on living creatures but also on decaying organic matter and plant roots. Dead and living matter in the soil environment, including plant roots, contribute to the maintenance of the food web.<br />
<br />
==3 Domains==<br />
[[Image:Big_Tree_Bold_Letters_white.png|frame|center|Figure 3.1 Phylogenetic Tree of the 3 Domains. From[http://phylogenomics.blogspot.com/2014_02_01_archive.html]]]<br />
<br />
===Carl Woese and Phylogeny===<br />
<br />
[[Image:Carlwoese1_0565_b.jpg|frame|center|Figure 3.2 Carl Woese. From[http://ofbacteriaandmen.blogspot.com/2013/01/the-new-biology-of-carl-woese.html]]] <br />
<br />
Carl Woese (Figure 3.2) was an American microbiologist famous for pioneering the technique of phylogenetic taxonomy through use of a 16S (for prokaryotic) and 18S (for eukaryotic) ribosomal RNA, also known as small subunit ribosomal RNA [46]. This refined Linnaean classification, taking out the guesswork classification by using a gene that was present in every living organism- the small subunit ribosomal RNA. This method of classification is comprehensive because all organisms possess this form of genetic material. Ssu rRNA is sequenced because the genes are highly conserved. Due to their functional constancy, some have variable regions to differentiate organisms, and are easy to sequence. This technique also elucidated the tree of life, which shows the three domains of microbial lineage diversity: Bacteria, Archaea, and Eukarya. DNA can be compared using a sample database that allows identification of unknown organisms to a species level.<br />
<br />
===Domain Bacteria===<br />
<br />
====Introduction to Bacteria==== <br />
Bacteria are single celled prokaryotic organisms that lack membrane bound organelles. They are involved in many important processes within the soil such as decomposition, [https://microbewiki.kenyon.edu/index.php/Bioremediation bioremediation], symbiosis and biological transformation of nutrients. They are present in all terrestrial soil environments.[1] Soil is a heterogenous environment that varies in moisture content, temperature, oxygen requirements, carbon source and many other bacterial growth conditions. Those wide ranging growth factors account for the enormous diversity in soil bacteria populations. One gram of soil can contain between 26,000 to 52,000 different bacterial species.[13] In the entire microbial world, only about 1 percent of bacterial species can be cultured under laboratory conditions which leaves an immense number of bacterial species yet to be described. [14]<br />
<br />
Classification based on phenotypic characteristics, such as cellular morphology, metabolism, gram staining, oxygen requirements, carbon source and other traits, was used more readily before modern DNA sequencing. But, phenotypic classification is still used and Bergey’s Manual of Systematic Bacteriology is the most widely used source for determining species based on characteristic species traits.<br />
<br />
Traditional species definitions are not as useful in bacteria. OTUs, or operational taxonomic units, based on DNA sequencing similarity, are more applicable to bacteria. Typically, those bacteria with 97 percent similar DNA sequence are classified within the same OTU.[15] The 16S small subunit ribosomal RNA is used to substantiate phylogenetic relationships between different bacterial groups.<br />
<br />
====Morphology====<br />
<br />
Bacterial cells measure approximately 1μm wide and 1-5μm long.[12] They are smaller than eukaryotic microbes.Due to their small size, bacteria can more easily adapt to changing soil environments than larger eukaryotes.[1] Most bacteria are singled celled, but actinomycetes grow in branching filaments. There are many different bacterial cell shapes. The most common are bacilli (rods), cocci (spheres), spirilla (spirals) and actinomycete (filaments).<br />
[[Image:bacteria_sizes.jpg|frame|center|Figure 3.3 Common cell shapes cocci, bacillus, and spirilla and relative sizes. From[http://www.ppdictionary.com/gnbac.htm]]]<br />
<br />
'''Flagella''' - There are many different types and different arrangement of flagella. Movement in soil environments is dependent on soil moisture content. Though movement in soil is limited, flagellar function is important to allow bacteria to find more favorable microsites.[1]<br />
<br />
'''Cell membrane''' - The cell membrane encloses the cytoplasm. It is semi-permeable phospholipid bilayer that regulates transport of nutrients into the cell and waste products out of the cell.<br />
<br />
'''Cell wall''' - Most bacteria have a rigid cell wall surrounding the cell membrane which protects the cell from osmotic lysis. The cell wall is made of a crosslinked polysaccharide, called peptidoglycan, that is found only in bacteria.[1] The cell wall gives the cell shape and structure, but it is porous enough to permit small water soluble molecules to flow through to the cell membrane surface.[1]<br />
<br />
*'''Gram positive''' bacteria have a thick cell wall made of several layers of peptidoglycan. The cell wall is the outermost structure, as they do not have an outer membrane. The thick cell wall structure make gram positive bacteria more resilient to osmotic shock. Gram positive bacteria can tolerate 5 to 10 times more turgor pressure than gram Gram negative bacteria.[1] Teichoic acids in the cell wall may also help to bind to cationic nutrients in soil surroundings.[1] <br />
<br />
*'''Gram negative''' bacteria have a thin cell wall surrounded by an outer membrane made of phospholipids and lipopolysaccharides. Polysaccharides of the outer membrane interact with surrounding cations and are involved in attachment of bacteria to soil particles. [1] Periplasm is a gel like substance that occupies the space between the outer membrane and the cell wall of gram negative bacteria.[1] The outer membrane and periplasmic space is thought to provide protection from environmental toxins.[1] Proteins within the periplasm are thought to begin the process of catalyzing hydrolysis of organic and toxic substances.[1] <br />
<br />
[[Image:gramposnegmembrane.jpg|frame|center| Figure 3.4 Illustration of Gram positive and Gram negative cell wall structures. From[http://micro.digitalproteus.com/morphology2.php]]]<br />
<br />
'''Endospores''' are made by ''Bacillus'' and ''Clostridium'' in response to environmental stress.[1] Endospores are extremely resistant structures that can withstand extreme temperatures up to 150℃.[12] They can also withstand extreme pressure, desiccation, radiation, pH and chemicals.[12] The endospore protects the bacterial DNA until environmental conditions are more favorable and germination can proceed. Soil is the most common habitat for endospore forming bacteria.[12]<br />
<br />
'''Extracellular polymers''' - Many bacteria secrete a slime layer or capsule made of polysaccharides or glycoproteins.[1] The outer polysaccharide coating of bacteria helps in attachment to surfaces and the formation of biofilms.[1] Bacterial capsule secretions play a big role in soil aggregation and soil structure.[1] When the carbon to nitrogen ratio within soils is high, microbes secrete the excess carbon as extracellular polysaccharides.[1]<br />
<br />
====Reproduction==== <br />
Most bacteria reproduce by binary fission.[12] The bacterial cell expands to twice the original cell size, duplicates the bacterial DNA and pinches off, producing two daughter cells. Each resultant daughter cell is a clone of the parent cell. Prokaryotic Archaea also reproduce by binary fission.<br />
<br />
*'''Spore formation:''' Actinomycetes are a large group of filamentous bacteria, primarily found in soil.[1] Actinomycetes are morphologically similar to fungi. Actinomycetes form long filaments called hyphae. Unlike most bacteria, the majority of actinomycetes reproduce using asexual spores called conidia.[1] Though they share many characteristic with fungi, actinomycetes are still prokaryotes. They are smaller than fungi and the cell wall contains peptidoglycan.[1] Actinomycetes break down a wide variety of organic compounds and play an important role in organic matter decomposition. [1] ''Streptomyces'', a subgroup within actinomycetes, produce geosmin, which gives soil the characteristic earthy smell.[12]<br />
<br />
====Metabolism==== <br />
<br />
Along with archaea, bacteria are the most metabolically diverse and employ many different nutritional strategies.[1]<br />
*Heterotrophs - Most bacteria are heterotrophic, obtaining carbon from preformed organic substances. [1] <br />
*Autotrophs - Carbon dioxide serves as the main source of carbon. Some cyanobacteria, nitrifying and sulfur-oxidizing bacteria are autotrophs.[1]<br />
*Organotrophs - Most bacteria obtain electrons from organic substances.[1]<br />
*Lithotrophs - Some cyanobacteria, nitrifying bacteria and sulfur-oxidizing bacteria obtain electrons from inorganic substances.[1]<br />
*Phototrophs - Cyanobacteria use light as the main source of metabolic energy.[1]<br />
*Chemotrophs - All other nonphotosynthetic bacteria do not rely on light for metabolic energy.[1]<br />
<br />
====Contributions to Biogeochemical Cycling==== <br />
<br />
Bacteria play a significant role in the cycling of a wide range of elements.<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Carbon_cycle '''Carbon Cycle:'''] <br />
<br />
*'''Carbon Assimilation''' is the process of fixing carbon dioxide into organic forms. Carbon fixation is performed by autotrophic bacteria, such as cyanobacteria.[1] Chemoautotrophic nitrifying bacteria, such as ''Nitrobacter, Nitrosospira'' and ''Nitrosomonas'', also fix carbon.[1] Sulfur oxidizing bacteria, such as ''Thiobacillus'', fix carbon as well.<br />
<br />
*'''Carbon Mineralization''' results from microbial decomposition of organic carbon compounds into inorganic forms. As the organic carbon substances, like plant matter, are decomposed, inorganic carbon dioxide is produced. Most bacteria are heterotrophs that perform carbon mineralization. When microorganisms die, they are decomposed by successive microbial generations. Peptidoglycan, the main component of bacterial cell walls, is utilized as a polysaccharide substrate by other heterotrophic soil microbes.[1]<br />
<br />
*'''Methanogenesis''' - Methanogenic bacteria produce methane from the reduction of carbon dioxide. They are all strict anaerobes that use carbon dioxide for the carbon source.[1] They can all use hydrogen as a source of energy and electron donor. [1]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle '''Nitrogen cycle:''']<br />
<br />
*'''Nitrogen fixation:''' ''Azotobacter'' is a free living nitrogen fixing bacteria.[1] ''Rhizobium'' lives in a mutualistic relationship with plants by fixing nitrogen within root the nodules of legumes.[1] ''Anabaena'' and ''Nostoc'' have specialized heterocyte structures where nitrogen fixation occurs.[1] <br />
<br />
*'''Nitrification:''' Nitrifying bacteria, such as ''Nitrobacter, Nitrosospira,'' and ''Nitrosomonas'', oxidize ammonium to nitrate.[1] <br />
<br />
*'''Denitrification:''' ''Alcaligenes, Flavobacterium'', and ''Pseudomonas'' are common soil denitrifying bacteria.[1]<br />
<br />
===Domain Archaea===<br />
<br />
====Introduction to Archaea====<br />
<br />
Vladimir Vernadsky decided, in 1926, that only two domains of life existed on Earth, Bacteria and Eukarya.[37] About 50 years later in 1977, Carl Woese and George Fox theorized that part of the bacterial domain possed multiple dissimilarities from bacteria and recognized it to be another domain of life, now called Archaea.[38] Woese and Fox’s theory regarding the differences of archaea were confirmed in 1990’s through the use of 16S rRNA and 18S rRNA.[38] <br />
<br />
Despite the strongly held belief, in the 1990s, that archaea only inhabited extreme environments, recent discoveries have suggested their presence in abundant numbers all throughout the Earth. It is suggested that Archaea play notable roles in maintaining nutrient cycles.[37] Various methods of research, such as cultivation, culture-independent techniques and isotope-based methods, have facilitated the study of domain Archaea in carbon and nitrogen cycling. [37]<br />
<br />
The use of genomic and biochemical data has permitted the study of archaeal structure.[37] Use of these research methods has shown that domain archaea and domain bacteria differ in cell wall characteristics yet, share various ways to transfer genetic information by replication and transcription from their common ancestor, Eukarya.[37] As of 2012, 116 genera of Archaea have been observed which consists of 450 species. Most of the archaeal species in these genera remains uncultivated, known only through its gene sequences and molecular surveys.[37]<br />
<br />
====Morphology==== <br />
Archaea are characterized by various cell sizes. They are most commonly found to be small organisms ranging from “0.1 to 15 μ diameter and up to 200 μ long.”[38] The shape of many archaea are similar to bacteria, including bacillus, cocci, spirilla and “plate-like forms.” [38] Their cell membranes have ether linked lipids with no periplasmic space, similar to gram-positive bacteria, and contain no intracellular organelles.[39]<br />
<br />
'''Flagella:''' Most motile archaea inhabit a motor rotary system that allows it to move its flagella through the chemical gradient similar to bacteria.[39] Despite its similarity in function and source of energy required for motility, the flagella of both archaea and bacteria differ in structure.[39] Archaeal flagella gets the energy for its movement by ATP and is composed of dependent filaments that rotate singularly. [40] Archaeal flagella are known to be thinner than bacteria flagellin.[40] Since, the archaeal common ancestor is not bacteria but eukarya, convergent evolution is a plausible explanations for the differences between bacterial and archaeal flagellin. [40]<br />
<br />
'''Membranes:''' Archaea have a cell membrane that protects the cytoplasm and the nucleic acids from the environment. The archaeal cell membrane has a lipid bilayer with glycol-ether lipids that are more stable than ester linkages and help some archaea that live in extreme environments to withstand such conditions.[39] Most archaeal species are surrounded by a cell wall which protects the cell membrane and maintains the archaeal structure.[41]<br />
<br />
====Reproduction====<br />
Archaeal organisms reproduce by binary fission since they do not have nucleases thus, the DNA chromosome in a Archaeal organism replicate, separate and create two daughter cells.[43] The process of binary fission can be seen in Figure (3.5) process begins the parent cell duplicating the DNA. The DNA material then goes to the sides of the cell where an invagination to the cell occurs allowing the cell to become two individual cells. Binary fission is a very fast reproduction process, that allows archaeal organisms to grow at an exponential rate.[44]<br />
<br />
[[Image:WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg|frame|center|Figure 3.5 Illustration of binary fission. From[https://d2jmvrsizmvf4x.cloudfront.net/WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg]]]<br />
<br />
====Metabolism==== <br />
Archaea share similar metabolic characteristics to bacteria. The metabolic pathways taken by all archaea shown in the (Figure 3.6) demonstrates the great diversity and variation amongst archaea. [38] The kinds of archaea that are seen in the environment and the metabolic pathways taken by some can be summarized in the image. <br />
<br />
*Photoautotrophs: use light as an energy source and carbon dioxide as the carbon source with the help of the Calvin Cycle.[38]<br />
*Chemoautotrophs: use inorganic chemicals as their energy source and carbon dioxide as carbon source. <br />
*Chemoheterotrophs: take organic chemicals as energy source and organic chemicals as carbon source. The pathways taken by chemoheterotrophs varies from respiration by the Krebs Cycle to fermentation. [38]<br />
*Photoheterotrophs: use light as their energy source and organic chemicals as their carbon source. <br />
<br />
Most archaea inhabiting in the soil environment are major contributors to the biogeochemical cycles.<br />
<br />
[[Image:2000px-Troph_flowchart.svg.png|thumbnail|center|Figure 3.6 Flowchart showing different metabolic pathways. From[https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Troph_flowchart.svg/2000px-Troph_flowchart.svg.png]]]<br />
<br />
====Contributions to the Cycle====<br />
Archaea play a significant role in the nutrient cycles that take place in the ecosystem as they account for about 1-5% of all the prokaryotes present in the soil environment.[42]<br />
<br />
'''Carbon Cycle:''' Archaea have an important role in the carbon cycle that takes place specifically in methane production, carbon mineralization and carbon assimilation all of all of which contribute to the soil’s carbon sink.[42] The carbon dense soil helps to make the soil organic matter rich and helps to form extracellular polymers which creates stable aggregates. For some microbes, an electron acceptor is need to carry out metabolic functions. [42] More info on [https://microbewiki.kenyon.edu/index.php/Carbon_cycle Carbon Cycle].<br />
<br />
*'''Carbon Assimilation:''' Involves the transformation of inorganic carbon into organic carbon compounds. This process is commonly done by autotrophic phyla ''Crenarchaeota, Thaumarchaeota'', and ''Euryarchaeota'' that use carbon dioxide/ bicarbonate converting it to organic compounds.[42] Of the autotrophic lineages observed in carbon assimilation the ''Thaumarchaeota'' are strict autotrophs, the ''Euryarchaeota'' and ''Crenarchaeota'' are facultative autotrophs and the ''Halobacteriales'' and ''Thermococcales'' are obligate heterotrophs.[42] <br />
<br />
*'''Carbon Mineralization:''' The process that converts organic carbon into the oxidized inorganic carbon, carbon dioxide is commonly done by both aerobes and anaerobes.[42] The heterotrophic microbes that use organic compounds as energy to oxidize the carbon source include, methanogens and methane-oxidizing archaea belonging to the phyla ''Euryarchaetota'', and ''Crenarchaeota''.[42] <br />
<br />
*'''Methanogenesis:''' production of methane, a major greenhouse gas in the Earth’s atmosphere is commonly done by archaea upon reducing an oxidized compound.[42] The phyla ''Euryarchaeota'' is the only phyla that consists of archaea that produce methane all of which form five class: ''Methanopyri, Methanococci, Methanobacteria, Methanomicrobia'' and ''Thermoplasmata''.[42] Methanogens are commonly found in anaerobic and aerobic conditions such as bodies of water, aerated soils and oxygenated waters.[42]<br />
<br />
'''Nitrogen Cycle :''' Archaea play a pivotal role in the Nitrogen cycle and help create nitrogenous products for the plants and microbes. More info on [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle Nitrogen cycle].<br />
<br />
*'''Nitrogen Fixation:''' Fixing nitrogen from the environment and converting it to organic nitrogen in the soil or to inorganic nitrogenous form since both organic and inorganic products are in short supply in the biosphere and are fixed by many archaeal organisms.[42] N2 fixation by the environment is usually done by three major archaeal classes ''Methanobactera, Methanococci'' and ''Methanomicrobia''.[42] <br />
<br />
*'''Nitrification:''' Converting the ammonia (NH4+) in the soil to nitrite (NO2-) produces nitrate (NO3-) as an intermediate. [42] The transformation of ammonia to first nitrate then to nitrite is a two step process that is done by different microbes. [42] Most common organisms involved in nitrification include ammonia-oxidizing archaea which are lithotrophic organisms mostly, of the ''Thaumarchaeota'' phylum from the archaea domain. <br />
<br />
*'''Denitrification :''' The conversion of atmospheric N2 using the electron acceptor NO3- or NO2- creating the formation of nitric oxide, nitrous oxide and/or N2.[42] The formation of the end product N2 may not always be produced but other intermediates NO and N2O, greenhouse gases may be produced.[42] Of the archaeal organisms that have been studied in denitrification process is done by ''Pyrobaculum aerophilum'' which accepts both NO3- and NO2- as an electron acceptor producing a variety of products NO2-, NO, N20 and N2.[42]<br />
<br />
===Domain Eukarya===<br />
<br />
====Fungi====<br />
<br />
=====Introduction=====<br />
<br />
'''Introduction'''<br />
<br />
Fungi comes from the ancient Greek word “sphongos” meaning sponge in reference to the mushroom cap [47]. Fungi have the general characteristics of being eukaryotic, heterotrophic, external absorbers of nutrients, containing a hyphal thallus, reproducing via spore, and being pleomorphic (producing several forms). Fungi are generally organoheterotrophs that can survive in low pH and stay active at low moisture content[46]. Fungi reside in the domain Eukarya with an estimated species of 1.5 million, and less than five percent of them have ever been described. The general phyla included within Kingdom Fungi include Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, Chytridiomycota, and Microsporidia [48].<br />
<br />
[[Image:magical-kingdom-620.jpg|frame|center|Figure 3.7 Fungi phyla hierarchy. From.[http://www.motherjones.com/environment/2009/11/fungi-family-tree]]]<br />
<br />
=====Morphology=====<br />
<br />
'''Morphology''' <br />
<br />
Fungi can be either unicellular (yeasts) or multicellular. All multicellular fungi are made up of small, filamentous particles called hyphae. Some hyphae have cross walls called septa, while others do not- this is a large basis of fungal identification. Fungal cells generally have multiple nuclei. Fungal cell walls are generally composed of chitin, a long carbohydrate polymer that adds rigidity and structural support to fungi [49]. <br />
<br />
=====Reproduction=====<br />
<br />
'''Reproduction'''<br />
<br />
Fungal reproduction can occur either sexually or asexually.<br />
<br />
'''Sexual reproduction''' can occur by homothallic or heterothallic mycelia.<br />
<br />
'''Asexual reproduction''' can occur by fragmentation, budding, or by producing spores (the most common method). <br />
<br />
*'''Spores:''' spores come in many different forms. One of the most well known are conidiospores, which are unicellular or multicellular spores that get released from the tip of the hyphae. <br />
<br />
'''Perfect fungi''' are those that can reproduce both sexually and asexually while imperfect fungi are those that can only reproduce asexually.<br />
<br />
*Sexual reproduction always includes the stages plasmogamy (fusion of two haploid cells), karyogamy (creation of a diploid zygote), and meiosis (gametes are created).<br />
<br />
=====Metabolism=====<br />
<br />
'''Metabolism'''<br />
<br />
Many different fungi display a myriad of metabolisms. There are primary metabolites that that help the fungi function properly, and secondary metabolites that are generally bioactive that are not the most pertinent to fungal growth (they can live without these). Secondary metabolites play a large role in chemistry today and can be manufactured into commonly used products such as new drugs. In general fungi are heterotrophic through release of extracellular enzymes into the neighboring environment to break complex molecules down into smaller ones. The materials are then absorbed and metabolized [50]. Fungi are sessile organisms that overcome their little to no movement through apical growth at the hyphal tip. Fungi are noted to grow almost everywhere on the Earth.<br />
<br />
=====Relevance to soil===== <br />
<br />
'''Relevance to soil'''<br />
<br />
Fungi include some of the most abundant biomass of microorganisms in numerous soils. They play an important role as decomposers within the soil food web through conversion of difficult to digest organic material into forms many other organisms can use [51]. Their hyphae can bind soil particles together and create aggregates that increase soil water holding capacity. They perform important functions from water dynamics to nutrient cycling and disease suppression. Soil fungi can be categorized into three different groups based on their actions: <br />
<br />
*decomposers: that convert dead organic material into fungal biomass<br />
<br />
*mutualists: which colonize plant roots and help solubilize phosphorous and bring soil nutrients<br />
<br />
*pathogens/ parasites: which help control diseases in soil via trapping organisms such as nematodes [51]. <br />
<br />
Fungi are seen common in intensively managed agricultural soils due to tillage disrupting hyphae. Fungi also play a very important role in the [https://microbewiki.kenyon.edu/index.php/Rhizosphere_Interactions rhizosphere], the region of soil that is greatly influenced by the plant root system. This area of soil which is concentrated in plant roots and fungal hyphae is known to support greater microbial activity.<br />
<br />
=====Protozoans=====<br />
<br />
'''Protozoans'''<br />
<br />
In general, Protozoans range from 5 to 500 µm in diameter, making them significantly larger than bacteria [21]. They are abundantly located near the surface of the soil (15cm deep) where roots are plentiful [21]. Many protozoans have two life cycles. One is their active form where they are motile and feed on prey. The other is the cyst form where they produce a thick coating to protect them from the environment and can go dormant for years. The protozoa are divided into 4 major categories: the ciliates, the flagellates, the heliozoans, and the amoebas [10]. <br />
<br />
======Ciliates======<br />
<br />
'''Cilliates:'''<br />
This group, within protozoans, is fairly diverse. A common feature shared amongst all of its members is the presence of at least one cilia at any stage of its development [10]. The cilia is used for movement and other things such as predation (tentacles). For movement, they use the massive amounts of tiny cilia to create wave like currents to propel the cell forwards. Most ciliates also have toxicysts which are used to capture prey [10]. Some ciliates even have a symbiotic relationship with algae living inside of them [10]. The algae use the CO2 produced by ciliates and turn it into O2 that can then be reused by the ciliates [10]. They are found in a wide array of habitats ranging from freshwater and soil to the rumen of Animals [22]. They are present in almost anywhere that contains water [23]. They are unicellular heterotrophs so they feed on bacteria and algae in their environment. Ciliates are one of the top predators in the microbial food web and are hypothesized to have been a major predatory group before animals evolved [23]. The large size of ciliates and their rigid cell structure make them less common in unsaturated soils than other types of protozoa.<br />
<br />
[[Image:2spiro.jpg|frame|center|Figure 3.8 Microscope image of ciliated protists. From[http://www.microscopy-uk.org.uk/mag/smallimag/2spiro.jpg]]]<br />
<br />
======Flagellates======<br />
<br />
'''Flagellates''' are one of the most commonly known protists. They are unicellular organisms that may be solitary, colonial, free living, or parasitic [24]. The hallmark feature of protists is that at some point in their life cycle, they possess a flagella. A flagellum is a long hair like structure that is used for locomotion, sensation, and sometimes predation [24]. The flagellum makes waves by whiplike lashing movements which propels the cell forwards. Flagellates also have a protective coating in the form of a thin pellicle to protect them from the environment [24]. <br />
<br />
[[Image:9703607_orig.jpg|frame|center|Figure 3.9 Illustration of flaggelates during different life cycle stages. From[http://diagnosticparasitology.weebly.com/uploads/3/9/5/4/3954522/9703607_orig.jpg]]]<br />
<br />
*'''Mastigophora:'''<br />
<br />
Mastigophora is a subphylum of flagellates. Being a member of the flagellates, their key feature is the flagellum. Their habitats include freshwater, soil, and can act as animal parasites as well [25]. They use pseudopodia, a long outward protrusion, to trap and funnel food from the environment into their cell bodies [25]. The Mastigophora are mainly known for their parasitism, which can take place in both humans and animals [25]. ''Typanosomes'' are an example of Mastigophora which causes African sleeping sickness [25]. ''Giardia lambli''a is another example that resides in the intestinal tract of warm-blooded animals and inflicts intestinal giardiases [25]. It is also a major contaminant of drinking water because it is resistant to chlorine, which is the most common water purifier [25]. Having a dormant cyst form also adds to its survival potential through filtration efforts [25].<br />
<br />
<br />
<br />
*'''Euglenids:'''<br />
<br />
Euglenids are one of the best known flagellates. They are found in freshwater and soil, as long as there are organic materials. They also participate in some symbiotic relationships with marine animals. Euglenid cells do not contain cell walls or other rigid membranes [26]. This gives the cell tremendous flexibility and allows it to change its shape to easily navigate through muddy terrain. Euglenids have two flagella, one which creates locomotion and movement for the cell [26]. The other flagellum does not protrude from the cell and is contained in the cell body [26].<br />
<br />
======Amoebas======<br />
<br />
'''Amoebas'''<br />
<br />
Amoebae are single celled eukaryotes present in many different types of environments. They are scattered throughout a variety of eukaryotic lineages and therefore are not monophyletic [27]. Amoebae range in size from 5 micrometers to 3 mm and don’t have a defined shape, commonly recognized for being polymorphic. They are motile through the use of pseudopodia, which stretch and pull the cell along with it. The pseudopodia are also used for feeding. They are able to sense prey that can be engulfed and engulf them via phagocytosis. The amoeba’s main prey consists of bacteria, algae, and other protozoa [28]. The prey is moved around within the cell via food vacuoles, a feature of amoebae [28]. Another key characteristic of amoebae are the large contractile vacuoles inside the cell. The purpose of the contractile vacuole is to osmoregulate by pumping excess water out of the cell. In times of turmoil, amoebae have an encysted form that helps them get through the tough times. This form is useful when there is low nutrient availability to limit energy consumption. There are two main forms an amoeba can be characterized as. They can either be testate or nontestate. Testate amoeba produce shells, or “tests”, that help identify their species since each species has a unique shell.<br />
<br />
[[Image:Amoeba_(PSF).png|frame|center|Figure 3.10 Amoeba morphology. From[https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Amoeba_(PSF).png/230px-Amoeba_(PSF).png]]]<br />
<br />
=====Slime Molds=====<br />
<br />
'''Slime molds''' were once classified as fungi, but have now been placed in their own phylogenetic groups. Slime molds are single cells that can live independently, but aggregate to form multicellular reproductive structures when necessary [29]. The fruiting body releases spores which germinate into new cells. Slime molds feed off of bacteria and are most commonly found in forests. They feed off of decaying vegetation as well so they can be seen on rotting logs and leaves.<br />
<br />
[[Image:28-30-cellslimemoldlife-l.jpg|frame|center|Figure 3.11 Illustration of slime mold life cycle. From[https://lichencolony.files.wordpress.com/2006/06/28-30-cellslimemoldlife-l.jpg]]]<br />
<br />
==Current Research== <br />
<br />
'''Bacteria:''' To showcase the great diversity of soil bacterial environments, cyanobacteria have been studied in both desert and polar regions. Cyanobacteria can survive in extreme conditions likely because of their long evolutionary past.[16] Dr. Patzelt and his colleagues studied the diverse cyanobacteria residing in the Atacama desert, one of the driest parts of the world. The diverse taxa found in the Atacama desert can withstand prolonged periods of extreme desiccation.[16] The cyanobacteria dominate the soil crusts, affecting soil stability, soil structure and soil fertility.[16] Cyanobacteria inhabiting the Antarctic and Arctic regions, show similar adaptations to extreme environments as the cyanobacteria found in the desert. The polar cyanobacteria are particularly adapted to high altitudes.[17] They can withstand high ultraviolet radiation, desiccation, and repeated freeze-thaw cycles.[17] The autotrophic cyanobacteria supports heterotrophic microbes, providing an important ecosystem service in an environment with low microbial activity.[17]<br />
<br />
'''Archaea:''' In 150 soil samples acquired from North and South America, about 150,000 species were observed.[45] Of these, over 2,500 were identified as archaea based on their ssu rRNA.[45] The archaeal species were further analyzed to understand their role in the soil environment. Of the archaeal groups, ''Crenarchaeota'' and ''Euryarchaeota'' were found.[45] Bates stated that, “Across the non-experimental soils examined the soil C:N ratio was the single best predictor of archaeal relative abundances” due to their influences in the nutrient cycles.[45]<br />
<br />
'''Fungi:''' Fungi have been in the public eye for a while now due to the many different types of secondary metabolites they produce. Some produce bioactive compounds that can inhibit growth of protozoa, bacteria, parasites, insects, and even other fungi. A large area of investigation is the uses of these chemicals for human interests in use from medicine to plant and animal toxins [52].<br />
<br />
'''Protozoa:''' It’s known that Protozoa stimulate plant growth in different ways. It’s suspected that the Protozoa take part in the microbial loop which is responsible for the nutrient production for plants [19]. However, new developments have shown that the Protozoa themselves are responsible for the nitrogen mineralization and that other bacteria have no effect on the plant’s nitrogen sources [19].<br />
<br />
==References==<br />
<br />
1. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). Principles and Applications of Soil Microbiology. New Jersey: Pearson Education Inc.<br />
<br />
2. Ingham, Elaine R. Ingham R. "Chapter 4: SOIL FUNGI." Soil Biology. Natural Resources Conservation Service Illinois, n.d. Web. 9 Feb. 2016<br />
<br />
3. Reid, Greg, and Percy Wong. "SOIL BACTERIA AND FUNGI - NEW SOUTH WALES." Soil Bacteria and Fungi. New South Wales Department of Primary Industries, 2005. Web. 11 Feb. 2016.<br />
<br />
4. "Fungi." Microbiology Online. Microbiology Society, n.d. Web. 11 Feb. 2016.<br />
<br />
5. Tortora, G.J., Funke, B.R., Case, C.L. (2012). “Microbiology an Introduction.” 11th ed. Pearson Benjamin Cummings, San Francisco.<br />
<br />
6. Rizzo, D. “Intro to Fungi.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
7. Rizzo, D. “Ascomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
8. Rizzo, D. “Basidiomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
9. Pegg G.F., Brady B.L. “Verticillium Wilts.” New York, CABI Publishing 2002. Google Books. Web. 11 Feb. 2016. http://books.google.com<br />
<br />
10. Hebert, Paul. "What Is a Protist / What Are Protozoa? - Encyclopedia of Life." Encyclopedia of Life. N.p., n.d. Web. 11 Feb. 2016.http://eol.org/info/456<br />
<br />
11. "MicrobeWorld." Protista. N.p., n.d. Web. 11 Feb. 2016. http://www.microbeworld.org/types-of-microbes/protista<br />
<br />
12. Madigan, M.T., Martinko, J.M. (2006). Brock Biology of Microorganisms. New Jersey: Pearson Prentice Hall.<br />
<br />
13. Roesch, L.F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H.; Camargo, F. A. O.; Farmerie, W. G.; Triplett, E. W.(2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1(4).283-290. <br />
<br />
14. Amann, R.I, Ludwig, W., Schleifer, K.H.(1995).Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology and Molecular Biology Reviews. 59(1). 143-169. <br />
<br />
15. Geers, D., Cohan, F.M., Lawrence J.G., Spratt, B.G., Coenye, T. Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005). Opinion: Re-evaluating prokaryotic species. Nature Reviews Microbiology. 3(9). 733-739.<br />
<br />
16. Patzelt, D.J., Hodac, L., Friedl, T., Pietrasiak, N., Johansen, J.R. (2014). Biodiversity of soil cyanobacteria in the hyper-arid Atacama Desert, Chile. Journal of phycology. 50(4). 698-710. <br />
<br />
17. Makhalanyane, T. P., Valverde, A., Velázquez, D., Gunnigle, E., Van Goethem, M. W., Quesada, A., & Cowan, D. A. (2015). Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats. Biodiversity and Conservation, 24(4), 819-840.<br />
<br />
18. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist>.<br />
<br />
19. Ekelund, Flemming; Saj, Stephane; Vestergård, Mette; Bertaux, Joanne; Mikola, Juha. (2009). “The “soil microbial loop” is not always needed to explain protozoan stimulation of plants”. Soil Biology & Biochemistry. Vol. 41 Issue 11, p2336-2342, 7p.<br />
<br />
20. Bonkowski, Michael. "Protozoa and Plant Growth: The Microbial Loop in Soil Revisited." New Phytologist New Phytol 162.3 (2004): 617-31. Web.<br />
<br />
21. Hoorman, James. "The Role of Soil Protozoa and Nematodes." Fact Sheet (n.d.): n. pag. Ohio State University, 2011. Web.<br />
<br />
22. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist<br />
<br />
23. Lynn, Denis H(Apr 2012) Ciliophora. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001966.pub3]<br />
<br />
24. "flagellate". Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc., 2016. Web. 23 Feb. 2016 <http://www.britannica.com/science/flagellate>.<br />
<br />
25. "Mastigophora." World of Microbiology and Immunology. 2003. Encyclopedia.com. 23 Feb. 2016<http://www.encyclopedia.com>.<br />
<br />
26. “Plant Life." : Euglenoids. N.p., n.d. Web. 23 Feb. 2016. <http://lifeofplant.blogspot.com/2011/04/euglenoids.html><br />
<br />
27. Parales, R.E. and Martin, M. (2015) Microbial Diversity Laboratory Manual, MIC 105L, Winter 2015. Department of Microbiology and Molecular Genetics, College of Biological Sciences, The University of California, Davis.<br />
<br />
28. Arnold, Paul. "What Does an Amoeba Eat? Plus Other Ameoba Info and Questions." Bright Hub. N.p., n.d. Web. 04 Mar. 2016.<br />
<br />
29. "MicrobeWorld." Slime Molds. N.p., n.d. Web. 24 Feb. 2016. <http://www.microbeworld.org/types-of-microbes/protista/slime-molds><br />
<br />
30. Leeuwenhoek., A. V. (2009, November 18). One gram of soil: A microbial biochemical gene library. Retrieved March 13, 2016, from http://www.ncbi.nlm.nih.gov/pubmed/19921459 <br />
<br />
31. Coleman, D. C., Crossley, D. A. & Hendrix, P. F. "Soil food webs: Detritivory and microbiology in soils," in Fundamentals of Soil Ecology, 2nd ed. (Elsevier, 2004) 236-241.<br />
<br />
32. Welcome to Agriinfo.in. (n.d.). Retrieved February 21, 2016, from http://agriinfo.in/?page=topic&superid=5&topicid=172 <br />
<br />
33. Gouthro, T., & Rice, D. (1987, December 15). Interaction Terminology. Retrieved February 21, 2016, from http://www.rpi.edu/dept/chem-eng/Biotech-Environ/MixCul/ecodefn.htm <br />
<br />
34. AMENSALISM. (n.d.). Retrieved February 21, 2016, from https://biostuds.wikispaces.com/AMENSALISM <br />
<br />
35. Natural Resources Conservation Service. (n.d.). Retrieved March 10, 2016, from <br />
http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053865 <br />
<br />
36. Ecological Linkages Between Aboveground and Belowground Biota. (n.d.). Retrieved March 10, 2016, from http://science.sciencemag.org/content/304/5677/1629 <br />
<br />
37. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf<br />
<br />
38. Kingdom Archaea. (n.d.). Retrieved March 10, 2016, from http://plantphys.info/organismal/lechtml/archaea.shtml <br />
<br />
39. What are Archaea? - Encyclopedia of Life. (n.d.). Retrieved March 10, 2016, from http://eol.org/info/457 <br />
<br />
40. Flagellum. (n.d.). Retrieved March 10, 2016, from http://www.newworldencyclopedia.org/entry/Flagellum#Archaeal_flagellum <br />
<br />
41. Archaea: Morphology. (n.d.). Retrieved March 10, 2016, from http://www.ucmp.berkeley.edu/archaea/archaeamm.html <br />
<br />
42. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf <br />
<br />
43. Archaea. (n.d.). Retrieved March 10, 2016, from http://www.eoearth.org/view/article/150172/ <br />
<br />
44. Binary Fission: Cell Division & Reproduction of Prokaryotes. (n.d.). Retrieved March 10, 2016, from http://www.scienceprofonline.com/microbi <br />
<br />
45. Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2010, November 18). Examining the global distribution of dominant archaeal populations in soil. Retrieved February 21, 2016, from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105767/<br />
<br />
46. Scow, K. M. "Lecture 1 Part 1." Lecture, Davis.<br />
<br />
47. Rizzo, D. "Lecture 1." Lecture, Davis.<br />
<br />
48. Rizzo, D. "Lecture 3." Lecture, Davis.<br />
<br />
49. C.J. Alexopoulos & C. W. Mims, Introductory Mycology 3rd edition. 1979. Wiley NY. Web accessed Mar 8, 2016 from http://www.ucmp.berkeley.edu/fungi/fungimm.html<br />
<br />
50. Rizzo, D. "Lecture 2." Lecture, Davis.<br />
<br />
51. Ingham, E. “Chapter 4: Soil Fungi” (2016) Oregon State University. Retrieved Feb. 20, 2016, from http://extension.illinois.edu/soil/SoilBiology/fungi.htm<br />
<br />
52. Keller, N., Turner, G., Bennett, J. “Fungal Secondary Metabolism- from Biochemistry to Genomics.” 2005 Nature Reviews Microbiology p/ 937 to 947.</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Introduction_to_Organisms&diff=132724
Introduction to Organisms
2018-01-08T05:56:39Z
<p>Kmscow: /* Soil Food Web and Microbial Interactions */</p>
<hr />
<div>{{Uncurated}}<br />
==Introduction== <br />
The soil ecosystem in an important environment that allows both plants and animals to survive, grow and reproduce. The significance of the soil as an ecosystem is at times overlooked despite its major contributions to the environment. The [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] is a complex and varied microbial habitat.[1] The plants and organisms inhabiting the soil contribute to its thriving diversity. Soil life is diverse in morphology, metabolism, size, and many other characteristics. Soil is a heterogeneous environment with various zones of rhizosphere, aggregates, organic matter and animal residues.[31] Given each zone is a small component of the larger soil ecosystem, rhizosphere accounts for only 5 to 7 percent of the soil environments but contains over “70 percent of the bacterial- and fungal-feeding nematodes.”[31] <br />
<br />
Since soil microbial diversity is immense, with all three domains of life: Archaea, Bacteria and Eukarya represented in the soil environment, it is not possible to discuss each microbial species (many of which have not even been described!). Only a few representative groups of each domain will be discussed to provide examples of the roles these organisms play in soil.<br />
<br />
==Soil Food Web and Microbial Interactions== <br />
<br />
To survive in a soil environment, an organism must be able to adapt to a constantly changing environment and to interactions with other organisms. One type of interaction shown in (Figure 2.1) is predation. Other common interactions in the soil environment are: <br />
<br />
:[[Image:soil_foodweb72.jpg|frame|center|Figure 2.1 Soil Food Web. From[http://www.exploringnature.org/graphics/foodwebs/soil_foodweb72.jpg]]]<br />
<br />
<br />
'''I. Commensalism:''' Organism (A) benefits from the presence of Organism (B) while (B) is unaffected by the presence of (A).[32]<br />
<br />
'''II. Mutualism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) and becomes a necessary association for each other’s survival. [32] [33]<br />
<br />
'''III. Synergism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) but the relationship is not necessary for survival.[33]<br />
<br />
'''IV. Competition:''' Depending on the organisms this interaction benefits organisms who can readily adapt to the environment and overcome any obstacles needed to survive, grow and reproduce.[33]<br />
<br />
'''V. Amensalism:''' An interaction in which Organisms (A) and (B) develop a partnership where (B) is unaffected by (A) but organism (A) is negatively affected by (B).[34]<br />
<br />
'''VI. Parasitism:''' Organism (A) benefits from Organism (B) but Organism (B) does not benefit positively from Organism (A). <br />
<br />
'''VII. Predation:''' “An interaction between organisms in which one benefits and one is harmed based on the ingestion of the smaller sized organism, the prey, by the larger organism, the predator.”[33]<br />
<br />
<br />
<br />
The soil food web consists of microbes, fauna (micro and macro) and plant roots, who play multiple essential roles in soil ecosystem. The interactions between members of the soil food web result not only in chemical processes such as nutrient cycling and biodegradation of pollutants, but also in creation of soil structure, e.g. of aggregates.[35].<br />
<br />
In (Figure 2.1), all three domains, Archaea, Bacteria, and Eukarya, are represented in the soil food web. Thel food web is not only dependent on living creatures but also on decaying organic matter and plant roots. Dead and living matter in the soil environment, including plant roots, contribute to the maintenance of the food web.<br />
<br />
==3 Domains==<br />
[[Image:Big_Tree_Bold_Letters_white.png|frame|center|Figure 3.1 Phylogenetic Tree of the 3 Domains. From[http://phylogenomics.blogspot.com/2014_02_01_archive.html]]]<br />
<br />
===Carl Woese and Phylogeny===<br />
<br />
[[Image:Carlwoese1_0565_b.jpg|frame|center|Figure 3.2 Carl Woese. From[http://ofbacteriaandmen.blogspot.com/2013/01/the-new-biology-of-carl-woese.html]]] <br />
<br />
Carl Woese (Figure 3.2) was an American microbiologist famous for pioneering the technique of phylogenetic taxonomy through use of a 16S (for prokaryotic) and 18S (for eukaryotic) ribosomal RNA, also known as small subunit ribosomal RNA [46]. This refined Linnaean classification, taking out the guesswork classification by using a gene that was present in every living organism- the small subunit ribosomal RNA. This method of classification is comprehensive because all organisms possess this form of genetic material. Ssu rRNA is sequenced because the genes are highly conserved. Due to their functional constancy, some have variable regions to differentiate organisms, and are easy to sequence. This technique also elucidated the tree of life, which shows the three domains of microbial lineage diversity: Bacteria, Archaea, and Eukarya. DNA can be compared using a sample database that allows identification of unknown organisms to a species level.<br />
<br />
===Domain Bacteria===<br />
<br />
====Introduction to Bacteria==== <br />
Bacteria are single celled prokaryotic organisms that lack membrane bound organelles. They are involved in many important processes within the soil such as decomposition, [https://microbewiki.kenyon.edu/index.php/Bioremediation bioremediation], symbiosis and biological transformation of nutrients. They are present in all terrestrial soil environments.[1] Soil is a heterogenous environment that varies in moisture content, temperature, oxygen requirements, carbon source and many other bacterial growth conditions. Those wide ranging growth factors account for the enormous diversity in soil bacteria populations. One gram of soil can contain between 26,000 to 52,000 different bacterial species.[13] In the entire microbial world, only about 1 percent of bacterial species can be cultured under laboratory conditions which leaves an immense number of bacterial species yet to be described. [14]<br />
<br />
Classification based on phenotypic characteristics, such as cellular morphology, metabolism, gram staining, oxygen requirements, carbon source and other traits, was used more readily before modern DNA sequencing. But, phenotypic classification is still used and Bergey’s Manual of Systematic Bacteriology is the most widely used source for determining species based on characteristic species traits.<br />
<br />
Traditional species definitions are not as useful in bacteria. OTUs, or operational taxonomic units, based on DNA sequencing similarity, are more applicable to bacteria. Typically, those bacteria with 97 percent similar DNA sequence are classified within the same OTU.[15] The 16S small subunit ribosomal RNA is used to substantiate phylogenetic relationships between different bacterial groups.<br />
<br />
====Morphology====<br />
<br />
Bacterial cells measure approximately 1μm wide and 1-5μm long.[12] They are smaller than eukaryotic microbes.Due to their small size, bacteria can more easily adapt to changing soil environments than larger eukaryotes.[1] Most bacteria are singled celled, but actinomycetes grow in branching filaments. There are many different bacterial cell shapes. The most common are bacilli (rods), cocci (spheres), spirilla (spirals) and actinomycete (filaments).<br />
[[Image:bacteria_sizes.jpg|frame|center|Figure 3.3 Common cell shapes cocci, bacillus, and spirilla and relative sizes. From[http://www.ppdictionary.com/gnbac.htm]]]<br />
<br />
'''Flagella''' - There are many different types and different arrangement of flagella. Movement in soil environments is dependent on soil moisture content. Though movement in soil is limited, flagellar function is important to allow bacteria to find more favorable microsites.[1]<br />
<br />
'''Cell membrane''' - The cell membrane encloses the cytoplasm. It is semi-permeable phospholipid bilayer that regulates transport of nutrients into the cell and waste products out of the cell.<br />
<br />
'''Cell wall''' - Most bacteria have a rigid cell wall surrounding the cell membrane which protects the cell from osmotic lysis. The cell wall is made of a crosslinked polysaccharide, called peptidoglycan, that is found only in bacteria.[1] The cell wall gives the cell shape and structure, but it is porous enough to permit small water soluble molecules to flow through to the cell membrane surface.[1]<br />
<br />
*'''Gram positive''' bacteria have a thick cell wall made of several layers of peptidoglycan. The cell wall is the outermost structure, as they do not have an outer membrane. The thick cell wall structure make gram positive bacteria more resilient to osmotic shock. Gram positive bacteria can tolerate 5 to 10 times more turgor pressure than gram Gram negative bacteria.[1] Teichoic acids in the cell wall may also help to bind to cationic nutrients in soil surroundings.[1] <br />
<br />
*'''Gram negative''' bacteria have a thin cell wall surrounded by an outer membrane made of phospholipids and lipopolysaccharides. Polysaccharides of the outer membrane interact with surrounding cations and are involved in attachment of bacteria to soil particles. [1] Periplasm is a gel like substance that occupies the space between the outer membrane and the cell wall of gram negative bacteria.[1] The outer membrane and periplasmic space is thought to provide protection from environmental toxins.[1] Proteins within the periplasm are thought to begin the process of catalyzing hydrolysis of organic and toxic substances.[1] <br />
<br />
[[Image:gramposnegmembrane.jpg|frame|center| Figure 3.4 Illustration of Gram positive and Gram negative cell wall structures. From[http://micro.digitalproteus.com/morphology2.php]]]<br />
<br />
'''Endospores''' are made by ''Bacillus'' and ''Clostridium'' in response to environmental stress.[1] Endospores are extremely resistant structures that can withstand extreme temperatures up to 150℃.[12] They can also withstand extreme pressure, desiccation, radiation, pH and chemicals.[12] The endospore protects the bacterial DNA until environmental conditions are more favorable and germination can proceed. Soil is the most common habitat for endospore forming bacteria.[12]<br />
<br />
'''Extracellular polymers''' - Many bacteria secrete a slime layer or capsule made of polysaccharides or glycoproteins.[1] The outer polysaccharide coating of bacteria helps in attachment to surfaces and the formation of biofilms.[1] Bacterial capsule secretions play a big role in soil aggregation and soil structure.[1] When the carbon to nitrogen ratio within soils is high, microbes secrete the excess carbon as extracellular polysaccharides.[1]<br />
<br />
====Reproduction==== <br />
Most bacteria reproduce by binary fission.[12] The bacterial cell expands to twice the original cell size, duplicates the bacterial DNA and pinches off, producing two daughter cells. Each resultant daughter cell is a clone of the parent cell. Prokaryotic Archaea also reproduce by binary fission.<br />
<br />
*'''Spore formation:''' Actinomycetes are a large group of filamentous bacteria, primarily found in soil.[1] Actinomycetes are morphologically similar to fungi. Actinomycetes form long filaments called hyphae. Unlike most bacteria, the majority of actinomycetes reproduce using asexual spores called conidia.[1] Though they share many characteristic with fungi, actinomycetes are still prokaryotes. They are smaller than fungi and the cell wall contains peptidoglycan.[1] Actinomycetes break down a wide variety of organic compounds and play an important role in organic matter decomposition. [1] ''Streptomyces'', a subgroup within actinomycetes, produce geosmin, which gives soil the characteristic earthy smell.[12]<br />
<br />
====Metabolism==== <br />
<br />
Along with archaea, bacteria are the most metabolically diverse and employ many different nutritional strategies.[1]<br />
*Heterotrophs - Most bacteria are heterotrophic, obtaining carbon from preformed organic substances. [1] <br />
*Autotrophs - Carbon dioxide serves as the main source of carbon. Some cyanobacteria, nitrifying and sulfur-oxidizing bacteria are autotrophs.[1]<br />
*Organotrophs - Most bacteria obtain electrons from organic substances.[1]<br />
*Lithotrophs - Some cyanobacteria, nitrifying bacteria and sulfur-oxidizing bacteria obtain electrons from inorganic substances.[1]<br />
*Phototrophs - Cyanobacteria use light as the main source of metabolic energy.[1]<br />
*Chemotrophs - All other nonphotosynthetic bacteria do not rely on light for metabolic energy.[1]<br />
<br />
====Contributions to Biogeochemical Cycling==== <br />
<br />
Bacteria play a significant role in the cycling of a wide range of elements.<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Carbon_cycle '''Carbon Cycle:'''] <br />
<br />
*'''Carbon Assimilation''' is the process of fixing carbon dioxide into organic forms. Carbon fixation is performed by autotrophic bacteria, such as cyanobacteria.[1] Chemoautotrophic nitrifying bacteria, such as ''Nitrobacter, Nitrosospira'' and ''Nitrosomonas'', also fix carbon.[1] Sulfur oxidizing bacteria, such as ''Thiobacillus'', fix carbon as well.<br />
<br />
*'''Carbon Mineralization''' results from microbial decomposition of organic carbon compounds into inorganic forms. As the organic carbon substances, like plant matter, are decomposed, inorganic carbon dioxide is produced. Most bacteria are heterotrophs that perform carbon mineralization. When microorganisms die, they are decomposed by successive microbial generations. Peptidoglycan, the main component of bacterial cell walls, is utilized as a polysaccharide substrate by other heterotrophic soil microbes.[1]<br />
<br />
*'''Methanogenesis''' - Methanogenic bacteria produce methane from the reduction of carbon dioxide. They are all strict anaerobes that use carbon dioxide for the carbon source.[1] They can all use hydrogen as a source of energy and electron donor. [1]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle '''Nitrogen cycle:''']<br />
<br />
*'''Nitrogen fixation:''' ''Azotobacter'' is a free living nitrogen fixing bacteria.[1] ''Rhizobium'' lives in a mutualistic relationship with plants by fixing nitrogen within root the nodules of legumes.[1] ''Anabaena'' and ''Nostoc'' have specialized heterocyte structures where nitrogen fixation occurs.[1] <br />
<br />
*'''Nitrification:''' Nitrifying bacteria, such as ''Nitrobacter, Nitrosospira,'' and ''Nitrosomonas'', oxidize ammonium to nitrate.[1] <br />
<br />
*'''Denitrification:''' ''Alcaligenes, Flavobacterium'', and ''Pseudomonas'' are common soil denitrifying bacteria.[1]<br />
<br />
===Domain Archaea===<br />
<br />
====Introduction to Archaea====<br />
<br />
Vladimir Vernadsky decided, in 1926, that only two domains of life existed on Earth, Bacteria and Eukarya.[37] About 50 years later in 1977, Carl Woese and George Fox theorized that part of the bacterial domain possed multiple dissimilarities from bacteria and recognized it to be another domain of life, now called Archaea.[38] Woese and Fox’s theory regarding the differences of archaea were confirmed in 1990’s through the use of 16S rRNA and 18S rRNA.[38] <br />
<br />
Despite the strongly held belief, in the 1990s, that archaea only inhabited extreme environments, recent discoveries have suggested their presence in abundant numbers all throughout the Earth. It is suggested that Archaea play notable roles in maintaining nutrient cycles.[37] Various methods of research, such as cultivation, culture-independent techniques and isotope-based methods, have facilitated the study of domain Archaea in carbon and nitrogen cycling. [37]<br />
<br />
The use of genomic and biochemical data has permitted the study of archaeal structure.[37] Use of these research methods has shown that domain archaea and domain bacteria differ in cell wall characteristics yet, share various ways to transfer genetic information by replication and transcription from their common ancestor, Eukarya.[37] As of 2012, 116 genera of Archaea have been observed which consists of 450 species. Most of the archaeal species in these genera remains uncultivated, known only through its gene sequences and molecular surveys.[37]<br />
<br />
====Morphology==== <br />
Archaea are characterized by various cell sizes. They are most commonly found to be small organisms ranging from “0.1 to 15 μ diameter and up to 200 μ long.”[38] The shape of many archaea are similar to bacteria, including bacillus, cocci, spirilla and “plate-like forms.” [38] Their cell membranes have ether linked lipids with no periplasmic space, similar to gram-positive bacteria, and contain no intracellular organelles.[39]<br />
<br />
'''Flagella:''' Most motile archaea inhabit a motor rotary system that allows it to move its flagella through the chemical gradient similar to bacteria.[39] Despite its similarity in function and source of energy required for motility, the flagella of both archaea and bacteria differ in structure.[39] Archaeal flagella gets the energy for its movement by ATP and is composed of dependent filaments that rotate singularly. [40] Archaeal flagella are known to be thinner than bacteria flagellin.[40] Since, the archaeal common ancestor is not bacteria but eukarya, convergent evolution is a plausible explanations for the differences between bacterial and archaeal flagellin. [40]<br />
<br />
'''Membranes:''' Archaea have a cell membrane that protects the cytoplasm and the nucleic acids from the environment. The archaeal cell membrane has a lipid bilayer with glycol-ether lipids that are more stable than ester linkages and help some archaea that live in extreme environments to withstand such conditions.[39] Most archaeal species are surrounded by a cell wall which protects the cell membrane and maintains the archaeal structure.[41]<br />
<br />
====Reproduction====<br />
Archaeal organisms reproduce by binary fission since they do not have nucleases thus, the DNA chromosome in a Archaeal organism replicate, separate and create two daughter cells.[43] The process of binary fission can be seen in Figure (3.5) process begins the parent cell duplicating the DNA. The DNA material then goes to the sides of the cell where an invagination to the cell occurs allowing the cell to become two individual cells. Binary fission is a very fast reproduction process, that allows archaeal organisms to grow at an exponential rate.[44]<br />
<br />
[[Image:WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg|frame|center|Figure 3.5 Illustration of binary fission. From[https://d2jmvrsizmvf4x.cloudfront.net/WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg]]]<br />
<br />
====Metabolism==== <br />
Archaea share similar metabolic characteristics to bacteria. The metabolic pathways taken by all archaea shown in the (Figure 3.6) demonstrates the great diversity and variation amongst archaea. [38] The kinds of archaea that are seen in the environment and the metabolic pathways taken by some can be summarized in the image. <br />
<br />
*Photoautotrophs: use light as an energy source and carbon dioxide as the carbon source with the help of the Calvin Cycle.[38]<br />
*Chemoautotrophs: use inorganic chemicals as their energy source and carbon dioxide as carbon source. <br />
*Chemoheterotrophs: take organic chemicals as energy source and organic chemicals as carbon source. The pathways taken by chemoheterotrophs varies from respiration by the Krebs Cycle to fermentation. [38]<br />
*Photoheterotrophs: use light as their energy source and organic chemicals as their carbon source. <br />
<br />
Most archaea inhabiting in the soil environment are major contributors to the biogeochemical cycles.<br />
<br />
[[Image:2000px-Troph_flowchart.svg.png|thumbnail|center|Figure 3.6 Flowchart showing different metabolic pathways. From[https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Troph_flowchart.svg/2000px-Troph_flowchart.svg.png]]]<br />
<br />
====Contributions to the Cycle====<br />
Archaea play a significant role in the nutrient cycles that take place in the ecosystem as they account for about 1-5% of all the prokaryotes present in the soil environment.[42]<br />
<br />
'''Carbon Cycle:''' Archaea have an important role in the carbon cycle that takes place specifically in methane production, carbon mineralization and carbon assimilation all of all of which contribute to the soil’s carbon sink.[42] The carbon dense soil helps to make the soil organic matter rich and helps to form extracellular polymers which creates stable aggregates. For some microbes, an electron acceptor is need to carry out metabolic functions. [42] More info on [https://microbewiki.kenyon.edu/index.php/Carbon_cycle Carbon Cycle].<br />
<br />
*'''Carbon Assimilation:''' Involves the transformation of inorganic carbon into organic carbon compounds. This process is commonly done by autotrophic phyla ''Crenarchaeota, Thaumarchaeota'', and ''Euryarchaeota'' that use carbon dioxide/ bicarbonate converting it to organic compounds.[42] Of the autotrophic lineages observed in carbon assimilation the ''Thaumarchaeota'' are strict autotrophs, the ''Euryarchaeota'' and ''Crenarchaeota'' are facultative autotrophs and the ''Halobacteriales'' and ''Thermococcales'' are obligate heterotrophs.[42] <br />
<br />
*'''Carbon Mineralization:''' The process that converts organic carbon into the oxidized inorganic carbon, carbon dioxide is commonly done by both aerobes and anaerobes.[42] The heterotrophic microbes that use organic compounds as energy to oxidize the carbon source include, methanogens and methane-oxidizing archaea belonging to the phyla ''Euryarchaetota'', and ''Crenarchaeota''.[42] <br />
<br />
*'''Methanogenesis:''' production of methane, a major greenhouse gas in the Earth’s atmosphere is commonly done by archaea upon reducing an oxidized compound.[42] The phyla ''Euryarchaeota'' is the only phyla that consists of archaea that produce methane all of which form five class: ''Methanopyri, Methanococci, Methanobacteria, Methanomicrobia'' and ''Thermoplasmata''.[42] Methanogens are commonly found in anaerobic and aerobic conditions such as bodies of water, aerated soils and oxygenated waters.[42]<br />
<br />
'''Nitrogen Cycle :''' Archaea play a pivotal role in the Nitrogen cycle and help create nitrogenous products for the plants and microbes. More info on [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle Nitrogen cycle].<br />
<br />
*'''Nitrogen Fixation:''' Fixing nitrogen from the environment and converting it to organic nitrogen in the soil or to inorganic nitrogenous form since both organic and inorganic products are in short supply in the biosphere and are fixed by many archaeal organisms.[42] N2 fixation by the environment is usually done by three major archaeal classes ''Methanobactera, Methanococci'' and ''Methanomicrobia''.[42] <br />
<br />
*'''Nitrification:''' Converting the ammonia (NH4+) in the soil to nitrite (NO2-) produces nitrate (NO3-) as an intermediate. [42] The transformation of ammonia to first nitrate then to nitrite is a two step process that is done by different microbes. [42] Most common organisms involved in nitrification include ammonia-oxidizing archaea which are lithotrophic organisms mostly, of the ''Thaumarchaeota'' phylum from the archaea domain. <br />
<br />
*'''Denitrification :''' The conversion of atmospheric N2 using the electron acceptor NO3- or NO2- creating the formation of nitric oxide, nitrous oxide and/or N2.[42] The formation of the end product N2 may not always be produced but other intermediates NO and N2O, greenhouse gases may be produced.[42] Of the archaeal organisms that have been studied in denitrification process is done by ''Pyrobaculum aerophilum'' which accepts both NO3- and NO2- as an electron acceptor producing a variety of products NO2-, NO, N20 and N2.[42]<br />
<br />
===Domain Eukarya===<br />
<br />
====Fungi====<br />
<br />
=====Introduction=====<br />
<br />
'''Introduction'''<br />
<br />
Fungi comes from the ancient Greek word “sphongos” meaning sponge in reference to the mushroom cap [47]. Fungi have the general characteristics of being eukaryotic, heterotrophic, external absorbers of nutrients, containing a hyphal thallus, reproducing via spore, and being pleomorphic (producing several forms). Fungi are generally organoheterotrophs that can survive in low pH and stay active at low moisture content[46]. Fungi reside in the domain Eukarya with an estimated species of 1.5 million, and less than five percent of them have ever been described. The general phyla included within Kingdom Fungi include Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, Chytridiomycota, and Microsporidia [48].<br />
<br />
[[Image:magical-kingdom-620.jpg|frame|center|Figure 3.7 Fungi phyla hierarchy. From.[http://www.motherjones.com/environment/2009/11/fungi-family-tree]]]<br />
<br />
=====Morphology=====<br />
<br />
'''Morphology''' <br />
<br />
Fungi can be either unicellular (yeasts) or multicellular. All multicellular fungi are made up of small, filamentous particles called hyphae. Some hyphae have cross walls called septa, while others do not- this is a large basis of fungal identification. Fungal cells generally have multiple nuclei. Fungal cell walls are generally composed of chitin, a long carbohydrate polymer that adds rigidity and structural support to fungi [49]. <br />
<br />
=====Reproduction=====<br />
<br />
'''Reproduction'''<br />
<br />
Fungal reproduction can occur either sexually or asexually.<br />
<br />
'''Sexual reproduction''' can occur by homothallic or heterothallic mycelia.<br />
<br />
'''Asexual reproduction''' can occur by fragmentation, budding, or by producing spores (the most common method). <br />
<br />
*'''Spores:''' spores come in many different forms. One of the most well known are conidiospores, which are unicellular or multicellular spores that get released from the tip of the hyphae. <br />
<br />
'''Perfect fungi''' are those that can reproduce both sexually and asexually while imperfect fungi are those that can only reproduce asexually.<br />
<br />
*Sexual reproduction always includes the stages plasmogamy (fusion of two haploid cells), karyogamy (creation of a diploid zygote), and meiosis (gametes are created).<br />
<br />
=====Metabolism=====<br />
<br />
'''Metabolism'''<br />
<br />
Many different fungi display a myriad of metabolisms. There are primary metabolites that that help the fungi function properly, and secondary metabolites that are generally bioactive that are not the most pertinent to fungal growth (they can live without these). Secondary metabolites play a large role in chemistry today and can be manufactured into commonly used products such as new drugs. In general fungi are heterotrophic through release of extracellular enzymes into the neighboring environment to break complex molecules down into smaller ones. The materials are then absorbed and metabolized [50]. Fungi are sessile organisms that overcome their little to no movement through apical growth at the hyphal tip. Fungi are noted to grow almost everywhere on the Earth.<br />
<br />
=====Relevance to soil===== <br />
<br />
'''Relevance to soil'''<br />
<br />
Fungi include some of the most abundant biomass of microorganisms in numerous soils. They play an important role as decomposers within the soil food web through conversion of difficult to digest organic material into forms many other organisms can use [51]. Their hyphae can bind soil particles together and create aggregates that increase soil water holding capacity. They perform important functions from water dynamics to nutrient cycling and disease suppression. Soil fungi can be categorized into three different groups based on their actions: <br />
<br />
*decomposers: that convert dead organic material into fungal biomass<br />
<br />
*mutualists: which colonize plant roots and help solubilize phosphorous and bring soil nutrients<br />
<br />
*pathogens/ parasites: which help control diseases in soil via trapping organisms such as nematodes [51]. <br />
<br />
Fungi are seen common in intensively managed agricultural soils due to tillage disrupting hyphae. Fungi also play a very important role in the [https://microbewiki.kenyon.edu/index.php/Rhizosphere_Interactions rhizosphere], the region of soil that is greatly influenced by the plant root system. This area of soil which is concentrated in plant roots and fungal hyphae is known to support greater microbial activity.<br />
<br />
=====Protozoans=====<br />
<br />
'''Protozoans'''<br />
<br />
In general, Protozoans range from 5 to 500 µm in diameter, making them significantly larger than bacteria [21]. They are abundantly located near the surface of the soil (15cm deep) where roots are plentiful [21]. Many protozoans have two life cycles. One is their active form where they are motile and feed on prey. The other is the cyst form where they produce a thick coating to protect them from the environment and can go dormant for years. The protozoa are divided into 4 major categories: the ciliates, the flagellates, the heliozoans, and the amoebas [10]. <br />
<br />
======Ciliates======<br />
<br />
'''Cilliates:'''<br />
This group, within protozoans, is fairly diverse. A common feature shared amongst all of its members is the presence of at least one cilia at any stage of its development [10]. The cilia is used for movement and other things such as predation (tentacles). For movement, they use the massive amounts of tiny cilia to create wave like currents to propel the cell forwards. Most ciliates also have toxicysts which are used to capture prey [10]. Some ciliates even have a symbiotic relationship with algae living inside of them [10]. The algae use the CO2 produced by ciliates and turn it into O2 that can then be reused by the ciliates [10]. They are found in a wide array of habitats ranging from freshwater and soil to the rumen of Animals [22]. They are present in almost anywhere that contains water [23]. They are unicellular heterotrophs so they feed on bacteria and algae in their environment. Ciliates are one of the top predators in the microbial food web and are hypothesized to have been a major predatory group before animals evolved [23]. Parasitic ciliates exist that can cause the death of animals and are increasingly becoming dangerous in water [23].<br />
<br />
[[Image:2spiro.jpg|frame|center|Figure 3.8 Microscope image of ciliated protists. From[http://www.microscopy-uk.org.uk/mag/smallimag/2spiro.jpg]]]<br />
<br />
======Flagellates======<br />
<br />
'''Flagellates''' are one of the most commonly known protists. They are unicellular organisms that may be solitary, colonial, free living, or parasitic [24]. The hallmark feature of protists is that at some point in their life cycle, they possess a flagella. A flagellum is a long hair like structure that is used for locomotion, sensation, and sometimes predation [24]. The flagellum makes waves by whiplike lashing movements which propels the cell forwards. Flagellates also have a protective coating in the form of a thin pellicle to protect them from the environment [24]. <br />
<br />
[[Image:9703607_orig.jpg|frame|center|Figure 3.9 Illustration of flaggelates during different life cycle stages. From[http://diagnosticparasitology.weebly.com/uploads/3/9/5/4/3954522/9703607_orig.jpg]]]<br />
<br />
*'''Mastigophora:'''<br />
<br />
Mastigophora is a subphylum of flagellates. Being a member of the flagellates, their key feature is the flagellum. Their habitats include freshwater, soil, and can act as animal parasites as well [25]. They use pseudopodia, a long outward protrusion, to trap and funnel food from the environment into their cell bodies [25]. The Mastigophora are mainly known for their parasitism, which can take place in both humans and animals [25]. ''Typanosomes'' are an example of Mastigophora which causes African sleeping sickness [25]. ''Giardia lambli''a is another example that resides in the intestinal tract of warm-blooded animals and inflicts intestinal giardiases [25]. It is also a major contaminant of drinking water because it is resistant to chlorine, which is the most common water purifier [25]. Having a dormant cyst form also adds to its survival potential through filtration efforts [25].<br />
<br />
<br />
<br />
*'''Euglenids:'''<br />
<br />
Euglenids are one of the best known flagellates. They are found in freshwater and soil, as long as there are organic materials. They also participate in some symbiotic relationships with marine animals. Euglenid cells do not contain cell walls or other rigid membranes [26]. This gives the cell tremendous flexibility and allows it to change its shape to easily navigate through muddy terrain. Euglenids have two flagella, one which creates locomotion and movement for the cell [26]. The other flagellum does not protrude from the cell and is contained in the cell body [26].<br />
<br />
======Amoebas======<br />
<br />
'''Amoebas'''<br />
<br />
Amoebae are single celled eukaryotes present in many different types of environments. They are scattered throughout a variety of eukaryotic lineages and therefore are not monophyletic [27]. Amoebae range in size from 5 micrometers to 3 mm and don’t have a defined shape, commonly recognized for being polymorphic. They are motile through the use of pseudopodia, which stretch and pull the cell along with it. The pseudopodia are also used for feeding. They are able to sense prey that can be engulfed and engulf them via phagocytosis. The amoeba’s main prey consists of bacteria, algae, and other protozoa [28]. The prey is moved around within the cell via food vacuoles, a feature of amoebae [28]. Another key characteristic of amoebae are the large contractile vacuoles inside the cell. The purpose of the contractile vacuole is to osmoregulate by pumping excess water out of the cell. In times of turmoil, amoebae have an encysted form that helps them get through the tough times. This form is useful when there is low nutrient availability to limit energy consumption. There are two main forms an amoeba can be characterized as. They can either be testate or nontestate. Testate amoeba produce shells, or “tests”, that help identify their species since each species has a unique shell.<br />
<br />
[[Image:Amoeba_(PSF).png|frame|center|Figure 3.10 Amoeba morphology. From[https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Amoeba_(PSF).png/230px-Amoeba_(PSF).png]]]<br />
<br />
=====Slime Molds=====<br />
<br />
'''Slime molds''' were once classified as fungi, but have now been placed in their own phylogenetic groups. Slime molds are single cells that can live independently, but aggregate to form multicellular reproductive structures when necessary [29]. The fruiting body releases spores which germinate into new cells. Slime molds feed off of bacteria and are most commonly found in forests. They feed off of decaying vegetation as well so they can be seen on rotting logs and leaves.<br />
<br />
[[Image:28-30-cellslimemoldlife-l.jpg|frame|center|Figure 3.11 Illustration of slime mold life cycle. From[https://lichencolony.files.wordpress.com/2006/06/28-30-cellslimemoldlife-l.jpg]]]<br />
<br />
==Current Research== <br />
<br />
'''Bacteria:''' To showcase the great diversity of soil bacterial environments, cyanobacteria have been studied in both desert and polar regions. Cyanobacteria can survive in extreme conditions likely because of their long evolutionary past.[16] Dr. Patzelt and his colleagues studied the diverse cyanobacteria residing in the Atacama desert, one of the driest parts of the world. The diverse taxa found in the Atacama desert can withstand prolonged periods of extreme desiccation.[16] The cyanobacteria dominate the soil crusts, affecting soil stability, soil structure and soil fertility.[16] Cyanobacteria inhabiting the Antarctic and Arctic regions, show similar adaptations to extreme environments as the cyanobacteria found in the desert. The polar cyanobacteria are particularly adapted to high altitudes.[17] They can withstand high ultraviolet radiation, desiccation, and repeated freeze-thaw cycles.[17] The autotrophic cyanobacteria supports heterotrophic microbes, providing an important ecosystem service in an environment with low microbial activity.[17]<br />
<br />
'''Archaea:''' In 150 soil samples acquired from North and South America, about 150,000 species were observed.[45] Of these, over 2,500 were identified as archaea based on their ssu rRNA.[45] The archaeal species were further analyzed to understand their role in the soil environment. Of the archaeal groups, ''Crenarchaeota'' and ''Euryarchaeota'' were found.[45] Bates stated that, “Across the non-experimental soils examined the soil C:N ratio was the single best predictor of archaeal relative abundances” due to their influences in the nutrient cycles.[45]<br />
<br />
'''Fungi:''' Fungi have been in the public eye for a while now due to the many different types of secondary metabolites they produce. Some produce bioactive compounds that can inhibit growth of protozoa, bacteria, parasites, insects, and even other fungi. A large area of investigation is the uses of these chemicals for human interests in use from medicine to plant and animal toxins [52].<br />
<br />
'''Protozoa:''' It’s known that Protozoa stimulate plant growth in different ways. It’s suspected that the Protozoa take part in the microbial loop which is responsible for the nutrient production for plants [19]. However, new developments have shown that the Protozoa themselves are responsible for the nitrogen mineralization and that other bacteria have no effect on the plant’s nitrogen sources [19].<br />
<br />
==References==<br />
<br />
1. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). Principles and Applications of Soil Microbiology. New Jersey: Pearson Education Inc.<br />
<br />
2. Ingham, Elaine R. Ingham R. "Chapter 4: SOIL FUNGI." Soil Biology. Natural Resources Conservation Service Illinois, n.d. Web. 9 Feb. 2016<br />
<br />
3. Reid, Greg, and Percy Wong. "SOIL BACTERIA AND FUNGI - NEW SOUTH WALES." Soil Bacteria and Fungi. New South Wales Department of Primary Industries, 2005. Web. 11 Feb. 2016.<br />
<br />
4. "Fungi." Microbiology Online. Microbiology Society, n.d. Web. 11 Feb. 2016.<br />
<br />
5. Tortora, G.J., Funke, B.R., Case, C.L. (2012). “Microbiology an Introduction.” 11th ed. Pearson Benjamin Cummings, San Francisco.<br />
<br />
6. Rizzo, D. “Intro to Fungi.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
7. Rizzo, D. “Ascomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
8. Rizzo, D. “Basidiomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
9. Pegg G.F., Brady B.L. “Verticillium Wilts.” New York, CABI Publishing 2002. Google Books. Web. 11 Feb. 2016. http://books.google.com<br />
<br />
10. Hebert, Paul. "What Is a Protist / What Are Protozoa? - Encyclopedia of Life." Encyclopedia of Life. N.p., n.d. Web. 11 Feb. 2016.http://eol.org/info/456<br />
<br />
11. "MicrobeWorld." Protista. N.p., n.d. Web. 11 Feb. 2016. http://www.microbeworld.org/types-of-microbes/protista<br />
<br />
12. Madigan, M.T., Martinko, J.M. (2006). Brock Biology of Microorganisms. New Jersey: Pearson Prentice Hall.<br />
<br />
13. Roesch, L.F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H.; Camargo, F. A. O.; Farmerie, W. G.; Triplett, E. W.(2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1(4).283-290. <br />
<br />
14. Amann, R.I, Ludwig, W., Schleifer, K.H.(1995).Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology and Molecular Biology Reviews. 59(1). 143-169. <br />
<br />
15. Geers, D., Cohan, F.M., Lawrence J.G., Spratt, B.G., Coenye, T. Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005). Opinion: Re-evaluating prokaryotic species. Nature Reviews Microbiology. 3(9). 733-739.<br />
<br />
16. Patzelt, D.J., Hodac, L., Friedl, T., Pietrasiak, N., Johansen, J.R. (2014). Biodiversity of soil cyanobacteria in the hyper-arid Atacama Desert, Chile. Journal of phycology. 50(4). 698-710. <br />
<br />
17. Makhalanyane, T. P., Valverde, A., Velázquez, D., Gunnigle, E., Van Goethem, M. W., Quesada, A., & Cowan, D. A. (2015). Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats. Biodiversity and Conservation, 24(4), 819-840.<br />
<br />
18. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist>.<br />
<br />
19. Ekelund, Flemming; Saj, Stephane; Vestergård, Mette; Bertaux, Joanne; Mikola, Juha. (2009). “The “soil microbial loop” is not always needed to explain protozoan stimulation of plants”. Soil Biology & Biochemistry. Vol. 41 Issue 11, p2336-2342, 7p.<br />
<br />
20. Bonkowski, Michael. "Protozoa and Plant Growth: The Microbial Loop in Soil Revisited." New Phytologist New Phytol 162.3 (2004): 617-31. Web.<br />
<br />
21. Hoorman, James. "The Role of Soil Protozoa and Nematodes." Fact Sheet (n.d.): n. pag. Ohio State University, 2011. Web.<br />
<br />
22. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist<br />
<br />
23. Lynn, Denis H(Apr 2012) Ciliophora. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001966.pub3]<br />
<br />
24. "flagellate". Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc., 2016. Web. 23 Feb. 2016 <http://www.britannica.com/science/flagellate>.<br />
<br />
25. "Mastigophora." World of Microbiology and Immunology. 2003. Encyclopedia.com. 23 Feb. 2016<http://www.encyclopedia.com>.<br />
<br />
26. “Plant Life." : Euglenoids. N.p., n.d. Web. 23 Feb. 2016. <http://lifeofplant.blogspot.com/2011/04/euglenoids.html><br />
<br />
27. Parales, R.E. and Martin, M. (2015) Microbial Diversity Laboratory Manual, MIC 105L, Winter 2015. Department of Microbiology and Molecular Genetics, College of Biological Sciences, The University of California, Davis.<br />
<br />
28. Arnold, Paul. "What Does an Amoeba Eat? Plus Other Ameoba Info and Questions." Bright Hub. N.p., n.d. Web. 04 Mar. 2016.<br />
<br />
29. "MicrobeWorld." Slime Molds. N.p., n.d. Web. 24 Feb. 2016. <http://www.microbeworld.org/types-of-microbes/protista/slime-molds><br />
<br />
30. Leeuwenhoek., A. V. (2009, November 18). One gram of soil: A microbial biochemical gene library. Retrieved March 13, 2016, from http://www.ncbi.nlm.nih.gov/pubmed/19921459 <br />
<br />
31. Coleman, D. C., Crossley, D. A. & Hendrix, P. F. "Soil food webs: Detritivory and microbiology in soils," in Fundamentals of Soil Ecology, 2nd ed. (Elsevier, 2004) 236-241.<br />
<br />
32. Welcome to Agriinfo.in. (n.d.). Retrieved February 21, 2016, from http://agriinfo.in/?page=topic&superid=5&topicid=172 <br />
<br />
33. Gouthro, T., & Rice, D. (1987, December 15). Interaction Terminology. Retrieved February 21, 2016, from http://www.rpi.edu/dept/chem-eng/Biotech-Environ/MixCul/ecodefn.htm <br />
<br />
34. AMENSALISM. (n.d.). Retrieved February 21, 2016, from https://biostuds.wikispaces.com/AMENSALISM <br />
<br />
35. Natural Resources Conservation Service. (n.d.). Retrieved March 10, 2016, from <br />
http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053865 <br />
<br />
36. Ecological Linkages Between Aboveground and Belowground Biota. (n.d.). Retrieved March 10, 2016, from http://science.sciencemag.org/content/304/5677/1629 <br />
<br />
37. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf<br />
<br />
38. Kingdom Archaea. (n.d.). Retrieved March 10, 2016, from http://plantphys.info/organismal/lechtml/archaea.shtml <br />
<br />
39. What are Archaea? - Encyclopedia of Life. (n.d.). Retrieved March 10, 2016, from http://eol.org/info/457 <br />
<br />
40. Flagellum. (n.d.). Retrieved March 10, 2016, from http://www.newworldencyclopedia.org/entry/Flagellum#Archaeal_flagellum <br />
<br />
41. Archaea: Morphology. (n.d.). Retrieved March 10, 2016, from http://www.ucmp.berkeley.edu/archaea/archaeamm.html <br />
<br />
42. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf <br />
<br />
43. Archaea. (n.d.). Retrieved March 10, 2016, from http://www.eoearth.org/view/article/150172/ <br />
<br />
44. Binary Fission: Cell Division & Reproduction of Prokaryotes. (n.d.). Retrieved March 10, 2016, from http://www.scienceprofonline.com/microbi <br />
<br />
45. Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2010, November 18). Examining the global distribution of dominant archaeal populations in soil. Retrieved February 21, 2016, from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105767/<br />
<br />
46. Scow, K. M. "Lecture 1 Part 1." Lecture, Davis.<br />
<br />
47. Rizzo, D. "Lecture 1." Lecture, Davis.<br />
<br />
48. Rizzo, D. "Lecture 3." Lecture, Davis.<br />
<br />
49. C.J. Alexopoulos & C. W. Mims, Introductory Mycology 3rd edition. 1979. Wiley NY. Web accessed Mar 8, 2016 from http://www.ucmp.berkeley.edu/fungi/fungimm.html<br />
<br />
50. Rizzo, D. "Lecture 2." Lecture, Davis.<br />
<br />
51. Ingham, E. “Chapter 4: Soil Fungi” (2016) Oregon State University. Retrieved Feb. 20, 2016, from http://extension.illinois.edu/soil/SoilBiology/fungi.htm<br />
<br />
52. Keller, N., Turner, G., Bennett, J. “Fungal Secondary Metabolism- from Biochemistry to Genomics.” 2005 Nature Reviews Microbiology p/ 937 to 947.</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Introduction_to_Organisms&diff=128511
Introduction to Organisms
2017-03-05T23:24:58Z
<p>Kmscow: /* Soil Food Web and Microbial Interactions */</p>
<hr />
<div>==Introduction== <br />
The soil ecosystem in an important environment that allows both plants and animals to survive, grow and reproduce. The significance of the soil as an ecosystem is at times overlooked despite its major contributions to the environment. The [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] is a complex and varied microbial habitat.[1] The plants and organisms inhabiting the soil contribute to its thriving diversity. Soil life is diverse in morphology, metabolism, size, and many other characteristics. Soil is a heterogeneous environment with various zones of rhizosphere, aggregates, organic matter and animal residues.[31] Given each zone is a small component of the larger soil ecosystem, rhizosphere accounts for only 5 to 7 percent of the soil environments but contains over “70 percent of the bacterial- and fungal-feeding nematodes.”[31] <br />
<br />
Since soil microbial diversity is immense, with all three domains of life: Archaea, Bacteria and Eukarya represented in the soil environment, it is not possible to discuss each microbial species (many of which have not even been described!). Only a few representative groups of each domain will be discussed to provide examples of the roles these organisms play in soil.<br />
<br />
==Soil Food Web and Microbial Interactions== <br />
<br />
To survive in a soil environment, an organism must be able to adapt to changing environments and organism interactions. One type of interaction shown in (Figure 2.1) is predation. Other common interactions in the soil environment are: <br />
<br />
:[[Image:soil_foodweb72.jpg|frame|center|Figure 2.1 Soil Food Web. From[http://www.exploringnature.org/graphics/foodwebs/soil_foodweb72.jpg]]]<br />
<br />
<br />
'''I. Commensalism:''' Organism (A) benefits from the presence of Organism (B) while (B) is unaffected by the presence of (A).[32]<br />
<br />
'''II. Mutualism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) and becomes a necessary association for each other’s survival. [32] [33]<br />
<br />
'''III. Synergism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) but the relationship is not necessary for survival.[33]<br />
<br />
'''IV. Competition:''' Depending on the organisms this interaction benefits organisms who can readily adapt to the environment and overcome any obstacles needed to survive, grow and reproduce.[33]<br />
<br />
'''V. Amensalism:''' An interaction in which Organisms (A) and (B) develop a partnership where (B) is unaffected by (A) but organism (A) is negatively affected by (B).[34]<br />
<br />
'''VI. Parasitism:''' Organism (A) benefits from Organism (B) but Organism (B) does not benefit positively from Organism (A). <br />
<br />
'''VII. Predation:''' “An interaction between organisms in which one benefits and one is harmed based on the ingestion of the smaller sized organism, the prey, by the larger organism, the predator.”[33]<br />
<br />
<br />
<br />
The soil food web consists of microbes who play multiple essential roles in soil ecosystem. The interactions observed in soil food web include not only based on biological interactions, which directly affects the nutrient cycling and degradation of pollutants, but also the creation of soil structure, e.g. of aggregates.[35] Soil organism activity, along with the presence of soil organic matter, create stabilizing aggregates.[35] The hyphae within the soil environment and the microbes help form large, stable aggregates in the soil habitat.[35] The production of specific nutrients, such as ammonium created by microbial metabolic functions, helps to enrich the the soil for plant use.[35] The biodiversity in the soil plays a pivotal role in degrading pollutants, and also prevents pathogens from inhabiting the soil environment through competition.[35] The food web in the soil environment is necessary to maintain the soil nutrients, biological activity, and detoxifying pollutants. <br />
<br />
In (Figure 2.1), all three domains, Archaea, Bacteria, and Eukarya, are represented in the soil food web. If one takes a closer look at the figure, the soil food web is not only dependent on small and large microbes but also dead organic matter and plant roots. Dead and living matter in the soil environment contribute to maintaining the food web. Plant residues contribute to the soil’s carbon source.[35] The plant residues either, release carbon dioxide to the environment, or contribute to the soil organic matter.<br />
<br />
==3 Domains==<br />
[[Image:Big_Tree_Bold_Letters_white.png|frame|center|Figure 3.1 Phylogenetic Tree of the 3 Domains. From[http://phylogenomics.blogspot.com/2014_02_01_archive.html]]]<br />
<br />
===Carl Woese and Phylogeny===<br />
<br />
[[Image:Carlwoese1_0565_b.jpg|frame|center|Figure 3.2 Carl Woese. From[http://ofbacteriaandmen.blogspot.com/2013/01/the-new-biology-of-carl-woese.html]]] <br />
<br />
Carl Woese (Figure 3.2) was an American microbiologist famous for pioneering the technique of phylogenetic taxonomy through use of a 16S (for prokaryotic) and 18S (for eukaryotic) ribosomal RNA, also known as small subunit ribosomal RNA [46]. This refined Linnaean classification, taking out the guesswork classification by using a gene that was present in every living organism- the small subunit ribosomal RNA. This method of classification is comprehensive because all organisms possess this form of genetic material. Ssu rRNA is sequenced because the genes are highly conserved. Due to their functional constancy, some have variable regions to differentiate organisms, and are easy to sequence. This technique also elucidated the tree of life, which shows the three domains of microbial lineage diversity: Bacteria, Archaea, and Eukarya. DNA can be compared using a sample database that allows identification of unknown organisms to a species level.<br />
<br />
===Domain Bacteria===<br />
<br />
====Introduction to Bacteria==== <br />
Bacteria are single celled prokaryotic organisms that lack membrane bound organelles. They are involved in many important processes within the soil such as decomposition, [https://microbewiki.kenyon.edu/index.php/Bioremediation bioremediation], symbiosis and biological transformation of nutrients. They are present in all terrestrial soil environments.[1] Soil is a heterogenous environment that varies in moisture content, temperature, oxygen requirements, carbon source and many other bacterial growth conditions. Those wide ranging growth factors account for the enormous diversity in soil bacteria populations. One gram of soil can contain between 26,000 to 52,000 different bacterial species.[13] In the entire microbial world, only about 1 percent of bacterial species can be cultured under laboratory conditions which leaves an immense number of bacterial species yet to be described. [14]<br />
<br />
Classification based on phenotypic characteristics, such as cellular morphology, metabolism, gram staining, oxygen requirements, carbon source and other traits, was used more readily before modern DNA sequencing. But, phenotypic classification is still used and Bergey’s Manual of Systematic Bacteriology is the most widely used source for determining species based on characteristic species traits.<br />
<br />
Traditional species definitions are not as useful in bacteria. OTUs, or operational taxonomic units, based on DNA sequencing similarity, are more applicable to bacteria. Typically, those bacteria with 97 percent similar DNA sequence are classified within the same OTU.[15] The 16S small subunit ribosomal RNA is used to substantiate phylogenetic relationships between different bacterial groups.<br />
<br />
====Morphology====<br />
<br />
Bacterial cells measure approximately 1μm wide and 1-5μm long.[12] They are smaller than eukaryotic microbes.Due to their small size, bacteria can more easily adapt to changing soil environments than larger eukaryotes.[1] Most bacteria are singled celled, but actinomycetes grow in branching filaments. There are many different bacterial cell shapes. The most common are bacilli (rods), cocci (spheres), spirilla (spirals) and actinomycete (filaments).<br />
[[Image:bacteria_sizes.jpg|frame|center|Figure 3.3 Common cell shapes cocci, bacillus, and spirilla and relative sizes. From[http://www.ppdictionary.com/gnbac.htm]]]<br />
<br />
'''Flagella''' - There are many different types and different arrangement of flagella. Movement in soil environments is dependent on soil moisture content. Though movement in soil is limited, flagellar function is important to allow bacteria to find more favorable microsites.[1]<br />
<br />
'''Cell membrane''' - The cell membrane encloses the cytoplasm. It is semi-permeable phospholipid bilayer that regulates transport of nutrients into the cell and waste products out of the cell.<br />
<br />
'''Cell wall''' - Most bacteria have a rigid cell wall surrounding the cell membrane which protects the cell from osmotic lysis. The cell wall is made of a crosslinked polysaccharide, called peptidoglycan, that is found only in bacteria.[1] The cell wall gives the cell shape and structure, but it is porous enough to permit small water soluble molecules to flow through to the cell membrane surface.[1]<br />
<br />
*'''Gram positive''' bacteria have a thick cell wall made of several layers of peptidoglycan. The cell wall is the outermost structure, as they do not have an outer membrane. The thick cell wall structure make gram positive bacteria more resilient to osmotic shock. Gram positive bacteria can tolerate 5 to 10 times more turgor pressure than gram Gram negative bacteria.[1] Teichoic acids in the cell wall may also help to bind to cationic nutrients in soil surroundings.[1] <br />
<br />
*'''Gram negative''' bacteria have a thin cell wall surrounded by an outer membrane made of phospholipids and lipopolysaccharides. Polysaccharides of the outer membrane interact with surrounding cations and are involved in attachment of bacteria to soil particles. [1] Periplasm is a gel like substance that occupies the space between the outer membrane and the cell wall of gram negative bacteria.[1] The outer membrane and periplasmic space is thought to provide protection from environmental toxins.[1] Proteins within the periplasm are thought to begin the process of catalyzing hydrolysis of organic and toxic substances.[1] <br />
<br />
[[Image:gramposnegmembrane.jpg|frame|center| Figure 3.4 Illustration of Gram positive and Gram negative cell wall structures. From[http://micro.digitalproteus.com/morphology2.php]]]<br />
<br />
'''Endospores''' are made by ''Bacillus'' and ''Clostridium'' in response to environmental stress.[1] Endospores are extremely resistant structures that can withstand extreme temperatures up to 150℃.[12] They can also withstand extreme pressure, desiccation, radiation, pH and chemicals.[12] The endospore protects the bacterial DNA until environmental conditions are more favorable and germination can proceed. Soil is the most common habitat for endospore forming bacteria.[12]<br />
<br />
'''Extracellular polymers''' - Many bacteria secrete a slime layer or capsule made of polysaccharides or glycoproteins.[1] The outer polysaccharide coating of bacteria helps in attachment to surfaces and the formation of biofilms.[1] Bacterial capsule secretions play a big role in soil aggregation and soil structure.[1] When the carbon to nitrogen ratio within soils is high, microbes secrete the excess carbon as extracellular polysaccharides.[1]<br />
<br />
====Reproduction==== <br />
Most bacteria reproduce by binary fission.[12] The bacterial cell expands to twice the original cell size, duplicates the bacterial DNA and pinches off, producing two daughter cells. Each resultant daughter cell is a clone of the parent cell. Prokaryotic Archaea also reproduce by binary fission.<br />
<br />
*'''Spore formation:''' Actinomycetes are a large group of filamentous bacteria, primarily found in soil.[1] Actinomycetes are morphologically similar to fungi. Actinomycetes form long filaments called hyphae. Unlike most bacteria, the majority of actinomycetes reproduce using asexual spores called conidia.[1] Though they share many characteristic with fungi, actinomycetes are still prokaryotes. They are smaller than fungi and the cell wall contains peptidoglycan.[1] Actinomycetes break down a wide variety of organic compounds and play an important role in organic matter decomposition. [1] ''Streptomyces'', a subgroup within actinomycetes, produce geosmin, which gives soil the characteristic earthy smell.[12]<br />
<br />
====Metabolism==== <br />
<br />
Along with archaea, bacteria are the most metabolically diverse and employ many different nutritional strategies.[1]<br />
*Heterotrophs - Most bacteria are heterotrophic, obtaining carbon from preformed organic substances. [1] <br />
*Autotrophs - Carbon dioxide serves as the main source of carbon. Some cyanobacteria, nitrifying and sulfur-oxidizing bacteria are autotrophs.[1]<br />
*Organotrophs - Most bacteria obtain electrons from organic substances.[1]<br />
*Lithotrophs - Some cyanobacteria, nitrifying bacteria and sulfur-oxidizing bacteria obtain electrons from inorganic substances.[1]<br />
*Phototrophs - Cyanobacteria use light as the main source of metabolic energy.[1]<br />
*Chemotrophs - All other nonphotosynthetic bacteria do not rely on light for metabolic energy.[1]<br />
<br />
====Contributions to Biogeochemical Cycling==== <br />
<br />
Bacteria play a significant role in the cycling of a wide range of elements.<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Carbon_cycle '''Carbon Cycle:'''] <br />
<br />
*'''Carbon Assimilation''' is the process of fixing carbon dioxide into organic forms. Carbon fixation is performed by autotrophic bacteria, such as cyanobacteria.[1] Chemoautotrophic nitrifying bacteria, such as ''Nitrobacter, Nitrosospira'' and ''Nitrosomonas'', also fix carbon.[1] Sulfur oxidizing bacteria, such as ''Thiobacillus'', fix carbon as well.<br />
<br />
*'''Carbon Mineralization''' results from microbial decomposition of organic carbon compounds into inorganic forms. As the organic carbon substances, like plant matter, are decomposed, inorganic carbon dioxide is produced. Most bacteria are heterotrophs that perform carbon mineralization. When microorganisms die, they are decomposed by successive microbial generations. Peptidoglycan, the main component of bacterial cell walls, is utilized as a polysaccharide substrate by other heterotrophic soil microbes.[1]<br />
<br />
*'''Methanogenesis''' - Methanogenic bacteria produce methane from the reduction of carbon dioxide. They are all strict anaerobes that use carbon dioxide for the carbon source.[1] They can all use hydrogen as a source of energy and electron donor. [1]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle '''Nitrogen cycle:''']<br />
<br />
*'''Nitrogen fixation:''' ''Azotobacter'' is a free living nitrogen fixing bacteria.[1] ''Rhizobium'' lives in a mutualistic relationship with plants by fixing nitrogen within root the nodules of legumes.[1] ''Anabaena'' and ''Nostoc'' have specialized heterocyte structures where nitrogen fixation occurs.[1] <br />
<br />
*'''Nitrification:''' Nitrifying bacteria, such as ''Nitrobacter, Nitrosospira,'' and ''Nitrosomonas'', oxidize ammonium to nitrate.[1] <br />
<br />
*'''Denitrification:''' ''Alcaligenes, Flavobacterium'', and ''Pseudomonas'' are common soil denitrifying bacteria.[1]<br />
<br />
===Domain Archaea===<br />
<br />
====Introduction to Archaea====<br />
<br />
Vladimir Vernadsky decided, in 1926, that only two domains of life existed on Earth, Bacteria and Eukarya.[37] About 50 years later in 1977, Carl Woese and George Fox theorized that part of the bacterial domain possed multiple dissimilarities from bacteria and recognized it to be another domain of life, now called Archaea.[38] Woese and Fox’s theory regarding the differences of archaea were confirmed in 1990’s through the use of 16S rRNA and 18S rRNA.[38] <br />
<br />
Despite the strongly held belief, in the 1990s, that archaea only inhabited extreme environments, recent discoveries have suggested their presence in abundant numbers all throughout the Earth. It is suggested that Archaea play notable roles in maintaining nutrient cycles.[37] Various methods of research, such as cultivation, culture-independent techniques and isotope-based methods, have facilitated the study of domain Archaea in carbon and nitrogen cycling. [37]<br />
<br />
The use of genomic and biochemical data has permitted the study of archaeal structure.[37] Use of these research methods has shown that domain archaea and domain bacteria differ in cell wall characteristics yet, share various ways to transfer genetic information by replication and transcription from their common ancestor, Eukarya.[37] As of 2012, 116 genera of Archaea have been observed which consists of 450 species. Most of the archaeal species in these genera remains uncultivated, known only through its gene sequences and molecular surveys.[37]<br />
<br />
====Morphology==== <br />
Archaea are characterized by various cell sizes. They are most commonly found to be small organisms ranging from “0.1 to 15 μ diameter and up to 200 μ long.”[38] The shape of many archaea are similar to bacteria, including bacillus, cocci, spirilla and “plate-like forms.” [38] Their cell membranes have ether linked lipids with no periplasmic space, similar to gram-positive bacteria, and contain no intracellular organelles.[39]<br />
<br />
'''Flagella:''' Most motile archaea inhabit a motor rotary system that allows it to move its flagella through the chemical gradient similar to bacteria.[39] Despite its similarity in function and source of energy required for motility, the flagella of both archaea and bacteria differ in structure.[39] Archaeal flagella gets the energy for its movement by ATP and is composed of dependent filaments that rotate singularly. [40] Archaeal flagella are known to be thinner than bacteria flagellin.[40] Since, the archaeal common ancestor is not bacteria but eukarya, convergent evolution is a plausible explanations for the differences between bacterial and archaeal flagellin. [40]<br />
<br />
'''Membranes:''' Archaea have a cell membrane that protects the cytoplasm and the nucleic acids from the environment. The archaeal cell membrane has a lipid bilayer with glycol-ether lipids that are more stable than ester linkages and help some archaea that live in extreme environments to withstand such conditions.[39] Most archaeal species are surrounded by a cell wall which protects the cell membrane and maintains the archaeal structure.[41]<br />
<br />
====Reproduction====<br />
Archaeal organisms reproduce by binary fission since they do not have nucleases thus, the DNA chromosome in a Archaeal organism replicate, separate and create two daughter cells.[43] The process of binary fission can be seen in Figure (3.5) process begins the parent cell duplicating the DNA. The DNA material then goes to the sides of the cell where an invagination to the cell occurs allowing the cell to become two individual cells. Binary fission is a very fast reproduction process, that allows archaeal organisms to grow at an exponential rate.[44]<br />
<br />
[[Image:WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg|frame|center|Figure 3.5 Illustration of binary fission. From[https://d2jmvrsizmvf4x.cloudfront.net/WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg]]]<br />
<br />
====Metabolism==== <br />
Archaea share similar metabolic characteristics to bacteria. The metabolic pathways taken by all archaea shown in the (Figure 3.6) demonstrates the great diversity and variation amongst archaea. [38] The kinds of archaea that are seen in the environment and the metabolic pathways taken by some can be summarized in the image. <br />
<br />
*Photoautotrophs: use light as an energy source and carbon dioxide as the carbon source with the help of the Calvin Cycle.[38]<br />
*Chemoautotrophs: use inorganic chemicals as their energy source and carbon dioxide as carbon source. <br />
*Chemoheterotrophs: take organic chemicals as energy source and organic chemicals as carbon source. The pathways taken by chemoheterotrophs varies from respiration by the Krebs Cycle to fermentation. [38]<br />
*Photoheterotrophs: use light as their energy source and organic chemicals as their carbon source. <br />
<br />
Most archaea inhabiting in the soil environment are major contributors to the biogeochemical cycles.<br />
<br />
[[Image:2000px-Troph_flowchart.svg.png|thumbnail|center|Figure 3.6 Flowchart showing different metabolic pathways. From[https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Troph_flowchart.svg/2000px-Troph_flowchart.svg.png]]]<br />
<br />
====Contributions to the Cycle====<br />
Archaea play a significant role in the nutrient cycles that take place in the ecosystem as they account for about 1-5% of all the prokaryotes present in the soil environment.[42]<br />
<br />
'''Carbon Cycle:''' Archaea have an important role in the carbon cycle that takes place specifically in methane production, carbon mineralization and carbon assimilation all of all of which contribute to the soil’s carbon sink.[42] The carbon dense soil helps to make the soil organic matter rich and helps to form extracellular polymers which creates stable aggregates. For some microbes, an electron acceptor is need to carry out metabolic functions. [42] More info on [https://microbewiki.kenyon.edu/index.php/Carbon_cycle Carbon Cycle].<br />
<br />
*'''Carbon Assimilation:''' Involves the transformation of inorganic carbon into organic carbon compounds. This process is commonly done by autotrophic phyla ''Crenarchaeota, Thaumarchaeota'', and ''Euryarchaeota'' that use carbon dioxide/ bicarbonate converting it to organic compounds.[42] Of the autotrophic lineages observed in carbon assimilation the ''Thaumarchaeota'' are strict autotrophs, the ''Euryarchaeota'' and ''Crenarchaeota'' are facultative autotrophs and the ''Halobacteriales'' and ''Thermococcales'' are obligate heterotrophs.[42] <br />
<br />
*'''Carbon Mineralization:''' The process that converts organic carbon into the oxidized inorganic carbon, carbon dioxide is commonly done by both aerobes and anaerobes.[42] The heterotrophic microbes that use organic compounds as energy to oxidize the carbon source include, methanogens and methane-oxidizing archaea belonging to the phyla ''Euryarchaetota'', and ''Crenarchaeota''.[42] <br />
<br />
*'''Methanogenesis:''' production of methane, a major greenhouse gas in the Earth’s atmosphere is commonly done by archaea upon reducing an oxidized compound.[42] The phyla ''Euryarchaeota'' is the only phyla that consists of archaea that produce methane all of which form five class: ''Methanopyri, Methanococci, Methanobacteria, Methanomicrobia'' and ''Thermoplasmata''.[42] Methanogens are commonly found in anaerobic and aerobic conditions such as bodies of water, aerated soils and oxygenated waters.[42]<br />
<br />
'''Nitrogen Cycle :''' Archaea play a pivotal role in the Nitrogen cycle and help create nitrogenous products for the plants and microbes. More info on [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle Nitrogen cycle].<br />
<br />
*'''Nitrogen Fixation:''' Fixing nitrogen from the environment and converting it to organic nitrogen in the soil or to inorganic nitrogenous form since both organic and inorganic products are in short supply in the biosphere and are fixed by many archaeal organisms.[42] N2 fixation by the environment is usually done by three major archaeal classes ''Methanobactera, Methanococci'' and ''Methanomicrobia''.[42] <br />
<br />
*'''Nitrification:''' Converting the ammonia (NH4+) in the soil to nitrite (NO2-) produces nitrate (NO3-) as an intermediate. [42] The transformation of ammonia to first nitrate then to nitrite is a two step process that is done by different microbes. [42] Most common organisms involved in nitrification include ammonia-oxidizing archaea which are lithotrophic organisms mostly, of the ''Thaumarchaeota'' phylum from the archaea domain. <br />
<br />
*'''Denitrification :''' The conversion of atmospheric N2 using the electron acceptor NO3- or NO2- creating the formation of nitric oxide, nitrous oxide and/or N2.[42] The formation of the end product N2 may not always be produced but other intermediates NO and N2O, greenhouse gases may be produced.[42] Of the archaeal organisms that have been studied in denitrification process is done by ''Pyrobaculum aerophilum'' which accepts both NO3- and NO2- as an electron acceptor producing a variety of products NO2-, NO, N20 and N2.[42]<br />
<br />
===Domain Eukarya===<br />
<br />
====Fungi====<br />
<br />
=====Introduction=====<br />
<br />
'''Introduction'''<br />
<br />
Fungi comes from the ancient Greek word “sphongos” meaning sponge in reference to the mushroom cap [47]. Fungi have the general characteristics of being eukaryotic, heterotrophic, external absorbers of nutrients, containing a hyphal thallus, reproducing via spore, and being pleomorphic (producing several forms). Fungi are generally organoheterotrophs that can survive in low pH and stay active at low moisture content[46]. Fungi reside in the domain Eukarya with an estimated species of 1.5 million, and less than five percent of them have ever been described. The general phyla included within Kingdom Fungi include Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, Chytridiomycota, and Microsporidia [48].<br />
<br />
[[Image:magical-kingdom-620.jpg|frame|center|Figure 3.7 Fungi phyla hierarchy. From.[http://www.motherjones.com/environment/2009/11/fungi-family-tree]]]<br />
<br />
=====Morphology=====<br />
<br />
'''Morphology''' <br />
<br />
Fungi can be either unicellular (yeasts) or multicellular. All multicellular fungi are made up of small, filamentous particles called hyphae. Some hyphae have cross walls called septa, while others do not- this is a large basis of fungal identification. Fungal cells generally have multiple nuclei. Fungal cell walls are generally composed of chitin, a long carbohydrate polymer that adds rigidity and structural support to fungi [49]. <br />
<br />
=====Reproduction=====<br />
<br />
'''Reproduction'''<br />
<br />
Fungal reproduction can occur either sexually or asexually.<br />
<br />
'''Sexual reproduction''' can occur by homothallic or heterothallic mycelia.<br />
<br />
'''Asexual reproduction''' can occur by fragmentation, budding, or by producing spores (the most common method). <br />
<br />
*'''Spores:''' spores come in many different forms. One of the most well known are conidiospores, which are unicellular or multicellular spores that get released from the tip of the hyphae. <br />
<br />
'''Perfect fungi''' are those that can reproduce both sexually and asexually while imperfect fungi are those that can only reproduce asexually.<br />
<br />
*Sexual reproduction always includes the stages plasmogamy (fusion of two haploid cells), karyogamy (creation of a diploid zygote), and meiosis (gametes are created).<br />
<br />
=====Metabolism=====<br />
<br />
'''Metabolism'''<br />
<br />
Many different fungi display a myriad of metabolisms. There are primary metabolites that that help the fungi function properly, and secondary metabolites that are generally bioactive that are not the most pertinent to fungal growth (they can live without these). Secondary metabolites play a large role in chemistry today and can be manufactured into commonly used products such as new drugs. In general fungi are heterotrophic through release of extracellular enzymes into the neighboring environment to break complex molecules down into smaller ones. The materials are then absorbed and metabolized [50]. Fungi are sessile organisms that overcome their little to no movement through apical growth at the hyphal tip. Fungi are noted to grow almost everywhere on the Earth.<br />
<br />
=====Relevance to soil===== <br />
<br />
'''Relevance to soil'''<br />
<br />
Fungi include some of the most abundant biomass of microorganisms in numerous soils. They play an important role as decomposers within the soil food web through conversion of difficult to digest organic material into forms many other organisms can use [51]. Their hyphae can bind soil particles together and create aggregates that increase soil water holding capacity. They perform important functions from water dynamics to nutrient cycling and disease suppression. Soil fungi can be categorized into three different groups based on their actions: <br />
<br />
*decomposers: that convert dead organic material into fungal biomass<br />
<br />
*mutualists: which colonize plant roots and help solubilize phosphorous and bring soil nutrients<br />
<br />
*pathogens/ parasites: which help control diseases in soil via trapping organisms such as nematodes [51]. <br />
<br />
Fungi are seen common in intensively managed agricultural soils due to tillage disrupting hyphae. Fungi also play a very important role in the [https://microbewiki.kenyon.edu/index.php/Rhizosphere_Interactions rhizosphere], the region of soil that is greatly influenced by the plant root system. This area of soil which is concentrated in plant roots and fungal hyphae is known to support greater microbial activity.<br />
<br />
=====Protozoans=====<br />
<br />
'''Protozoans'''<br />
<br />
In general, Protozoans range from 5 to 500 µm in diameter, making them significantly larger than bacteria [21]. They are abundantly located near the surface of the soil (15cm deep) where roots are plentiful [21]. Many protozoans have two life cycles. One is their active form where they are motile and feed on prey. The other is the cyst form where they produce a thick coating to protect them from the environment and can go dormant for years. The protozoa are divided into 4 major categories: the ciliates, the flagellates, the heliozoans, and the amoebas [10]. <br />
<br />
======Ciliates======<br />
<br />
'''Cilliates:'''<br />
This group, within protozoans, is fairly diverse. A common feature shared amongst all of its members is the presence of at least one cilia at any stage of its development [10]. The cilia is used for movement and other things such as predation (tentacles). For movement, they use the massive amounts of tiny cilia to create wave like currents to propel the cell forwards. Most ciliates also have toxicysts which are used to capture prey [10]. Some ciliates even have a symbiotic relationship with algae living inside of them [10]. The algae use the CO2 produced by ciliates and turn it into O2 that can then be reused by the ciliates [10]. They are found in a wide array of habitats ranging from freshwater and soil to the rumen of Animals [22]. They are present in almost anywhere that contains water [23]. They are unicellular heterotrophs so they feed on bacteria and algae in their environment. Ciliates are one of the top predators in the microbial food web and are hypothesized to have been a major predatory group before animals evolved [23]. Parasitic ciliates exist that can cause the death of animals and are increasingly becoming dangerous in water [23].<br />
<br />
[[Image:2spiro.jpg|frame|center|Figure 3.8 Microscope image of ciliated protists. From[http://www.microscopy-uk.org.uk/mag/smallimag/2spiro.jpg]]]<br />
<br />
======Flagellates======<br />
<br />
'''Flagellates''' are one of the most commonly known protists. They are unicellular organisms that may be solitary, colonial, free living, or parasitic [24]. The hallmark feature of protists is that at some point in their life cycle, they possess a flagella. A flagellum is a long hair like structure that is used for locomotion, sensation, and sometimes predation [24]. The flagellum makes waves by whiplike lashing movements which propels the cell forwards. Flagellates also have a protective coating in the form of a thin pellicle to protect them from the environment [24]. <br />
<br />
[[Image:9703607_orig.jpg|frame|center|Figure 3.9 Illustration of flaggelates during different life cycle stages. From[http://diagnosticparasitology.weebly.com/uploads/3/9/5/4/3954522/9703607_orig.jpg]]]<br />
<br />
*'''Mastigophora:'''<br />
<br />
Mastigophora is a subphylum of flagellates. Being a member of the flagellates, their key feature is the flagellum. Their habitats include freshwater, soil, and can act as animal parasites as well [25]. They use pseudopodia, a long outward protrusion, to trap and funnel food from the environment into their cell bodies [25]. The Mastigophora are mainly known for their parasitism, which can take place in both humans and animals [25]. ''Typanosomes'' are an example of Mastigophora which causes African sleeping sickness [25]. ''Giardia lambli''a is another example that resides in the intestinal tract of warm-blooded animals and inflicts intestinal giardiases [25]. It is also a major contaminant of drinking water because it is resistant to chlorine, which is the most common water purifier [25]. Having a dormant cyst form also adds to its survival potential through filtration efforts [25].<br />
<br />
<br />
<br />
*'''Euglenids:'''<br />
<br />
Euglenids are one of the best known flagellates. They are found in freshwater and soil, as long as there are organic materials. They also participate in some symbiotic relationships with marine animals. Euglenid cells do not contain cell walls or other rigid membranes [26]. This gives the cell tremendous flexibility and allows it to change its shape to easily navigate through muddy terrain. Euglenids have two flagella, one which creates locomotion and movement for the cell [26]. The other flagellum does not protrude from the cell and is contained in the cell body [26].<br />
<br />
======Amoebas======<br />
<br />
'''Amoebas'''<br />
<br />
Amoebae are single celled eukaryotes present in many different types of environments. They are scattered throughout a variety of eukaryotic lineages and therefore are not monophyletic [27]. Amoebae range in size from 5 micrometers to 3 mm and don’t have a defined shape, commonly recognized for being polymorphic. They are motile through the use of pseudopodia, which stretch and pull the cell along with it. The pseudopodia are also used for feeding. They are able to sense prey that can be engulfed and engulf them via phagocytosis. The amoeba’s main prey consists of bacteria, algae, and other protozoa [28]. The prey is moved around within the cell via food vacuoles, a feature of amoebae [28]. Another key characteristic of amoebae are the large contractile vacuoles inside the cell. The purpose of the contractile vacuole is to osmoregulate by pumping excess water out of the cell. In times of turmoil, amoebae have an encysted form that helps them get through the tough times. This form is useful when there is low nutrient availability to limit energy consumption. There are two main forms an amoeba can be characterized as. They can either be testate or nontestate. Testate amoeba produce shells, or “tests”, that help identify their species since each species has a unique shell.<br />
<br />
[[Image:Amoeba_(PSF).png|frame|center|Figure 3.10 Amoeba morphology. From[https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Amoeba_(PSF).png/230px-Amoeba_(PSF).png]]]<br />
<br />
=====Slime Molds=====<br />
<br />
'''Slime molds''' were once classified as fungi, but have now been placed in their own phylogenetic groups. Slime molds are single cells that can live independently, but aggregate to form multicellular reproductive structures when necessary [29]. The fruiting body releases spores which germinate into new cells. Slime molds feed off of bacteria and are most commonly found in forests. They feed off of decaying vegetation as well so they can be seen on rotting logs and leaves.<br />
<br />
[[Image:28-30-cellslimemoldlife-l.jpg|frame|center|Figure 3.11 Illustration of slime mold life cycle. From[https://lichencolony.files.wordpress.com/2006/06/28-30-cellslimemoldlife-l.jpg]]]<br />
<br />
==Current Research== <br />
<br />
'''Bacteria:''' To showcase the great diversity of soil bacterial environments, cyanobacteria have been studied in both desert and polar regions. Cyanobacteria can survive in extreme conditions likely because of their long evolutionary past.[16] Dr. Patzelt and his colleagues studied the diverse cyanobacteria residing in the Atacama desert, one of the driest parts of the world. The diverse taxa found in the Atacama desert can withstand prolonged periods of extreme desiccation.[16] The cyanobacteria dominate the soil crusts, affecting soil stability, soil structure and soil fertility.[16] Cyanobacteria inhabiting the Antarctic and Arctic regions, show similar adaptations to extreme environments as the cyanobacteria found in the desert. The polar cyanobacteria are particularly adapted to high altitudes.[17] They can withstand high ultraviolet radiation, desiccation, and repeated freeze-thaw cycles.[17] The autotrophic cyanobacteria supports heterotrophic microbes, providing an important ecosystem service in an environment with low microbial activity.[17]<br />
<br />
'''Archaea:''' In 150 soil samples acquired from North and South America, about 150,000 species were observed.[45] Of these, over 2,500 were identified as archaea based on their ssu rRNA.[45] The archaeal species were further analyzed to understand their role in the soil environment. Of the archaeal groups, ''Crenarchaeota'' and ''Euryarchaeota'' were found.[45] Bates stated that, “Across the non-experimental soils examined the soil C:N ratio was the single best predictor of archaeal relative abundances” due to their influences in the nutrient cycles.[45]<br />
<br />
'''Fungi:''' Fungi have been in the public eye for a while now due to the many different types of secondary metabolites they produce. Some produce bioactive compounds that can inhibit growth of protozoa, bacteria, parasites, insects, and even other fungi. A large area of investigation is the uses of these chemicals for human interests in use from medicine to plant and animal toxins [52].<br />
<br />
'''Protozoa:''' It’s known that Protozoa stimulate plant growth in different ways. It’s suspected that the Protozoa take part in the microbial loop which is responsible for the nutrient production for plants [19]. However, new developments have shown that the Protozoa themselves are responsible for the nitrogen mineralization and that other bacteria have no effect on the plant’s nitrogen sources [19].<br />
<br />
==References==<br />
<br />
1. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). Principles and Applications of Soil Microbiology. New Jersey: Pearson Education Inc.<br />
<br />
2. Ingham, Elaine R. Ingham R. "Chapter 4: SOIL FUNGI." Soil Biology. Natural Resources Conservation Service Illinois, n.d. Web. 9 Feb. 2016<br />
<br />
3. Reid, Greg, and Percy Wong. "SOIL BACTERIA AND FUNGI - NEW SOUTH WALES." Soil Bacteria and Fungi. New South Wales Department of Primary Industries, 2005. Web. 11 Feb. 2016.<br />
<br />
4. "Fungi." Microbiology Online. Microbiology Society, n.d. Web. 11 Feb. 2016.<br />
<br />
5. Tortora, G.J., Funke, B.R., Case, C.L. (2012). “Microbiology an Introduction.” 11th ed. Pearson Benjamin Cummings, San Francisco.<br />
<br />
6. Rizzo, D. “Intro to Fungi.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
7. Rizzo, D. “Ascomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
8. Rizzo, D. “Basidiomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
9. Pegg G.F., Brady B.L. “Verticillium Wilts.” New York, CABI Publishing 2002. Google Books. Web. 11 Feb. 2016. http://books.google.com<br />
<br />
10. Hebert, Paul. "What Is a Protist / What Are Protozoa? - Encyclopedia of Life." Encyclopedia of Life. N.p., n.d. Web. 11 Feb. 2016.http://eol.org/info/456<br />
<br />
11. "MicrobeWorld." Protista. N.p., n.d. Web. 11 Feb. 2016. http://www.microbeworld.org/types-of-microbes/protista<br />
<br />
12. Madigan, M.T., Martinko, J.M. (2006). Brock Biology of Microorganisms. New Jersey: Pearson Prentice Hall.<br />
<br />
13. Roesch, L.F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H.; Camargo, F. A. O.; Farmerie, W. G.; Triplett, E. W.(2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1(4).283-290. <br />
<br />
14. Amann, R.I, Ludwig, W., Schleifer, K.H.(1995).Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology and Molecular Biology Reviews. 59(1). 143-169. <br />
<br />
15. Geers, D., Cohan, F.M., Lawrence J.G., Spratt, B.G., Coenye, T. Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005). Opinion: Re-evaluating prokaryotic species. Nature Reviews Microbiology. 3(9). 733-739.<br />
<br />
16. Patzelt, D.J., Hodac, L., Friedl, T., Pietrasiak, N., Johansen, J.R. (2014). Biodiversity of soil cyanobacteria in the hyper-arid Atacama Desert, Chile. Journal of phycology. 50(4). 698-710. <br />
<br />
17. Makhalanyane, T. P., Valverde, A., Velázquez, D., Gunnigle, E., Van Goethem, M. W., Quesada, A., & Cowan, D. A. (2015). Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats. Biodiversity and Conservation, 24(4), 819-840.<br />
<br />
18. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist>.<br />
<br />
19. Ekelund, Flemming; Saj, Stephane; Vestergård, Mette; Bertaux, Joanne; Mikola, Juha. (2009). “The “soil microbial loop” is not always needed to explain protozoan stimulation of plants”. Soil Biology & Biochemistry. Vol. 41 Issue 11, p2336-2342, 7p.<br />
<br />
20. Bonkowski, Michael. "Protozoa and Plant Growth: The Microbial Loop in Soil Revisited." New Phytologist New Phytol 162.3 (2004): 617-31. Web.<br />
<br />
21. Hoorman, James. "The Role of Soil Protozoa and Nematodes." Fact Sheet (n.d.): n. pag. Ohio State University, 2011. Web.<br />
<br />
22. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist<br />
<br />
23. Lynn, Denis H(Apr 2012) Ciliophora. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001966.pub3]<br />
<br />
24. "flagellate". Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc., 2016. Web. 23 Feb. 2016 <http://www.britannica.com/science/flagellate>.<br />
<br />
25. "Mastigophora." World of Microbiology and Immunology. 2003. Encyclopedia.com. 23 Feb. 2016<http://www.encyclopedia.com>.<br />
<br />
26. “Plant Life." : Euglenoids. N.p., n.d. Web. 23 Feb. 2016. <http://lifeofplant.blogspot.com/2011/04/euglenoids.html><br />
<br />
27. Parales, R.E. and Martin, M. (2015) Microbial Diversity Laboratory Manual, MIC 105L, Winter 2015. Department of Microbiology and Molecular Genetics, College of Biological Sciences, The University of California, Davis.<br />
<br />
28. Arnold, Paul. "What Does an Amoeba Eat? Plus Other Ameoba Info and Questions." Bright Hub. N.p., n.d. Web. 04 Mar. 2016.<br />
<br />
29. "MicrobeWorld." Slime Molds. N.p., n.d. Web. 24 Feb. 2016. <http://www.microbeworld.org/types-of-microbes/protista/slime-molds><br />
<br />
30. Leeuwenhoek., A. V. (2009, November 18). One gram of soil: A microbial biochemical gene library. Retrieved March 13, 2016, from http://www.ncbi.nlm.nih.gov/pubmed/19921459 <br />
<br />
31. Coleman, D. C., Crossley, D. A. & Hendrix, P. F. "Soil food webs: Detritivory and microbiology in soils," in Fundamentals of Soil Ecology, 2nd ed. (Elsevier, 2004) 236-241.<br />
<br />
32. Welcome to Agriinfo.in. (n.d.). Retrieved February 21, 2016, from http://agriinfo.in/?page=topic&superid=5&topicid=172 <br />
<br />
33. Gouthro, T., & Rice, D. (1987, December 15). Interaction Terminology. Retrieved February 21, 2016, from http://www.rpi.edu/dept/chem-eng/Biotech-Environ/MixCul/ecodefn.htm <br />
<br />
34. AMENSALISM. (n.d.). Retrieved February 21, 2016, from https://biostuds.wikispaces.com/AMENSALISM <br />
<br />
35. Natural Resources Conservation Service. (n.d.). Retrieved March 10, 2016, from <br />
http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053865 <br />
<br />
36. Ecological Linkages Between Aboveground and Belowground Biota. (n.d.). Retrieved March 10, 2016, from http://science.sciencemag.org/content/304/5677/1629 <br />
<br />
37. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf<br />
<br />
38. Kingdom Archaea. (n.d.). Retrieved March 10, 2016, from http://plantphys.info/organismal/lechtml/archaea.shtml <br />
<br />
39. What are Archaea? - Encyclopedia of Life. (n.d.). Retrieved March 10, 2016, from http://eol.org/info/457 <br />
<br />
40. Flagellum. (n.d.). Retrieved March 10, 2016, from http://www.newworldencyclopedia.org/entry/Flagellum#Archaeal_flagellum <br />
<br />
41. Archaea: Morphology. (n.d.). Retrieved March 10, 2016, from http://www.ucmp.berkeley.edu/archaea/archaeamm.html <br />
<br />
42. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf <br />
<br />
43. Archaea. (n.d.). Retrieved March 10, 2016, from http://www.eoearth.org/view/article/150172/ <br />
<br />
44. Binary Fission: Cell Division & Reproduction of Prokaryotes. (n.d.). Retrieved March 10, 2016, from http://www.scienceprofonline.com/microbi <br />
<br />
45. Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2010, November 18). Examining the global distribution of dominant archaeal populations in soil. Retrieved February 21, 2016, from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105767/<br />
<br />
46. Scow, K. M. "Lecture 1 Part 1." Lecture, Davis.<br />
<br />
47. Rizzo, D. "Lecture 1." Lecture, Davis.<br />
<br />
48. Rizzo, D. "Lecture 3." Lecture, Davis.<br />
<br />
49. C.J. Alexopoulos & C. W. Mims, Introductory Mycology 3rd edition. 1979. Wiley NY. Web accessed Mar 8, 2016 from http://www.ucmp.berkeley.edu/fungi/fungimm.html<br />
<br />
50. Rizzo, D. "Lecture 2." Lecture, Davis.<br />
<br />
51. Ingham, E. “Chapter 4: Soil Fungi” (2016) Oregon State University. Retrieved Feb. 20, 2016, from http://extension.illinois.edu/soil/SoilBiology/fungi.htm<br />
<br />
52. Keller, N., Turner, G., Bennett, J. “Fungal Secondary Metabolism- from Biochemistry to Genomics.” 2005 Nature Reviews Microbiology p/ 937 to 947.</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Introduction_to_Organisms&diff=128510
Introduction to Organisms
2017-03-05T23:21:15Z
<p>Kmscow: /* Introduction */</p>
<hr />
<div>==Introduction== <br />
The soil ecosystem in an important environment that allows both plants and animals to survive, grow and reproduce. The significance of the soil as an ecosystem is at times overlooked despite its major contributions to the environment. The [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] is a complex and varied microbial habitat.[1] The plants and organisms inhabiting the soil contribute to its thriving diversity. Soil life is diverse in morphology, metabolism, size, and many other characteristics. Soil is a heterogeneous environment with various zones of rhizosphere, aggregates, organic matter and animal residues.[31] Given each zone is a small component of the larger soil ecosystem, rhizosphere accounts for only 5 to 7 percent of the soil environments but contains over “70 percent of the bacterial- and fungal-feeding nematodes.”[31] <br />
<br />
Since soil microbial diversity is immense, with all three domains of life: Archaea, Bacteria and Eukarya represented in the soil environment, it is not possible to discuss each microbial species (many of which have not even been described!). Only a few representative groups of each domain will be discussed to provide examples of the roles these organisms play in soil.<br />
<br />
==Soil Food Web and Microbial Interactions== <br />
<br />
To survive in a soil environment, an organism must be able to adapt to changing environments and organism interactions. The interactions seen between organisms allows only the fittest to survive, thrive, grow and reproduce in the soil. The only type of interaction shown in (Figure 2.1) is predation. Other common interactions in the soil environment are: <br />
<br />
:[[Image:soil_foodweb72.jpg|frame|center|Figure 2.1 Soil Food Web. From[http://www.exploringnature.org/graphics/foodwebs/soil_foodweb72.jpg]]]<br />
<br />
<br />
'''I. Commensalism:''' Organism (A) benefits from the presence of Organism (B) while (B) is unaffected by the presence of (A).[32]<br />
<br />
'''II. Mutualism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) and becomes a necessary association for each other’s survival. [32] [33]<br />
<br />
'''III. Synergism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) but the relationship is not necessary for survival.[33]<br />
<br />
'''IV. Competition:''' Depending on the organisms this interaction benefits organisms who can readily adapt to the environment and overcome any obstacles needed to survive, grow and reproduce.[33]<br />
<br />
'''V. Amensalism:''' An interaction in which Organisms (A) and (B) develop a partnership where (B) is unaffected by (A) but organism (A) is negatively affected by (B).[34]<br />
<br />
'''VI. Parasitism:''' Organism (A) benefits from Organism (B) but Organism (B) does not benefit positively from Organism (A). <br />
<br />
'''VII. Predation:''' “An interaction between organisms in which one benefits and one is harmed based on the ingestion of the smaller sized organism, the prey, by the larger organism, the predator.”[33]<br />
<br />
<br />
<br />
The soil food web consists of microbes which play an important role in maintaining the complexity of the soil environment. The interactions observed in the food web are not only based on predation, which directly affects the nutrient cycling and degradation of pollutants, but also the formation of aggregates.[35] The production of specific nutrients, such as ammonium created by microbial metabolic functions, helps to enrich the the soil for plant use.[35] Soil organism activity, along with the presence of soil organic matter, create stabilizing aggregates.[35] The hyphae within the soil environment and the microbes help form large, stable aggregates in the soil habitat.[35] The biodiversity in the soil plays a pivotal role in degrading pollutants, and also prevents pathogens from inhabiting the soil environment through competition.[35] The food web in the soil environment is necessary to maintain the soil nutrients, biological activity, and detoxifying pollutants. Thus, it directly maintains cultivation, productiveness and prosperity of the soil. <br />
<br />
In (Figure 2.1), all three domains, Archaea, Bacteria, and Eukarya, are represented in the soil food web. If one takes a closer look at the figure, the soil food web is not only dependent on small and large microbes but also dead organic matter and plant roots. Dead and living matter in the soil environment contribute to maintaining the food web. Plant residues also are apart of the soil food web. They contribute to the soil’s carbon source.[35] The plant residues either, release carbon dioxide to the environment, or contribute to the soil organic matter. Soil organic matter contributes to soil’s richness and helps to form aggregates.[35] The main focus in the image above is the diversity of organisms, both in domains and in size. The larger organisms are usually the predators. The smaller organisms eventually fall prey, due to their limited mobility, respiration, and size. The eukarya and small bacteria are apparent figures seen in the figure above, but archaea also contribute to the food cycle as they break down ammonia for plants to use. [35]<br />
<br />
The notable interactions of life that take place in the soil environment is evident both below-ground level, as seen in the figure 2.1, but also in the above-ground level.[36] Worms also impact the soil food web, acting as both drivers of the food web both belowground and aboveground.[36]<br />
<br />
==3 Domains==<br />
[[Image:Big_Tree_Bold_Letters_white.png|frame|center|Figure 3.1 Phylogenetic Tree of the 3 Domains. From[http://phylogenomics.blogspot.com/2014_02_01_archive.html]]]<br />
<br />
===Carl Woese and Phylogeny===<br />
<br />
[[Image:Carlwoese1_0565_b.jpg|frame|center|Figure 3.2 Carl Woese. From[http://ofbacteriaandmen.blogspot.com/2013/01/the-new-biology-of-carl-woese.html]]] <br />
<br />
Carl Woese (Figure 3.2) was an American microbiologist famous for pioneering the technique of phylogenetic taxonomy through use of a 16S (for prokaryotic) and 18S (for eukaryotic) ribosomal RNA, also known as small subunit ribosomal RNA [46]. This refined Linnaean classification, taking out the guesswork classification by using a gene that was present in every living organism- the small subunit ribosomal RNA. This method of classification is comprehensive because all organisms possess this form of genetic material. Ssu rRNA is sequenced because the genes are highly conserved. Due to their functional constancy, some have variable regions to differentiate organisms, and are easy to sequence. This technique also elucidated the tree of life, which shows the three domains of microbial lineage diversity: Bacteria, Archaea, and Eukarya. DNA can be compared using a sample database that allows identification of unknown organisms to a species level.<br />
<br />
===Domain Bacteria===<br />
<br />
====Introduction to Bacteria==== <br />
Bacteria are single celled prokaryotic organisms that lack membrane bound organelles. They are involved in many important processes within the soil such as decomposition, [https://microbewiki.kenyon.edu/index.php/Bioremediation bioremediation], symbiosis and biological transformation of nutrients. They are present in all terrestrial soil environments.[1] Soil is a heterogenous environment that varies in moisture content, temperature, oxygen requirements, carbon source and many other bacterial growth conditions. Those wide ranging growth factors account for the enormous diversity in soil bacteria populations. One gram of soil can contain between 26,000 to 52,000 different bacterial species.[13] In the entire microbial world, only about 1 percent of bacterial species can be cultured under laboratory conditions which leaves an immense number of bacterial species yet to be described. [14]<br />
<br />
Classification based on phenotypic characteristics, such as cellular morphology, metabolism, gram staining, oxygen requirements, carbon source and other traits, was used more readily before modern DNA sequencing. But, phenotypic classification is still used and Bergey’s Manual of Systematic Bacteriology is the most widely used source for determining species based on characteristic species traits.<br />
<br />
Traditional species definitions are not as useful in bacteria. OTUs, or operational taxonomic units, based on DNA sequencing similarity, are more applicable to bacteria. Typically, those bacteria with 97 percent similar DNA sequence are classified within the same OTU.[15] The 16S small subunit ribosomal RNA is used to substantiate phylogenetic relationships between different bacterial groups.<br />
<br />
====Morphology====<br />
<br />
Bacterial cells measure approximately 1μm wide and 1-5μm long.[12] They are smaller than eukaryotic microbes.Due to their small size, bacteria can more easily adapt to changing soil environments than larger eukaryotes.[1] Most bacteria are singled celled, but actinomycetes grow in branching filaments. There are many different bacterial cell shapes. The most common are bacilli (rods), cocci (spheres), spirilla (spirals) and actinomycete (filaments).<br />
[[Image:bacteria_sizes.jpg|frame|center|Figure 3.3 Common cell shapes cocci, bacillus, and spirilla and relative sizes. From[http://www.ppdictionary.com/gnbac.htm]]]<br />
<br />
'''Flagella''' - There are many different types and different arrangement of flagella. Movement in soil environments is dependent on soil moisture content. Though movement in soil is limited, flagellar function is important to allow bacteria to find more favorable microsites.[1]<br />
<br />
'''Cell membrane''' - The cell membrane encloses the cytoplasm. It is semi-permeable phospholipid bilayer that regulates transport of nutrients into the cell and waste products out of the cell.<br />
<br />
'''Cell wall''' - Most bacteria have a rigid cell wall surrounding the cell membrane which protects the cell from osmotic lysis. The cell wall is made of a crosslinked polysaccharide, called peptidoglycan, that is found only in bacteria.[1] The cell wall gives the cell shape and structure, but it is porous enough to permit small water soluble molecules to flow through to the cell membrane surface.[1]<br />
<br />
*'''Gram positive''' bacteria have a thick cell wall made of several layers of peptidoglycan. The cell wall is the outermost structure, as they do not have an outer membrane. The thick cell wall structure make gram positive bacteria more resilient to osmotic shock. Gram positive bacteria can tolerate 5 to 10 times more turgor pressure than gram Gram negative bacteria.[1] Teichoic acids in the cell wall may also help to bind to cationic nutrients in soil surroundings.[1] <br />
<br />
*'''Gram negative''' bacteria have a thin cell wall surrounded by an outer membrane made of phospholipids and lipopolysaccharides. Polysaccharides of the outer membrane interact with surrounding cations and are involved in attachment of bacteria to soil particles. [1] Periplasm is a gel like substance that occupies the space between the outer membrane and the cell wall of gram negative bacteria.[1] The outer membrane and periplasmic space is thought to provide protection from environmental toxins.[1] Proteins within the periplasm are thought to begin the process of catalyzing hydrolysis of organic and toxic substances.[1] <br />
<br />
[[Image:gramposnegmembrane.jpg|frame|center| Figure 3.4 Illustration of Gram positive and Gram negative cell wall structures. From[http://micro.digitalproteus.com/morphology2.php]]]<br />
<br />
'''Endospores''' are made by ''Bacillus'' and ''Clostridium'' in response to environmental stress.[1] Endospores are extremely resistant structures that can withstand extreme temperatures up to 150℃.[12] They can also withstand extreme pressure, desiccation, radiation, pH and chemicals.[12] The endospore protects the bacterial DNA until environmental conditions are more favorable and germination can proceed. Soil is the most common habitat for endospore forming bacteria.[12]<br />
<br />
'''Extracellular polymers''' - Many bacteria secrete a slime layer or capsule made of polysaccharides or glycoproteins.[1] The outer polysaccharide coating of bacteria helps in attachment to surfaces and the formation of biofilms.[1] Bacterial capsule secretions play a big role in soil aggregation and soil structure.[1] When the carbon to nitrogen ratio within soils is high, microbes secrete the excess carbon as extracellular polysaccharides.[1]<br />
<br />
====Reproduction==== <br />
Most bacteria reproduce by binary fission.[12] The bacterial cell expands to twice the original cell size, duplicates the bacterial DNA and pinches off, producing two daughter cells. Each resultant daughter cell is a clone of the parent cell. Prokaryotic Archaea also reproduce by binary fission.<br />
<br />
*'''Spore formation:''' Actinomycetes are a large group of filamentous bacteria, primarily found in soil.[1] Actinomycetes are morphologically similar to fungi. Actinomycetes form long filaments called hyphae. Unlike most bacteria, the majority of actinomycetes reproduce using asexual spores called conidia.[1] Though they share many characteristic with fungi, actinomycetes are still prokaryotes. They are smaller than fungi and the cell wall contains peptidoglycan.[1] Actinomycetes break down a wide variety of organic compounds and play an important role in organic matter decomposition. [1] ''Streptomyces'', a subgroup within actinomycetes, produce geosmin, which gives soil the characteristic earthy smell.[12]<br />
<br />
====Metabolism==== <br />
<br />
Along with archaea, bacteria are the most metabolically diverse and employ many different nutritional strategies.[1]<br />
*Heterotrophs - Most bacteria are heterotrophic, obtaining carbon from preformed organic substances. [1] <br />
*Autotrophs - Carbon dioxide serves as the main source of carbon. Some cyanobacteria, nitrifying and sulfur-oxidizing bacteria are autotrophs.[1]<br />
*Organotrophs - Most bacteria obtain electrons from organic substances.[1]<br />
*Lithotrophs - Some cyanobacteria, nitrifying bacteria and sulfur-oxidizing bacteria obtain electrons from inorganic substances.[1]<br />
*Phototrophs - Cyanobacteria use light as the main source of metabolic energy.[1]<br />
*Chemotrophs - All other nonphotosynthetic bacteria do not rely on light for metabolic energy.[1]<br />
<br />
====Contributions to Biogeochemical Cycling==== <br />
<br />
Bacteria play a significant role in the cycling of a wide range of elements.<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Carbon_cycle '''Carbon Cycle:'''] <br />
<br />
*'''Carbon Assimilation''' is the process of fixing carbon dioxide into organic forms. Carbon fixation is performed by autotrophic bacteria, such as cyanobacteria.[1] Chemoautotrophic nitrifying bacteria, such as ''Nitrobacter, Nitrosospira'' and ''Nitrosomonas'', also fix carbon.[1] Sulfur oxidizing bacteria, such as ''Thiobacillus'', fix carbon as well.<br />
<br />
*'''Carbon Mineralization''' results from microbial decomposition of organic carbon compounds into inorganic forms. As the organic carbon substances, like plant matter, are decomposed, inorganic carbon dioxide is produced. Most bacteria are heterotrophs that perform carbon mineralization. When microorganisms die, they are decomposed by successive microbial generations. Peptidoglycan, the main component of bacterial cell walls, is utilized as a polysaccharide substrate by other heterotrophic soil microbes.[1]<br />
<br />
*'''Methanogenesis''' - Methanogenic bacteria produce methane from the reduction of carbon dioxide. They are all strict anaerobes that use carbon dioxide for the carbon source.[1] They can all use hydrogen as a source of energy and electron donor. [1]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle '''Nitrogen cycle:''']<br />
<br />
*'''Nitrogen fixation:''' ''Azotobacter'' is a free living nitrogen fixing bacteria.[1] ''Rhizobium'' lives in a mutualistic relationship with plants by fixing nitrogen within root the nodules of legumes.[1] ''Anabaena'' and ''Nostoc'' have specialized heterocyte structures where nitrogen fixation occurs.[1] <br />
<br />
*'''Nitrification:''' Nitrifying bacteria, such as ''Nitrobacter, Nitrosospira,'' and ''Nitrosomonas'', oxidize ammonium to nitrate.[1] <br />
<br />
*'''Denitrification:''' ''Alcaligenes, Flavobacterium'', and ''Pseudomonas'' are common soil denitrifying bacteria.[1]<br />
<br />
===Domain Archaea===<br />
<br />
====Introduction to Archaea====<br />
<br />
Vladimir Vernadsky decided, in 1926, that only two domains of life existed on Earth, Bacteria and Eukarya.[37] About 50 years later in 1977, Carl Woese and George Fox theorized that part of the bacterial domain possed multiple dissimilarities from bacteria and recognized it to be another domain of life, now called Archaea.[38] Woese and Fox’s theory regarding the differences of archaea were confirmed in 1990’s through the use of 16S rRNA and 18S rRNA.[38] <br />
<br />
Despite the strongly held belief, in the 1990s, that archaea only inhabited extreme environments, recent discoveries have suggested their presence in abundant numbers all throughout the Earth. It is suggested that Archaea play notable roles in maintaining nutrient cycles.[37] Various methods of research, such as cultivation, culture-independent techniques and isotope-based methods, have facilitated the study of domain Archaea in carbon and nitrogen cycling. [37]<br />
<br />
The use of genomic and biochemical data has permitted the study of archaeal structure.[37] Use of these research methods has shown that domain archaea and domain bacteria differ in cell wall characteristics yet, share various ways to transfer genetic information by replication and transcription from their common ancestor, Eukarya.[37] As of 2012, 116 genera of Archaea have been observed which consists of 450 species. Most of the archaeal species in these genera remains uncultivated, known only through its gene sequences and molecular surveys.[37]<br />
<br />
====Morphology==== <br />
Archaea are characterized by various cell sizes. They are most commonly found to be small organisms ranging from “0.1 to 15 μ diameter and up to 200 μ long.”[38] The shape of many archaea are similar to bacteria, including bacillus, cocci, spirilla and “plate-like forms.” [38] Their cell membranes have ether linked lipids with no periplasmic space, similar to gram-positive bacteria, and contain no intracellular organelles.[39]<br />
<br />
'''Flagella:''' Most motile archaea inhabit a motor rotary system that allows it to move its flagella through the chemical gradient similar to bacteria.[39] Despite its similarity in function and source of energy required for motility, the flagella of both archaea and bacteria differ in structure.[39] Archaeal flagella gets the energy for its movement by ATP and is composed of dependent filaments that rotate singularly. [40] Archaeal flagella are known to be thinner than bacteria flagellin.[40] Since, the archaeal common ancestor is not bacteria but eukarya, convergent evolution is a plausible explanations for the differences between bacterial and archaeal flagellin. [40]<br />
<br />
'''Membranes:''' Archaea have a cell membrane that protects the cytoplasm and the nucleic acids from the environment. The archaeal cell membrane has a lipid bilayer with glycol-ether lipids that are more stable than ester linkages and help some archaea that live in extreme environments to withstand such conditions.[39] Most archaeal species are surrounded by a cell wall which protects the cell membrane and maintains the archaeal structure.[41]<br />
<br />
====Reproduction====<br />
Archaeal organisms reproduce by binary fission since they do not have nucleases thus, the DNA chromosome in a Archaeal organism replicate, separate and create two daughter cells.[43] The process of binary fission can be seen in Figure (3.5) process begins the parent cell duplicating the DNA. The DNA material then goes to the sides of the cell where an invagination to the cell occurs allowing the cell to become two individual cells. Binary fission is a very fast reproduction process, that allows archaeal organisms to grow at an exponential rate.[44]<br />
<br />
[[Image:WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg|frame|center|Figure 3.5 Illustration of binary fission. From[https://d2jmvrsizmvf4x.cloudfront.net/WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg]]]<br />
<br />
====Metabolism==== <br />
Archaea share similar metabolic characteristics to bacteria. The metabolic pathways taken by all archaea shown in the (Figure 3.6) demonstrates the great diversity and variation amongst archaea. [38] The kinds of archaea that are seen in the environment and the metabolic pathways taken by some can be summarized in the image. <br />
<br />
*Photoautotrophs: use light as an energy source and carbon dioxide as the carbon source with the help of the Calvin Cycle.[38]<br />
*Chemoautotrophs: use inorganic chemicals as their energy source and carbon dioxide as carbon source. <br />
*Chemoheterotrophs: take organic chemicals as energy source and organic chemicals as carbon source. The pathways taken by chemoheterotrophs varies from respiration by the Krebs Cycle to fermentation. [38]<br />
*Photoheterotrophs: use light as their energy source and organic chemicals as their carbon source. <br />
<br />
Most archaea inhabiting in the soil environment are major contributors to the biogeochemical cycles.<br />
<br />
[[Image:2000px-Troph_flowchart.svg.png|thumbnail|center|Figure 3.6 Flowchart showing different metabolic pathways. From[https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Troph_flowchart.svg/2000px-Troph_flowchart.svg.png]]]<br />
<br />
====Contributions to the Cycle====<br />
Archaea play a significant role in the nutrient cycles that take place in the ecosystem as they account for about 1-5% of all the prokaryotes present in the soil environment.[42]<br />
<br />
'''Carbon Cycle:''' Archaea have an important role in the carbon cycle that takes place specifically in methane production, carbon mineralization and carbon assimilation all of all of which contribute to the soil’s carbon sink.[42] The carbon dense soil helps to make the soil organic matter rich and helps to form extracellular polymers which creates stable aggregates. For some microbes, an electron acceptor is need to carry out metabolic functions. [42] More info on [https://microbewiki.kenyon.edu/index.php/Carbon_cycle Carbon Cycle].<br />
<br />
*'''Carbon Assimilation:''' Involves the transformation of inorganic carbon into organic carbon compounds. This process is commonly done by autotrophic phyla ''Crenarchaeota, Thaumarchaeota'', and ''Euryarchaeota'' that use carbon dioxide/ bicarbonate converting it to organic compounds.[42] Of the autotrophic lineages observed in carbon assimilation the ''Thaumarchaeota'' are strict autotrophs, the ''Euryarchaeota'' and ''Crenarchaeota'' are facultative autotrophs and the ''Halobacteriales'' and ''Thermococcales'' are obligate heterotrophs.[42] <br />
<br />
*'''Carbon Mineralization:''' The process that converts organic carbon into the oxidized inorganic carbon, carbon dioxide is commonly done by both aerobes and anaerobes.[42] The heterotrophic microbes that use organic compounds as energy to oxidize the carbon source include, methanogens and methane-oxidizing archaea belonging to the phyla ''Euryarchaetota'', and ''Crenarchaeota''.[42] <br />
<br />
*'''Methanogenesis:''' production of methane, a major greenhouse gas in the Earth’s atmosphere is commonly done by archaea upon reducing an oxidized compound.[42] The phyla ''Euryarchaeota'' is the only phyla that consists of archaea that produce methane all of which form five class: ''Methanopyri, Methanococci, Methanobacteria, Methanomicrobia'' and ''Thermoplasmata''.[42] Methanogens are commonly found in anaerobic and aerobic conditions such as bodies of water, aerated soils and oxygenated waters.[42]<br />
<br />
'''Nitrogen Cycle :''' Archaea play a pivotal role in the Nitrogen cycle and help create nitrogenous products for the plants and microbes. More info on [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle Nitrogen cycle].<br />
<br />
*'''Nitrogen Fixation:''' Fixing nitrogen from the environment and converting it to organic nitrogen in the soil or to inorganic nitrogenous form since both organic and inorganic products are in short supply in the biosphere and are fixed by many archaeal organisms.[42] N2 fixation by the environment is usually done by three major archaeal classes ''Methanobactera, Methanococci'' and ''Methanomicrobia''.[42] <br />
<br />
*'''Nitrification:''' Converting the ammonia (NH4+) in the soil to nitrite (NO2-) produces nitrate (NO3-) as an intermediate. [42] The transformation of ammonia to first nitrate then to nitrite is a two step process that is done by different microbes. [42] Most common organisms involved in nitrification include ammonia-oxidizing archaea which are lithotrophic organisms mostly, of the ''Thaumarchaeota'' phylum from the archaea domain. <br />
<br />
*'''Denitrification :''' The conversion of atmospheric N2 using the electron acceptor NO3- or NO2- creating the formation of nitric oxide, nitrous oxide and/or N2.[42] The formation of the end product N2 may not always be produced but other intermediates NO and N2O, greenhouse gases may be produced.[42] Of the archaeal organisms that have been studied in denitrification process is done by ''Pyrobaculum aerophilum'' which accepts both NO3- and NO2- as an electron acceptor producing a variety of products NO2-, NO, N20 and N2.[42]<br />
<br />
===Domain Eukarya===<br />
<br />
====Fungi====<br />
<br />
=====Introduction=====<br />
<br />
'''Introduction'''<br />
<br />
Fungi comes from the ancient Greek word “sphongos” meaning sponge in reference to the mushroom cap [47]. Fungi have the general characteristics of being eukaryotic, heterotrophic, external absorbers of nutrients, containing a hyphal thallus, reproducing via spore, and being pleomorphic (producing several forms). Fungi are generally organoheterotrophs that can survive in low pH and stay active at low moisture content[46]. Fungi reside in the domain Eukarya with an estimated species of 1.5 million, and less than five percent of them have ever been described. The general phyla included within Kingdom Fungi include Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, Chytridiomycota, and Microsporidia [48].<br />
<br />
[[Image:magical-kingdom-620.jpg|frame|center|Figure 3.7 Fungi phyla hierarchy. From.[http://www.motherjones.com/environment/2009/11/fungi-family-tree]]]<br />
<br />
=====Morphology=====<br />
<br />
'''Morphology''' <br />
<br />
Fungi can be either unicellular (yeasts) or multicellular. All multicellular fungi are made up of small, filamentous particles called hyphae. Some hyphae have cross walls called septa, while others do not- this is a large basis of fungal identification. Fungal cells generally have multiple nuclei. Fungal cell walls are generally composed of chitin, a long carbohydrate polymer that adds rigidity and structural support to fungi [49]. <br />
<br />
=====Reproduction=====<br />
<br />
'''Reproduction'''<br />
<br />
Fungal reproduction can occur either sexually or asexually.<br />
<br />
'''Sexual reproduction''' can occur by homothallic or heterothallic mycelia.<br />
<br />
'''Asexual reproduction''' can occur by fragmentation, budding, or by producing spores (the most common method). <br />
<br />
*'''Spores:''' spores come in many different forms. One of the most well known are conidiospores, which are unicellular or multicellular spores that get released from the tip of the hyphae. <br />
<br />
'''Perfect fungi''' are those that can reproduce both sexually and asexually while imperfect fungi are those that can only reproduce asexually.<br />
<br />
*Sexual reproduction always includes the stages plasmogamy (fusion of two haploid cells), karyogamy (creation of a diploid zygote), and meiosis (gametes are created).<br />
<br />
=====Metabolism=====<br />
<br />
'''Metabolism'''<br />
<br />
Many different fungi display a myriad of metabolisms. There are primary metabolites that that help the fungi function properly, and secondary metabolites that are generally bioactive that are not the most pertinent to fungal growth (they can live without these). Secondary metabolites play a large role in chemistry today and can be manufactured into commonly used products such as new drugs. In general fungi are heterotrophic through release of extracellular enzymes into the neighboring environment to break complex molecules down into smaller ones. The materials are then absorbed and metabolized [50]. Fungi are sessile organisms that overcome their little to no movement through apical growth at the hyphal tip. Fungi are noted to grow almost everywhere on the Earth.<br />
<br />
=====Relevance to soil===== <br />
<br />
'''Relevance to soil'''<br />
<br />
Fungi include some of the most abundant biomass of microorganisms in numerous soils. They play an important role as decomposers within the soil food web through conversion of difficult to digest organic material into forms many other organisms can use [51]. Their hyphae can bind soil particles together and create aggregates that increase soil water holding capacity. They perform important functions from water dynamics to nutrient cycling and disease suppression. Soil fungi can be categorized into three different groups based on their actions: <br />
<br />
*decomposers: that convert dead organic material into fungal biomass<br />
<br />
*mutualists: which colonize plant roots and help solubilize phosphorous and bring soil nutrients<br />
<br />
*pathogens/ parasites: which help control diseases in soil via trapping organisms such as nematodes [51]. <br />
<br />
Fungi are seen common in intensively managed agricultural soils due to tillage disrupting hyphae. Fungi also play a very important role in the [https://microbewiki.kenyon.edu/index.php/Rhizosphere_Interactions rhizosphere], the region of soil that is greatly influenced by the plant root system. This area of soil which is concentrated in plant roots and fungal hyphae is known to support greater microbial activity.<br />
<br />
=====Protozoans=====<br />
<br />
'''Protozoans'''<br />
<br />
In general, Protozoans range from 5 to 500 µm in diameter, making them significantly larger than bacteria [21]. They are abundantly located near the surface of the soil (15cm deep) where roots are plentiful [21]. Many protozoans have two life cycles. One is their active form where they are motile and feed on prey. The other is the cyst form where they produce a thick coating to protect them from the environment and can go dormant for years. The protozoa are divided into 4 major categories: the ciliates, the flagellates, the heliozoans, and the amoebas [10]. <br />
<br />
======Ciliates======<br />
<br />
'''Cilliates:'''<br />
This group, within protozoans, is fairly diverse. A common feature shared amongst all of its members is the presence of at least one cilia at any stage of its development [10]. The cilia is used for movement and other things such as predation (tentacles). For movement, they use the massive amounts of tiny cilia to create wave like currents to propel the cell forwards. Most ciliates also have toxicysts which are used to capture prey [10]. Some ciliates even have a symbiotic relationship with algae living inside of them [10]. The algae use the CO2 produced by ciliates and turn it into O2 that can then be reused by the ciliates [10]. They are found in a wide array of habitats ranging from freshwater and soil to the rumen of Animals [22]. They are present in almost anywhere that contains water [23]. They are unicellular heterotrophs so they feed on bacteria and algae in their environment. Ciliates are one of the top predators in the microbial food web and are hypothesized to have been a major predatory group before animals evolved [23]. Parasitic ciliates exist that can cause the death of animals and are increasingly becoming dangerous in water [23].<br />
<br />
[[Image:2spiro.jpg|frame|center|Figure 3.8 Microscope image of ciliated protists. From[http://www.microscopy-uk.org.uk/mag/smallimag/2spiro.jpg]]]<br />
<br />
======Flagellates======<br />
<br />
'''Flagellates''' are one of the most commonly known protists. They are unicellular organisms that may be solitary, colonial, free living, or parasitic [24]. The hallmark feature of protists is that at some point in their life cycle, they possess a flagella. A flagellum is a long hair like structure that is used for locomotion, sensation, and sometimes predation [24]. The flagellum makes waves by whiplike lashing movements which propels the cell forwards. Flagellates also have a protective coating in the form of a thin pellicle to protect them from the environment [24]. <br />
<br />
[[Image:9703607_orig.jpg|frame|center|Figure 3.9 Illustration of flaggelates during different life cycle stages. From[http://diagnosticparasitology.weebly.com/uploads/3/9/5/4/3954522/9703607_orig.jpg]]]<br />
<br />
*'''Mastigophora:'''<br />
<br />
Mastigophora is a subphylum of flagellates. Being a member of the flagellates, their key feature is the flagellum. Their habitats include freshwater, soil, and can act as animal parasites as well [25]. They use pseudopodia, a long outward protrusion, to trap and funnel food from the environment into their cell bodies [25]. The Mastigophora are mainly known for their parasitism, which can take place in both humans and animals [25]. ''Typanosomes'' are an example of Mastigophora which causes African sleeping sickness [25]. ''Giardia lambli''a is another example that resides in the intestinal tract of warm-blooded animals and inflicts intestinal giardiases [25]. It is also a major contaminant of drinking water because it is resistant to chlorine, which is the most common water purifier [25]. Having a dormant cyst form also adds to its survival potential through filtration efforts [25].<br />
<br />
<br />
<br />
*'''Euglenids:'''<br />
<br />
Euglenids are one of the best known flagellates. They are found in freshwater and soil, as long as there are organic materials. They also participate in some symbiotic relationships with marine animals. Euglenid cells do not contain cell walls or other rigid membranes [26]. This gives the cell tremendous flexibility and allows it to change its shape to easily navigate through muddy terrain. Euglenids have two flagella, one which creates locomotion and movement for the cell [26]. The other flagellum does not protrude from the cell and is contained in the cell body [26].<br />
<br />
======Amoebas======<br />
<br />
'''Amoebas'''<br />
<br />
Amoebae are single celled eukaryotes present in many different types of environments. They are scattered throughout a variety of eukaryotic lineages and therefore are not monophyletic [27]. Amoebae range in size from 5 micrometers to 3 mm and don’t have a defined shape, commonly recognized for being polymorphic. They are motile through the use of pseudopodia, which stretch and pull the cell along with it. The pseudopodia are also used for feeding. They are able to sense prey that can be engulfed and engulf them via phagocytosis. The amoeba’s main prey consists of bacteria, algae, and other protozoa [28]. The prey is moved around within the cell via food vacuoles, a feature of amoebae [28]. Another key characteristic of amoebae are the large contractile vacuoles inside the cell. The purpose of the contractile vacuole is to osmoregulate by pumping excess water out of the cell. In times of turmoil, amoebae have an encysted form that helps them get through the tough times. This form is useful when there is low nutrient availability to limit energy consumption. There are two main forms an amoeba can be characterized as. They can either be testate or nontestate. Testate amoeba produce shells, or “tests”, that help identify their species since each species has a unique shell.<br />
<br />
[[Image:Amoeba_(PSF).png|frame|center|Figure 3.10 Amoeba morphology. From[https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Amoeba_(PSF).png/230px-Amoeba_(PSF).png]]]<br />
<br />
=====Slime Molds=====<br />
<br />
'''Slime molds''' were once classified as fungi, but have now been placed in their own phylogenetic groups. Slime molds are single cells that can live independently, but aggregate to form multicellular reproductive structures when necessary [29]. The fruiting body releases spores which germinate into new cells. Slime molds feed off of bacteria and are most commonly found in forests. They feed off of decaying vegetation as well so they can be seen on rotting logs and leaves.<br />
<br />
[[Image:28-30-cellslimemoldlife-l.jpg|frame|center|Figure 3.11 Illustration of slime mold life cycle. From[https://lichencolony.files.wordpress.com/2006/06/28-30-cellslimemoldlife-l.jpg]]]<br />
<br />
==Current Research== <br />
<br />
'''Bacteria:''' To showcase the great diversity of soil bacterial environments, cyanobacteria have been studied in both desert and polar regions. Cyanobacteria can survive in extreme conditions likely because of their long evolutionary past.[16] Dr. Patzelt and his colleagues studied the diverse cyanobacteria residing in the Atacama desert, one of the driest parts of the world. The diverse taxa found in the Atacama desert can withstand prolonged periods of extreme desiccation.[16] The cyanobacteria dominate the soil crusts, affecting soil stability, soil structure and soil fertility.[16] Cyanobacteria inhabiting the Antarctic and Arctic regions, show similar adaptations to extreme environments as the cyanobacteria found in the desert. The polar cyanobacteria are particularly adapted to high altitudes.[17] They can withstand high ultraviolet radiation, desiccation, and repeated freeze-thaw cycles.[17] The autotrophic cyanobacteria supports heterotrophic microbes, providing an important ecosystem service in an environment with low microbial activity.[17]<br />
<br />
'''Archaea:''' In 150 soil samples acquired from North and South America, about 150,000 species were observed.[45] Of these, over 2,500 were identified as archaea based on their ssu rRNA.[45] The archaeal species were further analyzed to understand their role in the soil environment. Of the archaeal groups, ''Crenarchaeota'' and ''Euryarchaeota'' were found.[45] Bates stated that, “Across the non-experimental soils examined the soil C:N ratio was the single best predictor of archaeal relative abundances” due to their influences in the nutrient cycles.[45]<br />
<br />
'''Fungi:''' Fungi have been in the public eye for a while now due to the many different types of secondary metabolites they produce. Some produce bioactive compounds that can inhibit growth of protozoa, bacteria, parasites, insects, and even other fungi. A large area of investigation is the uses of these chemicals for human interests in use from medicine to plant and animal toxins [52].<br />
<br />
'''Protozoa:''' It’s known that Protozoa stimulate plant growth in different ways. It’s suspected that the Protozoa take part in the microbial loop which is responsible for the nutrient production for plants [19]. However, new developments have shown that the Protozoa themselves are responsible for the nitrogen mineralization and that other bacteria have no effect on the plant’s nitrogen sources [19].<br />
<br />
==References==<br />
<br />
1. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). Principles and Applications of Soil Microbiology. New Jersey: Pearson Education Inc.<br />
<br />
2. Ingham, Elaine R. Ingham R. "Chapter 4: SOIL FUNGI." Soil Biology. Natural Resources Conservation Service Illinois, n.d. Web. 9 Feb. 2016<br />
<br />
3. Reid, Greg, and Percy Wong. "SOIL BACTERIA AND FUNGI - NEW SOUTH WALES." Soil Bacteria and Fungi. New South Wales Department of Primary Industries, 2005. Web. 11 Feb. 2016.<br />
<br />
4. "Fungi." Microbiology Online. Microbiology Society, n.d. Web. 11 Feb. 2016.<br />
<br />
5. Tortora, G.J., Funke, B.R., Case, C.L. (2012). “Microbiology an Introduction.” 11th ed. Pearson Benjamin Cummings, San Francisco.<br />
<br />
6. Rizzo, D. “Intro to Fungi.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
7. Rizzo, D. “Ascomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
8. Rizzo, D. “Basidiomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
9. Pegg G.F., Brady B.L. “Verticillium Wilts.” New York, CABI Publishing 2002. Google Books. Web. 11 Feb. 2016. http://books.google.com<br />
<br />
10. Hebert, Paul. "What Is a Protist / What Are Protozoa? - Encyclopedia of Life." Encyclopedia of Life. N.p., n.d. Web. 11 Feb. 2016.http://eol.org/info/456<br />
<br />
11. "MicrobeWorld." Protista. N.p., n.d. Web. 11 Feb. 2016. http://www.microbeworld.org/types-of-microbes/protista<br />
<br />
12. Madigan, M.T., Martinko, J.M. (2006). Brock Biology of Microorganisms. New Jersey: Pearson Prentice Hall.<br />
<br />
13. Roesch, L.F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H.; Camargo, F. A. O.; Farmerie, W. G.; Triplett, E. W.(2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1(4).283-290. <br />
<br />
14. Amann, R.I, Ludwig, W., Schleifer, K.H.(1995).Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology and Molecular Biology Reviews. 59(1). 143-169. <br />
<br />
15. Geers, D., Cohan, F.M., Lawrence J.G., Spratt, B.G., Coenye, T. Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005). Opinion: Re-evaluating prokaryotic species. Nature Reviews Microbiology. 3(9). 733-739.<br />
<br />
16. Patzelt, D.J., Hodac, L., Friedl, T., Pietrasiak, N., Johansen, J.R. (2014). Biodiversity of soil cyanobacteria in the hyper-arid Atacama Desert, Chile. Journal of phycology. 50(4). 698-710. <br />
<br />
17. Makhalanyane, T. P., Valverde, A., Velázquez, D., Gunnigle, E., Van Goethem, M. W., Quesada, A., & Cowan, D. A. (2015). Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats. Biodiversity and Conservation, 24(4), 819-840.<br />
<br />
18. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist>.<br />
<br />
19. Ekelund, Flemming; Saj, Stephane; Vestergård, Mette; Bertaux, Joanne; Mikola, Juha. (2009). “The “soil microbial loop” is not always needed to explain protozoan stimulation of plants”. Soil Biology & Biochemistry. Vol. 41 Issue 11, p2336-2342, 7p.<br />
<br />
20. Bonkowski, Michael. "Protozoa and Plant Growth: The Microbial Loop in Soil Revisited." New Phytologist New Phytol 162.3 (2004): 617-31. Web.<br />
<br />
21. Hoorman, James. "The Role of Soil Protozoa and Nematodes." Fact Sheet (n.d.): n. pag. Ohio State University, 2011. Web.<br />
<br />
22. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist<br />
<br />
23. Lynn, Denis H(Apr 2012) Ciliophora. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001966.pub3]<br />
<br />
24. "flagellate". Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc., 2016. Web. 23 Feb. 2016 <http://www.britannica.com/science/flagellate>.<br />
<br />
25. "Mastigophora." World of Microbiology and Immunology. 2003. Encyclopedia.com. 23 Feb. 2016<http://www.encyclopedia.com>.<br />
<br />
26. “Plant Life." : Euglenoids. N.p., n.d. Web. 23 Feb. 2016. <http://lifeofplant.blogspot.com/2011/04/euglenoids.html><br />
<br />
27. Parales, R.E. and Martin, M. (2015) Microbial Diversity Laboratory Manual, MIC 105L, Winter 2015. Department of Microbiology and Molecular Genetics, College of Biological Sciences, The University of California, Davis.<br />
<br />
28. Arnold, Paul. "What Does an Amoeba Eat? Plus Other Ameoba Info and Questions." Bright Hub. N.p., n.d. Web. 04 Mar. 2016.<br />
<br />
29. "MicrobeWorld." Slime Molds. N.p., n.d. Web. 24 Feb. 2016. <http://www.microbeworld.org/types-of-microbes/protista/slime-molds><br />
<br />
30. Leeuwenhoek., A. V. (2009, November 18). One gram of soil: A microbial biochemical gene library. Retrieved March 13, 2016, from http://www.ncbi.nlm.nih.gov/pubmed/19921459 <br />
<br />
31. Coleman, D. C., Crossley, D. A. & Hendrix, P. F. "Soil food webs: Detritivory and microbiology in soils," in Fundamentals of Soil Ecology, 2nd ed. (Elsevier, 2004) 236-241.<br />
<br />
32. Welcome to Agriinfo.in. (n.d.). Retrieved February 21, 2016, from http://agriinfo.in/?page=topic&superid=5&topicid=172 <br />
<br />
33. Gouthro, T., & Rice, D. (1987, December 15). Interaction Terminology. Retrieved February 21, 2016, from http://www.rpi.edu/dept/chem-eng/Biotech-Environ/MixCul/ecodefn.htm <br />
<br />
34. AMENSALISM. (n.d.). Retrieved February 21, 2016, from https://biostuds.wikispaces.com/AMENSALISM <br />
<br />
35. Natural Resources Conservation Service. (n.d.). Retrieved March 10, 2016, from <br />
http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053865 <br />
<br />
36. Ecological Linkages Between Aboveground and Belowground Biota. (n.d.). Retrieved March 10, 2016, from http://science.sciencemag.org/content/304/5677/1629 <br />
<br />
37. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf<br />
<br />
38. Kingdom Archaea. (n.d.). Retrieved March 10, 2016, from http://plantphys.info/organismal/lechtml/archaea.shtml <br />
<br />
39. What are Archaea? - Encyclopedia of Life. (n.d.). Retrieved March 10, 2016, from http://eol.org/info/457 <br />
<br />
40. Flagellum. (n.d.). Retrieved March 10, 2016, from http://www.newworldencyclopedia.org/entry/Flagellum#Archaeal_flagellum <br />
<br />
41. Archaea: Morphology. (n.d.). Retrieved March 10, 2016, from http://www.ucmp.berkeley.edu/archaea/archaeamm.html <br />
<br />
42. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf <br />
<br />
43. Archaea. (n.d.). Retrieved March 10, 2016, from http://www.eoearth.org/view/article/150172/ <br />
<br />
44. Binary Fission: Cell Division & Reproduction of Prokaryotes. (n.d.). Retrieved March 10, 2016, from http://www.scienceprofonline.com/microbi <br />
<br />
45. Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2010, November 18). Examining the global distribution of dominant archaeal populations in soil. Retrieved February 21, 2016, from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105767/<br />
<br />
46. Scow, K. M. "Lecture 1 Part 1." Lecture, Davis.<br />
<br />
47. Rizzo, D. "Lecture 1." Lecture, Davis.<br />
<br />
48. Rizzo, D. "Lecture 3." Lecture, Davis.<br />
<br />
49. C.J. Alexopoulos & C. W. Mims, Introductory Mycology 3rd edition. 1979. Wiley NY. Web accessed Mar 8, 2016 from http://www.ucmp.berkeley.edu/fungi/fungimm.html<br />
<br />
50. Rizzo, D. "Lecture 2." Lecture, Davis.<br />
<br />
51. Ingham, E. “Chapter 4: Soil Fungi” (2016) Oregon State University. Retrieved Feb. 20, 2016, from http://extension.illinois.edu/soil/SoilBiology/fungi.htm<br />
<br />
52. Keller, N., Turner, G., Bennett, J. “Fungal Secondary Metabolism- from Biochemistry to Genomics.” 2005 Nature Reviews Microbiology p/ 937 to 947.</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Introduction_to_Organisms&diff=128509
Introduction to Organisms
2017-03-05T23:14:29Z
<p>Kmscow: /* Contributions to the Cycle */</p>
<hr />
<div>==Introduction== <br />
The soil ecosystem in an important environment that allows both plants and animals to survive, grow and reproduce. The significance of the soil as an ecosystem is at times overlooked despite its major contributions to the environment. The [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] is a complex and varied microbial habitat.[1] The plants and organisms inhabiting the soil contribute to its thriving diversity. Soil life is diverse in morphology, metabolism, size, and many other characteristics. It is believed that “there is sufficient [microbial] DNA in 1 g of soil to extend 1,598km.” [30] Soil is a heterogeneous environment with various zones of rhizosphere, aggregates, organic matter and animal residues.[31] Given each zone is a small component of the larger soil ecosystem, rhizosphere accounts for only 5 to 7 percent of the soil environments but contains over “70 percent of the bacterial- and fungal-feeding nematodes.”[31] <br />
<br />
Since, all three domains of life: archaea, bacteria and eukarya, inhabit the soil environment it is difficult to observe each microbe individually within the soil ecosystem.Only a few representative groups of each domain will be discussed to provide examples of the roles these organisms play in soil. This page attempts to outline the major microbial groups within the diverse soil environment.The interactions between soil microbes amongst the soil microbial diversity. The concept of survival of the fittest is seen in the soil food web, which allows only a selective few with the correct nutrients to thrive in a soil environment. The interactions of soil microbes is not only a part of nature but it also only selects those organisms that are fit for survival, growth and reproduction. The soil food web and symbiotic relationships are used to explain the dynamic interactions between soil organisms.<br />
<br />
==Soil Food Web and Microbial Interactions== <br />
<br />
To survive in a soil environment, an organism must be able to adapt to changing environments and organism interactions. The interactions seen between organisms allows only the fittest to survive, thrive, grow and reproduce in the soil. The only type of interaction shown in (Figure 2.1) is predation. Other common interactions in the soil environment are: <br />
<br />
:[[Image:soil_foodweb72.jpg|frame|center|Figure 2.1 Soil Food Web. From[http://www.exploringnature.org/graphics/foodwebs/soil_foodweb72.jpg]]]<br />
<br />
<br />
'''I. Commensalism:''' Organism (A) benefits from the presence of Organism (B) while (B) is unaffected by the presence of (A).[32]<br />
<br />
'''II. Mutualism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) and becomes a necessary association for each other’s survival. [32] [33]<br />
<br />
'''III. Synergism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) but the relationship is not necessary for survival.[33]<br />
<br />
'''IV. Competition:''' Depending on the organisms this interaction benefits organisms who can readily adapt to the environment and overcome any obstacles needed to survive, grow and reproduce.[33]<br />
<br />
'''V. Amensalism:''' An interaction in which Organisms (A) and (B) develop a partnership where (B) is unaffected by (A) but organism (A) is negatively affected by (B).[34]<br />
<br />
'''VI. Parasitism:''' Organism (A) benefits from Organism (B) but Organism (B) does not benefit positively from Organism (A). <br />
<br />
'''VII. Predation:''' “An interaction between organisms in which one benefits and one is harmed based on the ingestion of the smaller sized organism, the prey, by the larger organism, the predator.”[33]<br />
<br />
<br />
<br />
The soil food web consists of microbes which play an important role in maintaining the complexity of the soil environment. The interactions observed in the food web are not only based on predation, which directly affects the nutrient cycling and degradation of pollutants, but also the formation of aggregates.[35] The production of specific nutrients, such as ammonium created by microbial metabolic functions, helps to enrich the the soil for plant use.[35] Soil organism activity, along with the presence of soil organic matter, create stabilizing aggregates.[35] The hyphae within the soil environment and the microbes help form large, stable aggregates in the soil habitat.[35] The biodiversity in the soil plays a pivotal role in degrading pollutants, and also prevents pathogens from inhabiting the soil environment through competition.[35] The food web in the soil environment is necessary to maintain the soil nutrients, biological activity, and detoxifying pollutants. Thus, it directly maintains cultivation, productiveness and prosperity of the soil. <br />
<br />
In (Figure 2.1), all three domains, Archaea, Bacteria, and Eukarya, are represented in the soil food web. If one takes a closer look at the figure, the soil food web is not only dependent on small and large microbes but also dead organic matter and plant roots. Dead and living matter in the soil environment contribute to maintaining the food web. Plant residues also are apart of the soil food web. They contribute to the soil’s carbon source.[35] The plant residues either, release carbon dioxide to the environment, or contribute to the soil organic matter. Soil organic matter contributes to soil’s richness and helps to form aggregates.[35] The main focus in the image above is the diversity of organisms, both in domains and in size. The larger organisms are usually the predators. The smaller organisms eventually fall prey, due to their limited mobility, respiration, and size. The eukarya and small bacteria are apparent figures seen in the figure above, but archaea also contribute to the food cycle as they break down ammonia for plants to use. [35]<br />
<br />
The notable interactions of life that take place in the soil environment is evident both below-ground level, as seen in the figure 2.1, but also in the above-ground level.[36] Worms also impact the soil food web, acting as both drivers of the food web both belowground and aboveground.[36]<br />
<br />
==3 Domains==<br />
[[Image:Big_Tree_Bold_Letters_white.png|frame|center|Figure 3.1 Phylogenetic Tree of the 3 Domains. From[http://phylogenomics.blogspot.com/2014_02_01_archive.html]]]<br />
<br />
===Carl Woese and Phylogeny===<br />
<br />
[[Image:Carlwoese1_0565_b.jpg|frame|center|Figure 3.2 Carl Woese. From[http://ofbacteriaandmen.blogspot.com/2013/01/the-new-biology-of-carl-woese.html]]] <br />
<br />
Carl Woese (Figure 3.2) was an American microbiologist famous for pioneering the technique of phylogenetic taxonomy through use of a 16S (for prokaryotic) and 18S (for eukaryotic) ribosomal RNA, also known as small subunit ribosomal RNA [46]. This refined Linnaean classification, taking out the guesswork classification by using a gene that was present in every living organism- the small subunit ribosomal RNA. This method of classification is comprehensive because all organisms possess this form of genetic material. Ssu rRNA is sequenced because the genes are highly conserved. Due to their functional constancy, some have variable regions to differentiate organisms, and are easy to sequence. This technique also elucidated the tree of life, which shows the three domains of microbial lineage diversity: Bacteria, Archaea, and Eukarya. DNA can be compared using a sample database that allows identification of unknown organisms to a species level.<br />
<br />
===Domain Bacteria===<br />
<br />
====Introduction to Bacteria==== <br />
Bacteria are single celled prokaryotic organisms that lack membrane bound organelles. They are involved in many important processes within the soil such as decomposition, [https://microbewiki.kenyon.edu/index.php/Bioremediation bioremediation], symbiosis and biological transformation of nutrients. They are present in all terrestrial soil environments.[1] Soil is a heterogenous environment that varies in moisture content, temperature, oxygen requirements, carbon source and many other bacterial growth conditions. Those wide ranging growth factors account for the enormous diversity in soil bacteria populations. One gram of soil can contain between 26,000 to 52,000 different bacterial species.[13] In the entire microbial world, only about 1 percent of bacterial species can be cultured under laboratory conditions which leaves an immense number of bacterial species yet to be described. [14]<br />
<br />
Classification based on phenotypic characteristics, such as cellular morphology, metabolism, gram staining, oxygen requirements, carbon source and other traits, was used more readily before modern DNA sequencing. But, phenotypic classification is still used and Bergey’s Manual of Systematic Bacteriology is the most widely used source for determining species based on characteristic species traits.<br />
<br />
Traditional species definitions are not as useful in bacteria. OTUs, or operational taxonomic units, based on DNA sequencing similarity, are more applicable to bacteria. Typically, those bacteria with 97 percent similar DNA sequence are classified within the same OTU.[15] The 16S small subunit ribosomal RNA is used to substantiate phylogenetic relationships between different bacterial groups.<br />
<br />
====Morphology====<br />
<br />
Bacterial cells measure approximately 1μm wide and 1-5μm long.[12] They are smaller than eukaryotic microbes.Due to their small size, bacteria can more easily adapt to changing soil environments than larger eukaryotes.[1] Most bacteria are singled celled, but actinomycetes grow in branching filaments. There are many different bacterial cell shapes. The most common are bacilli (rods), cocci (spheres), spirilla (spirals) and actinomycete (filaments).<br />
[[Image:bacteria_sizes.jpg|frame|center|Figure 3.3 Common cell shapes cocci, bacillus, and spirilla and relative sizes. From[http://www.ppdictionary.com/gnbac.htm]]]<br />
<br />
'''Flagella''' - There are many different types and different arrangement of flagella. Movement in soil environments is dependent on soil moisture content. Though movement in soil is limited, flagellar function is important to allow bacteria to find more favorable microsites.[1]<br />
<br />
'''Cell membrane''' - The cell membrane encloses the cytoplasm. It is semi-permeable phospholipid bilayer that regulates transport of nutrients into the cell and waste products out of the cell.<br />
<br />
'''Cell wall''' - Most bacteria have a rigid cell wall surrounding the cell membrane which protects the cell from osmotic lysis. The cell wall is made of a crosslinked polysaccharide, called peptidoglycan, that is found only in bacteria.[1] The cell wall gives the cell shape and structure, but it is porous enough to permit small water soluble molecules to flow through to the cell membrane surface.[1]<br />
<br />
*'''Gram positive''' bacteria have a thick cell wall made of several layers of peptidoglycan. The cell wall is the outermost structure, as they do not have an outer membrane. The thick cell wall structure make gram positive bacteria more resilient to osmotic shock. Gram positive bacteria can tolerate 5 to 10 times more turgor pressure than gram Gram negative bacteria.[1] Teichoic acids in the cell wall may also help to bind to cationic nutrients in soil surroundings.[1] <br />
<br />
*'''Gram negative''' bacteria have a thin cell wall surrounded by an outer membrane made of phospholipids and lipopolysaccharides. Polysaccharides of the outer membrane interact with surrounding cations and are involved in attachment of bacteria to soil particles. [1] Periplasm is a gel like substance that occupies the space between the outer membrane and the cell wall of gram negative bacteria.[1] The outer membrane and periplasmic space is thought to provide protection from environmental toxins.[1] Proteins within the periplasm are thought to begin the process of catalyzing hydrolysis of organic and toxic substances.[1] <br />
<br />
[[Image:gramposnegmembrane.jpg|frame|center| Figure 3.4 Illustration of Gram positive and Gram negative cell wall structures. From[http://micro.digitalproteus.com/morphology2.php]]]<br />
<br />
'''Endospores''' are made by ''Bacillus'' and ''Clostridium'' in response to environmental stress.[1] Endospores are extremely resistant structures that can withstand extreme temperatures up to 150℃.[12] They can also withstand extreme pressure, desiccation, radiation, pH and chemicals.[12] The endospore protects the bacterial DNA until environmental conditions are more favorable and germination can proceed. Soil is the most common habitat for endospore forming bacteria.[12]<br />
<br />
'''Extracellular polymers''' - Many bacteria secrete a slime layer or capsule made of polysaccharides or glycoproteins.[1] The outer polysaccharide coating of bacteria helps in attachment to surfaces and the formation of biofilms.[1] Bacterial capsule secretions play a big role in soil aggregation and soil structure.[1] When the carbon to nitrogen ratio within soils is high, microbes secrete the excess carbon as extracellular polysaccharides.[1]<br />
<br />
====Reproduction==== <br />
Most bacteria reproduce by binary fission.[12] The bacterial cell expands to twice the original cell size, duplicates the bacterial DNA and pinches off, producing two daughter cells. Each resultant daughter cell is a clone of the parent cell. Prokaryotic Archaea also reproduce by binary fission.<br />
<br />
*'''Spore formation:''' Actinomycetes are a large group of filamentous bacteria, primarily found in soil.[1] Actinomycetes are morphologically similar to fungi. Actinomycetes form long filaments called hyphae. Unlike most bacteria, the majority of actinomycetes reproduce using asexual spores called conidia.[1] Though they share many characteristic with fungi, actinomycetes are still prokaryotes. They are smaller than fungi and the cell wall contains peptidoglycan.[1] Actinomycetes break down a wide variety of organic compounds and play an important role in organic matter decomposition. [1] ''Streptomyces'', a subgroup within actinomycetes, produce geosmin, which gives soil the characteristic earthy smell.[12]<br />
<br />
====Metabolism==== <br />
<br />
Along with archaea, bacteria are the most metabolically diverse and employ many different nutritional strategies.[1]<br />
*Heterotrophs - Most bacteria are heterotrophic, obtaining carbon from preformed organic substances. [1] <br />
*Autotrophs - Carbon dioxide serves as the main source of carbon. Some cyanobacteria, nitrifying and sulfur-oxidizing bacteria are autotrophs.[1]<br />
*Organotrophs - Most bacteria obtain electrons from organic substances.[1]<br />
*Lithotrophs - Some cyanobacteria, nitrifying bacteria and sulfur-oxidizing bacteria obtain electrons from inorganic substances.[1]<br />
*Phototrophs - Cyanobacteria use light as the main source of metabolic energy.[1]<br />
*Chemotrophs - All other nonphotosynthetic bacteria do not rely on light for metabolic energy.[1]<br />
<br />
====Contributions to Biogeochemical Cycling==== <br />
<br />
Bacteria play a significant role in the cycling of a wide range of elements.<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Carbon_cycle '''Carbon Cycle:'''] <br />
<br />
*'''Carbon Assimilation''' is the process of fixing carbon dioxide into organic forms. Carbon fixation is performed by autotrophic bacteria, such as cyanobacteria.[1] Chemoautotrophic nitrifying bacteria, such as ''Nitrobacter, Nitrosospira'' and ''Nitrosomonas'', also fix carbon.[1] Sulfur oxidizing bacteria, such as ''Thiobacillus'', fix carbon as well.<br />
<br />
*'''Carbon Mineralization''' results from microbial decomposition of organic carbon compounds into inorganic forms. As the organic carbon substances, like plant matter, are decomposed, inorganic carbon dioxide is produced. Most bacteria are heterotrophs that perform carbon mineralization. When microorganisms die, they are decomposed by successive microbial generations. Peptidoglycan, the main component of bacterial cell walls, is utilized as a polysaccharide substrate by other heterotrophic soil microbes.[1]<br />
<br />
*'''Methanogenesis''' - Methanogenic bacteria produce methane from the reduction of carbon dioxide. They are all strict anaerobes that use carbon dioxide for the carbon source.[1] They can all use hydrogen as a source of energy and electron donor. [1]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle '''Nitrogen cycle:''']<br />
<br />
*'''Nitrogen fixation:''' ''Azotobacter'' is a free living nitrogen fixing bacteria.[1] ''Rhizobium'' lives in a mutualistic relationship with plants by fixing nitrogen within root the nodules of legumes.[1] ''Anabaena'' and ''Nostoc'' have specialized heterocyte structures where nitrogen fixation occurs.[1] <br />
<br />
*'''Nitrification:''' Nitrifying bacteria, such as ''Nitrobacter, Nitrosospira,'' and ''Nitrosomonas'', oxidize ammonium to nitrate.[1] <br />
<br />
*'''Denitrification:''' ''Alcaligenes, Flavobacterium'', and ''Pseudomonas'' are common soil denitrifying bacteria.[1]<br />
<br />
===Domain Archaea===<br />
<br />
====Introduction to Archaea====<br />
<br />
Vladimir Vernadsky decided, in 1926, that only two domains of life existed on Earth, Bacteria and Eukarya.[37] About 50 years later in 1977, Carl Woese and George Fox theorized that part of the bacterial domain possed multiple dissimilarities from bacteria and recognized it to be another domain of life, now called Archaea.[38] Woese and Fox’s theory regarding the differences of archaea were confirmed in 1990’s through the use of 16S rRNA and 18S rRNA.[38] <br />
<br />
Despite the strongly held belief, in the 1990s, that archaea only inhabited extreme environments, recent discoveries have suggested their presence in abundant numbers all throughout the Earth. It is suggested that Archaea play notable roles in maintaining nutrient cycles.[37] Various methods of research, such as cultivation, culture-independent techniques and isotope-based methods, have facilitated the study of domain Archaea in carbon and nitrogen cycling. [37]<br />
<br />
The use of genomic and biochemical data has permitted the study of archaeal structure.[37] Use of these research methods has shown that domain archaea and domain bacteria differ in cell wall characteristics yet, share various ways to transfer genetic information by replication and transcription from their common ancestor, Eukarya.[37] As of 2012, 116 genera of Archaea have been observed which consists of 450 species. Most of the archaeal species in these genera remains uncultivated, known only through its gene sequences and molecular surveys.[37]<br />
<br />
====Morphology==== <br />
Archaea are characterized by various cell sizes. They are most commonly found to be small organisms ranging from “0.1 to 15 μ diameter and up to 200 μ long.”[38] The shape of many archaea are similar to bacteria, including bacillus, cocci, spirilla and “plate-like forms.” [38] Their cell membranes have ether linked lipids with no periplasmic space, similar to gram-positive bacteria, and contain no intracellular organelles.[39]<br />
<br />
'''Flagella:''' Most motile archaea inhabit a motor rotary system that allows it to move its flagella through the chemical gradient similar to bacteria.[39] Despite its similarity in function and source of energy required for motility, the flagella of both archaea and bacteria differ in structure.[39] Archaeal flagella gets the energy for its movement by ATP and is composed of dependent filaments that rotate singularly. [40] Archaeal flagella are known to be thinner than bacteria flagellin.[40] Since, the archaeal common ancestor is not bacteria but eukarya, convergent evolution is a plausible explanations for the differences between bacterial and archaeal flagellin. [40]<br />
<br />
'''Membranes:''' Archaea have a cell membrane that protects the cytoplasm and the nucleic acids from the environment. The archaeal cell membrane has a lipid bilayer with glycol-ether lipids that are more stable than ester linkages and help some archaea that live in extreme environments to withstand such conditions.[39] Most archaeal species are surrounded by a cell wall which protects the cell membrane and maintains the archaeal structure.[41]<br />
<br />
====Reproduction====<br />
Archaeal organisms reproduce by binary fission since they do not have nucleases thus, the DNA chromosome in a Archaeal organism replicate, separate and create two daughter cells.[43] The process of binary fission can be seen in Figure (3.5) process begins the parent cell duplicating the DNA. The DNA material then goes to the sides of the cell where an invagination to the cell occurs allowing the cell to become two individual cells. Binary fission is a very fast reproduction process, that allows archaeal organisms to grow at an exponential rate.[44]<br />
<br />
[[Image:WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg|frame|center|Figure 3.5 Illustration of binary fission. From[https://d2jmvrsizmvf4x.cloudfront.net/WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg]]]<br />
<br />
====Metabolism==== <br />
Archaea share similar metabolic characteristics to bacteria. The metabolic pathways taken by all archaea shown in the (Figure 3.6) demonstrates the great diversity and variation amongst archaea. [38] The kinds of archaea that are seen in the environment and the metabolic pathways taken by some can be summarized in the image. <br />
<br />
*Photoautotrophs: use light as an energy source and carbon dioxide as the carbon source with the help of the Calvin Cycle.[38]<br />
*Chemoautotrophs: use inorganic chemicals as their energy source and carbon dioxide as carbon source. <br />
*Chemoheterotrophs: take organic chemicals as energy source and organic chemicals as carbon source. The pathways taken by chemoheterotrophs varies from respiration by the Krebs Cycle to fermentation. [38]<br />
*Photoheterotrophs: use light as their energy source and organic chemicals as their carbon source. <br />
<br />
Most archaea inhabiting in the soil environment are major contributors to the biogeochemical cycles.<br />
<br />
[[Image:2000px-Troph_flowchart.svg.png|thumbnail|center|Figure 3.6 Flowchart showing different metabolic pathways. From[https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Troph_flowchart.svg/2000px-Troph_flowchart.svg.png]]]<br />
<br />
====Contributions to the Cycle====<br />
Archaea play a significant role in the nutrient cycles that take place in the ecosystem as they account for about 1-5% of all the prokaryotes present in the soil environment.[42]<br />
<br />
'''Carbon Cycle:''' Archaea have an important role in the carbon cycle that takes place specifically in methane production, carbon mineralization and carbon assimilation all of all of which contribute to the soil’s carbon sink.[42] The carbon dense soil helps to make the soil organic matter rich and helps to form extracellular polymers which creates stable aggregates. For some microbes, an electron acceptor is need to carry out metabolic functions. [42] More info on [https://microbewiki.kenyon.edu/index.php/Carbon_cycle Carbon Cycle].<br />
<br />
*'''Carbon Assimilation:''' Involves the transformation of inorganic carbon into organic carbon compounds. This process is commonly done by autotrophic phyla ''Crenarchaeota, Thaumarchaeota'', and ''Euryarchaeota'' that use carbon dioxide/ bicarbonate converting it to organic compounds.[42] Of the autotrophic lineages observed in carbon assimilation the ''Thaumarchaeota'' are strict autotrophs, the ''Euryarchaeota'' and ''Crenarchaeota'' are facultative autotrophs and the ''Halobacteriales'' and ''Thermococcales'' are obligate heterotrophs.[42] <br />
<br />
*'''Carbon Mineralization:''' The process that converts organic carbon into the oxidized inorganic carbon, carbon dioxide is commonly done by both aerobes and anaerobes.[42] The heterotrophic microbes that use organic compounds as energy to oxidize the carbon source include, methanogens and methane-oxidizing archaea belonging to the phyla ''Euryarchaetota'', and ''Crenarchaeota''.[42] <br />
<br />
*'''Methanogenesis:''' production of methane, a major greenhouse gas in the Earth’s atmosphere is commonly done by archaea upon reducing an oxidized compound.[42] The phyla ''Euryarchaeota'' is the only phyla that consists of archaea that produce methane all of which form five class: ''Methanopyri, Methanococci, Methanobacteria, Methanomicrobia'' and ''Thermoplasmata''.[42] Methanogens are commonly found in anaerobic and aerobic conditions such as bodies of water, aerated soils and oxygenated waters.[42]<br />
<br />
'''Nitrogen Cycle :''' Archaea play a pivotal role in the Nitrogen cycle and help create nitrogenous products for the plants and microbes. More info on [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle Nitrogen cycle].<br />
<br />
*'''Nitrogen Fixation:''' Fixing nitrogen from the environment and converting it to organic nitrogen in the soil or to inorganic nitrogenous form since both organic and inorganic products are in short supply in the biosphere and are fixed by many archaeal organisms.[42] N2 fixation by the environment is usually done by three major archaeal classes ''Methanobactera, Methanococci'' and ''Methanomicrobia''.[42] <br />
<br />
*'''Nitrification:''' Converting the ammonia (NH4+) in the soil to nitrite (NO2-) produces nitrate (NO3-) as an intermediate. [42] The transformation of ammonia to first nitrate then to nitrite is a two step process that is done by different microbes. [42] Most common organisms involved in nitrification include ammonia-oxidizing archaea which are lithotrophic organisms mostly, of the ''Thaumarchaeota'' phylum from the archaea domain. <br />
<br />
*'''Denitrification :''' The conversion of atmospheric N2 using the electron acceptor NO3- or NO2- creating the formation of nitric oxide, nitrous oxide and/or N2.[42] The formation of the end product N2 may not always be produced but other intermediates NO and N2O, greenhouse gases may be produced.[42] Of the archaeal organisms that have been studied in denitrification process is done by ''Pyrobaculum aerophilum'' which accepts both NO3- and NO2- as an electron acceptor producing a variety of products NO2-, NO, N20 and N2.[42]<br />
<br />
===Domain Eukarya===<br />
<br />
====Fungi====<br />
<br />
=====Introduction=====<br />
<br />
'''Introduction'''<br />
<br />
Fungi comes from the ancient Greek word “sphongos” meaning sponge in reference to the mushroom cap [47]. Fungi have the general characteristics of being eukaryotic, heterotrophic, external absorbers of nutrients, containing a hyphal thallus, reproducing via spore, and being pleomorphic (producing several forms). Fungi are generally organoheterotrophs that can survive in low pH and stay active at low moisture content[46]. Fungi reside in the domain Eukarya with an estimated species of 1.5 million, and less than five percent of them have ever been described. The general phyla included within Kingdom Fungi include Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, Chytridiomycota, and Microsporidia [48].<br />
<br />
[[Image:magical-kingdom-620.jpg|frame|center|Figure 3.7 Fungi phyla hierarchy. From.[http://www.motherjones.com/environment/2009/11/fungi-family-tree]]]<br />
<br />
=====Morphology=====<br />
<br />
'''Morphology''' <br />
<br />
Fungi can be either unicellular (yeasts) or multicellular. All multicellular fungi are made up of small, filamentous particles called hyphae. Some hyphae have cross walls called septa, while others do not- this is a large basis of fungal identification. Fungal cells generally have multiple nuclei. Fungal cell walls are generally composed of chitin, a long carbohydrate polymer that adds rigidity and structural support to fungi [49]. <br />
<br />
=====Reproduction=====<br />
<br />
'''Reproduction'''<br />
<br />
Fungal reproduction can occur either sexually or asexually.<br />
<br />
'''Sexual reproduction''' can occur by homothallic or heterothallic mycelia.<br />
<br />
'''Asexual reproduction''' can occur by fragmentation, budding, or by producing spores (the most common method). <br />
<br />
*'''Spores:''' spores come in many different forms. One of the most well known are conidiospores, which are unicellular or multicellular spores that get released from the tip of the hyphae. <br />
<br />
'''Perfect fungi''' are those that can reproduce both sexually and asexually while imperfect fungi are those that can only reproduce asexually.<br />
<br />
*Sexual reproduction always includes the stages plasmogamy (fusion of two haploid cells), karyogamy (creation of a diploid zygote), and meiosis (gametes are created).<br />
<br />
=====Metabolism=====<br />
<br />
'''Metabolism'''<br />
<br />
Many different fungi display a myriad of metabolisms. There are primary metabolites that that help the fungi function properly, and secondary metabolites that are generally bioactive that are not the most pertinent to fungal growth (they can live without these). Secondary metabolites play a large role in chemistry today and can be manufactured into commonly used products such as new drugs. In general fungi are heterotrophic through release of extracellular enzymes into the neighboring environment to break complex molecules down into smaller ones. The materials are then absorbed and metabolized [50]. Fungi are sessile organisms that overcome their little to no movement through apical growth at the hyphal tip. Fungi are noted to grow almost everywhere on the Earth.<br />
<br />
=====Relevance to soil===== <br />
<br />
'''Relevance to soil'''<br />
<br />
Fungi include some of the most abundant biomass of microorganisms in numerous soils. They play an important role as decomposers within the soil food web through conversion of difficult to digest organic material into forms many other organisms can use [51]. Their hyphae can bind soil particles together and create aggregates that increase soil water holding capacity. They perform important functions from water dynamics to nutrient cycling and disease suppression. Soil fungi can be categorized into three different groups based on their actions: <br />
<br />
*decomposers: that convert dead organic material into fungal biomass<br />
<br />
*mutualists: which colonize plant roots and help solubilize phosphorous and bring soil nutrients<br />
<br />
*pathogens/ parasites: which help control diseases in soil via trapping organisms such as nematodes [51]. <br />
<br />
Fungi are seen common in intensively managed agricultural soils due to tillage disrupting hyphae. Fungi also play a very important role in the [https://microbewiki.kenyon.edu/index.php/Rhizosphere_Interactions rhizosphere], the region of soil that is greatly influenced by the plant root system. This area of soil which is concentrated in plant roots and fungal hyphae is known to support greater microbial activity.<br />
<br />
=====Protozoans=====<br />
<br />
'''Protozoans'''<br />
<br />
In general, Protozoans range from 5 to 500 µm in diameter, making them significantly larger than bacteria [21]. They are abundantly located near the surface of the soil (15cm deep) where roots are plentiful [21]. Many protozoans have two life cycles. One is their active form where they are motile and feed on prey. The other is the cyst form where they produce a thick coating to protect them from the environment and can go dormant for years. The protozoa are divided into 4 major categories: the ciliates, the flagellates, the heliozoans, and the amoebas [10]. <br />
<br />
======Ciliates======<br />
<br />
'''Cilliates:'''<br />
This group, within protozoans, is fairly diverse. A common feature shared amongst all of its members is the presence of at least one cilia at any stage of its development [10]. The cilia is used for movement and other things such as predation (tentacles). For movement, they use the massive amounts of tiny cilia to create wave like currents to propel the cell forwards. Most ciliates also have toxicysts which are used to capture prey [10]. Some ciliates even have a symbiotic relationship with algae living inside of them [10]. The algae use the CO2 produced by ciliates and turn it into O2 that can then be reused by the ciliates [10]. They are found in a wide array of habitats ranging from freshwater and soil to the rumen of Animals [22]. They are present in almost anywhere that contains water [23]. They are unicellular heterotrophs so they feed on bacteria and algae in their environment. Ciliates are one of the top predators in the microbial food web and are hypothesized to have been a major predatory group before animals evolved [23]. Parasitic ciliates exist that can cause the death of animals and are increasingly becoming dangerous in water [23].<br />
<br />
[[Image:2spiro.jpg|frame|center|Figure 3.8 Microscope image of ciliated protists. From[http://www.microscopy-uk.org.uk/mag/smallimag/2spiro.jpg]]]<br />
<br />
======Flagellates======<br />
<br />
'''Flagellates''' are one of the most commonly known protists. They are unicellular organisms that may be solitary, colonial, free living, or parasitic [24]. The hallmark feature of protists is that at some point in their life cycle, they possess a flagella. A flagellum is a long hair like structure that is used for locomotion, sensation, and sometimes predation [24]. The flagellum makes waves by whiplike lashing movements which propels the cell forwards. Flagellates also have a protective coating in the form of a thin pellicle to protect them from the environment [24]. <br />
<br />
[[Image:9703607_orig.jpg|frame|center|Figure 3.9 Illustration of flaggelates during different life cycle stages. From[http://diagnosticparasitology.weebly.com/uploads/3/9/5/4/3954522/9703607_orig.jpg]]]<br />
<br />
*'''Mastigophora:'''<br />
<br />
Mastigophora is a subphylum of flagellates. Being a member of the flagellates, their key feature is the flagellum. Their habitats include freshwater, soil, and can act as animal parasites as well [25]. They use pseudopodia, a long outward protrusion, to trap and funnel food from the environment into their cell bodies [25]. The Mastigophora are mainly known for their parasitism, which can take place in both humans and animals [25]. ''Typanosomes'' are an example of Mastigophora which causes African sleeping sickness [25]. ''Giardia lambli''a is another example that resides in the intestinal tract of warm-blooded animals and inflicts intestinal giardiases [25]. It is also a major contaminant of drinking water because it is resistant to chlorine, which is the most common water purifier [25]. Having a dormant cyst form also adds to its survival potential through filtration efforts [25].<br />
<br />
<br />
<br />
*'''Euglenids:'''<br />
<br />
Euglenids are one of the best known flagellates. They are found in freshwater and soil, as long as there are organic materials. They also participate in some symbiotic relationships with marine animals. Euglenid cells do not contain cell walls or other rigid membranes [26]. This gives the cell tremendous flexibility and allows it to change its shape to easily navigate through muddy terrain. Euglenids have two flagella, one which creates locomotion and movement for the cell [26]. The other flagellum does not protrude from the cell and is contained in the cell body [26].<br />
<br />
======Amoebas======<br />
<br />
'''Amoebas'''<br />
<br />
Amoebae are single celled eukaryotes present in many different types of environments. They are scattered throughout a variety of eukaryotic lineages and therefore are not monophyletic [27]. Amoebae range in size from 5 micrometers to 3 mm and don’t have a defined shape, commonly recognized for being polymorphic. They are motile through the use of pseudopodia, which stretch and pull the cell along with it. The pseudopodia are also used for feeding. They are able to sense prey that can be engulfed and engulf them via phagocytosis. The amoeba’s main prey consists of bacteria, algae, and other protozoa [28]. The prey is moved around within the cell via food vacuoles, a feature of amoebae [28]. Another key characteristic of amoebae are the large contractile vacuoles inside the cell. The purpose of the contractile vacuole is to osmoregulate by pumping excess water out of the cell. In times of turmoil, amoebae have an encysted form that helps them get through the tough times. This form is useful when there is low nutrient availability to limit energy consumption. There are two main forms an amoeba can be characterized as. They can either be testate or nontestate. Testate amoeba produce shells, or “tests”, that help identify their species since each species has a unique shell.<br />
<br />
[[Image:Amoeba_(PSF).png|frame|center|Figure 3.10 Amoeba morphology. From[https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Amoeba_(PSF).png/230px-Amoeba_(PSF).png]]]<br />
<br />
=====Slime Molds=====<br />
<br />
'''Slime molds''' were once classified as fungi, but have now been placed in their own phylogenetic groups. Slime molds are single cells that can live independently, but aggregate to form multicellular reproductive structures when necessary [29]. The fruiting body releases spores which germinate into new cells. Slime molds feed off of bacteria and are most commonly found in forests. They feed off of decaying vegetation as well so they can be seen on rotting logs and leaves.<br />
<br />
[[Image:28-30-cellslimemoldlife-l.jpg|frame|center|Figure 3.11 Illustration of slime mold life cycle. From[https://lichencolony.files.wordpress.com/2006/06/28-30-cellslimemoldlife-l.jpg]]]<br />
<br />
==Current Research== <br />
<br />
'''Bacteria:''' To showcase the great diversity of soil bacterial environments, cyanobacteria have been studied in both desert and polar regions. Cyanobacteria can survive in extreme conditions likely because of their long evolutionary past.[16] Dr. Patzelt and his colleagues studied the diverse cyanobacteria residing in the Atacama desert, one of the driest parts of the world. The diverse taxa found in the Atacama desert can withstand prolonged periods of extreme desiccation.[16] The cyanobacteria dominate the soil crusts, affecting soil stability, soil structure and soil fertility.[16] Cyanobacteria inhabiting the Antarctic and Arctic regions, show similar adaptations to extreme environments as the cyanobacteria found in the desert. The polar cyanobacteria are particularly adapted to high altitudes.[17] They can withstand high ultraviolet radiation, desiccation, and repeated freeze-thaw cycles.[17] The autotrophic cyanobacteria supports heterotrophic microbes, providing an important ecosystem service in an environment with low microbial activity.[17]<br />
<br />
'''Archaea:''' In 150 soil samples acquired from North and South America, about 150,000 species were observed.[45] Of these, over 2,500 were identified as archaea based on their ssu rRNA.[45] The archaeal species were further analyzed to understand their role in the soil environment. Of the archaeal groups, ''Crenarchaeota'' and ''Euryarchaeota'' were found.[45] Bates stated that, “Across the non-experimental soils examined the soil C:N ratio was the single best predictor of archaeal relative abundances” due to their influences in the nutrient cycles.[45]<br />
<br />
'''Fungi:''' Fungi have been in the public eye for a while now due to the many different types of secondary metabolites they produce. Some produce bioactive compounds that can inhibit growth of protozoa, bacteria, parasites, insects, and even other fungi. A large area of investigation is the uses of these chemicals for human interests in use from medicine to plant and animal toxins [52].<br />
<br />
'''Protozoa:''' It’s known that Protozoa stimulate plant growth in different ways. It’s suspected that the Protozoa take part in the microbial loop which is responsible for the nutrient production for plants [19]. However, new developments have shown that the Protozoa themselves are responsible for the nitrogen mineralization and that other bacteria have no effect on the plant’s nitrogen sources [19].<br />
<br />
==References==<br />
<br />
1. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). Principles and Applications of Soil Microbiology. New Jersey: Pearson Education Inc.<br />
<br />
2. Ingham, Elaine R. Ingham R. "Chapter 4: SOIL FUNGI." Soil Biology. Natural Resources Conservation Service Illinois, n.d. Web. 9 Feb. 2016<br />
<br />
3. Reid, Greg, and Percy Wong. "SOIL BACTERIA AND FUNGI - NEW SOUTH WALES." Soil Bacteria and Fungi. New South Wales Department of Primary Industries, 2005. Web. 11 Feb. 2016.<br />
<br />
4. "Fungi." Microbiology Online. Microbiology Society, n.d. Web. 11 Feb. 2016.<br />
<br />
5. Tortora, G.J., Funke, B.R., Case, C.L. (2012). “Microbiology an Introduction.” 11th ed. Pearson Benjamin Cummings, San Francisco.<br />
<br />
6. Rizzo, D. “Intro to Fungi.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
7. Rizzo, D. “Ascomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
8. Rizzo, D. “Basidiomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
9. Pegg G.F., Brady B.L. “Verticillium Wilts.” New York, CABI Publishing 2002. Google Books. Web. 11 Feb. 2016. http://books.google.com<br />
<br />
10. Hebert, Paul. "What Is a Protist / What Are Protozoa? - Encyclopedia of Life." Encyclopedia of Life. N.p., n.d. Web. 11 Feb. 2016.http://eol.org/info/456<br />
<br />
11. "MicrobeWorld." Protista. N.p., n.d. Web. 11 Feb. 2016. http://www.microbeworld.org/types-of-microbes/protista<br />
<br />
12. Madigan, M.T., Martinko, J.M. (2006). Brock Biology of Microorganisms. New Jersey: Pearson Prentice Hall.<br />
<br />
13. Roesch, L.F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H.; Camargo, F. A. O.; Farmerie, W. G.; Triplett, E. W.(2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1(4).283-290. <br />
<br />
14. Amann, R.I, Ludwig, W., Schleifer, K.H.(1995).Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology and Molecular Biology Reviews. 59(1). 143-169. <br />
<br />
15. Geers, D., Cohan, F.M., Lawrence J.G., Spratt, B.G., Coenye, T. Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005). Opinion: Re-evaluating prokaryotic species. Nature Reviews Microbiology. 3(9). 733-739.<br />
<br />
16. Patzelt, D.J., Hodac, L., Friedl, T., Pietrasiak, N., Johansen, J.R. (2014). Biodiversity of soil cyanobacteria in the hyper-arid Atacama Desert, Chile. Journal of phycology. 50(4). 698-710. <br />
<br />
17. Makhalanyane, T. P., Valverde, A., Velázquez, D., Gunnigle, E., Van Goethem, M. W., Quesada, A., & Cowan, D. A. (2015). Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats. Biodiversity and Conservation, 24(4), 819-840.<br />
<br />
18. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist>.<br />
<br />
19. Ekelund, Flemming; Saj, Stephane; Vestergård, Mette; Bertaux, Joanne; Mikola, Juha. (2009). “The “soil microbial loop” is not always needed to explain protozoan stimulation of plants”. Soil Biology & Biochemistry. Vol. 41 Issue 11, p2336-2342, 7p.<br />
<br />
20. Bonkowski, Michael. "Protozoa and Plant Growth: The Microbial Loop in Soil Revisited." New Phytologist New Phytol 162.3 (2004): 617-31. Web.<br />
<br />
21. Hoorman, James. "The Role of Soil Protozoa and Nematodes." Fact Sheet (n.d.): n. pag. Ohio State University, 2011. Web.<br />
<br />
22. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist<br />
<br />
23. Lynn, Denis H(Apr 2012) Ciliophora. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001966.pub3]<br />
<br />
24. "flagellate". Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc., 2016. Web. 23 Feb. 2016 <http://www.britannica.com/science/flagellate>.<br />
<br />
25. "Mastigophora." World of Microbiology and Immunology. 2003. Encyclopedia.com. 23 Feb. 2016<http://www.encyclopedia.com>.<br />
<br />
26. “Plant Life." : Euglenoids. N.p., n.d. Web. 23 Feb. 2016. <http://lifeofplant.blogspot.com/2011/04/euglenoids.html><br />
<br />
27. Parales, R.E. and Martin, M. (2015) Microbial Diversity Laboratory Manual, MIC 105L, Winter 2015. Department of Microbiology and Molecular Genetics, College of Biological Sciences, The University of California, Davis.<br />
<br />
28. Arnold, Paul. "What Does an Amoeba Eat? Plus Other Ameoba Info and Questions." Bright Hub. N.p., n.d. Web. 04 Mar. 2016.<br />
<br />
29. "MicrobeWorld." Slime Molds. N.p., n.d. Web. 24 Feb. 2016. <http://www.microbeworld.org/types-of-microbes/protista/slime-molds><br />
<br />
30. Leeuwenhoek., A. V. (2009, November 18). One gram of soil: A microbial biochemical gene library. Retrieved March 13, 2016, from http://www.ncbi.nlm.nih.gov/pubmed/19921459 <br />
<br />
31. Coleman, D. C., Crossley, D. A. & Hendrix, P. F. "Soil food webs: Detritivory and microbiology in soils," in Fundamentals of Soil Ecology, 2nd ed. (Elsevier, 2004) 236-241.<br />
<br />
32. Welcome to Agriinfo.in. (n.d.). Retrieved February 21, 2016, from http://agriinfo.in/?page=topic&superid=5&topicid=172 <br />
<br />
33. Gouthro, T., & Rice, D. (1987, December 15). Interaction Terminology. Retrieved February 21, 2016, from http://www.rpi.edu/dept/chem-eng/Biotech-Environ/MixCul/ecodefn.htm <br />
<br />
34. AMENSALISM. (n.d.). Retrieved February 21, 2016, from https://biostuds.wikispaces.com/AMENSALISM <br />
<br />
35. Natural Resources Conservation Service. (n.d.). Retrieved March 10, 2016, from <br />
http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053865 <br />
<br />
36. Ecological Linkages Between Aboveground and Belowground Biota. (n.d.). Retrieved March 10, 2016, from http://science.sciencemag.org/content/304/5677/1629 <br />
<br />
37. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf<br />
<br />
38. Kingdom Archaea. (n.d.). Retrieved March 10, 2016, from http://plantphys.info/organismal/lechtml/archaea.shtml <br />
<br />
39. What are Archaea? - Encyclopedia of Life. (n.d.). Retrieved March 10, 2016, from http://eol.org/info/457 <br />
<br />
40. Flagellum. (n.d.). Retrieved March 10, 2016, from http://www.newworldencyclopedia.org/entry/Flagellum#Archaeal_flagellum <br />
<br />
41. Archaea: Morphology. (n.d.). Retrieved March 10, 2016, from http://www.ucmp.berkeley.edu/archaea/archaeamm.html <br />
<br />
42. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf <br />
<br />
43. Archaea. (n.d.). Retrieved March 10, 2016, from http://www.eoearth.org/view/article/150172/ <br />
<br />
44. Binary Fission: Cell Division & Reproduction of Prokaryotes. (n.d.). Retrieved March 10, 2016, from http://www.scienceprofonline.com/microbi <br />
<br />
45. Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2010, November 18). Examining the global distribution of dominant archaeal populations in soil. Retrieved February 21, 2016, from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105767/<br />
<br />
46. Scow, K. M. "Lecture 1 Part 1." Lecture, Davis.<br />
<br />
47. Rizzo, D. "Lecture 1." Lecture, Davis.<br />
<br />
48. Rizzo, D. "Lecture 3." Lecture, Davis.<br />
<br />
49. C.J. Alexopoulos & C. W. Mims, Introductory Mycology 3rd edition. 1979. Wiley NY. Web accessed Mar 8, 2016 from http://www.ucmp.berkeley.edu/fungi/fungimm.html<br />
<br />
50. Rizzo, D. "Lecture 2." Lecture, Davis.<br />
<br />
51. Ingham, E. “Chapter 4: Soil Fungi” (2016) Oregon State University. Retrieved Feb. 20, 2016, from http://extension.illinois.edu/soil/SoilBiology/fungi.htm<br />
<br />
52. Keller, N., Turner, G., Bennett, J. “Fungal Secondary Metabolism- from Biochemistry to Genomics.” 2005 Nature Reviews Microbiology p/ 937 to 947.</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Introduction_to_Organisms&diff=128508
Introduction to Organisms
2017-03-05T23:13:49Z
<p>Kmscow: /* Reproduction */</p>
<hr />
<div>==Introduction== <br />
The soil ecosystem in an important environment that allows both plants and animals to survive, grow and reproduce. The significance of the soil as an ecosystem is at times overlooked despite its major contributions to the environment. The [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] is a complex and varied microbial habitat.[1] The plants and organisms inhabiting the soil contribute to its thriving diversity. Soil life is diverse in morphology, metabolism, size, and many other characteristics. It is believed that “there is sufficient [microbial] DNA in 1 g of soil to extend 1,598km.” [30] Soil is a heterogeneous environment with various zones of rhizosphere, aggregates, organic matter and animal residues.[31] Given each zone is a small component of the larger soil ecosystem, rhizosphere accounts for only 5 to 7 percent of the soil environments but contains over “70 percent of the bacterial- and fungal-feeding nematodes.”[31] <br />
<br />
Since, all three domains of life: archaea, bacteria and eukarya, inhabit the soil environment it is difficult to observe each microbe individually within the soil ecosystem.Only a few representative groups of each domain will be discussed to provide examples of the roles these organisms play in soil. This page attempts to outline the major microbial groups within the diverse soil environment.The interactions between soil microbes amongst the soil microbial diversity. The concept of survival of the fittest is seen in the soil food web, which allows only a selective few with the correct nutrients to thrive in a soil environment. The interactions of soil microbes is not only a part of nature but it also only selects those organisms that are fit for survival, growth and reproduction. The soil food web and symbiotic relationships are used to explain the dynamic interactions between soil organisms.<br />
<br />
==Soil Food Web and Microbial Interactions== <br />
<br />
To survive in a soil environment, an organism must be able to adapt to changing environments and organism interactions. The interactions seen between organisms allows only the fittest to survive, thrive, grow and reproduce in the soil. The only type of interaction shown in (Figure 2.1) is predation. Other common interactions in the soil environment are: <br />
<br />
:[[Image:soil_foodweb72.jpg|frame|center|Figure 2.1 Soil Food Web. From[http://www.exploringnature.org/graphics/foodwebs/soil_foodweb72.jpg]]]<br />
<br />
<br />
'''I. Commensalism:''' Organism (A) benefits from the presence of Organism (B) while (B) is unaffected by the presence of (A).[32]<br />
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'''II. Mutualism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) and becomes a necessary association for each other’s survival. [32] [33]<br />
<br />
'''III. Synergism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) but the relationship is not necessary for survival.[33]<br />
<br />
'''IV. Competition:''' Depending on the organisms this interaction benefits organisms who can readily adapt to the environment and overcome any obstacles needed to survive, grow and reproduce.[33]<br />
<br />
'''V. Amensalism:''' An interaction in which Organisms (A) and (B) develop a partnership where (B) is unaffected by (A) but organism (A) is negatively affected by (B).[34]<br />
<br />
'''VI. Parasitism:''' Organism (A) benefits from Organism (B) but Organism (B) does not benefit positively from Organism (A). <br />
<br />
'''VII. Predation:''' “An interaction between organisms in which one benefits and one is harmed based on the ingestion of the smaller sized organism, the prey, by the larger organism, the predator.”[33]<br />
<br />
<br />
<br />
The soil food web consists of microbes which play an important role in maintaining the complexity of the soil environment. The interactions observed in the food web are not only based on predation, which directly affects the nutrient cycling and degradation of pollutants, but also the formation of aggregates.[35] The production of specific nutrients, such as ammonium created by microbial metabolic functions, helps to enrich the the soil for plant use.[35] Soil organism activity, along with the presence of soil organic matter, create stabilizing aggregates.[35] The hyphae within the soil environment and the microbes help form large, stable aggregates in the soil habitat.[35] The biodiversity in the soil plays a pivotal role in degrading pollutants, and also prevents pathogens from inhabiting the soil environment through competition.[35] The food web in the soil environment is necessary to maintain the soil nutrients, biological activity, and detoxifying pollutants. Thus, it directly maintains cultivation, productiveness and prosperity of the soil. <br />
<br />
In (Figure 2.1), all three domains, Archaea, Bacteria, and Eukarya, are represented in the soil food web. If one takes a closer look at the figure, the soil food web is not only dependent on small and large microbes but also dead organic matter and plant roots. Dead and living matter in the soil environment contribute to maintaining the food web. Plant residues also are apart of the soil food web. They contribute to the soil’s carbon source.[35] The plant residues either, release carbon dioxide to the environment, or contribute to the soil organic matter. Soil organic matter contributes to soil’s richness and helps to form aggregates.[35] The main focus in the image above is the diversity of organisms, both in domains and in size. The larger organisms are usually the predators. The smaller organisms eventually fall prey, due to their limited mobility, respiration, and size. The eukarya and small bacteria are apparent figures seen in the figure above, but archaea also contribute to the food cycle as they break down ammonia for plants to use. [35]<br />
<br />
The notable interactions of life that take place in the soil environment is evident both below-ground level, as seen in the figure 2.1, but also in the above-ground level.[36] Worms also impact the soil food web, acting as both drivers of the food web both belowground and aboveground.[36]<br />
<br />
==3 Domains==<br />
[[Image:Big_Tree_Bold_Letters_white.png|frame|center|Figure 3.1 Phylogenetic Tree of the 3 Domains. From[http://phylogenomics.blogspot.com/2014_02_01_archive.html]]]<br />
<br />
===Carl Woese and Phylogeny===<br />
<br />
[[Image:Carlwoese1_0565_b.jpg|frame|center|Figure 3.2 Carl Woese. From[http://ofbacteriaandmen.blogspot.com/2013/01/the-new-biology-of-carl-woese.html]]] <br />
<br />
Carl Woese (Figure 3.2) was an American microbiologist famous for pioneering the technique of phylogenetic taxonomy through use of a 16S (for prokaryotic) and 18S (for eukaryotic) ribosomal RNA, also known as small subunit ribosomal RNA [46]. This refined Linnaean classification, taking out the guesswork classification by using a gene that was present in every living organism- the small subunit ribosomal RNA. This method of classification is comprehensive because all organisms possess this form of genetic material. Ssu rRNA is sequenced because the genes are highly conserved. Due to their functional constancy, some have variable regions to differentiate organisms, and are easy to sequence. This technique also elucidated the tree of life, which shows the three domains of microbial lineage diversity: Bacteria, Archaea, and Eukarya. DNA can be compared using a sample database that allows identification of unknown organisms to a species level.<br />
<br />
===Domain Bacteria===<br />
<br />
====Introduction to Bacteria==== <br />
Bacteria are single celled prokaryotic organisms that lack membrane bound organelles. They are involved in many important processes within the soil such as decomposition, [https://microbewiki.kenyon.edu/index.php/Bioremediation bioremediation], symbiosis and biological transformation of nutrients. They are present in all terrestrial soil environments.[1] Soil is a heterogenous environment that varies in moisture content, temperature, oxygen requirements, carbon source and many other bacterial growth conditions. Those wide ranging growth factors account for the enormous diversity in soil bacteria populations. One gram of soil can contain between 26,000 to 52,000 different bacterial species.[13] In the entire microbial world, only about 1 percent of bacterial species can be cultured under laboratory conditions which leaves an immense number of bacterial species yet to be described. [14]<br />
<br />
Classification based on phenotypic characteristics, such as cellular morphology, metabolism, gram staining, oxygen requirements, carbon source and other traits, was used more readily before modern DNA sequencing. But, phenotypic classification is still used and Bergey’s Manual of Systematic Bacteriology is the most widely used source for determining species based on characteristic species traits.<br />
<br />
Traditional species definitions are not as useful in bacteria. OTUs, or operational taxonomic units, based on DNA sequencing similarity, are more applicable to bacteria. Typically, those bacteria with 97 percent similar DNA sequence are classified within the same OTU.[15] The 16S small subunit ribosomal RNA is used to substantiate phylogenetic relationships between different bacterial groups.<br />
<br />
====Morphology====<br />
<br />
Bacterial cells measure approximately 1μm wide and 1-5μm long.[12] They are smaller than eukaryotic microbes.Due to their small size, bacteria can more easily adapt to changing soil environments than larger eukaryotes.[1] Most bacteria are singled celled, but actinomycetes grow in branching filaments. There are many different bacterial cell shapes. The most common are bacilli (rods), cocci (spheres), spirilla (spirals) and actinomycete (filaments).<br />
[[Image:bacteria_sizes.jpg|frame|center|Figure 3.3 Common cell shapes cocci, bacillus, and spirilla and relative sizes. From[http://www.ppdictionary.com/gnbac.htm]]]<br />
<br />
'''Flagella''' - There are many different types and different arrangement of flagella. Movement in soil environments is dependent on soil moisture content. Though movement in soil is limited, flagellar function is important to allow bacteria to find more favorable microsites.[1]<br />
<br />
'''Cell membrane''' - The cell membrane encloses the cytoplasm. It is semi-permeable phospholipid bilayer that regulates transport of nutrients into the cell and waste products out of the cell.<br />
<br />
'''Cell wall''' - Most bacteria have a rigid cell wall surrounding the cell membrane which protects the cell from osmotic lysis. The cell wall is made of a crosslinked polysaccharide, called peptidoglycan, that is found only in bacteria.[1] The cell wall gives the cell shape and structure, but it is porous enough to permit small water soluble molecules to flow through to the cell membrane surface.[1]<br />
<br />
*'''Gram positive''' bacteria have a thick cell wall made of several layers of peptidoglycan. The cell wall is the outermost structure, as they do not have an outer membrane. The thick cell wall structure make gram positive bacteria more resilient to osmotic shock. Gram positive bacteria can tolerate 5 to 10 times more turgor pressure than gram Gram negative bacteria.[1] Teichoic acids in the cell wall may also help to bind to cationic nutrients in soil surroundings.[1] <br />
<br />
*'''Gram negative''' bacteria have a thin cell wall surrounded by an outer membrane made of phospholipids and lipopolysaccharides. Polysaccharides of the outer membrane interact with surrounding cations and are involved in attachment of bacteria to soil particles. [1] Periplasm is a gel like substance that occupies the space between the outer membrane and the cell wall of gram negative bacteria.[1] The outer membrane and periplasmic space is thought to provide protection from environmental toxins.[1] Proteins within the periplasm are thought to begin the process of catalyzing hydrolysis of organic and toxic substances.[1] <br />
<br />
[[Image:gramposnegmembrane.jpg|frame|center| Figure 3.4 Illustration of Gram positive and Gram negative cell wall structures. From[http://micro.digitalproteus.com/morphology2.php]]]<br />
<br />
'''Endospores''' are made by ''Bacillus'' and ''Clostridium'' in response to environmental stress.[1] Endospores are extremely resistant structures that can withstand extreme temperatures up to 150℃.[12] They can also withstand extreme pressure, desiccation, radiation, pH and chemicals.[12] The endospore protects the bacterial DNA until environmental conditions are more favorable and germination can proceed. Soil is the most common habitat for endospore forming bacteria.[12]<br />
<br />
'''Extracellular polymers''' - Many bacteria secrete a slime layer or capsule made of polysaccharides or glycoproteins.[1] The outer polysaccharide coating of bacteria helps in attachment to surfaces and the formation of biofilms.[1] Bacterial capsule secretions play a big role in soil aggregation and soil structure.[1] When the carbon to nitrogen ratio within soils is high, microbes secrete the excess carbon as extracellular polysaccharides.[1]<br />
<br />
====Reproduction==== <br />
Most bacteria reproduce by binary fission.[12] The bacterial cell expands to twice the original cell size, duplicates the bacterial DNA and pinches off, producing two daughter cells. Each resultant daughter cell is a clone of the parent cell. Prokaryotic Archaea also reproduce by binary fission.<br />
<br />
*'''Spore formation:''' Actinomycetes are a large group of filamentous bacteria, primarily found in soil.[1] Actinomycetes are morphologically similar to fungi. Actinomycetes form long filaments called hyphae. Unlike most bacteria, the majority of actinomycetes reproduce using asexual spores called conidia.[1] Though they share many characteristic with fungi, actinomycetes are still prokaryotes. They are smaller than fungi and the cell wall contains peptidoglycan.[1] Actinomycetes break down a wide variety of organic compounds and play an important role in organic matter decomposition. [1] ''Streptomyces'', a subgroup within actinomycetes, produce geosmin, which gives soil the characteristic earthy smell.[12]<br />
<br />
====Metabolism==== <br />
<br />
Along with archaea, bacteria are the most metabolically diverse and employ many different nutritional strategies.[1]<br />
*Heterotrophs - Most bacteria are heterotrophic, obtaining carbon from preformed organic substances. [1] <br />
*Autotrophs - Carbon dioxide serves as the main source of carbon. Some cyanobacteria, nitrifying and sulfur-oxidizing bacteria are autotrophs.[1]<br />
*Organotrophs - Most bacteria obtain electrons from organic substances.[1]<br />
*Lithotrophs - Some cyanobacteria, nitrifying bacteria and sulfur-oxidizing bacteria obtain electrons from inorganic substances.[1]<br />
*Phototrophs - Cyanobacteria use light as the main source of metabolic energy.[1]<br />
*Chemotrophs - All other nonphotosynthetic bacteria do not rely on light for metabolic energy.[1]<br />
<br />
====Contributions to the Cycle==== <br />
<br />
Bacteria play a significant role in the cycling of a wide range of elements.<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Carbon_cycle '''Carbon Cycle:'''] <br />
<br />
*'''Carbon Assimilation''' is the process of fixing carbon dioxide into organic forms. Carbon fixation is performed by autotrophic bacteria, such as cyanobacteria.[1] Chemoautotrophic nitrifying bacteria, such as ''Nitrobacter, Nitrosospira'' and ''Nitrosomonas'', also fix carbon.[1] Sulfur oxidizing bacteria, such as ''Thiobacillus'', fix carbon as well.<br />
<br />
*'''Carbon Mineralization''' results from microbial decomposition of organic carbon compounds into inorganic forms. As the organic carbon substances, like plant matter, are decomposed, inorganic carbon dioxide is produced. Most bacteria are heterotrophs that perform carbon mineralization. When microorganisms die, they are decomposed by successive microbial generations. Peptidoglycan, the main component of bacterial cell walls, is utilized as a polysaccharide substrate by other heterotrophic soil microbes.[1]<br />
<br />
*'''Methanogenesis''' - Methanogenic bacteria produce methane from the reduction of carbon dioxide. They are all strict anaerobes that use carbon dioxide for the carbon source.[1] They can all use hydrogen as a source of energy and electron donor. [1]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle '''Nitrogen cycle:''']<br />
<br />
*'''Nitrogen fixation:''' ''Azotobacter'' is a free living nitrogen fixing bacteria.[1] ''Rhizobium'' lives in a mutualistic relationship with plants by fixing nitrogen within root the nodules of legumes.[1] ''Anabaena'' and ''Nostoc'' have specialized heterocyte structures where nitrogen fixation occurs.[1] <br />
<br />
*'''Nitrification:''' Nitrifying bacteria, such as ''Nitrobacter, Nitrosospira,'' and ''Nitrosomonas'', oxidize ammonium to nitrate.[1] <br />
<br />
*'''Denitrification:''' ''Alcaligenes, Flavobacterium'', and ''Pseudomonas'' are common soil denitrifying bacteria.[1]<br />
<br />
===Domain Archaea===<br />
<br />
====Introduction to Archaea====<br />
<br />
Vladimir Vernadsky decided, in 1926, that only two domains of life existed on Earth, Bacteria and Eukarya.[37] About 50 years later in 1977, Carl Woese and George Fox theorized that part of the bacterial domain possed multiple dissimilarities from bacteria and recognized it to be another domain of life, now called Archaea.[38] Woese and Fox’s theory regarding the differences of archaea were confirmed in 1990’s through the use of 16S rRNA and 18S rRNA.[38] <br />
<br />
Despite the strongly held belief, in the 1990s, that archaea only inhabited extreme environments, recent discoveries have suggested their presence in abundant numbers all throughout the Earth. It is suggested that Archaea play notable roles in maintaining nutrient cycles.[37] Various methods of research, such as cultivation, culture-independent techniques and isotope-based methods, have facilitated the study of domain Archaea in carbon and nitrogen cycling. [37]<br />
<br />
The use of genomic and biochemical data has permitted the study of archaeal structure.[37] Use of these research methods has shown that domain archaea and domain bacteria differ in cell wall characteristics yet, share various ways to transfer genetic information by replication and transcription from their common ancestor, Eukarya.[37] As of 2012, 116 genera of Archaea have been observed which consists of 450 species. Most of the archaeal species in these genera remains uncultivated, known only through its gene sequences and molecular surveys.[37]<br />
<br />
====Morphology==== <br />
Archaea are characterized by various cell sizes. They are most commonly found to be small organisms ranging from “0.1 to 15 μ diameter and up to 200 μ long.”[38] The shape of many archaea are similar to bacteria, including bacillus, cocci, spirilla and “plate-like forms.” [38] Their cell membranes have ether linked lipids with no periplasmic space, similar to gram-positive bacteria, and contain no intracellular organelles.[39]<br />
<br />
'''Flagella:''' Most motile archaea inhabit a motor rotary system that allows it to move its flagella through the chemical gradient similar to bacteria.[39] Despite its similarity in function and source of energy required for motility, the flagella of both archaea and bacteria differ in structure.[39] Archaeal flagella gets the energy for its movement by ATP and is composed of dependent filaments that rotate singularly. [40] Archaeal flagella are known to be thinner than bacteria flagellin.[40] Since, the archaeal common ancestor is not bacteria but eukarya, convergent evolution is a plausible explanations for the differences between bacterial and archaeal flagellin. [40]<br />
<br />
'''Membranes:''' Archaea have a cell membrane that protects the cytoplasm and the nucleic acids from the environment. The archaeal cell membrane has a lipid bilayer with glycol-ether lipids that are more stable than ester linkages and help some archaea that live in extreme environments to withstand such conditions.[39] Most archaeal species are surrounded by a cell wall which protects the cell membrane and maintains the archaeal structure.[41]<br />
<br />
====Reproduction====<br />
Archaeal organisms reproduce by binary fission since they do not have nucleases thus, the DNA chromosome in a Archaeal organism replicate, separate and create two daughter cells.[43] The process of binary fission can be seen in Figure (3.5) process begins the parent cell duplicating the DNA. The DNA material then goes to the sides of the cell where an invagination to the cell occurs allowing the cell to become two individual cells. Binary fission is a very fast reproduction process, that allows archaeal organisms to grow at an exponential rate.[44]<br />
<br />
[[Image:WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg|frame|center|Figure 3.5 Illustration of binary fission. From[https://d2jmvrsizmvf4x.cloudfront.net/WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg]]]<br />
<br />
====Metabolism==== <br />
Archaea share similar metabolic characteristics to bacteria. The metabolic pathways taken by all archaea shown in the (Figure 3.6) demonstrates the great diversity and variation amongst archaea. [38] The kinds of archaea that are seen in the environment and the metabolic pathways taken by some can be summarized in the image. <br />
<br />
*Photoautotrophs: use light as an energy source and carbon dioxide as the carbon source with the help of the Calvin Cycle.[38]<br />
*Chemoautotrophs: use inorganic chemicals as their energy source and carbon dioxide as carbon source. <br />
*Chemoheterotrophs: take organic chemicals as energy source and organic chemicals as carbon source. The pathways taken by chemoheterotrophs varies from respiration by the Krebs Cycle to fermentation. [38]<br />
*Photoheterotrophs: use light as their energy source and organic chemicals as their carbon source. <br />
<br />
Most archaea inhabiting in the soil environment are major contributors to the biogeochemical cycles.<br />
<br />
[[Image:2000px-Troph_flowchart.svg.png|thumbnail|center|Figure 3.6 Flowchart showing different metabolic pathways. From[https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Troph_flowchart.svg/2000px-Troph_flowchart.svg.png]]]<br />
<br />
====Contributions to the Cycle====<br />
Archaea play a significant role in the nutrient cycles that take place in the ecosystem as they account for about 1-5% of all the prokaryotes present in the soil environment.[42]<br />
<br />
'''Carbon Cycle:''' Archaea have an important role in the carbon cycle that takes place specifically in methane production, carbon mineralization and carbon assimilation all of all of which contribute to the soil’s carbon sink.[42] The carbon dense soil helps to make the soil organic matter rich and helps to form extracellular polymers which creates stable aggregates. For some microbes, an electron acceptor is need to carry out metabolic functions. [42] More info on [https://microbewiki.kenyon.edu/index.php/Carbon_cycle Carbon Cycle].<br />
<br />
*'''Carbon Assimilation:''' Involves the transformation of inorganic carbon into organic carbon compounds. This process is commonly done by autotrophic phyla ''Crenarchaeota, Thaumarchaeota'', and ''Euryarchaeota'' that use carbon dioxide/ bicarbonate converting it to organic compounds.[42] Of the autotrophic lineages observed in carbon assimilation the ''Thaumarchaeota'' are strict autotrophs, the ''Euryarchaeota'' and ''Crenarchaeota'' are facultative autotrophs and the ''Halobacteriales'' and ''Thermococcales'' are obligate heterotrophs.[42] <br />
<br />
*'''Carbon Mineralization:''' The process that converts organic carbon into the oxidized inorganic carbon, carbon dioxide is commonly done by both aerobes and anaerobes.[42] The heterotrophic microbes that use organic compounds as energy to oxidize the carbon source include, methanogens and methane-oxidizing archaea belonging to the phyla ''Euryarchaetota'', and ''Crenarchaeota''.[42] <br />
<br />
*'''Methanogenesis:''' production of methane, a major greenhouse gas in the Earth’s atmosphere is commonly done by archaea upon reducing an oxidized compound.[42] The phyla ''Euryarchaeota'' is the only phyla that consists of archaea that produce methane all of which form five class: ''Methanopyri, Methanococci, Methanobacteria, Methanomicrobia'' and ''Thermoplasmata''.[42] Methanogens are commonly found in anaerobic and aerobic conditions such as bodies of water, aerated soils and oxygenated waters.[42]<br />
<br />
'''Nitrogen Cycle :''' Archaea play a pivotal role in the Nitrogen cycle and help create nitrogenous products for the plants and microbes. More info on [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle Nitrogen cycle].<br />
<br />
*'''Nitrogen Fixation:''' Fixing nitrogen from the environment and converting it to organic nitrogen in the soil or to inorganic nitrogenous form since both organic and inorganic products are in short supply in the biosphere and are fixed by many archaeal organisms.[42] N2 fixation by the environment is usually done by three major archaeal classes ''Methanobactera, Methanococci'' and ''Methanomicrobia''.[42] <br />
<br />
*'''Nitrification:''' Converting the ammonia (NH4+) in the soil to nitrite (NO2-) produces nitrate (NO3-) as an intermediate. [42] The transformation of ammonia to first nitrate then to nitrite is a two step process that is done by different microbes. [42] Most common organisms involved in nitrification include ammonia-oxidizing archaea which are lithotrophic organisms mostly, of the ''Thaumarchaeota'' phylum from the archaea domain. <br />
<br />
*'''Denitrification :''' The conversion of atmospheric N2 using the electron acceptor NO3- or NO2- creating the formation of nitric oxide, nitrous oxide and/or N2.[42] The formation of the end product N2 may not always be produced but other intermediates NO and N2O, greenhouse gases may be produced.[42] Of the archaeal organisms that have been studied in denitrification process is done by ''Pyrobaculum aerophilum'' which accepts both NO3- and NO2- as an electron acceptor producing a variety of products NO2-, NO, N20 and N2.[42]<br />
<br />
===Domain Eukarya===<br />
<br />
====Fungi====<br />
<br />
=====Introduction=====<br />
<br />
'''Introduction'''<br />
<br />
Fungi comes from the ancient Greek word “sphongos” meaning sponge in reference to the mushroom cap [47]. Fungi have the general characteristics of being eukaryotic, heterotrophic, external absorbers of nutrients, containing a hyphal thallus, reproducing via spore, and being pleomorphic (producing several forms). Fungi are generally organoheterotrophs that can survive in low pH and stay active at low moisture content[46]. Fungi reside in the domain Eukarya with an estimated species of 1.5 million, and less than five percent of them have ever been described. The general phyla included within Kingdom Fungi include Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, Chytridiomycota, and Microsporidia [48].<br />
<br />
[[Image:magical-kingdom-620.jpg|frame|center|Figure 3.7 Fungi phyla hierarchy. From.[http://www.motherjones.com/environment/2009/11/fungi-family-tree]]]<br />
<br />
=====Morphology=====<br />
<br />
'''Morphology''' <br />
<br />
Fungi can be either unicellular (yeasts) or multicellular. All multicellular fungi are made up of small, filamentous particles called hyphae. Some hyphae have cross walls called septa, while others do not- this is a large basis of fungal identification. Fungal cells generally have multiple nuclei. Fungal cell walls are generally composed of chitin, a long carbohydrate polymer that adds rigidity and structural support to fungi [49]. <br />
<br />
=====Reproduction=====<br />
<br />
'''Reproduction'''<br />
<br />
Fungal reproduction can occur either sexually or asexually.<br />
<br />
'''Sexual reproduction''' can occur by homothallic or heterothallic mycelia.<br />
<br />
'''Asexual reproduction''' can occur by fragmentation, budding, or by producing spores (the most common method). <br />
<br />
*'''Spores:''' spores come in many different forms. One of the most well known are conidiospores, which are unicellular or multicellular spores that get released from the tip of the hyphae. <br />
<br />
'''Perfect fungi''' are those that can reproduce both sexually and asexually while imperfect fungi are those that can only reproduce asexually.<br />
<br />
*Sexual reproduction always includes the stages plasmogamy (fusion of two haploid cells), karyogamy (creation of a diploid zygote), and meiosis (gametes are created).<br />
<br />
=====Metabolism=====<br />
<br />
'''Metabolism'''<br />
<br />
Many different fungi display a myriad of metabolisms. There are primary metabolites that that help the fungi function properly, and secondary metabolites that are generally bioactive that are not the most pertinent to fungal growth (they can live without these). Secondary metabolites play a large role in chemistry today and can be manufactured into commonly used products such as new drugs. In general fungi are heterotrophic through release of extracellular enzymes into the neighboring environment to break complex molecules down into smaller ones. The materials are then absorbed and metabolized [50]. Fungi are sessile organisms that overcome their little to no movement through apical growth at the hyphal tip. Fungi are noted to grow almost everywhere on the Earth.<br />
<br />
=====Relevance to soil===== <br />
<br />
'''Relevance to soil'''<br />
<br />
Fungi include some of the most abundant biomass of microorganisms in numerous soils. They play an important role as decomposers within the soil food web through conversion of difficult to digest organic material into forms many other organisms can use [51]. Their hyphae can bind soil particles together and create aggregates that increase soil water holding capacity. They perform important functions from water dynamics to nutrient cycling and disease suppression. Soil fungi can be categorized into three different groups based on their actions: <br />
<br />
*decomposers: that convert dead organic material into fungal biomass<br />
<br />
*mutualists: which colonize plant roots and help solubilize phosphorous and bring soil nutrients<br />
<br />
*pathogens/ parasites: which help control diseases in soil via trapping organisms such as nematodes [51]. <br />
<br />
Fungi are seen common in intensively managed agricultural soils due to tillage disrupting hyphae. Fungi also play a very important role in the [https://microbewiki.kenyon.edu/index.php/Rhizosphere_Interactions rhizosphere], the region of soil that is greatly influenced by the plant root system. This area of soil which is concentrated in plant roots and fungal hyphae is known to support greater microbial activity.<br />
<br />
=====Protozoans=====<br />
<br />
'''Protozoans'''<br />
<br />
In general, Protozoans range from 5 to 500 µm in diameter, making them significantly larger than bacteria [21]. They are abundantly located near the surface of the soil (15cm deep) where roots are plentiful [21]. Many protozoans have two life cycles. One is their active form where they are motile and feed on prey. The other is the cyst form where they produce a thick coating to protect them from the environment and can go dormant for years. The protozoa are divided into 4 major categories: the ciliates, the flagellates, the heliozoans, and the amoebas [10]. <br />
<br />
======Ciliates======<br />
<br />
'''Cilliates:'''<br />
This group, within protozoans, is fairly diverse. A common feature shared amongst all of its members is the presence of at least one cilia at any stage of its development [10]. The cilia is used for movement and other things such as predation (tentacles). For movement, they use the massive amounts of tiny cilia to create wave like currents to propel the cell forwards. Most ciliates also have toxicysts which are used to capture prey [10]. Some ciliates even have a symbiotic relationship with algae living inside of them [10]. The algae use the CO2 produced by ciliates and turn it into O2 that can then be reused by the ciliates [10]. They are found in a wide array of habitats ranging from freshwater and soil to the rumen of Animals [22]. They are present in almost anywhere that contains water [23]. They are unicellular heterotrophs so they feed on bacteria and algae in their environment. Ciliates are one of the top predators in the microbial food web and are hypothesized to have been a major predatory group before animals evolved [23]. Parasitic ciliates exist that can cause the death of animals and are increasingly becoming dangerous in water [23].<br />
<br />
[[Image:2spiro.jpg|frame|center|Figure 3.8 Microscope image of ciliated protists. From[http://www.microscopy-uk.org.uk/mag/smallimag/2spiro.jpg]]]<br />
<br />
======Flagellates======<br />
<br />
'''Flagellates''' are one of the most commonly known protists. They are unicellular organisms that may be solitary, colonial, free living, or parasitic [24]. The hallmark feature of protists is that at some point in their life cycle, they possess a flagella. A flagellum is a long hair like structure that is used for locomotion, sensation, and sometimes predation [24]. The flagellum makes waves by whiplike lashing movements which propels the cell forwards. Flagellates also have a protective coating in the form of a thin pellicle to protect them from the environment [24]. <br />
<br />
[[Image:9703607_orig.jpg|frame|center|Figure 3.9 Illustration of flaggelates during different life cycle stages. From[http://diagnosticparasitology.weebly.com/uploads/3/9/5/4/3954522/9703607_orig.jpg]]]<br />
<br />
*'''Mastigophora:'''<br />
<br />
Mastigophora is a subphylum of flagellates. Being a member of the flagellates, their key feature is the flagellum. Their habitats include freshwater, soil, and can act as animal parasites as well [25]. They use pseudopodia, a long outward protrusion, to trap and funnel food from the environment into their cell bodies [25]. The Mastigophora are mainly known for their parasitism, which can take place in both humans and animals [25]. ''Typanosomes'' are an example of Mastigophora which causes African sleeping sickness [25]. ''Giardia lambli''a is another example that resides in the intestinal tract of warm-blooded animals and inflicts intestinal giardiases [25]. It is also a major contaminant of drinking water because it is resistant to chlorine, which is the most common water purifier [25]. Having a dormant cyst form also adds to its survival potential through filtration efforts [25].<br />
<br />
<br />
<br />
*'''Euglenids:'''<br />
<br />
Euglenids are one of the best known flagellates. They are found in freshwater and soil, as long as there are organic materials. They also participate in some symbiotic relationships with marine animals. Euglenid cells do not contain cell walls or other rigid membranes [26]. This gives the cell tremendous flexibility and allows it to change its shape to easily navigate through muddy terrain. Euglenids have two flagella, one which creates locomotion and movement for the cell [26]. The other flagellum does not protrude from the cell and is contained in the cell body [26].<br />
<br />
======Amoebas======<br />
<br />
'''Amoebas'''<br />
<br />
Amoebae are single celled eukaryotes present in many different types of environments. They are scattered throughout a variety of eukaryotic lineages and therefore are not monophyletic [27]. Amoebae range in size from 5 micrometers to 3 mm and don’t have a defined shape, commonly recognized for being polymorphic. They are motile through the use of pseudopodia, which stretch and pull the cell along with it. The pseudopodia are also used for feeding. They are able to sense prey that can be engulfed and engulf them via phagocytosis. The amoeba’s main prey consists of bacteria, algae, and other protozoa [28]. The prey is moved around within the cell via food vacuoles, a feature of amoebae [28]. Another key characteristic of amoebae are the large contractile vacuoles inside the cell. The purpose of the contractile vacuole is to osmoregulate by pumping excess water out of the cell. In times of turmoil, amoebae have an encysted form that helps them get through the tough times. This form is useful when there is low nutrient availability to limit energy consumption. There are two main forms an amoeba can be characterized as. They can either be testate or nontestate. Testate amoeba produce shells, or “tests”, that help identify their species since each species has a unique shell.<br />
<br />
[[Image:Amoeba_(PSF).png|frame|center|Figure 3.10 Amoeba morphology. From[https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Amoeba_(PSF).png/230px-Amoeba_(PSF).png]]]<br />
<br />
=====Slime Molds=====<br />
<br />
'''Slime molds''' were once classified as fungi, but have now been placed in their own phylogenetic groups. Slime molds are single cells that can live independently, but aggregate to form multicellular reproductive structures when necessary [29]. The fruiting body releases spores which germinate into new cells. Slime molds feed off of bacteria and are most commonly found in forests. They feed off of decaying vegetation as well so they can be seen on rotting logs and leaves.<br />
<br />
[[Image:28-30-cellslimemoldlife-l.jpg|frame|center|Figure 3.11 Illustration of slime mold life cycle. From[https://lichencolony.files.wordpress.com/2006/06/28-30-cellslimemoldlife-l.jpg]]]<br />
<br />
==Current Research== <br />
<br />
'''Bacteria:''' To showcase the great diversity of soil bacterial environments, cyanobacteria have been studied in both desert and polar regions. Cyanobacteria can survive in extreme conditions likely because of their long evolutionary past.[16] Dr. Patzelt and his colleagues studied the diverse cyanobacteria residing in the Atacama desert, one of the driest parts of the world. The diverse taxa found in the Atacama desert can withstand prolonged periods of extreme desiccation.[16] The cyanobacteria dominate the soil crusts, affecting soil stability, soil structure and soil fertility.[16] Cyanobacteria inhabiting the Antarctic and Arctic regions, show similar adaptations to extreme environments as the cyanobacteria found in the desert. The polar cyanobacteria are particularly adapted to high altitudes.[17] They can withstand high ultraviolet radiation, desiccation, and repeated freeze-thaw cycles.[17] The autotrophic cyanobacteria supports heterotrophic microbes, providing an important ecosystem service in an environment with low microbial activity.[17]<br />
<br />
'''Archaea:''' In 150 soil samples acquired from North and South America, about 150,000 species were observed.[45] Of these, over 2,500 were identified as archaea based on their ssu rRNA.[45] The archaeal species were further analyzed to understand their role in the soil environment. Of the archaeal groups, ''Crenarchaeota'' and ''Euryarchaeota'' were found.[45] Bates stated that, “Across the non-experimental soils examined the soil C:N ratio was the single best predictor of archaeal relative abundances” due to their influences in the nutrient cycles.[45]<br />
<br />
'''Fungi:''' Fungi have been in the public eye for a while now due to the many different types of secondary metabolites they produce. Some produce bioactive compounds that can inhibit growth of protozoa, bacteria, parasites, insects, and even other fungi. A large area of investigation is the uses of these chemicals for human interests in use from medicine to plant and animal toxins [52].<br />
<br />
'''Protozoa:''' It’s known that Protozoa stimulate plant growth in different ways. It’s suspected that the Protozoa take part in the microbial loop which is responsible for the nutrient production for plants [19]. However, new developments have shown that the Protozoa themselves are responsible for the nitrogen mineralization and that other bacteria have no effect on the plant’s nitrogen sources [19].<br />
<br />
==References==<br />
<br />
1. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). Principles and Applications of Soil Microbiology. New Jersey: Pearson Education Inc.<br />
<br />
2. Ingham, Elaine R. Ingham R. "Chapter 4: SOIL FUNGI." Soil Biology. Natural Resources Conservation Service Illinois, n.d. Web. 9 Feb. 2016<br />
<br />
3. Reid, Greg, and Percy Wong. "SOIL BACTERIA AND FUNGI - NEW SOUTH WALES." Soil Bacteria and Fungi. New South Wales Department of Primary Industries, 2005. Web. 11 Feb. 2016.<br />
<br />
4. "Fungi." Microbiology Online. Microbiology Society, n.d. Web. 11 Feb. 2016.<br />
<br />
5. Tortora, G.J., Funke, B.R., Case, C.L. (2012). “Microbiology an Introduction.” 11th ed. Pearson Benjamin Cummings, San Francisco.<br />
<br />
6. Rizzo, D. “Intro to Fungi.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
7. Rizzo, D. “Ascomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
8. Rizzo, D. “Basidiomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
9. Pegg G.F., Brady B.L. “Verticillium Wilts.” New York, CABI Publishing 2002. Google Books. Web. 11 Feb. 2016. http://books.google.com<br />
<br />
10. Hebert, Paul. "What Is a Protist / What Are Protozoa? - Encyclopedia of Life." Encyclopedia of Life. N.p., n.d. Web. 11 Feb. 2016.http://eol.org/info/456<br />
<br />
11. "MicrobeWorld." Protista. N.p., n.d. Web. 11 Feb. 2016. http://www.microbeworld.org/types-of-microbes/protista<br />
<br />
12. Madigan, M.T., Martinko, J.M. (2006). Brock Biology of Microorganisms. New Jersey: Pearson Prentice Hall.<br />
<br />
13. Roesch, L.F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H.; Camargo, F. A. O.; Farmerie, W. G.; Triplett, E. W.(2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1(4).283-290. <br />
<br />
14. Amann, R.I, Ludwig, W., Schleifer, K.H.(1995).Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology and Molecular Biology Reviews. 59(1). 143-169. <br />
<br />
15. Geers, D., Cohan, F.M., Lawrence J.G., Spratt, B.G., Coenye, T. Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005). Opinion: Re-evaluating prokaryotic species. Nature Reviews Microbiology. 3(9). 733-739.<br />
<br />
16. Patzelt, D.J., Hodac, L., Friedl, T., Pietrasiak, N., Johansen, J.R. (2014). Biodiversity of soil cyanobacteria in the hyper-arid Atacama Desert, Chile. Journal of phycology. 50(4). 698-710. <br />
<br />
17. Makhalanyane, T. P., Valverde, A., Velázquez, D., Gunnigle, E., Van Goethem, M. W., Quesada, A., & Cowan, D. A. (2015). Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats. Biodiversity and Conservation, 24(4), 819-840.<br />
<br />
18. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist>.<br />
<br />
19. Ekelund, Flemming; Saj, Stephane; Vestergård, Mette; Bertaux, Joanne; Mikola, Juha. (2009). “The “soil microbial loop” is not always needed to explain protozoan stimulation of plants”. Soil Biology & Biochemistry. Vol. 41 Issue 11, p2336-2342, 7p.<br />
<br />
20. Bonkowski, Michael. "Protozoa and Plant Growth: The Microbial Loop in Soil Revisited." New Phytologist New Phytol 162.3 (2004): 617-31. Web.<br />
<br />
21. Hoorman, James. "The Role of Soil Protozoa and Nematodes." Fact Sheet (n.d.): n. pag. Ohio State University, 2011. Web.<br />
<br />
22. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist<br />
<br />
23. Lynn, Denis H(Apr 2012) Ciliophora. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001966.pub3]<br />
<br />
24. "flagellate". Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc., 2016. Web. 23 Feb. 2016 <http://www.britannica.com/science/flagellate>.<br />
<br />
25. "Mastigophora." World of Microbiology and Immunology. 2003. Encyclopedia.com. 23 Feb. 2016<http://www.encyclopedia.com>.<br />
<br />
26. “Plant Life." : Euglenoids. N.p., n.d. Web. 23 Feb. 2016. <http://lifeofplant.blogspot.com/2011/04/euglenoids.html><br />
<br />
27. Parales, R.E. and Martin, M. (2015) Microbial Diversity Laboratory Manual, MIC 105L, Winter 2015. Department of Microbiology and Molecular Genetics, College of Biological Sciences, The University of California, Davis.<br />
<br />
28. Arnold, Paul. "What Does an Amoeba Eat? Plus Other Ameoba Info and Questions." Bright Hub. N.p., n.d. Web. 04 Mar. 2016.<br />
<br />
29. "MicrobeWorld." Slime Molds. N.p., n.d. Web. 24 Feb. 2016. <http://www.microbeworld.org/types-of-microbes/protista/slime-molds><br />
<br />
30. Leeuwenhoek., A. V. (2009, November 18). One gram of soil: A microbial biochemical gene library. Retrieved March 13, 2016, from http://www.ncbi.nlm.nih.gov/pubmed/19921459 <br />
<br />
31. Coleman, D. C., Crossley, D. A. & Hendrix, P. F. "Soil food webs: Detritivory and microbiology in soils," in Fundamentals of Soil Ecology, 2nd ed. (Elsevier, 2004) 236-241.<br />
<br />
32. Welcome to Agriinfo.in. (n.d.). Retrieved February 21, 2016, from http://agriinfo.in/?page=topic&superid=5&topicid=172 <br />
<br />
33. Gouthro, T., & Rice, D. (1987, December 15). Interaction Terminology. Retrieved February 21, 2016, from http://www.rpi.edu/dept/chem-eng/Biotech-Environ/MixCul/ecodefn.htm <br />
<br />
34. AMENSALISM. (n.d.). Retrieved February 21, 2016, from https://biostuds.wikispaces.com/AMENSALISM <br />
<br />
35. Natural Resources Conservation Service. (n.d.). Retrieved March 10, 2016, from <br />
http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053865 <br />
<br />
36. Ecological Linkages Between Aboveground and Belowground Biota. (n.d.). Retrieved March 10, 2016, from http://science.sciencemag.org/content/304/5677/1629 <br />
<br />
37. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf<br />
<br />
38. Kingdom Archaea. (n.d.). Retrieved March 10, 2016, from http://plantphys.info/organismal/lechtml/archaea.shtml <br />
<br />
39. What are Archaea? - Encyclopedia of Life. (n.d.). Retrieved March 10, 2016, from http://eol.org/info/457 <br />
<br />
40. Flagellum. (n.d.). Retrieved March 10, 2016, from http://www.newworldencyclopedia.org/entry/Flagellum#Archaeal_flagellum <br />
<br />
41. Archaea: Morphology. (n.d.). Retrieved March 10, 2016, from http://www.ucmp.berkeley.edu/archaea/archaeamm.html <br />
<br />
42. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf <br />
<br />
43. Archaea. (n.d.). Retrieved March 10, 2016, from http://www.eoearth.org/view/article/150172/ <br />
<br />
44. Binary Fission: Cell Division & Reproduction of Prokaryotes. (n.d.). Retrieved March 10, 2016, from http://www.scienceprofonline.com/microbi <br />
<br />
45. Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2010, November 18). Examining the global distribution of dominant archaeal populations in soil. Retrieved February 21, 2016, from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105767/<br />
<br />
46. Scow, K. M. "Lecture 1 Part 1." Lecture, Davis.<br />
<br />
47. Rizzo, D. "Lecture 1." Lecture, Davis.<br />
<br />
48. Rizzo, D. "Lecture 3." Lecture, Davis.<br />
<br />
49. C.J. Alexopoulos & C. W. Mims, Introductory Mycology 3rd edition. 1979. Wiley NY. Web accessed Mar 8, 2016 from http://www.ucmp.berkeley.edu/fungi/fungimm.html<br />
<br />
50. Rizzo, D. "Lecture 2." Lecture, Davis.<br />
<br />
51. Ingham, E. “Chapter 4: Soil Fungi” (2016) Oregon State University. Retrieved Feb. 20, 2016, from http://extension.illinois.edu/soil/SoilBiology/fungi.htm<br />
<br />
52. Keller, N., Turner, G., Bennett, J. “Fungal Secondary Metabolism- from Biochemistry to Genomics.” 2005 Nature Reviews Microbiology p/ 937 to 947.</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Introduction_to_Organisms&diff=128507
Introduction to Organisms
2017-03-05T23:12:29Z
<p>Kmscow: /* Protista */</p>
<hr />
<div>==Introduction== <br />
The soil ecosystem in an important environment that allows both plants and animals to survive, grow and reproduce. The significance of the soil as an ecosystem is at times overlooked despite its major contributions to the environment. The [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] is a complex and varied microbial habitat.[1] The plants and organisms inhabiting the soil contribute to its thriving diversity. Soil life is diverse in morphology, metabolism, size, and many other characteristics. It is believed that “there is sufficient [microbial] DNA in 1 g of soil to extend 1,598km.” [30] Soil is a heterogeneous environment with various zones of rhizosphere, aggregates, organic matter and animal residues.[31] Given each zone is a small component of the larger soil ecosystem, rhizosphere accounts for only 5 to 7 percent of the soil environments but contains over “70 percent of the bacterial- and fungal-feeding nematodes.”[31] <br />
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Since, all three domains of life: archaea, bacteria and eukarya, inhabit the soil environment it is difficult to observe each microbe individually within the soil ecosystem.Only a few representative groups of each domain will be discussed to provide examples of the roles these organisms play in soil. This page attempts to outline the major microbial groups within the diverse soil environment.The interactions between soil microbes amongst the soil microbial diversity. The concept of survival of the fittest is seen in the soil food web, which allows only a selective few with the correct nutrients to thrive in a soil environment. The interactions of soil microbes is not only a part of nature but it also only selects those organisms that are fit for survival, growth and reproduction. The soil food web and symbiotic relationships are used to explain the dynamic interactions between soil organisms.<br />
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==Soil Food Web and Microbial Interactions== <br />
<br />
To survive in a soil environment, an organism must be able to adapt to changing environments and organism interactions. The interactions seen between organisms allows only the fittest to survive, thrive, grow and reproduce in the soil. The only type of interaction shown in (Figure 2.1) is predation. Other common interactions in the soil environment are: <br />
<br />
:[[Image:soil_foodweb72.jpg|frame|center|Figure 2.1 Soil Food Web. From[http://www.exploringnature.org/graphics/foodwebs/soil_foodweb72.jpg]]]<br />
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<br />
'''I. Commensalism:''' Organism (A) benefits from the presence of Organism (B) while (B) is unaffected by the presence of (A).[32]<br />
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'''II. Mutualism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) and becomes a necessary association for each other’s survival. [32] [33]<br />
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'''III. Synergism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) but the relationship is not necessary for survival.[33]<br />
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'''IV. Competition:''' Depending on the organisms this interaction benefits organisms who can readily adapt to the environment and overcome any obstacles needed to survive, grow and reproduce.[33]<br />
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'''V. Amensalism:''' An interaction in which Organisms (A) and (B) develop a partnership where (B) is unaffected by (A) but organism (A) is negatively affected by (B).[34]<br />
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'''VI. Parasitism:''' Organism (A) benefits from Organism (B) but Organism (B) does not benefit positively from Organism (A). <br />
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'''VII. Predation:''' “An interaction between organisms in which one benefits and one is harmed based on the ingestion of the smaller sized organism, the prey, by the larger organism, the predator.”[33]<br />
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<br />
<br />
The soil food web consists of microbes which play an important role in maintaining the complexity of the soil environment. The interactions observed in the food web are not only based on predation, which directly affects the nutrient cycling and degradation of pollutants, but also the formation of aggregates.[35] The production of specific nutrients, such as ammonium created by microbial metabolic functions, helps to enrich the the soil for plant use.[35] Soil organism activity, along with the presence of soil organic matter, create stabilizing aggregates.[35] The hyphae within the soil environment and the microbes help form large, stable aggregates in the soil habitat.[35] The biodiversity in the soil plays a pivotal role in degrading pollutants, and also prevents pathogens from inhabiting the soil environment through competition.[35] The food web in the soil environment is necessary to maintain the soil nutrients, biological activity, and detoxifying pollutants. Thus, it directly maintains cultivation, productiveness and prosperity of the soil. <br />
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In (Figure 2.1), all three domains, Archaea, Bacteria, and Eukarya, are represented in the soil food web. If one takes a closer look at the figure, the soil food web is not only dependent on small and large microbes but also dead organic matter and plant roots. Dead and living matter in the soil environment contribute to maintaining the food web. Plant residues also are apart of the soil food web. They contribute to the soil’s carbon source.[35] The plant residues either, release carbon dioxide to the environment, or contribute to the soil organic matter. Soil organic matter contributes to soil’s richness and helps to form aggregates.[35] The main focus in the image above is the diversity of organisms, both in domains and in size. The larger organisms are usually the predators. The smaller organisms eventually fall prey, due to their limited mobility, respiration, and size. The eukarya and small bacteria are apparent figures seen in the figure above, but archaea also contribute to the food cycle as they break down ammonia for plants to use. [35]<br />
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The notable interactions of life that take place in the soil environment is evident both below-ground level, as seen in the figure 2.1, but also in the above-ground level.[36] Worms also impact the soil food web, acting as both drivers of the food web both belowground and aboveground.[36]<br />
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==3 Domains==<br />
[[Image:Big_Tree_Bold_Letters_white.png|frame|center|Figure 3.1 Phylogenetic Tree of the 3 Domains. From[http://phylogenomics.blogspot.com/2014_02_01_archive.html]]]<br />
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===Carl Woese and Phylogeny===<br />
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[[Image:Carlwoese1_0565_b.jpg|frame|center|Figure 3.2 Carl Woese. From[http://ofbacteriaandmen.blogspot.com/2013/01/the-new-biology-of-carl-woese.html]]] <br />
<br />
Carl Woese (Figure 3.2) was an American microbiologist famous for pioneering the technique of phylogenetic taxonomy through use of a 16S (for prokaryotic) and 18S (for eukaryotic) ribosomal RNA, also known as small subunit ribosomal RNA [46]. This refined Linnaean classification, taking out the guesswork classification by using a gene that was present in every living organism- the small subunit ribosomal RNA. This method of classification is comprehensive because all organisms possess this form of genetic material. Ssu rRNA is sequenced because the genes are highly conserved. Due to their functional constancy, some have variable regions to differentiate organisms, and are easy to sequence. This technique also elucidated the tree of life, which shows the three domains of microbial lineage diversity: Bacteria, Archaea, and Eukarya. DNA can be compared using a sample database that allows identification of unknown organisms to a species level.<br />
<br />
===Domain Bacteria===<br />
<br />
====Introduction to Bacteria==== <br />
Bacteria are single celled prokaryotic organisms that lack membrane bound organelles. They are involved in many important processes within the soil such as decomposition, [https://microbewiki.kenyon.edu/index.php/Bioremediation bioremediation], symbiosis and biological transformation of nutrients. They are present in all terrestrial soil environments.[1] Soil is a heterogenous environment that varies in moisture content, temperature, oxygen requirements, carbon source and many other bacterial growth conditions. Those wide ranging growth factors account for the enormous diversity in soil bacteria populations. One gram of soil can contain between 26,000 to 52,000 different bacterial species.[13] In the entire microbial world, only about 1 percent of bacterial species can be cultured under laboratory conditions which leaves an immense number of bacterial species yet to be described. [14]<br />
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Classification based on phenotypic characteristics, such as cellular morphology, metabolism, gram staining, oxygen requirements, carbon source and other traits, was used more readily before modern DNA sequencing. But, phenotypic classification is still used and Bergey’s Manual of Systematic Bacteriology is the most widely used source for determining species based on characteristic species traits.<br />
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Traditional species definitions are not as useful in bacteria. OTUs, or operational taxonomic units, based on DNA sequencing similarity, are more applicable to bacteria. Typically, those bacteria with 97 percent similar DNA sequence are classified within the same OTU.[15] The 16S small subunit ribosomal RNA is used to substantiate phylogenetic relationships between different bacterial groups.<br />
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====Morphology====<br />
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Bacterial cells measure approximately 1μm wide and 1-5μm long.[12] They are smaller than eukaryotic microbes.Due to their small size, bacteria can more easily adapt to changing soil environments than larger eukaryotes.[1] Most bacteria are singled celled, but actinomycetes grow in branching filaments. There are many different bacterial cell shapes. The most common are bacilli (rods), cocci (spheres), spirilla (spirals) and actinomycete (filaments).<br />
[[Image:bacteria_sizes.jpg|frame|center|Figure 3.3 Common cell shapes cocci, bacillus, and spirilla and relative sizes. From[http://www.ppdictionary.com/gnbac.htm]]]<br />
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'''Flagella''' - There are many different types and different arrangement of flagella. Movement in soil environments is dependent on soil moisture content. Though movement in soil is limited, flagellar function is important to allow bacteria to find more favorable microsites.[1]<br />
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'''Cell membrane''' - The cell membrane encloses the cytoplasm. It is semi-permeable phospholipid bilayer that regulates transport of nutrients into the cell and waste products out of the cell.<br />
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'''Cell wall''' - Most bacteria have a rigid cell wall surrounding the cell membrane which protects the cell from osmotic lysis. The cell wall is made of a crosslinked polysaccharide, called peptidoglycan, that is found only in bacteria.[1] The cell wall gives the cell shape and structure, but it is porous enough to permit small water soluble molecules to flow through to the cell membrane surface.[1]<br />
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*'''Gram positive''' bacteria have a thick cell wall made of several layers of peptidoglycan. The cell wall is the outermost structure, as they do not have an outer membrane. The thick cell wall structure make gram positive bacteria more resilient to osmotic shock. Gram positive bacteria can tolerate 5 to 10 times more turgor pressure than gram Gram negative bacteria.[1] Teichoic acids in the cell wall may also help to bind to cationic nutrients in soil surroundings.[1] <br />
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*'''Gram negative''' bacteria have a thin cell wall surrounded by an outer membrane made of phospholipids and lipopolysaccharides. Polysaccharides of the outer membrane interact with surrounding cations and are involved in attachment of bacteria to soil particles. [1] Periplasm is a gel like substance that occupies the space between the outer membrane and the cell wall of gram negative bacteria.[1] The outer membrane and periplasmic space is thought to provide protection from environmental toxins.[1] Proteins within the periplasm are thought to begin the process of catalyzing hydrolysis of organic and toxic substances.[1] <br />
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[[Image:gramposnegmembrane.jpg|frame|center| Figure 3.4 Illustration of Gram positive and Gram negative cell wall structures. From[http://micro.digitalproteus.com/morphology2.php]]]<br />
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'''Endospores''' are made by ''Bacillus'' and ''Clostridium'' in response to environmental stress.[1] Endospores are extremely resistant structures that can withstand extreme temperatures up to 150℃.[12] They can also withstand extreme pressure, desiccation, radiation, pH and chemicals.[12] The endospore protects the bacterial DNA until environmental conditions are more favorable and germination can proceed. Soil is the most common habitat for endospore forming bacteria.[12]<br />
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'''Extracellular polymers''' - Many bacteria secrete a slime layer or capsule made of polysaccharides or glycoproteins.[1] The outer polysaccharide coating of bacteria helps in attachment to surfaces and the formation of biofilms.[1] Bacterial capsule secretions play a big role in soil aggregation and soil structure.[1] When the carbon to nitrogen ratio within soils is high, microbes secrete the excess carbon as extracellular polysaccharides.[1]<br />
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====Reproduction==== <br />
Most bacteria reproduce by binary fission.[12] The bacterial cell expands to twice the original cell size, duplicates the bacterial DNA and pinches off, producing two daughter cells. Each resultant daughter cell is a clone of the parent cell. Prokaryotic Archaea also reproduce by binary fission.<br />
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*'''Spore formation:''' Actinomycetes are a large group of filamentous bacteria, primarily found in soil.[1] Actinomycetes are morphologically similar to fungi. Actinomycetes form long filaments called hyphae. Unlike most bacteria, the majority of actinomycetes reproduce using asexual spores called conidia.[1] Though they share many characteristic with fungi, actinomycetes are still prokaryotes. They are smaller than fungi and the cell wall contains peptidoglycan.[1] Actinomycetes break down a wide variety of organic compounds and play an important role in organic matter decomposition. [1] ''Streptomyces'', a subgroup within actinomycetes, produce geosmin, which gives soil the characteristic earthy smell.[12]<br />
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====Metabolism==== <br />
<br />
Along with archaea, bacteria are the most metabolically diverse and employ many different nutritional strategies.[1]<br />
*Heterotrophs - Most bacteria are heterotrophic, obtaining carbon from preformed organic substances. [1] <br />
*Autotrophs - Carbon dioxide serves as the main source of carbon. Some cyanobacteria, nitrifying and sulfur-oxidizing bacteria are autotrophs.[1]<br />
*Organotrophs - Most bacteria obtain electrons from organic substances.[1]<br />
*Lithotrophs - Some cyanobacteria, nitrifying bacteria and sulfur-oxidizing bacteria obtain electrons from inorganic substances.[1]<br />
*Phototrophs - Cyanobacteria use light as the main source of metabolic energy.[1]<br />
*Chemotrophs - All other nonphotosynthetic bacteria do not rely on light for metabolic energy.[1]<br />
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====Contributions to the Cycle==== <br />
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Bacteria play a significant role in the cycling of a wide range of elements.<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Carbon_cycle '''Carbon Cycle:'''] <br />
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*'''Carbon Assimilation''' is the process of fixing carbon dioxide into organic forms. Carbon fixation is performed by autotrophic bacteria, such as cyanobacteria.[1] Chemoautotrophic nitrifying bacteria, such as ''Nitrobacter, Nitrosospira'' and ''Nitrosomonas'', also fix carbon.[1] Sulfur oxidizing bacteria, such as ''Thiobacillus'', fix carbon as well.<br />
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*'''Carbon Mineralization''' results from microbial decomposition of organic carbon compounds into inorganic forms. As the organic carbon substances, like plant matter, are decomposed, inorganic carbon dioxide is produced. Most bacteria are heterotrophs that perform carbon mineralization. When microorganisms die, they are decomposed by successive microbial generations. Peptidoglycan, the main component of bacterial cell walls, is utilized as a polysaccharide substrate by other heterotrophic soil microbes.[1]<br />
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*'''Methanogenesis''' - Methanogenic bacteria produce methane from the reduction of carbon dioxide. They are all strict anaerobes that use carbon dioxide for the carbon source.[1] They can all use hydrogen as a source of energy and electron donor. [1]<br />
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[https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle '''Nitrogen cycle:''']<br />
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*'''Nitrogen fixation:''' ''Azotobacter'' is a free living nitrogen fixing bacteria.[1] ''Rhizobium'' lives in a mutualistic relationship with plants by fixing nitrogen within root the nodules of legumes.[1] ''Anabaena'' and ''Nostoc'' have specialized heterocyte structures where nitrogen fixation occurs.[1] <br />
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*'''Nitrification:''' Nitrifying bacteria, such as ''Nitrobacter, Nitrosospira,'' and ''Nitrosomonas'', oxidize ammonium to nitrate.[1] <br />
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*'''Denitrification:''' ''Alcaligenes, Flavobacterium'', and ''Pseudomonas'' are common soil denitrifying bacteria.[1]<br />
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===Domain Archaea===<br />
<br />
====Introduction to Archaea====<br />
<br />
Vladimir Vernadsky decided, in 1926, that only two domains of life existed on Earth, Bacteria and Eukarya.[37] About 50 years later in 1977, Carl Woese and George Fox theorized that part of the bacterial domain possed multiple dissimilarities from bacteria and recognized it to be another domain of life, now called Archaea.[38] Woese and Fox’s theory regarding the differences of archaea were confirmed in 1990’s through the use of 16S rRNA and 18S rRNA.[38] <br />
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Despite the strongly held belief, in the 1990s, that archaea only inhabited extreme environments, recent discoveries have suggested their presence in abundant numbers all throughout the Earth. It is suggested that Archaea play notable roles in maintaining nutrient cycles.[37] Various methods of research, such as cultivation, culture-independent techniques and isotope-based methods, have facilitated the study of domain Archaea in carbon and nitrogen cycling. [37]<br />
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The use of genomic and biochemical data has permitted the study of archaeal structure.[37] Use of these research methods has shown that domain archaea and domain bacteria differ in cell wall characteristics yet, share various ways to transfer genetic information by replication and transcription from their common ancestor, Eukarya.[37] As of 2012, 116 genera of Archaea have been observed which consists of 450 species. Most of the archaeal species in these genera remains uncultivated, known only through its gene sequences and molecular surveys.[37]<br />
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====Morphology==== <br />
Archaea are characterized by various cell sizes. They are most commonly found to be small organisms ranging from “0.1 to 15 μ diameter and up to 200 μ long.”[38] The shape of many archaea are similar to bacteria, including bacillus, cocci, spirilla and “plate-like forms.” [38] Their cell membranes have ether linked lipids with no periplasmic space, similar to gram-positive bacteria, and contain no intracellular organelles.[39]<br />
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'''Flagella:''' Most motile archaea inhabit a motor rotary system that allows it to move its flagella through the chemical gradient similar to bacteria.[39] Despite its similarity in function and source of energy required for motility, the flagella of both archaea and bacteria differ in structure.[39] Archaeal flagella gets the energy for its movement by ATP and is composed of dependent filaments that rotate singularly. [40] Archaeal flagella are known to be thinner than bacteria flagellin.[40] Since, the archaeal common ancestor is not bacteria but eukarya, convergent evolution is a plausible explanations for the differences between bacterial and archaeal flagellin. [40]<br />
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'''Membranes:''' Archaea have a cell membrane that protects the cytoplasm and the nucleic acids from the environment. The archaeal cell membrane has a lipid bilayer with glycol-ether lipids that are more stable than ester linkages and help some archaea that live in extreme environments to withstand such conditions.[39] Most archaeal species are surrounded by a cell wall which protects the cell membrane and maintains the archaeal structure.[41]<br />
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====Reproduction====<br />
Archaeal organisms reproduce by binary fission since they do not have nucleases thus, the DNA chromosome in a Archaeal organism replicate, separate and create two daughter cells.[43] The process of binary fission can be seen in Figure (3.5) process begins the parent cell duplicating the DNA. The DNA material then goes to the sides of the cell where an invagination to the cell occurs allowing the cell to become two individual cells. Binary fission is a very fast reproduction process, that allows archaeal organisms to grow at an exponential rate.[44]<br />
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[[Image:WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg|frame|center|Figure 3.5 Illustration of binary fission. From[https://d2jmvrsizmvf4x.cloudfront.net/WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg]]]<br />
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====Metabolism==== <br />
Archaea share similar metabolic characteristics to bacteria. The metabolic pathways taken by all archaea shown in the (Figure 3.6) demonstrates the great diversity and variation amongst archaea. [38] The kinds of archaea that are seen in the environment and the metabolic pathways taken by some can be summarized in the image. <br />
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*Photoautotrophs: use light as an energy source and carbon dioxide as the carbon source with the help of the Calvin Cycle.[38]<br />
*Chemoautotrophs: use inorganic chemicals as their energy source and carbon dioxide as carbon source. <br />
*Chemoheterotrophs: take organic chemicals as energy source and organic chemicals as carbon source. The pathways taken by chemoheterotrophs varies from respiration by the Krebs Cycle to fermentation. [38]<br />
*Photoheterotrophs: use light as their energy source and organic chemicals as their carbon source. <br />
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Most archaea inhabiting in the soil environment are major contributors to the biogeochemical cycles.<br />
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[[Image:2000px-Troph_flowchart.svg.png|thumbnail|center|Figure 3.6 Flowchart showing different metabolic pathways. From[https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Troph_flowchart.svg/2000px-Troph_flowchart.svg.png]]]<br />
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====Contributions to the Cycle====<br />
Archaea play a significant role in the nutrient cycles that take place in the ecosystem as they account for about 1-5% of all the prokaryotes present in the soil environment.[42]<br />
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'''Carbon Cycle:''' Archaea have an important role in the carbon cycle that takes place specifically in methane production, carbon mineralization and carbon assimilation all of all of which contribute to the soil’s carbon sink.[42] The carbon dense soil helps to make the soil organic matter rich and helps to form extracellular polymers which creates stable aggregates. For some microbes, an electron acceptor is need to carry out metabolic functions. [42] More info on [https://microbewiki.kenyon.edu/index.php/Carbon_cycle Carbon Cycle].<br />
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*'''Carbon Assimilation:''' Involves the transformation of inorganic carbon into organic carbon compounds. This process is commonly done by autotrophic phyla ''Crenarchaeota, Thaumarchaeota'', and ''Euryarchaeota'' that use carbon dioxide/ bicarbonate converting it to organic compounds.[42] Of the autotrophic lineages observed in carbon assimilation the ''Thaumarchaeota'' are strict autotrophs, the ''Euryarchaeota'' and ''Crenarchaeota'' are facultative autotrophs and the ''Halobacteriales'' and ''Thermococcales'' are obligate heterotrophs.[42] <br />
<br />
*'''Carbon Mineralization:''' The process that converts organic carbon into the oxidized inorganic carbon, carbon dioxide is commonly done by both aerobes and anaerobes.[42] The heterotrophic microbes that use organic compounds as energy to oxidize the carbon source include, methanogens and methane-oxidizing archaea belonging to the phyla ''Euryarchaetota'', and ''Crenarchaeota''.[42] <br />
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*'''Methanogenesis:''' production of methane, a major greenhouse gas in the Earth’s atmosphere is commonly done by archaea upon reducing an oxidized compound.[42] The phyla ''Euryarchaeota'' is the only phyla that consists of archaea that produce methane all of which form five class: ''Methanopyri, Methanococci, Methanobacteria, Methanomicrobia'' and ''Thermoplasmata''.[42] Methanogens are commonly found in anaerobic and aerobic conditions such as bodies of water, aerated soils and oxygenated waters.[42]<br />
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'''Nitrogen Cycle :''' Archaea play a pivotal role in the Nitrogen cycle and help create nitrogenous products for the plants and microbes. More info on [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle Nitrogen cycle].<br />
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*'''Nitrogen Fixation:''' Fixing nitrogen from the environment and converting it to organic nitrogen in the soil or to inorganic nitrogenous form since both organic and inorganic products are in short supply in the biosphere and are fixed by many archaeal organisms.[42] N2 fixation by the environment is usually done by three major archaeal classes ''Methanobactera, Methanococci'' and ''Methanomicrobia''.[42] <br />
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*'''Nitrification:''' Converting the ammonia (NH4+) in the soil to nitrite (NO2-) produces nitrate (NO3-) as an intermediate. [42] The transformation of ammonia to first nitrate then to nitrite is a two step process that is done by different microbes. [42] Most common organisms involved in nitrification include ammonia-oxidizing archaea which are lithotrophic organisms mostly, of the ''Thaumarchaeota'' phylum from the archaea domain. <br />
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*'''Denitrification :''' The conversion of atmospheric N2 using the electron acceptor NO3- or NO2- creating the formation of nitric oxide, nitrous oxide and/or N2.[42] The formation of the end product N2 may not always be produced but other intermediates NO and N2O, greenhouse gases may be produced.[42] Of the archaeal organisms that have been studied in denitrification process is done by ''Pyrobaculum aerophilum'' which accepts both NO3- and NO2- as an electron acceptor producing a variety of products NO2-, NO, N20 and N2.[42]<br />
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===Domain Eukarya===<br />
<br />
====Fungi====<br />
<br />
=====Introduction=====<br />
<br />
'''Introduction'''<br />
<br />
Fungi comes from the ancient Greek word “sphongos” meaning sponge in reference to the mushroom cap [47]. Fungi have the general characteristics of being eukaryotic, heterotrophic, external absorbers of nutrients, containing a hyphal thallus, reproducing via spore, and being pleomorphic (producing several forms). Fungi are generally organoheterotrophs that can survive in low pH and stay active at low moisture content[46]. Fungi reside in the domain Eukarya with an estimated species of 1.5 million, and less than five percent of them have ever been described. The general phyla included within Kingdom Fungi include Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, Chytridiomycota, and Microsporidia [48].<br />
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[[Image:magical-kingdom-620.jpg|frame|center|Figure 3.7 Fungi phyla hierarchy. From.[http://www.motherjones.com/environment/2009/11/fungi-family-tree]]]<br />
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=====Morphology=====<br />
<br />
'''Morphology''' <br />
<br />
Fungi can be either unicellular (yeasts) or multicellular. All multicellular fungi are made up of small, filamentous particles called hyphae. Some hyphae have cross walls called septa, while others do not- this is a large basis of fungal identification. Fungal cells generally have multiple nuclei. Fungal cell walls are generally composed of chitin, a long carbohydrate polymer that adds rigidity and structural support to fungi [49]. <br />
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=====Reproduction=====<br />
<br />
'''Reproduciton'''<br />
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Fungal reproduction can occur either sexually or asexually.<br />
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'''Sexual reproduction''' can occur by homothallic or heterothallic mycelia.<br />
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'''Asexual reproduction''' can occur by fragmentation, budding, or by producing spores (the most common method). <br />
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*'''Spores:''' spores come in many different forms. One of the most well known are conidiospores, which are unicellular or multicellular spores that get released from the tip of the hyphae. <br />
<br />
'''Perfect fungi''' are those that can reproduce both sexually and asexually while imperfect fungi are those that can only reproduce asexually.<br />
<br />
*Sexual reproduction always includes the stages plasmogamy (fusion of two haploid cells), karyogamy (creation of a diploid zygote), and meiosis (gametes are created).<br />
<br />
=====Metabolism=====<br />
<br />
'''Metabolism'''<br />
<br />
Many different fungi display a myriad of metabolisms. There are primary metabolites that that help the fungi function properly, and secondary metabolites that are generally bioactive that are not the most pertinent to fungal growth (they can live without these). Secondary metabolites play a large role in chemistry today and can be manufactured into commonly used products such as new drugs. In general fungi are heterotrophic through release of extracellular enzymes into the neighboring environment to break complex molecules down into smaller ones. The materials are then absorbed and metabolized [50]. Fungi are sessile organisms that overcome their little to no movement through apical growth at the hyphal tip. Fungi are noted to grow almost everywhere on the Earth.<br />
<br />
=====Relevance to soil===== <br />
<br />
'''Relevance to soil'''<br />
<br />
Fungi include some of the most abundant biomass of microorganisms in numerous soils. They play an important role as decomposers within the soil food web through conversion of difficult to digest organic material into forms many other organisms can use [51]. Their hyphae can bind soil particles together and create aggregates that increase soil water holding capacity. They perform important functions from water dynamics to nutrient cycling and disease suppression. Soil fungi can be categorized into three different groups based on their actions: <br />
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*decomposers: that convert dead organic material into fungal biomass<br />
<br />
*mutualists: which colonize plant roots and help solubilize phosphorous and bring soil nutrients<br />
<br />
*pathogens/ parasites: which help control diseases in soil via trapping organisms such as nematodes [51]. <br />
<br />
Fungi are seen common in intensively managed agricultural soils due to tillage disrupting hyphae. Fungi also play a very important role in the [https://microbewiki.kenyon.edu/index.php/Rhizosphere_Interactions rhizosphere], the region of soil that is greatly influenced by the plant root system. This area of soil which is concentrated in plant roots and fungal hyphae is known to support greater microbial activity.<br />
<br />
=====Protozoans=====<br />
<br />
'''Protozoans'''<br />
<br />
In general, Protozoans range from 5 to 500 µm in diameter, making them significantly larger than bacteria [21]. They are abundantly located near the surface of the soil (15cm deep) where roots are plentiful [21]. Many protozoans have two life cycles. One is their active form where they are motile and feed on prey. The other is the cyst form where they produce a thick coating to protect them from the environment and can go dormant for years. The protozoa are divided into 4 major categories: the ciliates, the flagellates, the heliozoans, and the amoebas [10]. <br />
<br />
======Ciliates======<br />
<br />
'''Cilliates:'''<br />
This group, within protozoans, is fairly diverse. A common feature shared amongst all of its members is the presence of at least one cilia at any stage of its development [10]. The cilia is used for movement and other things such as predation (tentacles). For movement, they use the massive amounts of tiny cilia to create wave like currents to propel the cell forwards. Most ciliates also have toxicysts which are used to capture prey [10]. Some ciliates even have a symbiotic relationship with algae living inside of them [10]. The algae use the CO2 produced by ciliates and turn it into O2 that can then be reused by the ciliates [10]. They are found in a wide array of habitats ranging from freshwater and soil to the rumen of Animals [22]. They are present in almost anywhere that contains water [23]. They are unicellular heterotrophs so they feed on bacteria and algae in their environment. Ciliates are one of the top predators in the microbial food web and are hypothesized to have been a major predatory group before animals evolved [23]. Parasitic ciliates exist that can cause the death of animals and are increasingly becoming dangerous in water [23].<br />
<br />
[[Image:2spiro.jpg|frame|center|Figure 3.8 Microscope image of ciliated protists. From[http://www.microscopy-uk.org.uk/mag/smallimag/2spiro.jpg]]]<br />
<br />
======Flagellates======<br />
<br />
'''Flagellates''' are one of the most commonly known protists. They are unicellular organisms that may be solitary, colonial, free living, or parasitic [24]. The hallmark feature of protists is that at some point in their life cycle, they possess a flagella. A flagellum is a long hair like structure that is used for locomotion, sensation, and sometimes predation [24]. The flagellum makes waves by whiplike lashing movements which propels the cell forwards. Flagellates also have a protective coating in the form of a thin pellicle to protect them from the environment [24]. <br />
<br />
[[Image:9703607_orig.jpg|frame|center|Figure 3.9 Illustration of flaggelates during different life cycle stages. From[http://diagnosticparasitology.weebly.com/uploads/3/9/5/4/3954522/9703607_orig.jpg]]]<br />
<br />
*'''Mastigophora:'''<br />
<br />
Mastigophora is a subphylum of flagellates. Being a member of the flagellates, their key feature is the flagellum. Their habitats include freshwater, soil, and can act as animal parasites as well [25]. They use pseudopodia, a long outward protrusion, to trap and funnel food from the environment into their cell bodies [25]. The Mastigophora are mainly known for their parasitism, which can take place in both humans and animals [25]. ''Typanosomes'' are an example of Mastigophora which causes African sleeping sickness [25]. ''Giardia lambli''a is another example that resides in the intestinal tract of warm-blooded animals and inflicts intestinal giardiases [25]. It is also a major contaminant of drinking water because it is resistant to chlorine, which is the most common water purifier [25]. Having a dormant cyst form also adds to its survival potential through filtration efforts [25].<br />
<br />
<br />
<br />
*'''Euglenids:'''<br />
<br />
Euglenids are one of the best known flagellates. They are found in freshwater and soil, as long as there are organic materials. They also participate in some symbiotic relationships with marine animals. Euglenid cells do not contain cell walls or other rigid membranes [26]. This gives the cell tremendous flexibility and allows it to change its shape to easily navigate through muddy terrain. Euglenids have two flagella, one which creates locomotion and movement for the cell [26]. The other flagellum does not protrude from the cell and is contained in the cell body [26].<br />
<br />
======Amoebas======<br />
<br />
'''Amoebas'''<br />
<br />
Amoebae are single celled eukaryotes present in many different types of environments. They are scattered throughout a variety of eukaryotic lineages and therefore are not monophyletic [27]. Amoebae range in size from 5 micrometers to 3 mm and don’t have a defined shape, commonly recognized for being polymorphic. They are motile through the use of pseudopodia, which stretch and pull the cell along with it. The pseudopodia are also used for feeding. They are able to sense prey that can be engulfed and engulf them via phagocytosis. The amoeba’s main prey consists of bacteria, algae, and other protozoa [28]. The prey is moved around within the cell via food vacuoles, a feature of amoebae [28]. Another key characteristic of amoebae are the large contractile vacuoles inside the cell. The purpose of the contractile vacuole is to osmoregulate by pumping excess water out of the cell. In times of turmoil, amoebae have an encysted form that helps them get through the tough times. This form is useful when there is low nutrient availability to limit energy consumption. There are two main forms an amoeba can be characterized as. They can either be testate or nontestate. Testate amoeba produce shells, or “tests”, that help identify their species since each species has a unique shell.<br />
<br />
[[Image:Amoeba_(PSF).png|frame|center|Figure 3.10 Amoeba morphology. From[https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Amoeba_(PSF).png/230px-Amoeba_(PSF).png]]]<br />
<br />
=====Slime Molds=====<br />
<br />
'''Slime molds''' were once classified as fungi, but have now been placed in their own phylogenetic groups. Slime molds are single cells that can live independently, but aggregate to form multicellular reproductive structures when necessary [29]. The fruiting body releases spores which germinate into new cells. Slime molds feed off of bacteria and are most commonly found in forests. They feed off of decaying vegetation as well so they can be seen on rotting logs and leaves.<br />
<br />
[[Image:28-30-cellslimemoldlife-l.jpg|frame|center|Figure 3.11 Illustration of slime mold life cycle. From[https://lichencolony.files.wordpress.com/2006/06/28-30-cellslimemoldlife-l.jpg]]]<br />
<br />
==Current Research== <br />
<br />
'''Bacteria:''' To showcase the great diversity of soil bacterial environments, cyanobacteria have been studied in both desert and polar regions. Cyanobacteria can survive in extreme conditions likely because of their long evolutionary past.[16] Dr. Patzelt and his colleagues studied the diverse cyanobacteria residing in the Atacama desert, one of the driest parts of the world. The diverse taxa found in the Atacama desert can withstand prolonged periods of extreme desiccation.[16] The cyanobacteria dominate the soil crusts, affecting soil stability, soil structure and soil fertility.[16] Cyanobacteria inhabiting the Antarctic and Arctic regions, show similar adaptations to extreme environments as the cyanobacteria found in the desert. The polar cyanobacteria are particularly adapted to high altitudes.[17] They can withstand high ultraviolet radiation, desiccation, and repeated freeze-thaw cycles.[17] The autotrophic cyanobacteria supports heterotrophic microbes, providing an important ecosystem service in an environment with low microbial activity.[17]<br />
<br />
'''Archaea:''' In 150 soil samples acquired from North and South America, about 150,000 species were observed.[45] Of these, over 2,500 were identified as archaea based on their ssu rRNA.[45] The archaeal species were further analyzed to understand their role in the soil environment. Of the archaeal groups, ''Crenarchaeota'' and ''Euryarchaeota'' were found.[45] Bates stated that, “Across the non-experimental soils examined the soil C:N ratio was the single best predictor of archaeal relative abundances” due to their influences in the nutrient cycles.[45]<br />
<br />
'''Fungi:''' Fungi have been in the public eye for a while now due to the many different types of secondary metabolites they produce. Some produce bioactive compounds that can inhibit growth of protozoa, bacteria, parasites, insects, and even other fungi. A large area of investigation is the uses of these chemicals for human interests in use from medicine to plant and animal toxins [52].<br />
<br />
'''Protozoa:''' It’s known that Protozoa stimulate plant growth in different ways. It’s suspected that the Protozoa take part in the microbial loop which is responsible for the nutrient production for plants [19]. However, new developments have shown that the Protozoa themselves are responsible for the nitrogen mineralization and that other bacteria have no effect on the plant’s nitrogen sources [19].<br />
<br />
==References==<br />
<br />
1. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). Principles and Applications of Soil Microbiology. New Jersey: Pearson Education Inc.<br />
<br />
2. Ingham, Elaine R. Ingham R. "Chapter 4: SOIL FUNGI." Soil Biology. Natural Resources Conservation Service Illinois, n.d. Web. 9 Feb. 2016<br />
<br />
3. Reid, Greg, and Percy Wong. "SOIL BACTERIA AND FUNGI - NEW SOUTH WALES." Soil Bacteria and Fungi. New South Wales Department of Primary Industries, 2005. Web. 11 Feb. 2016.<br />
<br />
4. "Fungi." Microbiology Online. Microbiology Society, n.d. Web. 11 Feb. 2016.<br />
<br />
5. Tortora, G.J., Funke, B.R., Case, C.L. (2012). “Microbiology an Introduction.” 11th ed. Pearson Benjamin Cummings, San Francisco.<br />
<br />
6. Rizzo, D. “Intro to Fungi.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
7. Rizzo, D. “Ascomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
8. Rizzo, D. “Basidiomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
9. Pegg G.F., Brady B.L. “Verticillium Wilts.” New York, CABI Publishing 2002. Google Books. Web. 11 Feb. 2016. http://books.google.com<br />
<br />
10. Hebert, Paul. "What Is a Protist / What Are Protozoa? - Encyclopedia of Life." Encyclopedia of Life. N.p., n.d. Web. 11 Feb. 2016.http://eol.org/info/456<br />
<br />
11. "MicrobeWorld." Protista. N.p., n.d. Web. 11 Feb. 2016. http://www.microbeworld.org/types-of-microbes/protista<br />
<br />
12. Madigan, M.T., Martinko, J.M. (2006). Brock Biology of Microorganisms. New Jersey: Pearson Prentice Hall.<br />
<br />
13. Roesch, L.F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H.; Camargo, F. A. O.; Farmerie, W. G.; Triplett, E. W.(2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1(4).283-290. <br />
<br />
14. Amann, R.I, Ludwig, W., Schleifer, K.H.(1995).Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology and Molecular Biology Reviews. 59(1). 143-169. <br />
<br />
15. Geers, D., Cohan, F.M., Lawrence J.G., Spratt, B.G., Coenye, T. Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005). Opinion: Re-evaluating prokaryotic species. Nature Reviews Microbiology. 3(9). 733-739.<br />
<br />
16. Patzelt, D.J., Hodac, L., Friedl, T., Pietrasiak, N., Johansen, J.R. (2014). Biodiversity of soil cyanobacteria in the hyper-arid Atacama Desert, Chile. Journal of phycology. 50(4). 698-710. <br />
<br />
17. Makhalanyane, T. P., Valverde, A., Velázquez, D., Gunnigle, E., Van Goethem, M. W., Quesada, A., & Cowan, D. A. (2015). Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats. Biodiversity and Conservation, 24(4), 819-840.<br />
<br />
18. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist>.<br />
<br />
19. Ekelund, Flemming; Saj, Stephane; Vestergård, Mette; Bertaux, Joanne; Mikola, Juha. (2009). “The “soil microbial loop” is not always needed to explain protozoan stimulation of plants”. Soil Biology & Biochemistry. Vol. 41 Issue 11, p2336-2342, 7p.<br />
<br />
20. Bonkowski, Michael. "Protozoa and Plant Growth: The Microbial Loop in Soil Revisited." New Phytologist New Phytol 162.3 (2004): 617-31. Web.<br />
<br />
21. Hoorman, James. "The Role of Soil Protozoa and Nematodes." Fact Sheet (n.d.): n. pag. Ohio State University, 2011. Web.<br />
<br />
22. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist<br />
<br />
23. Lynn, Denis H(Apr 2012) Ciliophora. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001966.pub3]<br />
<br />
24. "flagellate". Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc., 2016. Web. 23 Feb. 2016 <http://www.britannica.com/science/flagellate>.<br />
<br />
25. "Mastigophora." World of Microbiology and Immunology. 2003. Encyclopedia.com. 23 Feb. 2016<http://www.encyclopedia.com>.<br />
<br />
26. “Plant Life." : Euglenoids. N.p., n.d. Web. 23 Feb. 2016. <http://lifeofplant.blogspot.com/2011/04/euglenoids.html><br />
<br />
27. Parales, R.E. and Martin, M. (2015) Microbial Diversity Laboratory Manual, MIC 105L, Winter 2015. Department of Microbiology and Molecular Genetics, College of Biological Sciences, The University of California, Davis.<br />
<br />
28. Arnold, Paul. "What Does an Amoeba Eat? Plus Other Ameoba Info and Questions." Bright Hub. N.p., n.d. Web. 04 Mar. 2016.<br />
<br />
29. "MicrobeWorld." Slime Molds. N.p., n.d. Web. 24 Feb. 2016. <http://www.microbeworld.org/types-of-microbes/protista/slime-molds><br />
<br />
30. Leeuwenhoek., A. V. (2009, November 18). One gram of soil: A microbial biochemical gene library. Retrieved March 13, 2016, from http://www.ncbi.nlm.nih.gov/pubmed/19921459 <br />
<br />
31. Coleman, D. C., Crossley, D. A. & Hendrix, P. F. "Soil food webs: Detritivory and microbiology in soils," in Fundamentals of Soil Ecology, 2nd ed. (Elsevier, 2004) 236-241.<br />
<br />
32. Welcome to Agriinfo.in. (n.d.). Retrieved February 21, 2016, from http://agriinfo.in/?page=topic&superid=5&topicid=172 <br />
<br />
33. Gouthro, T., & Rice, D. (1987, December 15). Interaction Terminology. Retrieved February 21, 2016, from http://www.rpi.edu/dept/chem-eng/Biotech-Environ/MixCul/ecodefn.htm <br />
<br />
34. AMENSALISM. (n.d.). Retrieved February 21, 2016, from https://biostuds.wikispaces.com/AMENSALISM <br />
<br />
35. Natural Resources Conservation Service. (n.d.). Retrieved March 10, 2016, from <br />
http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053865 <br />
<br />
36. Ecological Linkages Between Aboveground and Belowground Biota. (n.d.). Retrieved March 10, 2016, from http://science.sciencemag.org/content/304/5677/1629 <br />
<br />
37. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf<br />
<br />
38. Kingdom Archaea. (n.d.). Retrieved March 10, 2016, from http://plantphys.info/organismal/lechtml/archaea.shtml <br />
<br />
39. What are Archaea? - Encyclopedia of Life. (n.d.). Retrieved March 10, 2016, from http://eol.org/info/457 <br />
<br />
40. Flagellum. (n.d.). Retrieved March 10, 2016, from http://www.newworldencyclopedia.org/entry/Flagellum#Archaeal_flagellum <br />
<br />
41. Archaea: Morphology. (n.d.). Retrieved March 10, 2016, from http://www.ucmp.berkeley.edu/archaea/archaeamm.html <br />
<br />
42. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf <br />
<br />
43. Archaea. (n.d.). Retrieved March 10, 2016, from http://www.eoearth.org/view/article/150172/ <br />
<br />
44. Binary Fission: Cell Division & Reproduction of Prokaryotes. (n.d.). Retrieved March 10, 2016, from http://www.scienceprofonline.com/microbi <br />
<br />
45. Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2010, November 18). Examining the global distribution of dominant archaeal populations in soil. Retrieved February 21, 2016, from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105767/<br />
<br />
46. Scow, K. M. "Lecture 1 Part 1." Lecture, Davis.<br />
<br />
47. Rizzo, D. "Lecture 1." Lecture, Davis.<br />
<br />
48. Rizzo, D. "Lecture 3." Lecture, Davis.<br />
<br />
49. C.J. Alexopoulos & C. W. Mims, Introductory Mycology 3rd edition. 1979. Wiley NY. Web accessed Mar 8, 2016 from http://www.ucmp.berkeley.edu/fungi/fungimm.html<br />
<br />
50. Rizzo, D. "Lecture 2." Lecture, Davis.<br />
<br />
51. Ingham, E. “Chapter 4: Soil Fungi” (2016) Oregon State University. Retrieved Feb. 20, 2016, from http://extension.illinois.edu/soil/SoilBiology/fungi.htm<br />
<br />
52. Keller, N., Turner, G., Bennett, J. “Fungal Secondary Metabolism- from Biochemistry to Genomics.” 2005 Nature Reviews Microbiology p/ 937 to 947.</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Introduction_to_Organisms&diff=128506
Introduction to Organisms
2017-03-05T23:11:32Z
<p>Kmscow: /* Protozoans */</p>
<hr />
<div>==Introduction== <br />
The soil ecosystem in an important environment that allows both plants and animals to survive, grow and reproduce. The significance of the soil as an ecosystem is at times overlooked despite its major contributions to the environment. The [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] is a complex and varied microbial habitat.[1] The plants and organisms inhabiting the soil contribute to its thriving diversity. Soil life is diverse in morphology, metabolism, size, and many other characteristics. It is believed that “there is sufficient [microbial] DNA in 1 g of soil to extend 1,598km.” [30] Soil is a heterogeneous environment with various zones of rhizosphere, aggregates, organic matter and animal residues.[31] Given each zone is a small component of the larger soil ecosystem, rhizosphere accounts for only 5 to 7 percent of the soil environments but contains over “70 percent of the bacterial- and fungal-feeding nematodes.”[31] <br />
<br />
Since, all three domains of life: archaea, bacteria and eukarya, inhabit the soil environment it is difficult to observe each microbe individually within the soil ecosystem.Only a few representative groups of each domain will be discussed to provide examples of the roles these organisms play in soil. This page attempts to outline the major microbial groups within the diverse soil environment.The interactions between soil microbes amongst the soil microbial diversity. The concept of survival of the fittest is seen in the soil food web, which allows only a selective few with the correct nutrients to thrive in a soil environment. The interactions of soil microbes is not only a part of nature but it also only selects those organisms that are fit for survival, growth and reproduction. The soil food web and symbiotic relationships are used to explain the dynamic interactions between soil organisms.<br />
<br />
==Soil Food Web and Microbial Interactions== <br />
<br />
To survive in a soil environment, an organism must be able to adapt to changing environments and organism interactions. The interactions seen between organisms allows only the fittest to survive, thrive, grow and reproduce in the soil. The only type of interaction shown in (Figure 2.1) is predation. Other common interactions in the soil environment are: <br />
<br />
:[[Image:soil_foodweb72.jpg|frame|center|Figure 2.1 Soil Food Web. From[http://www.exploringnature.org/graphics/foodwebs/soil_foodweb72.jpg]]]<br />
<br />
<br />
'''I. Commensalism:''' Organism (A) benefits from the presence of Organism (B) while (B) is unaffected by the presence of (A).[32]<br />
<br />
'''II. Mutualism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) and becomes a necessary association for each other’s survival. [32] [33]<br />
<br />
'''III. Synergism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) but the relationship is not necessary for survival.[33]<br />
<br />
'''IV. Competition:''' Depending on the organisms this interaction benefits organisms who can readily adapt to the environment and overcome any obstacles needed to survive, grow and reproduce.[33]<br />
<br />
'''V. Amensalism:''' An interaction in which Organisms (A) and (B) develop a partnership where (B) is unaffected by (A) but organism (A) is negatively affected by (B).[34]<br />
<br />
'''VI. Parasitism:''' Organism (A) benefits from Organism (B) but Organism (B) does not benefit positively from Organism (A). <br />
<br />
'''VII. Predation:''' “An interaction between organisms in which one benefits and one is harmed based on the ingestion of the smaller sized organism, the prey, by the larger organism, the predator.”[33]<br />
<br />
<br />
<br />
The soil food web consists of microbes which play an important role in maintaining the complexity of the soil environment. The interactions observed in the food web are not only based on predation, which directly affects the nutrient cycling and degradation of pollutants, but also the formation of aggregates.[35] The production of specific nutrients, such as ammonium created by microbial metabolic functions, helps to enrich the the soil for plant use.[35] Soil organism activity, along with the presence of soil organic matter, create stabilizing aggregates.[35] The hyphae within the soil environment and the microbes help form large, stable aggregates in the soil habitat.[35] The biodiversity in the soil plays a pivotal role in degrading pollutants, and also prevents pathogens from inhabiting the soil environment through competition.[35] The food web in the soil environment is necessary to maintain the soil nutrients, biological activity, and detoxifying pollutants. Thus, it directly maintains cultivation, productiveness and prosperity of the soil. <br />
<br />
In (Figure 2.1), all three domains, Archaea, Bacteria, and Eukarya, are represented in the soil food web. If one takes a closer look at the figure, the soil food web is not only dependent on small and large microbes but also dead organic matter and plant roots. Dead and living matter in the soil environment contribute to maintaining the food web. Plant residues also are apart of the soil food web. They contribute to the soil’s carbon source.[35] The plant residues either, release carbon dioxide to the environment, or contribute to the soil organic matter. Soil organic matter contributes to soil’s richness and helps to form aggregates.[35] The main focus in the image above is the diversity of organisms, both in domains and in size. The larger organisms are usually the predators. The smaller organisms eventually fall prey, due to their limited mobility, respiration, and size. The eukarya and small bacteria are apparent figures seen in the figure above, but archaea also contribute to the food cycle as they break down ammonia for plants to use. [35]<br />
<br />
The notable interactions of life that take place in the soil environment is evident both below-ground level, as seen in the figure 2.1, but also in the above-ground level.[36] Worms also impact the soil food web, acting as both drivers of the food web both belowground and aboveground.[36]<br />
<br />
==3 Domains==<br />
[[Image:Big_Tree_Bold_Letters_white.png|frame|center|Figure 3.1 Phylogenetic Tree of the 3 Domains. From[http://phylogenomics.blogspot.com/2014_02_01_archive.html]]]<br />
<br />
===Carl Woese and Phylogeny===<br />
<br />
[[Image:Carlwoese1_0565_b.jpg|frame|center|Figure 3.2 Carl Woese. From[http://ofbacteriaandmen.blogspot.com/2013/01/the-new-biology-of-carl-woese.html]]] <br />
<br />
Carl Woese (Figure 3.2) was an American microbiologist famous for pioneering the technique of phylogenetic taxonomy through use of a 16S (for prokaryotic) and 18S (for eukaryotic) ribosomal RNA, also known as small subunit ribosomal RNA [46]. This refined Linnaean classification, taking out the guesswork classification by using a gene that was present in every living organism- the small subunit ribosomal RNA. This method of classification is comprehensive because all organisms possess this form of genetic material. Ssu rRNA is sequenced because the genes are highly conserved. Due to their functional constancy, some have variable regions to differentiate organisms, and are easy to sequence. This technique also elucidated the tree of life, which shows the three domains of microbial lineage diversity: Bacteria, Archaea, and Eukarya. DNA can be compared using a sample database that allows identification of unknown organisms to a species level.<br />
<br />
===Domain Bacteria===<br />
<br />
====Introduction to Bacteria==== <br />
Bacteria are single celled prokaryotic organisms that lack membrane bound organelles. They are involved in many important processes within the soil such as decomposition, [https://microbewiki.kenyon.edu/index.php/Bioremediation bioremediation], symbiosis and biological transformation of nutrients. They are present in all terrestrial soil environments.[1] Soil is a heterogenous environment that varies in moisture content, temperature, oxygen requirements, carbon source and many other bacterial growth conditions. Those wide ranging growth factors account for the enormous diversity in soil bacteria populations. One gram of soil can contain between 26,000 to 52,000 different bacterial species.[13] In the entire microbial world, only about 1 percent of bacterial species can be cultured under laboratory conditions which leaves an immense number of bacterial species yet to be described. [14]<br />
<br />
Classification based on phenotypic characteristics, such as cellular morphology, metabolism, gram staining, oxygen requirements, carbon source and other traits, was used more readily before modern DNA sequencing. But, phenotypic classification is still used and Bergey’s Manual of Systematic Bacteriology is the most widely used source for determining species based on characteristic species traits.<br />
<br />
Traditional species definitions are not as useful in bacteria. OTUs, or operational taxonomic units, based on DNA sequencing similarity, are more applicable to bacteria. Typically, those bacteria with 97 percent similar DNA sequence are classified within the same OTU.[15] The 16S small subunit ribosomal RNA is used to substantiate phylogenetic relationships between different bacterial groups.<br />
<br />
====Morphology====<br />
<br />
Bacterial cells measure approximately 1μm wide and 1-5μm long.[12] They are smaller than eukaryotic microbes.Due to their small size, bacteria can more easily adapt to changing soil environments than larger eukaryotes.[1] Most bacteria are singled celled, but actinomycetes grow in branching filaments. There are many different bacterial cell shapes. The most common are bacilli (rods), cocci (spheres), spirilla (spirals) and actinomycete (filaments).<br />
[[Image:bacteria_sizes.jpg|frame|center|Figure 3.3 Common cell shapes cocci, bacillus, and spirilla and relative sizes. From[http://www.ppdictionary.com/gnbac.htm]]]<br />
<br />
'''Flagella''' - There are many different types and different arrangement of flagella. Movement in soil environments is dependent on soil moisture content. Though movement in soil is limited, flagellar function is important to allow bacteria to find more favorable microsites.[1]<br />
<br />
'''Cell membrane''' - The cell membrane encloses the cytoplasm. It is semi-permeable phospholipid bilayer that regulates transport of nutrients into the cell and waste products out of the cell.<br />
<br />
'''Cell wall''' - Most bacteria have a rigid cell wall surrounding the cell membrane which protects the cell from osmotic lysis. The cell wall is made of a crosslinked polysaccharide, called peptidoglycan, that is found only in bacteria.[1] The cell wall gives the cell shape and structure, but it is porous enough to permit small water soluble molecules to flow through to the cell membrane surface.[1]<br />
<br />
*'''Gram positive''' bacteria have a thick cell wall made of several layers of peptidoglycan. The cell wall is the outermost structure, as they do not have an outer membrane. The thick cell wall structure make gram positive bacteria more resilient to osmotic shock. Gram positive bacteria can tolerate 5 to 10 times more turgor pressure than gram Gram negative bacteria.[1] Teichoic acids in the cell wall may also help to bind to cationic nutrients in soil surroundings.[1] <br />
<br />
*'''Gram negative''' bacteria have a thin cell wall surrounded by an outer membrane made of phospholipids and lipopolysaccharides. Polysaccharides of the outer membrane interact with surrounding cations and are involved in attachment of bacteria to soil particles. [1] Periplasm is a gel like substance that occupies the space between the outer membrane and the cell wall of gram negative bacteria.[1] The outer membrane and periplasmic space is thought to provide protection from environmental toxins.[1] Proteins within the periplasm are thought to begin the process of catalyzing hydrolysis of organic and toxic substances.[1] <br />
<br />
[[Image:gramposnegmembrane.jpg|frame|center| Figure 3.4 Illustration of Gram positive and Gram negative cell wall structures. From[http://micro.digitalproteus.com/morphology2.php]]]<br />
<br />
'''Endospores''' are made by ''Bacillus'' and ''Clostridium'' in response to environmental stress.[1] Endospores are extremely resistant structures that can withstand extreme temperatures up to 150℃.[12] They can also withstand extreme pressure, desiccation, radiation, pH and chemicals.[12] The endospore protects the bacterial DNA until environmental conditions are more favorable and germination can proceed. Soil is the most common habitat for endospore forming bacteria.[12]<br />
<br />
'''Extracellular polymers''' - Many bacteria secrete a slime layer or capsule made of polysaccharides or glycoproteins.[1] The outer polysaccharide coating of bacteria helps in attachment to surfaces and the formation of biofilms.[1] Bacterial capsule secretions play a big role in soil aggregation and soil structure.[1] When the carbon to nitrogen ratio within soils is high, microbes secrete the excess carbon as extracellular polysaccharides.[1]<br />
<br />
====Reproduction==== <br />
Most bacteria reproduce by binary fission.[12] The bacterial cell expands to twice the original cell size, duplicates the bacterial DNA and pinches off, producing two daughter cells. Each resultant daughter cell is a clone of the parent cell. Prokaryotic Archaea also reproduce by binary fission.<br />
<br />
*'''Spore formation:''' Actinomycetes are a large group of filamentous bacteria, primarily found in soil.[1] Actinomycetes are morphologically similar to fungi. Actinomycetes form long filaments called hyphae. Unlike most bacteria, the majority of actinomycetes reproduce using asexual spores called conidia.[1] Though they share many characteristic with fungi, actinomycetes are still prokaryotes. They are smaller than fungi and the cell wall contains peptidoglycan.[1] Actinomycetes break down a wide variety of organic compounds and play an important role in organic matter decomposition. [1] ''Streptomyces'', a subgroup within actinomycetes, produce geosmin, which gives soil the characteristic earthy smell.[12]<br />
<br />
====Metabolism==== <br />
<br />
Along with archaea, bacteria are the most metabolically diverse and employ many different nutritional strategies.[1]<br />
*Heterotrophs - Most bacteria are heterotrophic, obtaining carbon from preformed organic substances. [1] <br />
*Autotrophs - Carbon dioxide serves as the main source of carbon. Some cyanobacteria, nitrifying and sulfur-oxidizing bacteria are autotrophs.[1]<br />
*Organotrophs - Most bacteria obtain electrons from organic substances.[1]<br />
*Lithotrophs - Some cyanobacteria, nitrifying bacteria and sulfur-oxidizing bacteria obtain electrons from inorganic substances.[1]<br />
*Phototrophs - Cyanobacteria use light as the main source of metabolic energy.[1]<br />
*Chemotrophs - All other nonphotosynthetic bacteria do not rely on light for metabolic energy.[1]<br />
<br />
====Contributions to the Cycle==== <br />
<br />
Bacteria play a significant role in the cycling of a wide range of elements.<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Carbon_cycle '''Carbon Cycle:'''] <br />
<br />
*'''Carbon Assimilation''' is the process of fixing carbon dioxide into organic forms. Carbon fixation is performed by autotrophic bacteria, such as cyanobacteria.[1] Chemoautotrophic nitrifying bacteria, such as ''Nitrobacter, Nitrosospira'' and ''Nitrosomonas'', also fix carbon.[1] Sulfur oxidizing bacteria, such as ''Thiobacillus'', fix carbon as well.<br />
<br />
*'''Carbon Mineralization''' results from microbial decomposition of organic carbon compounds into inorganic forms. As the organic carbon substances, like plant matter, are decomposed, inorganic carbon dioxide is produced. Most bacteria are heterotrophs that perform carbon mineralization. When microorganisms die, they are decomposed by successive microbial generations. Peptidoglycan, the main component of bacterial cell walls, is utilized as a polysaccharide substrate by other heterotrophic soil microbes.[1]<br />
<br />
*'''Methanogenesis''' - Methanogenic bacteria produce methane from the reduction of carbon dioxide. They are all strict anaerobes that use carbon dioxide for the carbon source.[1] They can all use hydrogen as a source of energy and electron donor. [1]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle '''Nitrogen cycle:''']<br />
<br />
*'''Nitrogen fixation:''' ''Azotobacter'' is a free living nitrogen fixing bacteria.[1] ''Rhizobium'' lives in a mutualistic relationship with plants by fixing nitrogen within root the nodules of legumes.[1] ''Anabaena'' and ''Nostoc'' have specialized heterocyte structures where nitrogen fixation occurs.[1] <br />
<br />
*'''Nitrification:''' Nitrifying bacteria, such as ''Nitrobacter, Nitrosospira,'' and ''Nitrosomonas'', oxidize ammonium to nitrate.[1] <br />
<br />
*'''Denitrification:''' ''Alcaligenes, Flavobacterium'', and ''Pseudomonas'' are common soil denitrifying bacteria.[1]<br />
<br />
===Domain Archaea===<br />
<br />
====Introduction to Archaea====<br />
<br />
Vladimir Vernadsky decided, in 1926, that only two domains of life existed on Earth, Bacteria and Eukarya.[37] About 50 years later in 1977, Carl Woese and George Fox theorized that part of the bacterial domain possed multiple dissimilarities from bacteria and recognized it to be another domain of life, now called Archaea.[38] Woese and Fox’s theory regarding the differences of archaea were confirmed in 1990’s through the use of 16S rRNA and 18S rRNA.[38] <br />
<br />
Despite the strongly held belief, in the 1990s, that archaea only inhabited extreme environments, recent discoveries have suggested their presence in abundant numbers all throughout the Earth. It is suggested that Archaea play notable roles in maintaining nutrient cycles.[37] Various methods of research, such as cultivation, culture-independent techniques and isotope-based methods, have facilitated the study of domain Archaea in carbon and nitrogen cycling. [37]<br />
<br />
The use of genomic and biochemical data has permitted the study of archaeal structure.[37] Use of these research methods has shown that domain archaea and domain bacteria differ in cell wall characteristics yet, share various ways to transfer genetic information by replication and transcription from their common ancestor, Eukarya.[37] As of 2012, 116 genera of Archaea have been observed which consists of 450 species. Most of the archaeal species in these genera remains uncultivated, known only through its gene sequences and molecular surveys.[37]<br />
<br />
====Morphology==== <br />
Archaea are characterized by various cell sizes. They are most commonly found to be small organisms ranging from “0.1 to 15 μ diameter and up to 200 μ long.”[38] The shape of many archaea are similar to bacteria, including bacillus, cocci, spirilla and “plate-like forms.” [38] Their cell membranes have ether linked lipids with no periplasmic space, similar to gram-positive bacteria, and contain no intracellular organelles.[39]<br />
<br />
'''Flagella:''' Most motile archaea inhabit a motor rotary system that allows it to move its flagella through the chemical gradient similar to bacteria.[39] Despite its similarity in function and source of energy required for motility, the flagella of both archaea and bacteria differ in structure.[39] Archaeal flagella gets the energy for its movement by ATP and is composed of dependent filaments that rotate singularly. [40] Archaeal flagella are known to be thinner than bacteria flagellin.[40] Since, the archaeal common ancestor is not bacteria but eukarya, convergent evolution is a plausible explanations for the differences between bacterial and archaeal flagellin. [40]<br />
<br />
'''Membranes:''' Archaea have a cell membrane that protects the cytoplasm and the nucleic acids from the environment. The archaeal cell membrane has a lipid bilayer with glycol-ether lipids that are more stable than ester linkages and help some archaea that live in extreme environments to withstand such conditions.[39] Most archaeal species are surrounded by a cell wall which protects the cell membrane and maintains the archaeal structure.[41]<br />
<br />
====Reproduction====<br />
Archaeal organisms reproduce by binary fission since they do not have nucleases thus, the DNA chromosome in a Archaeal organism replicate, separate and create two daughter cells.[43] The process of binary fission can be seen in Figure (3.5) process begins the parent cell duplicating the DNA. The DNA material then goes to the sides of the cell where an invagination to the cell occurs allowing the cell to become two individual cells. Binary fission is a very fast reproduction process, that allows archaeal organisms to grow at an exponential rate.[44]<br />
<br />
[[Image:WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg|frame|center|Figure 3.5 Illustration of binary fission. From[https://d2jmvrsizmvf4x.cloudfront.net/WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg]]]<br />
<br />
====Metabolism==== <br />
Archaea share similar metabolic characteristics to bacteria. The metabolic pathways taken by all archaea shown in the (Figure 3.6) demonstrates the great diversity and variation amongst archaea. [38] The kinds of archaea that are seen in the environment and the metabolic pathways taken by some can be summarized in the image. <br />
<br />
*Photoautotrophs: use light as an energy source and carbon dioxide as the carbon source with the help of the Calvin Cycle.[38]<br />
*Chemoautotrophs: use inorganic chemicals as their energy source and carbon dioxide as carbon source. <br />
*Chemoheterotrophs: take organic chemicals as energy source and organic chemicals as carbon source. The pathways taken by chemoheterotrophs varies from respiration by the Krebs Cycle to fermentation. [38]<br />
*Photoheterotrophs: use light as their energy source and organic chemicals as their carbon source. <br />
<br />
Most archaea inhabiting in the soil environment are major contributors to the biogeochemical cycles.<br />
<br />
[[Image:2000px-Troph_flowchart.svg.png|thumbnail|center|Figure 3.6 Flowchart showing different metabolic pathways. From[https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Troph_flowchart.svg/2000px-Troph_flowchart.svg.png]]]<br />
<br />
====Contributions to the Cycle====<br />
Archaea play a significant role in the nutrient cycles that take place in the ecosystem as they account for about 1-5% of all the prokaryotes present in the soil environment.[42]<br />
<br />
'''Carbon Cycle:''' Archaea have an important role in the carbon cycle that takes place specifically in methane production, carbon mineralization and carbon assimilation all of all of which contribute to the soil’s carbon sink.[42] The carbon dense soil helps to make the soil organic matter rich and helps to form extracellular polymers which creates stable aggregates. For some microbes, an electron acceptor is need to carry out metabolic functions. [42] More info on [https://microbewiki.kenyon.edu/index.php/Carbon_cycle Carbon Cycle].<br />
<br />
*'''Carbon Assimilation:''' Involves the transformation of inorganic carbon into organic carbon compounds. This process is commonly done by autotrophic phyla ''Crenarchaeota, Thaumarchaeota'', and ''Euryarchaeota'' that use carbon dioxide/ bicarbonate converting it to organic compounds.[42] Of the autotrophic lineages observed in carbon assimilation the ''Thaumarchaeota'' are strict autotrophs, the ''Euryarchaeota'' and ''Crenarchaeota'' are facultative autotrophs and the ''Halobacteriales'' and ''Thermococcales'' are obligate heterotrophs.[42] <br />
<br />
*'''Carbon Mineralization:''' The process that converts organic carbon into the oxidized inorganic carbon, carbon dioxide is commonly done by both aerobes and anaerobes.[42] The heterotrophic microbes that use organic compounds as energy to oxidize the carbon source include, methanogens and methane-oxidizing archaea belonging to the phyla ''Euryarchaetota'', and ''Crenarchaeota''.[42] <br />
<br />
*'''Methanogenesis:''' production of methane, a major greenhouse gas in the Earth’s atmosphere is commonly done by archaea upon reducing an oxidized compound.[42] The phyla ''Euryarchaeota'' is the only phyla that consists of archaea that produce methane all of which form five class: ''Methanopyri, Methanococci, Methanobacteria, Methanomicrobia'' and ''Thermoplasmata''.[42] Methanogens are commonly found in anaerobic and aerobic conditions such as bodies of water, aerated soils and oxygenated waters.[42]<br />
<br />
'''Nitrogen Cycle :''' Archaea play a pivotal role in the Nitrogen cycle and help create nitrogenous products for the plants and microbes. More info on [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle Nitrogen cycle].<br />
<br />
*'''Nitrogen Fixation:''' Fixing nitrogen from the environment and converting it to organic nitrogen in the soil or to inorganic nitrogenous form since both organic and inorganic products are in short supply in the biosphere and are fixed by many archaeal organisms.[42] N2 fixation by the environment is usually done by three major archaeal classes ''Methanobactera, Methanococci'' and ''Methanomicrobia''.[42] <br />
<br />
*'''Nitrification:''' Converting the ammonia (NH4+) in the soil to nitrite (NO2-) produces nitrate (NO3-) as an intermediate. [42] The transformation of ammonia to first nitrate then to nitrite is a two step process that is done by different microbes. [42] Most common organisms involved in nitrification include ammonia-oxidizing archaea which are lithotrophic organisms mostly, of the ''Thaumarchaeota'' phylum from the archaea domain. <br />
<br />
*'''Denitrification :''' The conversion of atmospheric N2 using the electron acceptor NO3- or NO2- creating the formation of nitric oxide, nitrous oxide and/or N2.[42] The formation of the end product N2 may not always be produced but other intermediates NO and N2O, greenhouse gases may be produced.[42] Of the archaeal organisms that have been studied in denitrification process is done by ''Pyrobaculum aerophilum'' which accepts both NO3- and NO2- as an electron acceptor producing a variety of products NO2-, NO, N20 and N2.[42]<br />
<br />
===Domain Eukarya===<br />
<br />
====Fungi====<br />
<br />
=====Introduction=====<br />
<br />
'''Introduction'''<br />
<br />
Fungi comes from the ancient Greek word “sphongos” meaning sponge in reference to the mushroom cap [47]. Fungi have the general characteristics of being eukaryotic, heterotrophic, external absorbers of nutrients, containing a hyphal thallus, reproducing via spore, and being pleomorphic (producing several forms). Fungi are generally organoheterotrophs that can survive in low pH and stay active at low moisture content[46]. Fungi reside in the domain Eukarya with an estimated species of 1.5 million, and less than five percent of them have ever been described. The general phyla included within Kingdom Fungi include Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, Chytridiomycota, and Microsporidia [48].<br />
<br />
[[Image:magical-kingdom-620.jpg|frame|center|Figure 3.7 Fungi phyla hierarchy. From.[http://www.motherjones.com/environment/2009/11/fungi-family-tree]]]<br />
<br />
=====Morphology=====<br />
<br />
'''Morphology''' <br />
<br />
Fungi can be either unicellular (yeasts) or multicellular. All multicellular fungi are made up of small, filamentous particles called hyphae. Some hyphae have cross walls called septa, while others do not- this is a large basis of fungal identification. Fungal cells generally have multiple nuclei. Fungal cell walls are generally composed of chitin, a long carbohydrate polymer that adds rigidity and structural support to fungi [49]. <br />
<br />
=====Reproduction=====<br />
<br />
'''Reproduciton'''<br />
<br />
Fungal reproduction can occur either sexually or asexually.<br />
<br />
'''Sexual reproduction''' can occur by homothallic or heterothallic mycelia.<br />
<br />
'''Asexual reproduction''' can occur by fragmentation, budding, or by producing spores (the most common method). <br />
<br />
*'''Spores:''' spores come in many different forms. One of the most well known are conidiospores, which are unicellular or multicellular spores that get released from the tip of the hyphae. <br />
<br />
'''Perfect fungi''' are those that can reproduce both sexually and asexually while imperfect fungi are those that can only reproduce asexually.<br />
<br />
*Sexual reproduction always includes the stages plasmogamy (fusion of two haploid cells), karyogamy (creation of a diploid zygote), and meiosis (gametes are created).<br />
<br />
=====Metabolism=====<br />
<br />
'''Metabolism'''<br />
<br />
Many different fungi display a myriad of metabolisms. There are primary metabolites that that help the fungi function properly, and secondary metabolites that are generally bioactive that are not the most pertinent to fungal growth (they can live without these). Secondary metabolites play a large role in chemistry today and can be manufactured into commonly used products such as new drugs. In general fungi are heterotrophic through release of extracellular enzymes into the neighboring environment to break complex molecules down into smaller ones. The materials are then absorbed and metabolized [50]. Fungi are sessile organisms that overcome their little to no movement through apical growth at the hyphal tip. Fungi are noted to grow almost everywhere on the Earth.<br />
<br />
=====Relevance to soil===== <br />
<br />
'''Relevance to soil'''<br />
<br />
Fungi include some of the most abundant biomass of microorganisms in numerous soils. They play an important role as decomposers within the soil food web through conversion of difficult to digest organic material into forms many other organisms can use [51]. Their hyphae can bind soil particles together and create aggregates that increase soil water holding capacity. They perform important functions from water dynamics to nutrient cycling and disease suppression. Soil fungi can be categorized into three different groups based on their actions: <br />
<br />
*decomposers: that convert dead organic material into fungal biomass<br />
<br />
*mutualists: which colonize plant roots and help solubilize phosphorous and bring soil nutrients<br />
<br />
*pathogens/ parasites: which help control diseases in soil via trapping organisms such as nematodes [51]. <br />
<br />
Fungi are seen common in intensively managed agricultural soils due to tillage disrupting hyphae. Fungi also play a very important role in the [https://microbewiki.kenyon.edu/index.php/Rhizosphere_Interactions rhizosphere], the region of soil that is greatly influenced by the plant root system. This area of soil which is concentrated in plant roots and fungal hyphae is known to support greater microbial activity.<br />
<br />
====Protista====<br />
<br />
Protists are mainly eukaryotic unicellular organisms. They used to belong to their own kingdom Protista, but are now known to be paraphyletic [18]. Protists are made up of protozoa, unicellular algae, and slime molds. The protozoa are divided into 4 major categories: the ciliates, the flagellates, the heliozoans, and the amoebas [10]. They are so small that they don’t need any specialized organelles in order to survive and can survive at low oxygen levels because of this. They are also known to use a contractile vacuole to remove excess water from their cells [10]. <br />
<br />
=====Protozoans=====<br />
<br />
'''Protozoans'''<br />
<br />
In general, Protozoans range from 5 to 500 µm in diameter, making them significantly larger than bacteria [21]. They are abundantly located near the surface of the soil (15cm deep) where roots are plentiful [21]. Many protozoans have two life cycles. One is their active form where they are motile and feed on prey. The other is the cyst form where they produce a thick coating to protect them from the environment and can go dormant for years.<br />
<br />
======Ciliates======<br />
<br />
'''Cilliates:'''<br />
This group, within protozoans, is fairly diverse. A common feature shared amongst all of its members is the presence of at least one cilia at any stage of its development [10]. The cilia is used for movement and other things such as predation (tentacles). For movement, they use the massive amounts of tiny cilia to create wave like currents to propel the cell forwards. Most ciliates also have toxicysts which are used to capture prey [10]. Some ciliates even have a symbiotic relationship with algae living inside of them [10]. The algae use the CO2 produced by ciliates and turn it into O2 that can then be reused by the ciliates [10]. They are found in a wide array of habitats ranging from freshwater and soil to the rumen of Animals [22]. They are present in almost anywhere that contains water [23]. They are unicellular heterotrophs so they feed on bacteria and algae in their environment. Ciliates are one of the top predators in the microbial food web and are hypothesized to have been a major predatory group before animals evolved [23]. Parasitic ciliates exist that can cause the death of animals and are increasingly becoming dangerous in water [23].<br />
<br />
[[Image:2spiro.jpg|frame|center|Figure 3.8 Microscope image of ciliated protists. From[http://www.microscopy-uk.org.uk/mag/smallimag/2spiro.jpg]]]<br />
<br />
======Flagellates======<br />
<br />
'''Flagellates''' are one of the most commonly known protists. They are unicellular organisms that may be solitary, colonial, free living, or parasitic [24]. The hallmark feature of protists is that at some point in their life cycle, they possess a flagella. A flagellum is a long hair like structure that is used for locomotion, sensation, and sometimes predation [24]. The flagellum makes waves by whiplike lashing movements which propels the cell forwards. Flagellates also have a protective coating in the form of a thin pellicle to protect them from the environment [24]. <br />
<br />
[[Image:9703607_orig.jpg|frame|center|Figure 3.9 Illustration of flaggelates during different life cycle stages. From[http://diagnosticparasitology.weebly.com/uploads/3/9/5/4/3954522/9703607_orig.jpg]]]<br />
<br />
*'''Mastigophora:'''<br />
<br />
Mastigophora is a subphylum of flagellates. Being a member of the flagellates, their key feature is the flagellum. Their habitats include freshwater, soil, and can act as animal parasites as well [25]. They use pseudopodia, a long outward protrusion, to trap and funnel food from the environment into their cell bodies [25]. The Mastigophora are mainly known for their parasitism, which can take place in both humans and animals [25]. ''Typanosomes'' are an example of Mastigophora which causes African sleeping sickness [25]. ''Giardia lambli''a is another example that resides in the intestinal tract of warm-blooded animals and inflicts intestinal giardiases [25]. It is also a major contaminant of drinking water because it is resistant to chlorine, which is the most common water purifier [25]. Having a dormant cyst form also adds to its survival potential through filtration efforts [25].<br />
<br />
<br />
<br />
*'''Euglenids:'''<br />
<br />
Euglenids are one of the best known flagellates. They are found in freshwater and soil, as long as there are organic materials. They also participate in some symbiotic relationships with marine animals. Euglenid cells do not contain cell walls or other rigid membranes [26]. This gives the cell tremendous flexibility and allows it to change its shape to easily navigate through muddy terrain. Euglenids have two flagella, one which creates locomotion and movement for the cell [26]. The other flagellum does not protrude from the cell and is contained in the cell body [26].<br />
<br />
======Amoebas======<br />
<br />
'''Amoebas'''<br />
<br />
Amoebae are single celled eukaryotes present in many different types of environments. They are scattered throughout a variety of eukaryotic lineages and therefore are not monophyletic [27]. Amoebae range in size from 5 micrometers to 3 mm and don’t have a defined shape, commonly recognized for being polymorphic. They are motile through the use of pseudopodia, which stretch and pull the cell along with it. The pseudopodia are also used for feeding. They are able to sense prey that can be engulfed and engulf them via phagocytosis. The amoeba’s main prey consists of bacteria, algae, and other protozoa [28]. The prey is moved around within the cell via food vacuoles, a feature of amoebae [28]. Another key characteristic of amoebae are the large contractile vacuoles inside the cell. The purpose of the contractile vacuole is to osmoregulate by pumping excess water out of the cell. In times of turmoil, amoebae have an encysted form that helps them get through the tough times. This form is useful when there is low nutrient availability to limit energy consumption. There are two main forms an amoeba can be characterized as. They can either be testate or nontestate. Testate amoeba produce shells, or “tests”, that help identify their species since each species has a unique shell.<br />
<br />
[[Image:Amoeba_(PSF).png|frame|center|Figure 3.10 Amoeba morphology. From[https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Amoeba_(PSF).png/230px-Amoeba_(PSF).png]]]<br />
<br />
=====Slime Molds=====<br />
<br />
'''Slime molds''' were once classified as fungi, but have now been placed in their own phylogenetic groups. Slime molds are single cells that can live independently, but aggregate to form multicellular reproductive structures when necessary [29]. The fruiting body releases spores which germinate into new cells. Slime molds feed off of bacteria and are most commonly found in forests. They feed off of decaying vegetation as well so they can be seen on rotting logs and leaves.<br />
<br />
[[Image:28-30-cellslimemoldlife-l.jpg|frame|center|Figure 3.11 Illustration of slime mold life cycle. From[https://lichencolony.files.wordpress.com/2006/06/28-30-cellslimemoldlife-l.jpg]]]<br />
<br />
==Current Research== <br />
<br />
'''Bacteria:''' To showcase the great diversity of soil bacterial environments, cyanobacteria have been studied in both desert and polar regions. Cyanobacteria can survive in extreme conditions likely because of their long evolutionary past.[16] Dr. Patzelt and his colleagues studied the diverse cyanobacteria residing in the Atacama desert, one of the driest parts of the world. The diverse taxa found in the Atacama desert can withstand prolonged periods of extreme desiccation.[16] The cyanobacteria dominate the soil crusts, affecting soil stability, soil structure and soil fertility.[16] Cyanobacteria inhabiting the Antarctic and Arctic regions, show similar adaptations to extreme environments as the cyanobacteria found in the desert. The polar cyanobacteria are particularly adapted to high altitudes.[17] They can withstand high ultraviolet radiation, desiccation, and repeated freeze-thaw cycles.[17] The autotrophic cyanobacteria supports heterotrophic microbes, providing an important ecosystem service in an environment with low microbial activity.[17]<br />
<br />
'''Archaea:''' In 150 soil samples acquired from North and South America, about 150,000 species were observed.[45] Of these, over 2,500 were identified as archaea based on their ssu rRNA.[45] The archaeal species were further analyzed to understand their role in the soil environment. Of the archaeal groups, ''Crenarchaeota'' and ''Euryarchaeota'' were found.[45] Bates stated that, “Across the non-experimental soils examined the soil C:N ratio was the single best predictor of archaeal relative abundances” due to their influences in the nutrient cycles.[45]<br />
<br />
'''Fungi:''' Fungi have been in the public eye for a while now due to the many different types of secondary metabolites they produce. Some produce bioactive compounds that can inhibit growth of protozoa, bacteria, parasites, insects, and even other fungi. A large area of investigation is the uses of these chemicals for human interests in use from medicine to plant and animal toxins [52].<br />
<br />
'''Protozoa:''' It’s known that Protozoa stimulate plant growth in different ways. It’s suspected that the Protozoa take part in the microbial loop which is responsible for the nutrient production for plants [19]. However, new developments have shown that the Protozoa themselves are responsible for the nitrogen mineralization and that other bacteria have no effect on the plant’s nitrogen sources [19].<br />
<br />
==References==<br />
<br />
1. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). Principles and Applications of Soil Microbiology. New Jersey: Pearson Education Inc.<br />
<br />
2. Ingham, Elaine R. Ingham R. "Chapter 4: SOIL FUNGI." Soil Biology. Natural Resources Conservation Service Illinois, n.d. Web. 9 Feb. 2016<br />
<br />
3. Reid, Greg, and Percy Wong. "SOIL BACTERIA AND FUNGI - NEW SOUTH WALES." Soil Bacteria and Fungi. New South Wales Department of Primary Industries, 2005. Web. 11 Feb. 2016.<br />
<br />
4. "Fungi." Microbiology Online. Microbiology Society, n.d. Web. 11 Feb. 2016.<br />
<br />
5. Tortora, G.J., Funke, B.R., Case, C.L. (2012). “Microbiology an Introduction.” 11th ed. Pearson Benjamin Cummings, San Francisco.<br />
<br />
6. Rizzo, D. “Intro to Fungi.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
7. Rizzo, D. “Ascomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
8. Rizzo, D. “Basidiomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
9. Pegg G.F., Brady B.L. “Verticillium Wilts.” New York, CABI Publishing 2002. Google Books. Web. 11 Feb. 2016. http://books.google.com<br />
<br />
10. Hebert, Paul. "What Is a Protist / What Are Protozoa? - Encyclopedia of Life." Encyclopedia of Life. N.p., n.d. Web. 11 Feb. 2016.http://eol.org/info/456<br />
<br />
11. "MicrobeWorld." Protista. N.p., n.d. Web. 11 Feb. 2016. http://www.microbeworld.org/types-of-microbes/protista<br />
<br />
12. Madigan, M.T., Martinko, J.M. (2006). Brock Biology of Microorganisms. New Jersey: Pearson Prentice Hall.<br />
<br />
13. Roesch, L.F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H.; Camargo, F. A. O.; Farmerie, W. G.; Triplett, E. W.(2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1(4).283-290. <br />
<br />
14. Amann, R.I, Ludwig, W., Schleifer, K.H.(1995).Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology and Molecular Biology Reviews. 59(1). 143-169. <br />
<br />
15. Geers, D., Cohan, F.M., Lawrence J.G., Spratt, B.G., Coenye, T. Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005). Opinion: Re-evaluating prokaryotic species. Nature Reviews Microbiology. 3(9). 733-739.<br />
<br />
16. Patzelt, D.J., Hodac, L., Friedl, T., Pietrasiak, N., Johansen, J.R. (2014). Biodiversity of soil cyanobacteria in the hyper-arid Atacama Desert, Chile. Journal of phycology. 50(4). 698-710. <br />
<br />
17. Makhalanyane, T. P., Valverde, A., Velázquez, D., Gunnigle, E., Van Goethem, M. W., Quesada, A., & Cowan, D. A. (2015). Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats. Biodiversity and Conservation, 24(4), 819-840.<br />
<br />
18. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist>.<br />
<br />
19. Ekelund, Flemming; Saj, Stephane; Vestergård, Mette; Bertaux, Joanne; Mikola, Juha. (2009). “The “soil microbial loop” is not always needed to explain protozoan stimulation of plants”. Soil Biology & Biochemistry. Vol. 41 Issue 11, p2336-2342, 7p.<br />
<br />
20. Bonkowski, Michael. "Protozoa and Plant Growth: The Microbial Loop in Soil Revisited." New Phytologist New Phytol 162.3 (2004): 617-31. Web.<br />
<br />
21. Hoorman, James. "The Role of Soil Protozoa and Nematodes." Fact Sheet (n.d.): n. pag. Ohio State University, 2011. Web.<br />
<br />
22. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist<br />
<br />
23. Lynn, Denis H(Apr 2012) Ciliophora. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001966.pub3]<br />
<br />
24. "flagellate". Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc., 2016. Web. 23 Feb. 2016 <http://www.britannica.com/science/flagellate>.<br />
<br />
25. "Mastigophora." World of Microbiology and Immunology. 2003. Encyclopedia.com. 23 Feb. 2016<http://www.encyclopedia.com>.<br />
<br />
26. “Plant Life." : Euglenoids. N.p., n.d. Web. 23 Feb. 2016. <http://lifeofplant.blogspot.com/2011/04/euglenoids.html><br />
<br />
27. Parales, R.E. and Martin, M. (2015) Microbial Diversity Laboratory Manual, MIC 105L, Winter 2015. Department of Microbiology and Molecular Genetics, College of Biological Sciences, The University of California, Davis.<br />
<br />
28. Arnold, Paul. "What Does an Amoeba Eat? Plus Other Ameoba Info and Questions." Bright Hub. N.p., n.d. Web. 04 Mar. 2016.<br />
<br />
29. "MicrobeWorld." Slime Molds. N.p., n.d. Web. 24 Feb. 2016. <http://www.microbeworld.org/types-of-microbes/protista/slime-molds><br />
<br />
30. Leeuwenhoek., A. V. (2009, November 18). One gram of soil: A microbial biochemical gene library. Retrieved March 13, 2016, from http://www.ncbi.nlm.nih.gov/pubmed/19921459 <br />
<br />
31. Coleman, D. C., Crossley, D. A. & Hendrix, P. F. "Soil food webs: Detritivory and microbiology in soils," in Fundamentals of Soil Ecology, 2nd ed. (Elsevier, 2004) 236-241.<br />
<br />
32. Welcome to Agriinfo.in. (n.d.). Retrieved February 21, 2016, from http://agriinfo.in/?page=topic&superid=5&topicid=172 <br />
<br />
33. Gouthro, T., & Rice, D. (1987, December 15). Interaction Terminology. Retrieved February 21, 2016, from http://www.rpi.edu/dept/chem-eng/Biotech-Environ/MixCul/ecodefn.htm <br />
<br />
34. AMENSALISM. (n.d.). Retrieved February 21, 2016, from https://biostuds.wikispaces.com/AMENSALISM <br />
<br />
35. Natural Resources Conservation Service. (n.d.). Retrieved March 10, 2016, from <br />
http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053865 <br />
<br />
36. Ecological Linkages Between Aboveground and Belowground Biota. (n.d.). Retrieved March 10, 2016, from http://science.sciencemag.org/content/304/5677/1629 <br />
<br />
37. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf<br />
<br />
38. Kingdom Archaea. (n.d.). Retrieved March 10, 2016, from http://plantphys.info/organismal/lechtml/archaea.shtml <br />
<br />
39. What are Archaea? - Encyclopedia of Life. (n.d.). Retrieved March 10, 2016, from http://eol.org/info/457 <br />
<br />
40. Flagellum. (n.d.). Retrieved March 10, 2016, from http://www.newworldencyclopedia.org/entry/Flagellum#Archaeal_flagellum <br />
<br />
41. Archaea: Morphology. (n.d.). Retrieved March 10, 2016, from http://www.ucmp.berkeley.edu/archaea/archaeamm.html <br />
<br />
42. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf <br />
<br />
43. Archaea. (n.d.). Retrieved March 10, 2016, from http://www.eoearth.org/view/article/150172/ <br />
<br />
44. Binary Fission: Cell Division & Reproduction of Prokaryotes. (n.d.). Retrieved March 10, 2016, from http://www.scienceprofonline.com/microbi <br />
<br />
45. Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2010, November 18). Examining the global distribution of dominant archaeal populations in soil. Retrieved February 21, 2016, from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105767/<br />
<br />
46. Scow, K. M. "Lecture 1 Part 1." Lecture, Davis.<br />
<br />
47. Rizzo, D. "Lecture 1." Lecture, Davis.<br />
<br />
48. Rizzo, D. "Lecture 3." Lecture, Davis.<br />
<br />
49. C.J. Alexopoulos & C. W. Mims, Introductory Mycology 3rd edition. 1979. Wiley NY. Web accessed Mar 8, 2016 from http://www.ucmp.berkeley.edu/fungi/fungimm.html<br />
<br />
50. Rizzo, D. "Lecture 2." Lecture, Davis.<br />
<br />
51. Ingham, E. “Chapter 4: Soil Fungi” (2016) Oregon State University. Retrieved Feb. 20, 2016, from http://extension.illinois.edu/soil/SoilBiology/fungi.htm<br />
<br />
52. Keller, N., Turner, G., Bennett, J. “Fungal Secondary Metabolism- from Biochemistry to Genomics.” 2005 Nature Reviews Microbiology p/ 937 to 947.</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Introduction_to_Organisms&diff=128505
Introduction to Organisms
2017-03-05T23:09:32Z
<p>Kmscow: /* Slime Molds */</p>
<hr />
<div>==Introduction== <br />
The soil ecosystem in an important environment that allows both plants and animals to survive, grow and reproduce. The significance of the soil as an ecosystem is at times overlooked despite its major contributions to the environment. The [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] is a complex and varied microbial habitat.[1] The plants and organisms inhabiting the soil contribute to its thriving diversity. Soil life is diverse in morphology, metabolism, size, and many other characteristics. It is believed that “there is sufficient [microbial] DNA in 1 g of soil to extend 1,598km.” [30] Soil is a heterogeneous environment with various zones of rhizosphere, aggregates, organic matter and animal residues.[31] Given each zone is a small component of the larger soil ecosystem, rhizosphere accounts for only 5 to 7 percent of the soil environments but contains over “70 percent of the bacterial- and fungal-feeding nematodes.”[31] <br />
<br />
Since, all three domains of life: archaea, bacteria and eukarya, inhabit the soil environment it is difficult to observe each microbe individually within the soil ecosystem.Only a few representative groups of each domain will be discussed to provide examples of the roles these organisms play in soil. This page attempts to outline the major microbial groups within the diverse soil environment.The interactions between soil microbes amongst the soil microbial diversity. The concept of survival of the fittest is seen in the soil food web, which allows only a selective few with the correct nutrients to thrive in a soil environment. The interactions of soil microbes is not only a part of nature but it also only selects those organisms that are fit for survival, growth and reproduction. The soil food web and symbiotic relationships are used to explain the dynamic interactions between soil organisms.<br />
<br />
==Soil Food Web and Microbial Interactions== <br />
<br />
To survive in a soil environment, an organism must be able to adapt to changing environments and organism interactions. The interactions seen between organisms allows only the fittest to survive, thrive, grow and reproduce in the soil. The only type of interaction shown in (Figure 2.1) is predation. Other common interactions in the soil environment are: <br />
<br />
:[[Image:soil_foodweb72.jpg|frame|center|Figure 2.1 Soil Food Web. From[http://www.exploringnature.org/graphics/foodwebs/soil_foodweb72.jpg]]]<br />
<br />
<br />
'''I. Commensalism:''' Organism (A) benefits from the presence of Organism (B) while (B) is unaffected by the presence of (A).[32]<br />
<br />
'''II. Mutualism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) and becomes a necessary association for each other’s survival. [32] [33]<br />
<br />
'''III. Synergism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) but the relationship is not necessary for survival.[33]<br />
<br />
'''IV. Competition:''' Depending on the organisms this interaction benefits organisms who can readily adapt to the environment and overcome any obstacles needed to survive, grow and reproduce.[33]<br />
<br />
'''V. Amensalism:''' An interaction in which Organisms (A) and (B) develop a partnership where (B) is unaffected by (A) but organism (A) is negatively affected by (B).[34]<br />
<br />
'''VI. Parasitism:''' Organism (A) benefits from Organism (B) but Organism (B) does not benefit positively from Organism (A). <br />
<br />
'''VII. Predation:''' “An interaction between organisms in which one benefits and one is harmed based on the ingestion of the smaller sized organism, the prey, by the larger organism, the predator.”[33]<br />
<br />
<br />
<br />
The soil food web consists of microbes which play an important role in maintaining the complexity of the soil environment. The interactions observed in the food web are not only based on predation, which directly affects the nutrient cycling and degradation of pollutants, but also the formation of aggregates.[35] The production of specific nutrients, such as ammonium created by microbial metabolic functions, helps to enrich the the soil for plant use.[35] Soil organism activity, along with the presence of soil organic matter, create stabilizing aggregates.[35] The hyphae within the soil environment and the microbes help form large, stable aggregates in the soil habitat.[35] The biodiversity in the soil plays a pivotal role in degrading pollutants, and also prevents pathogens from inhabiting the soil environment through competition.[35] The food web in the soil environment is necessary to maintain the soil nutrients, biological activity, and detoxifying pollutants. Thus, it directly maintains cultivation, productiveness and prosperity of the soil. <br />
<br />
In (Figure 2.1), all three domains, Archaea, Bacteria, and Eukarya, are represented in the soil food web. If one takes a closer look at the figure, the soil food web is not only dependent on small and large microbes but also dead organic matter and plant roots. Dead and living matter in the soil environment contribute to maintaining the food web. Plant residues also are apart of the soil food web. They contribute to the soil’s carbon source.[35] The plant residues either, release carbon dioxide to the environment, or contribute to the soil organic matter. Soil organic matter contributes to soil’s richness and helps to form aggregates.[35] The main focus in the image above is the diversity of organisms, both in domains and in size. The larger organisms are usually the predators. The smaller organisms eventually fall prey, due to their limited mobility, respiration, and size. The eukarya and small bacteria are apparent figures seen in the figure above, but archaea also contribute to the food cycle as they break down ammonia for plants to use. [35]<br />
<br />
The notable interactions of life that take place in the soil environment is evident both below-ground level, as seen in the figure 2.1, but also in the above-ground level.[36] Worms also impact the soil food web, acting as both drivers of the food web both belowground and aboveground.[36]<br />
<br />
==3 Domains==<br />
[[Image:Big_Tree_Bold_Letters_white.png|frame|center|Figure 3.1 Phylogenetic Tree of the 3 Domains. From[http://phylogenomics.blogspot.com/2014_02_01_archive.html]]]<br />
<br />
===Carl Woese and Phylogeny===<br />
<br />
[[Image:Carlwoese1_0565_b.jpg|frame|center|Figure 3.2 Carl Woese. From[http://ofbacteriaandmen.blogspot.com/2013/01/the-new-biology-of-carl-woese.html]]] <br />
<br />
Carl Woese (Figure 3.2) was an American microbiologist famous for pioneering the technique of phylogenetic taxonomy through use of a 16S (for prokaryotic) and 18S (for eukaryotic) ribosomal RNA, also known as small subunit ribosomal RNA [46]. This refined Linnaean classification, taking out the guesswork classification by using a gene that was present in every living organism- the small subunit ribosomal RNA. This method of classification is comprehensive because all organisms possess this form of genetic material. Ssu rRNA is sequenced because the genes are highly conserved. Due to their functional constancy, some have variable regions to differentiate organisms, and are easy to sequence. This technique also elucidated the tree of life, which shows the three domains of microbial lineage diversity: Bacteria, Archaea, and Eukarya. DNA can be compared using a sample database that allows identification of unknown organisms to a species level.<br />
<br />
===Domain Bacteria===<br />
<br />
====Introduction to Bacteria==== <br />
Bacteria are single celled prokaryotic organisms that lack membrane bound organelles. They are involved in many important processes within the soil such as decomposition, [https://microbewiki.kenyon.edu/index.php/Bioremediation bioremediation], symbiosis and biological transformation of nutrients. They are present in all terrestrial soil environments.[1] Soil is a heterogenous environment that varies in moisture content, temperature, oxygen requirements, carbon source and many other bacterial growth conditions. Those wide ranging growth factors account for the enormous diversity in soil bacteria populations. One gram of soil can contain between 26,000 to 52,000 different bacterial species.[13] In the entire microbial world, only about 1 percent of bacterial species can be cultured under laboratory conditions which leaves an immense number of bacterial species yet to be described. [14]<br />
<br />
Classification based on phenotypic characteristics, such as cellular morphology, metabolism, gram staining, oxygen requirements, carbon source and other traits, was used more readily before modern DNA sequencing. But, phenotypic classification is still used and Bergey’s Manual of Systematic Bacteriology is the most widely used source for determining species based on characteristic species traits.<br />
<br />
Traditional species definitions are not as useful in bacteria. OTUs, or operational taxonomic units, based on DNA sequencing similarity, are more applicable to bacteria. Typically, those bacteria with 97 percent similar DNA sequence are classified within the same OTU.[15] The 16S small subunit ribosomal RNA is used to substantiate phylogenetic relationships between different bacterial groups.<br />
<br />
====Morphology====<br />
<br />
Bacterial cells measure approximately 1μm wide and 1-5μm long.[12] They are smaller than eukaryotic microbes.Due to their small size, bacteria can more easily adapt to changing soil environments than larger eukaryotes.[1] Most bacteria are singled celled, but actinomycetes grow in branching filaments. There are many different bacterial cell shapes. The most common are bacilli (rods), cocci (spheres), spirilla (spirals) and actinomycete (filaments).<br />
[[Image:bacteria_sizes.jpg|frame|center|Figure 3.3 Common cell shapes cocci, bacillus, and spirilla and relative sizes. From[http://www.ppdictionary.com/gnbac.htm]]]<br />
<br />
'''Flagella''' - There are many different types and different arrangement of flagella. Movement in soil environments is dependent on soil moisture content. Though movement in soil is limited, flagellar function is important to allow bacteria to find more favorable microsites.[1]<br />
<br />
'''Cell membrane''' - The cell membrane encloses the cytoplasm. It is semi-permeable phospholipid bilayer that regulates transport of nutrients into the cell and waste products out of the cell.<br />
<br />
'''Cell wall''' - Most bacteria have a rigid cell wall surrounding the cell membrane which protects the cell from osmotic lysis. The cell wall is made of a crosslinked polysaccharide, called peptidoglycan, that is found only in bacteria.[1] The cell wall gives the cell shape and structure, but it is porous enough to permit small water soluble molecules to flow through to the cell membrane surface.[1]<br />
<br />
*'''Gram positive''' bacteria have a thick cell wall made of several layers of peptidoglycan. The cell wall is the outermost structure, as they do not have an outer membrane. The thick cell wall structure make gram positive bacteria more resilient to osmotic shock. Gram positive bacteria can tolerate 5 to 10 times more turgor pressure than gram Gram negative bacteria.[1] Teichoic acids in the cell wall may also help to bind to cationic nutrients in soil surroundings.[1] <br />
<br />
*'''Gram negative''' bacteria have a thin cell wall surrounded by an outer membrane made of phospholipids and lipopolysaccharides. Polysaccharides of the outer membrane interact with surrounding cations and are involved in attachment of bacteria to soil particles. [1] Periplasm is a gel like substance that occupies the space between the outer membrane and the cell wall of gram negative bacteria.[1] The outer membrane and periplasmic space is thought to provide protection from environmental toxins.[1] Proteins within the periplasm are thought to begin the process of catalyzing hydrolysis of organic and toxic substances.[1] <br />
<br />
[[Image:gramposnegmembrane.jpg|frame|center| Figure 3.4 Illustration of Gram positive and Gram negative cell wall structures. From[http://micro.digitalproteus.com/morphology2.php]]]<br />
<br />
'''Endospores''' are made by ''Bacillus'' and ''Clostridium'' in response to environmental stress.[1] Endospores are extremely resistant structures that can withstand extreme temperatures up to 150℃.[12] They can also withstand extreme pressure, desiccation, radiation, pH and chemicals.[12] The endospore protects the bacterial DNA until environmental conditions are more favorable and germination can proceed. Soil is the most common habitat for endospore forming bacteria.[12]<br />
<br />
'''Extracellular polymers''' - Many bacteria secrete a slime layer or capsule made of polysaccharides or glycoproteins.[1] The outer polysaccharide coating of bacteria helps in attachment to surfaces and the formation of biofilms.[1] Bacterial capsule secretions play a big role in soil aggregation and soil structure.[1] When the carbon to nitrogen ratio within soils is high, microbes secrete the excess carbon as extracellular polysaccharides.[1]<br />
<br />
====Reproduction==== <br />
Most bacteria reproduce by binary fission.[12] The bacterial cell expands to twice the original cell size, duplicates the bacterial DNA and pinches off, producing two daughter cells. Each resultant daughter cell is a clone of the parent cell. Prokaryotic Archaea also reproduce by binary fission.<br />
<br />
*'''Spore formation:''' Actinomycetes are a large group of filamentous bacteria, primarily found in soil.[1] Actinomycetes are morphologically similar to fungi. Actinomycetes form long filaments called hyphae. Unlike most bacteria, the majority of actinomycetes reproduce using asexual spores called conidia.[1] Though they share many characteristic with fungi, actinomycetes are still prokaryotes. They are smaller than fungi and the cell wall contains peptidoglycan.[1] Actinomycetes break down a wide variety of organic compounds and play an important role in organic matter decomposition. [1] ''Streptomyces'', a subgroup within actinomycetes, produce geosmin, which gives soil the characteristic earthy smell.[12]<br />
<br />
====Metabolism==== <br />
<br />
Along with archaea, bacteria are the most metabolically diverse and employ many different nutritional strategies.[1]<br />
*Heterotrophs - Most bacteria are heterotrophic, obtaining carbon from preformed organic substances. [1] <br />
*Autotrophs - Carbon dioxide serves as the main source of carbon. Some cyanobacteria, nitrifying and sulfur-oxidizing bacteria are autotrophs.[1]<br />
*Organotrophs - Most bacteria obtain electrons from organic substances.[1]<br />
*Lithotrophs - Some cyanobacteria, nitrifying bacteria and sulfur-oxidizing bacteria obtain electrons from inorganic substances.[1]<br />
*Phototrophs - Cyanobacteria use light as the main source of metabolic energy.[1]<br />
*Chemotrophs - All other nonphotosynthetic bacteria do not rely on light for metabolic energy.[1]<br />
<br />
====Contributions to the Cycle==== <br />
<br />
Bacteria play a significant role in the cycling of a wide range of elements.<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Carbon_cycle '''Carbon Cycle:'''] <br />
<br />
*'''Carbon Assimilation''' is the process of fixing carbon dioxide into organic forms. Carbon fixation is performed by autotrophic bacteria, such as cyanobacteria.[1] Chemoautotrophic nitrifying bacteria, such as ''Nitrobacter, Nitrosospira'' and ''Nitrosomonas'', also fix carbon.[1] Sulfur oxidizing bacteria, such as ''Thiobacillus'', fix carbon as well.<br />
<br />
*'''Carbon Mineralization''' results from microbial decomposition of organic carbon compounds into inorganic forms. As the organic carbon substances, like plant matter, are decomposed, inorganic carbon dioxide is produced. Most bacteria are heterotrophs that perform carbon mineralization. When microorganisms die, they are decomposed by successive microbial generations. Peptidoglycan, the main component of bacterial cell walls, is utilized as a polysaccharide substrate by other heterotrophic soil microbes.[1]<br />
<br />
*'''Methanogenesis''' - Methanogenic bacteria produce methane from the reduction of carbon dioxide. They are all strict anaerobes that use carbon dioxide for the carbon source.[1] They can all use hydrogen as a source of energy and electron donor. [1]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle '''Nitrogen cycle:''']<br />
<br />
*'''Nitrogen fixation:''' ''Azotobacter'' is a free living nitrogen fixing bacteria.[1] ''Rhizobium'' lives in a mutualistic relationship with plants by fixing nitrogen within root the nodules of legumes.[1] ''Anabaena'' and ''Nostoc'' have specialized heterocyte structures where nitrogen fixation occurs.[1] <br />
<br />
*'''Nitrification:''' Nitrifying bacteria, such as ''Nitrobacter, Nitrosospira,'' and ''Nitrosomonas'', oxidize ammonium to nitrate.[1] <br />
<br />
*'''Denitrification:''' ''Alcaligenes, Flavobacterium'', and ''Pseudomonas'' are common soil denitrifying bacteria.[1]<br />
<br />
===Domain Archaea===<br />
<br />
====Introduction to Archaea====<br />
<br />
Vladimir Vernadsky decided, in 1926, that only two domains of life existed on Earth, Bacteria and Eukarya.[37] About 50 years later in 1977, Carl Woese and George Fox theorized that part of the bacterial domain possed multiple dissimilarities from bacteria and recognized it to be another domain of life, now called Archaea.[38] Woese and Fox’s theory regarding the differences of archaea were confirmed in 1990’s through the use of 16S rRNA and 18S rRNA.[38] <br />
<br />
Despite the strongly held belief, in the 1990s, that archaea only inhabited extreme environments, recent discoveries have suggested their presence in abundant numbers all throughout the Earth. It is suggested that Archaea play notable roles in maintaining nutrient cycles.[37] Various methods of research, such as cultivation, culture-independent techniques and isotope-based methods, have facilitated the study of domain Archaea in carbon and nitrogen cycling. [37]<br />
<br />
The use of genomic and biochemical data has permitted the study of archaeal structure.[37] Use of these research methods has shown that domain archaea and domain bacteria differ in cell wall characteristics yet, share various ways to transfer genetic information by replication and transcription from their common ancestor, Eukarya.[37] As of 2012, 116 genera of Archaea have been observed which consists of 450 species. Most of the archaeal species in these genera remains uncultivated, known only through its gene sequences and molecular surveys.[37]<br />
<br />
====Morphology==== <br />
Archaea are characterized by various cell sizes. They are most commonly found to be small organisms ranging from “0.1 to 15 μ diameter and up to 200 μ long.”[38] The shape of many archaea are similar to bacteria, including bacillus, cocci, spirilla and “plate-like forms.” [38] Their cell membranes have ether linked lipids with no periplasmic space, similar to gram-positive bacteria, and contain no intracellular organelles.[39]<br />
<br />
'''Flagella:''' Most motile archaea inhabit a motor rotary system that allows it to move its flagella through the chemical gradient similar to bacteria.[39] Despite its similarity in function and source of energy required for motility, the flagella of both archaea and bacteria differ in structure.[39] Archaeal flagella gets the energy for its movement by ATP and is composed of dependent filaments that rotate singularly. [40] Archaeal flagella are known to be thinner than bacteria flagellin.[40] Since, the archaeal common ancestor is not bacteria but eukarya, convergent evolution is a plausible explanations for the differences between bacterial and archaeal flagellin. [40]<br />
<br />
'''Membranes:''' Archaea have a cell membrane that protects the cytoplasm and the nucleic acids from the environment. The archaeal cell membrane has a lipid bilayer with glycol-ether lipids that are more stable than ester linkages and help some archaea that live in extreme environments to withstand such conditions.[39] Most archaeal species are surrounded by a cell wall which protects the cell membrane and maintains the archaeal structure.[41]<br />
<br />
====Reproduction====<br />
Archaeal organisms reproduce by binary fission since they do not have nucleases thus, the DNA chromosome in a Archaeal organism replicate, separate and create two daughter cells.[43] The process of binary fission can be seen in Figure (3.5) process begins the parent cell duplicating the DNA. The DNA material then goes to the sides of the cell where an invagination to the cell occurs allowing the cell to become two individual cells. Binary fission is a very fast reproduction process, that allows archaeal organisms to grow at an exponential rate.[44]<br />
<br />
[[Image:WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg|frame|center|Figure 3.5 Illustration of binary fission. From[https://d2jmvrsizmvf4x.cloudfront.net/WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg]]]<br />
<br />
====Metabolism==== <br />
Archaea share similar metabolic characteristics to bacteria. The metabolic pathways taken by all archaea shown in the (Figure 3.6) demonstrates the great diversity and variation amongst archaea. [38] The kinds of archaea that are seen in the environment and the metabolic pathways taken by some can be summarized in the image. <br />
<br />
*Photoautotrophs: use light as an energy source and carbon dioxide as the carbon source with the help of the Calvin Cycle.[38]<br />
*Chemoautotrophs: use inorganic chemicals as their energy source and carbon dioxide as carbon source. <br />
*Chemoheterotrophs: take organic chemicals as energy source and organic chemicals as carbon source. The pathways taken by chemoheterotrophs varies from respiration by the Krebs Cycle to fermentation. [38]<br />
*Photoheterotrophs: use light as their energy source and organic chemicals as their carbon source. <br />
<br />
Most archaea inhabiting in the soil environment are major contributors to the biogeochemical cycles.<br />
<br />
[[Image:2000px-Troph_flowchart.svg.png|thumbnail|center|Figure 3.6 Flowchart showing different metabolic pathways. From[https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Troph_flowchart.svg/2000px-Troph_flowchart.svg.png]]]<br />
<br />
====Contributions to the Cycle====<br />
Archaea play a significant role in the nutrient cycles that take place in the ecosystem as they account for about 1-5% of all the prokaryotes present in the soil environment.[42]<br />
<br />
'''Carbon Cycle:''' Archaea have an important role in the carbon cycle that takes place specifically in methane production, carbon mineralization and carbon assimilation all of all of which contribute to the soil’s carbon sink.[42] The carbon dense soil helps to make the soil organic matter rich and helps to form extracellular polymers which creates stable aggregates. For some microbes, an electron acceptor is need to carry out metabolic functions. [42] More info on [https://microbewiki.kenyon.edu/index.php/Carbon_cycle Carbon Cycle].<br />
<br />
*'''Carbon Assimilation:''' Involves the transformation of inorganic carbon into organic carbon compounds. This process is commonly done by autotrophic phyla ''Crenarchaeota, Thaumarchaeota'', and ''Euryarchaeota'' that use carbon dioxide/ bicarbonate converting it to organic compounds.[42] Of the autotrophic lineages observed in carbon assimilation the ''Thaumarchaeota'' are strict autotrophs, the ''Euryarchaeota'' and ''Crenarchaeota'' are facultative autotrophs and the ''Halobacteriales'' and ''Thermococcales'' are obligate heterotrophs.[42] <br />
<br />
*'''Carbon Mineralization:''' The process that converts organic carbon into the oxidized inorganic carbon, carbon dioxide is commonly done by both aerobes and anaerobes.[42] The heterotrophic microbes that use organic compounds as energy to oxidize the carbon source include, methanogens and methane-oxidizing archaea belonging to the phyla ''Euryarchaetota'', and ''Crenarchaeota''.[42] <br />
<br />
*'''Methanogenesis:''' production of methane, a major greenhouse gas in the Earth’s atmosphere is commonly done by archaea upon reducing an oxidized compound.[42] The phyla ''Euryarchaeota'' is the only phyla that consists of archaea that produce methane all of which form five class: ''Methanopyri, Methanococci, Methanobacteria, Methanomicrobia'' and ''Thermoplasmata''.[42] Methanogens are commonly found in anaerobic and aerobic conditions such as bodies of water, aerated soils and oxygenated waters.[42]<br />
<br />
'''Nitrogen Cycle :''' Archaea play a pivotal role in the Nitrogen cycle and help create nitrogenous products for the plants and microbes. More info on [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle Nitrogen cycle].<br />
<br />
*'''Nitrogen Fixation:''' Fixing nitrogen from the environment and converting it to organic nitrogen in the soil or to inorganic nitrogenous form since both organic and inorganic products are in short supply in the biosphere and are fixed by many archaeal organisms.[42] N2 fixation by the environment is usually done by three major archaeal classes ''Methanobactera, Methanococci'' and ''Methanomicrobia''.[42] <br />
<br />
*'''Nitrification:''' Converting the ammonia (NH4+) in the soil to nitrite (NO2-) produces nitrate (NO3-) as an intermediate. [42] The transformation of ammonia to first nitrate then to nitrite is a two step process that is done by different microbes. [42] Most common organisms involved in nitrification include ammonia-oxidizing archaea which are lithotrophic organisms mostly, of the ''Thaumarchaeota'' phylum from the archaea domain. <br />
<br />
*'''Denitrification :''' The conversion of atmospheric N2 using the electron acceptor NO3- or NO2- creating the formation of nitric oxide, nitrous oxide and/or N2.[42] The formation of the end product N2 may not always be produced but other intermediates NO and N2O, greenhouse gases may be produced.[42] Of the archaeal organisms that have been studied in denitrification process is done by ''Pyrobaculum aerophilum'' which accepts both NO3- and NO2- as an electron acceptor producing a variety of products NO2-, NO, N20 and N2.[42]<br />
<br />
===Domain Eukarya===<br />
<br />
====Fungi====<br />
<br />
=====Introduction=====<br />
<br />
'''Introduction'''<br />
<br />
Fungi comes from the ancient Greek word “sphongos” meaning sponge in reference to the mushroom cap [47]. Fungi have the general characteristics of being eukaryotic, heterotrophic, external absorbers of nutrients, containing a hyphal thallus, reproducing via spore, and being pleomorphic (producing several forms). Fungi are generally organoheterotrophs that can survive in low pH and stay active at low moisture content[46]. Fungi reside in the domain Eukarya with an estimated species of 1.5 million, and less than five percent of them have ever been described. The general phyla included within Kingdom Fungi include Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, Chytridiomycota, and Microsporidia [48].<br />
<br />
[[Image:magical-kingdom-620.jpg|frame|center|Figure 3.7 Fungi phyla hierarchy. From.[http://www.motherjones.com/environment/2009/11/fungi-family-tree]]]<br />
<br />
=====Morphology=====<br />
<br />
'''Morphology''' <br />
<br />
Fungi can be either unicellular (yeasts) or multicellular. All multicellular fungi are made up of small, filamentous particles called hyphae. Some hyphae have cross walls called septa, while others do not- this is a large basis of fungal identification. Fungal cells generally have multiple nuclei. Fungal cell walls are generally composed of chitin, a long carbohydrate polymer that adds rigidity and structural support to fungi [49]. <br />
<br />
=====Reproduction=====<br />
<br />
'''Reproduciton'''<br />
<br />
Fungal reproduction can occur either sexually or asexually.<br />
<br />
'''Sexual reproduction''' can occur by homothallic or heterothallic mycelia.<br />
<br />
'''Asexual reproduction''' can occur by fragmentation, budding, or by producing spores (the most common method). <br />
<br />
*'''Spores:''' spores come in many different forms. One of the most well known are conidiospores, which are unicellular or multicellular spores that get released from the tip of the hyphae. <br />
<br />
'''Perfect fungi''' are those that can reproduce both sexually and asexually while imperfect fungi are those that can only reproduce asexually.<br />
<br />
*Sexual reproduction always includes the stages plasmogamy (fusion of two haploid cells), karyogamy (creation of a diploid zygote), and meiosis (gametes are created).<br />
<br />
=====Metabolism=====<br />
<br />
'''Metabolism'''<br />
<br />
Many different fungi display a myriad of metabolisms. There are primary metabolites that that help the fungi function properly, and secondary metabolites that are generally bioactive that are not the most pertinent to fungal growth (they can live without these). Secondary metabolites play a large role in chemistry today and can be manufactured into commonly used products such as new drugs. In general fungi are heterotrophic through release of extracellular enzymes into the neighboring environment to break complex molecules down into smaller ones. The materials are then absorbed and metabolized [50]. Fungi are sessile organisms that overcome their little to no movement through apical growth at the hyphal tip. Fungi are noted to grow almost everywhere on the Earth.<br />
<br />
=====Relevance to soil===== <br />
<br />
'''Relevance to soil'''<br />
<br />
Fungi include some of the most abundant biomass of microorganisms in numerous soils. They play an important role as decomposers within the soil food web through conversion of difficult to digest organic material into forms many other organisms can use [51]. Their hyphae can bind soil particles together and create aggregates that increase soil water holding capacity. They perform important functions from water dynamics to nutrient cycling and disease suppression. Soil fungi can be categorized into three different groups based on their actions: <br />
<br />
*decomposers: that convert dead organic material into fungal biomass<br />
<br />
*mutualists: which colonize plant roots and help solubilize phosphorous and bring soil nutrients<br />
<br />
*pathogens/ parasites: which help control diseases in soil via trapping organisms such as nematodes [51]. <br />
<br />
Fungi are seen common in intensively managed agricultural soils due to tillage disrupting hyphae. Fungi also play a very important role in the [https://microbewiki.kenyon.edu/index.php/Rhizosphere_Interactions rhizosphere], the region of soil that is greatly influenced by the plant root system. This area of soil which is concentrated in plant roots and fungal hyphae is known to support greater microbial activity.<br />
<br />
====Protista====<br />
<br />
Protists are mainly eukaryotic unicellular organisms. They used to belong to their own kingdom Protista, but are now known to be paraphyletic [18]. Protists are made up of protozoa, unicellular algae, and slime molds. The protozoa are divided into 4 major categories: the ciliates, the flagellates, the heliozoans, and the amoebas [10]. They are so small that they don’t need any specialized organelles in order to survive and can survive at low oxygen levels because of this. They are also known to use a contractile vacuole to remove excess water from their cells [10]. <br />
<br />
=====Protozoans=====<br />
<br />
'''Protozoans'''<br />
<br />
The microbial loop is a subsection of the microbial food web that accounts for the dissolved organic matter of systems. It’s suggested that Protozoa have an important role in the maintenance of soil nutrients, specifically nitrogen. A common known characteristic of protozoans is that they stimulate plant growth [19]. It’s hypothesized that they do this through the manipulation of nitrogen levels. In the presence of Protozoa, shoot biomass and shoot N levels are increased [20]. The protozoa is said to stimulate the mineralization of nitrogen via the microbial loop [20]. The indirect effects protozoans have on the nitrogen cycle are thought to be more important than the direct effects it has. This is because grazing stimulates microbial mineralization processes that in turn speeds up the nutrient cycles [20].<br />
<br />
In general, Protozoans range from 5 to 500 µm in diameter, making them significantly larger than bacteria [21]. They are abundantly located near the surface of the soil (15cm deep) where roots are plentiful [21]. Most protozoans have two life cycles. One is their active form where they are motile and feed on prey. The other is the cyst form where they produce a thick coating to protect them from the environment and can go dormant for years.<br />
<br />
======Ciliates======<br />
<br />
'''Cilliates:'''<br />
This group, within protozoans, is fairly diverse. A common feature shared amongst all of its members is the presence of at least one cilia at any stage of its development [10]. The cilia is used for movement and other things such as predation (tentacles). For movement, they use the massive amounts of tiny cilia to create wave like currents to propel the cell forwards. Most ciliates also have toxicysts which are used to capture prey [10]. Some ciliates even have a symbiotic relationship with algae living inside of them [10]. The algae use the CO2 produced by ciliates and turn it into O2 that can then be reused by the ciliates [10]. They are found in a wide array of habitats ranging from freshwater and soil to the rumen of Animals [22]. They are present in almost anywhere that contains water [23]. They are unicellular heterotrophs so they feed on bacteria and algae in their environment. Ciliates are one of the top predators in the microbial food web and are hypothesized to have been a major predatory group before animals evolved [23]. Parasitic ciliates exist that can cause the death of animals and are increasingly becoming dangerous in water [23].<br />
<br />
[[Image:2spiro.jpg|frame|center|Figure 3.8 Microscope image of ciliated protists. From[http://www.microscopy-uk.org.uk/mag/smallimag/2spiro.jpg]]]<br />
<br />
======Flagellates======<br />
<br />
'''Flagellates''' are one of the most commonly known protists. They are unicellular organisms that may be solitary, colonial, free living, or parasitic [24]. The hallmark feature of protists is that at some point in their life cycle, they possess a flagella. A flagellum is a long hair like structure that is used for locomotion, sensation, and sometimes predation [24]. The flagellum makes waves by whiplike lashing movements which propels the cell forwards. Flagellates also have a protective coating in the form of a thin pellicle to protect them from the environment [24]. <br />
<br />
[[Image:9703607_orig.jpg|frame|center|Figure 3.9 Illustration of flaggelates during different life cycle stages. From[http://diagnosticparasitology.weebly.com/uploads/3/9/5/4/3954522/9703607_orig.jpg]]]<br />
<br />
*'''Mastigophora:'''<br />
<br />
Mastigophora is a subphylum of flagellates. Being a member of the flagellates, their key feature is the flagellum. Their habitats include freshwater, soil, and can act as animal parasites as well [25]. They use pseudopodia, a long outward protrusion, to trap and funnel food from the environment into their cell bodies [25]. The Mastigophora are mainly known for their parasitism, which can take place in both humans and animals [25]. ''Typanosomes'' are an example of Mastigophora which causes African sleeping sickness [25]. ''Giardia lambli''a is another example that resides in the intestinal tract of warm-blooded animals and inflicts intestinal giardiases [25]. It is also a major contaminant of drinking water because it is resistant to chlorine, which is the most common water purifier [25]. Having a dormant cyst form also adds to its survival potential through filtration efforts [25].<br />
<br />
<br />
<br />
*'''Euglenids:'''<br />
<br />
Euglenids are one of the best known flagellates. They are found in freshwater and soil, as long as there are organic materials. They also participate in some symbiotic relationships with marine animals. Euglenid cells do not contain cell walls or other rigid membranes [26]. This gives the cell tremendous flexibility and allows it to change its shape to easily navigate through muddy terrain. Euglenids have two flagella, one which creates locomotion and movement for the cell [26]. The other flagellum does not protrude from the cell and is contained in the cell body [26].<br />
<br />
======Amoebas======<br />
<br />
'''Amoebas'''<br />
<br />
Amoebae are single celled eukaryotes present in many different types of environments. They are scattered throughout a variety of eukaryotic lineages and therefore are not monophyletic [27]. Amoebae range in size from 5 micrometers to 3 mm and don’t have a defined shape, commonly recognized for being polymorphic. They are motile through the use of pseudopodia, which stretch and pull the cell along with it. The pseudopodia are also used for feeding. They are able to sense prey that can be engulfed and engulf them via phagocytosis. The amoeba’s main prey consists of bacteria, algae, and other protozoa [28]. The prey is moved around within the cell via food vacuoles, a feature of amoebae [28]. Another key characteristic of amoebae are the large contractile vacuoles inside the cell. The purpose of the contractile vacuole is to osmoregulate by pumping excess water out of the cell. In times of turmoil, amoebae have an encysted form that helps them get through the tough times. This form is useful when there is low nutrient availability to limit energy consumption. There are two main forms an amoeba can be characterized as. They can either be testate or nontestate. Testate amoeba produce shells, or “tests”, that help identify their species since each species has a unique shell.<br />
<br />
[[Image:Amoeba_(PSF).png|frame|center|Figure 3.10 Amoeba morphology. From[https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Amoeba_(PSF).png/230px-Amoeba_(PSF).png]]]<br />
<br />
=====Slime Molds=====<br />
<br />
'''Slime molds''' were once classified as fungi, but have now been placed in their own phylogenetic groups. Slime molds are single cells that can live independently, but aggregate to form multicellular reproductive structures when necessary [29]. The fruiting body releases spores which germinate into new cells. Slime molds feed off of bacteria and are most commonly found in forests. They feed off of decaying vegetation as well so they can be seen on rotting logs and leaves.<br />
<br />
[[Image:28-30-cellslimemoldlife-l.jpg|frame|center|Figure 3.11 Illustration of slime mold life cycle. From[https://lichencolony.files.wordpress.com/2006/06/28-30-cellslimemoldlife-l.jpg]]]<br />
<br />
==Current Research== <br />
<br />
'''Bacteria:''' To showcase the great diversity of soil bacterial environments, cyanobacteria have been studied in both desert and polar regions. Cyanobacteria can survive in extreme conditions likely because of their long evolutionary past.[16] Dr. Patzelt and his colleagues studied the diverse cyanobacteria residing in the Atacama desert, one of the driest parts of the world. The diverse taxa found in the Atacama desert can withstand prolonged periods of extreme desiccation.[16] The cyanobacteria dominate the soil crusts, affecting soil stability, soil structure and soil fertility.[16] Cyanobacteria inhabiting the Antarctic and Arctic regions, show similar adaptations to extreme environments as the cyanobacteria found in the desert. The polar cyanobacteria are particularly adapted to high altitudes.[17] They can withstand high ultraviolet radiation, desiccation, and repeated freeze-thaw cycles.[17] The autotrophic cyanobacteria supports heterotrophic microbes, providing an important ecosystem service in an environment with low microbial activity.[17]<br />
<br />
'''Archaea:''' In 150 soil samples acquired from North and South America, about 150,000 species were observed.[45] Of these, over 2,500 were identified as archaea based on their ssu rRNA.[45] The archaeal species were further analyzed to understand their role in the soil environment. Of the archaeal groups, ''Crenarchaeota'' and ''Euryarchaeota'' were found.[45] Bates stated that, “Across the non-experimental soils examined the soil C:N ratio was the single best predictor of archaeal relative abundances” due to their influences in the nutrient cycles.[45]<br />
<br />
'''Fungi:''' Fungi have been in the public eye for a while now due to the many different types of secondary metabolites they produce. Some produce bioactive compounds that can inhibit growth of protozoa, bacteria, parasites, insects, and even other fungi. A large area of investigation is the uses of these chemicals for human interests in use from medicine to plant and animal toxins [52].<br />
<br />
'''Protozoa:''' It’s known that Protozoa stimulate plant growth in different ways. It’s suspected that the Protozoa take part in the microbial loop which is responsible for the nutrient production for plants [19]. However, new developments have shown that the Protozoa themselves are responsible for the nitrogen mineralization and that other bacteria have no effect on the plant’s nitrogen sources [19].<br />
<br />
==References==<br />
<br />
1. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). Principles and Applications of Soil Microbiology. New Jersey: Pearson Education Inc.<br />
<br />
2. Ingham, Elaine R. Ingham R. "Chapter 4: SOIL FUNGI." Soil Biology. Natural Resources Conservation Service Illinois, n.d. Web. 9 Feb. 2016<br />
<br />
3. Reid, Greg, and Percy Wong. "SOIL BACTERIA AND FUNGI - NEW SOUTH WALES." Soil Bacteria and Fungi. New South Wales Department of Primary Industries, 2005. Web. 11 Feb. 2016.<br />
<br />
4. "Fungi." Microbiology Online. Microbiology Society, n.d. Web. 11 Feb. 2016.<br />
<br />
5. Tortora, G.J., Funke, B.R., Case, C.L. (2012). “Microbiology an Introduction.” 11th ed. Pearson Benjamin Cummings, San Francisco.<br />
<br />
6. Rizzo, D. “Intro to Fungi.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
7. Rizzo, D. “Ascomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
8. Rizzo, D. “Basidiomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
9. Pegg G.F., Brady B.L. “Verticillium Wilts.” New York, CABI Publishing 2002. Google Books. Web. 11 Feb. 2016. http://books.google.com<br />
<br />
10. Hebert, Paul. "What Is a Protist / What Are Protozoa? - Encyclopedia of Life." Encyclopedia of Life. N.p., n.d. Web. 11 Feb. 2016.http://eol.org/info/456<br />
<br />
11. "MicrobeWorld." Protista. N.p., n.d. Web. 11 Feb. 2016. http://www.microbeworld.org/types-of-microbes/protista<br />
<br />
12. Madigan, M.T., Martinko, J.M. (2006). Brock Biology of Microorganisms. New Jersey: Pearson Prentice Hall.<br />
<br />
13. Roesch, L.F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H.; Camargo, F. A. O.; Farmerie, W. G.; Triplett, E. W.(2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1(4).283-290. <br />
<br />
14. Amann, R.I, Ludwig, W., Schleifer, K.H.(1995).Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology and Molecular Biology Reviews. 59(1). 143-169. <br />
<br />
15. Geers, D., Cohan, F.M., Lawrence J.G., Spratt, B.G., Coenye, T. Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005). Opinion: Re-evaluating prokaryotic species. Nature Reviews Microbiology. 3(9). 733-739.<br />
<br />
16. Patzelt, D.J., Hodac, L., Friedl, T., Pietrasiak, N., Johansen, J.R. (2014). Biodiversity of soil cyanobacteria in the hyper-arid Atacama Desert, Chile. Journal of phycology. 50(4). 698-710. <br />
<br />
17. Makhalanyane, T. P., Valverde, A., Velázquez, D., Gunnigle, E., Van Goethem, M. W., Quesada, A., & Cowan, D. A. (2015). Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats. Biodiversity and Conservation, 24(4), 819-840.<br />
<br />
18. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist>.<br />
<br />
19. Ekelund, Flemming; Saj, Stephane; Vestergård, Mette; Bertaux, Joanne; Mikola, Juha. (2009). “The “soil microbial loop” is not always needed to explain protozoan stimulation of plants”. Soil Biology & Biochemistry. Vol. 41 Issue 11, p2336-2342, 7p.<br />
<br />
20. Bonkowski, Michael. "Protozoa and Plant Growth: The Microbial Loop in Soil Revisited." New Phytologist New Phytol 162.3 (2004): 617-31. Web.<br />
<br />
21. Hoorman, James. "The Role of Soil Protozoa and Nematodes." Fact Sheet (n.d.): n. pag. Ohio State University, 2011. Web.<br />
<br />
22. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist<br />
<br />
23. Lynn, Denis H(Apr 2012) Ciliophora. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001966.pub3]<br />
<br />
24. "flagellate". Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc., 2016. Web. 23 Feb. 2016 <http://www.britannica.com/science/flagellate>.<br />
<br />
25. "Mastigophora." World of Microbiology and Immunology. 2003. Encyclopedia.com. 23 Feb. 2016<http://www.encyclopedia.com>.<br />
<br />
26. “Plant Life." : Euglenoids. N.p., n.d. Web. 23 Feb. 2016. <http://lifeofplant.blogspot.com/2011/04/euglenoids.html><br />
<br />
27. Parales, R.E. and Martin, M. (2015) Microbial Diversity Laboratory Manual, MIC 105L, Winter 2015. Department of Microbiology and Molecular Genetics, College of Biological Sciences, The University of California, Davis.<br />
<br />
28. Arnold, Paul. "What Does an Amoeba Eat? Plus Other Ameoba Info and Questions." Bright Hub. N.p., n.d. Web. 04 Mar. 2016.<br />
<br />
29. "MicrobeWorld." Slime Molds. N.p., n.d. Web. 24 Feb. 2016. <http://www.microbeworld.org/types-of-microbes/protista/slime-molds><br />
<br />
30. Leeuwenhoek., A. V. (2009, November 18). One gram of soil: A microbial biochemical gene library. Retrieved March 13, 2016, from http://www.ncbi.nlm.nih.gov/pubmed/19921459 <br />
<br />
31. Coleman, D. C., Crossley, D. A. & Hendrix, P. F. "Soil food webs: Detritivory and microbiology in soils," in Fundamentals of Soil Ecology, 2nd ed. (Elsevier, 2004) 236-241.<br />
<br />
32. Welcome to Agriinfo.in. (n.d.). Retrieved February 21, 2016, from http://agriinfo.in/?page=topic&superid=5&topicid=172 <br />
<br />
33. Gouthro, T., & Rice, D. (1987, December 15). Interaction Terminology. Retrieved February 21, 2016, from http://www.rpi.edu/dept/chem-eng/Biotech-Environ/MixCul/ecodefn.htm <br />
<br />
34. AMENSALISM. (n.d.). Retrieved February 21, 2016, from https://biostuds.wikispaces.com/AMENSALISM <br />
<br />
35. Natural Resources Conservation Service. (n.d.). Retrieved March 10, 2016, from <br />
http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053865 <br />
<br />
36. Ecological Linkages Between Aboveground and Belowground Biota. (n.d.). Retrieved March 10, 2016, from http://science.sciencemag.org/content/304/5677/1629 <br />
<br />
37. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf<br />
<br />
38. Kingdom Archaea. (n.d.). Retrieved March 10, 2016, from http://plantphys.info/organismal/lechtml/archaea.shtml <br />
<br />
39. What are Archaea? - Encyclopedia of Life. (n.d.). Retrieved March 10, 2016, from http://eol.org/info/457 <br />
<br />
40. Flagellum. (n.d.). Retrieved March 10, 2016, from http://www.newworldencyclopedia.org/entry/Flagellum#Archaeal_flagellum <br />
<br />
41. Archaea: Morphology. (n.d.). Retrieved March 10, 2016, from http://www.ucmp.berkeley.edu/archaea/archaeamm.html <br />
<br />
42. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf <br />
<br />
43. Archaea. (n.d.). Retrieved March 10, 2016, from http://www.eoearth.org/view/article/150172/ <br />
<br />
44. Binary Fission: Cell Division & Reproduction of Prokaryotes. (n.d.). Retrieved March 10, 2016, from http://www.scienceprofonline.com/microbi <br />
<br />
45. Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2010, November 18). Examining the global distribution of dominant archaeal populations in soil. Retrieved February 21, 2016, from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105767/<br />
<br />
46. Scow, K. M. "Lecture 1 Part 1." Lecture, Davis.<br />
<br />
47. Rizzo, D. "Lecture 1." Lecture, Davis.<br />
<br />
48. Rizzo, D. "Lecture 3." Lecture, Davis.<br />
<br />
49. C.J. Alexopoulos & C. W. Mims, Introductory Mycology 3rd edition. 1979. Wiley NY. Web accessed Mar 8, 2016 from http://www.ucmp.berkeley.edu/fungi/fungimm.html<br />
<br />
50. Rizzo, D. "Lecture 2." Lecture, Davis.<br />
<br />
51. Ingham, E. “Chapter 4: Soil Fungi” (2016) Oregon State University. Retrieved Feb. 20, 2016, from http://extension.illinois.edu/soil/SoilBiology/fungi.htm<br />
<br />
52. Keller, N., Turner, G., Bennett, J. “Fungal Secondary Metabolism- from Biochemistry to Genomics.” 2005 Nature Reviews Microbiology p/ 937 to 947.</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Introduction_to_Organisms&diff=128504
Introduction to Organisms
2017-03-05T23:09:18Z
<p>Kmscow: /* Slime Molds */</p>
<hr />
<div>==Introduction== <br />
The soil ecosystem in an important environment that allows both plants and animals to survive, grow and reproduce. The significance of the soil as an ecosystem is at times overlooked despite its major contributions to the environment. The [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] is a complex and varied microbial habitat.[1] The plants and organisms inhabiting the soil contribute to its thriving diversity. Soil life is diverse in morphology, metabolism, size, and many other characteristics. It is believed that “there is sufficient [microbial] DNA in 1 g of soil to extend 1,598km.” [30] Soil is a heterogeneous environment with various zones of rhizosphere, aggregates, organic matter and animal residues.[31] Given each zone is a small component of the larger soil ecosystem, rhizosphere accounts for only 5 to 7 percent of the soil environments but contains over “70 percent of the bacterial- and fungal-feeding nematodes.”[31] <br />
<br />
Since, all three domains of life: archaea, bacteria and eukarya, inhabit the soil environment it is difficult to observe each microbe individually within the soil ecosystem.Only a few representative groups of each domain will be discussed to provide examples of the roles these organisms play in soil. This page attempts to outline the major microbial groups within the diverse soil environment.The interactions between soil microbes amongst the soil microbial diversity. The concept of survival of the fittest is seen in the soil food web, which allows only a selective few with the correct nutrients to thrive in a soil environment. The interactions of soil microbes is not only a part of nature but it also only selects those organisms that are fit for survival, growth and reproduction. The soil food web and symbiotic relationships are used to explain the dynamic interactions between soil organisms.<br />
<br />
==Soil Food Web and Microbial Interactions== <br />
<br />
To survive in a soil environment, an organism must be able to adapt to changing environments and organism interactions. The interactions seen between organisms allows only the fittest to survive, thrive, grow and reproduce in the soil. The only type of interaction shown in (Figure 2.1) is predation. Other common interactions in the soil environment are: <br />
<br />
:[[Image:soil_foodweb72.jpg|frame|center|Figure 2.1 Soil Food Web. From[http://www.exploringnature.org/graphics/foodwebs/soil_foodweb72.jpg]]]<br />
<br />
<br />
'''I. Commensalism:''' Organism (A) benefits from the presence of Organism (B) while (B) is unaffected by the presence of (A).[32]<br />
<br />
'''II. Mutualism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) and becomes a necessary association for each other’s survival. [32] [33]<br />
<br />
'''III. Synergism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) but the relationship is not necessary for survival.[33]<br />
<br />
'''IV. Competition:''' Depending on the organisms this interaction benefits organisms who can readily adapt to the environment and overcome any obstacles needed to survive, grow and reproduce.[33]<br />
<br />
'''V. Amensalism:''' An interaction in which Organisms (A) and (B) develop a partnership where (B) is unaffected by (A) but organism (A) is negatively affected by (B).[34]<br />
<br />
'''VI. Parasitism:''' Organism (A) benefits from Organism (B) but Organism (B) does not benefit positively from Organism (A). <br />
<br />
'''VII. Predation:''' “An interaction between organisms in which one benefits and one is harmed based on the ingestion of the smaller sized organism, the prey, by the larger organism, the predator.”[33]<br />
<br />
<br />
<br />
The soil food web consists of microbes which play an important role in maintaining the complexity of the soil environment. The interactions observed in the food web are not only based on predation, which directly affects the nutrient cycling and degradation of pollutants, but also the formation of aggregates.[35] The production of specific nutrients, such as ammonium created by microbial metabolic functions, helps to enrich the the soil for plant use.[35] Soil organism activity, along with the presence of soil organic matter, create stabilizing aggregates.[35] The hyphae within the soil environment and the microbes help form large, stable aggregates in the soil habitat.[35] The biodiversity in the soil plays a pivotal role in degrading pollutants, and also prevents pathogens from inhabiting the soil environment through competition.[35] The food web in the soil environment is necessary to maintain the soil nutrients, biological activity, and detoxifying pollutants. Thus, it directly maintains cultivation, productiveness and prosperity of the soil. <br />
<br />
In (Figure 2.1), all three domains, Archaea, Bacteria, and Eukarya, are represented in the soil food web. If one takes a closer look at the figure, the soil food web is not only dependent on small and large microbes but also dead organic matter and plant roots. Dead and living matter in the soil environment contribute to maintaining the food web. Plant residues also are apart of the soil food web. They contribute to the soil’s carbon source.[35] The plant residues either, release carbon dioxide to the environment, or contribute to the soil organic matter. Soil organic matter contributes to soil’s richness and helps to form aggregates.[35] The main focus in the image above is the diversity of organisms, both in domains and in size. The larger organisms are usually the predators. The smaller organisms eventually fall prey, due to their limited mobility, respiration, and size. The eukarya and small bacteria are apparent figures seen in the figure above, but archaea also contribute to the food cycle as they break down ammonia for plants to use. [35]<br />
<br />
The notable interactions of life that take place in the soil environment is evident both below-ground level, as seen in the figure 2.1, but also in the above-ground level.[36] Worms also impact the soil food web, acting as both drivers of the food web both belowground and aboveground.[36]<br />
<br />
==3 Domains==<br />
[[Image:Big_Tree_Bold_Letters_white.png|frame|center|Figure 3.1 Phylogenetic Tree of the 3 Domains. From[http://phylogenomics.blogspot.com/2014_02_01_archive.html]]]<br />
<br />
===Carl Woese and Phylogeny===<br />
<br />
[[Image:Carlwoese1_0565_b.jpg|frame|center|Figure 3.2 Carl Woese. From[http://ofbacteriaandmen.blogspot.com/2013/01/the-new-biology-of-carl-woese.html]]] <br />
<br />
Carl Woese (Figure 3.2) was an American microbiologist famous for pioneering the technique of phylogenetic taxonomy through use of a 16S (for prokaryotic) and 18S (for eukaryotic) ribosomal RNA, also known as small subunit ribosomal RNA [46]. This refined Linnaean classification, taking out the guesswork classification by using a gene that was present in every living organism- the small subunit ribosomal RNA. This method of classification is comprehensive because all organisms possess this form of genetic material. Ssu rRNA is sequenced because the genes are highly conserved. Due to their functional constancy, some have variable regions to differentiate organisms, and are easy to sequence. This technique also elucidated the tree of life, which shows the three domains of microbial lineage diversity: Bacteria, Archaea, and Eukarya. DNA can be compared using a sample database that allows identification of unknown organisms to a species level.<br />
<br />
===Domain Bacteria===<br />
<br />
====Introduction to Bacteria==== <br />
Bacteria are single celled prokaryotic organisms that lack membrane bound organelles. They are involved in many important processes within the soil such as decomposition, [https://microbewiki.kenyon.edu/index.php/Bioremediation bioremediation], symbiosis and biological transformation of nutrients. They are present in all terrestrial soil environments.[1] Soil is a heterogenous environment that varies in moisture content, temperature, oxygen requirements, carbon source and many other bacterial growth conditions. Those wide ranging growth factors account for the enormous diversity in soil bacteria populations. One gram of soil can contain between 26,000 to 52,000 different bacterial species.[13] In the entire microbial world, only about 1 percent of bacterial species can be cultured under laboratory conditions which leaves an immense number of bacterial species yet to be described. [14]<br />
<br />
Classification based on phenotypic characteristics, such as cellular morphology, metabolism, gram staining, oxygen requirements, carbon source and other traits, was used more readily before modern DNA sequencing. But, phenotypic classification is still used and Bergey’s Manual of Systematic Bacteriology is the most widely used source for determining species based on characteristic species traits.<br />
<br />
Traditional species definitions are not as useful in bacteria. OTUs, or operational taxonomic units, based on DNA sequencing similarity, are more applicable to bacteria. Typically, those bacteria with 97 percent similar DNA sequence are classified within the same OTU.[15] The 16S small subunit ribosomal RNA is used to substantiate phylogenetic relationships between different bacterial groups.<br />
<br />
====Morphology====<br />
<br />
Bacterial cells measure approximately 1μm wide and 1-5μm long.[12] They are smaller than eukaryotic microbes.Due to their small size, bacteria can more easily adapt to changing soil environments than larger eukaryotes.[1] Most bacteria are singled celled, but actinomycetes grow in branching filaments. There are many different bacterial cell shapes. The most common are bacilli (rods), cocci (spheres), spirilla (spirals) and actinomycete (filaments).<br />
[[Image:bacteria_sizes.jpg|frame|center|Figure 3.3 Common cell shapes cocci, bacillus, and spirilla and relative sizes. From[http://www.ppdictionary.com/gnbac.htm]]]<br />
<br />
'''Flagella''' - There are many different types and different arrangement of flagella. Movement in soil environments is dependent on soil moisture content. Though movement in soil is limited, flagellar function is important to allow bacteria to find more favorable microsites.[1]<br />
<br />
'''Cell membrane''' - The cell membrane encloses the cytoplasm. It is semi-permeable phospholipid bilayer that regulates transport of nutrients into the cell and waste products out of the cell.<br />
<br />
'''Cell wall''' - Most bacteria have a rigid cell wall surrounding the cell membrane which protects the cell from osmotic lysis. The cell wall is made of a crosslinked polysaccharide, called peptidoglycan, that is found only in bacteria.[1] The cell wall gives the cell shape and structure, but it is porous enough to permit small water soluble molecules to flow through to the cell membrane surface.[1]<br />
<br />
*'''Gram positive''' bacteria have a thick cell wall made of several layers of peptidoglycan. The cell wall is the outermost structure, as they do not have an outer membrane. The thick cell wall structure make gram positive bacteria more resilient to osmotic shock. Gram positive bacteria can tolerate 5 to 10 times more turgor pressure than gram Gram negative bacteria.[1] Teichoic acids in the cell wall may also help to bind to cationic nutrients in soil surroundings.[1] <br />
<br />
*'''Gram negative''' bacteria have a thin cell wall surrounded by an outer membrane made of phospholipids and lipopolysaccharides. Polysaccharides of the outer membrane interact with surrounding cations and are involved in attachment of bacteria to soil particles. [1] Periplasm is a gel like substance that occupies the space between the outer membrane and the cell wall of gram negative bacteria.[1] The outer membrane and periplasmic space is thought to provide protection from environmental toxins.[1] Proteins within the periplasm are thought to begin the process of catalyzing hydrolysis of organic and toxic substances.[1] <br />
<br />
[[Image:gramposnegmembrane.jpg|frame|center| Figure 3.4 Illustration of Gram positive and Gram negative cell wall structures. From[http://micro.digitalproteus.com/morphology2.php]]]<br />
<br />
'''Endospores''' are made by ''Bacillus'' and ''Clostridium'' in response to environmental stress.[1] Endospores are extremely resistant structures that can withstand extreme temperatures up to 150℃.[12] They can also withstand extreme pressure, desiccation, radiation, pH and chemicals.[12] The endospore protects the bacterial DNA until environmental conditions are more favorable and germination can proceed. Soil is the most common habitat for endospore forming bacteria.[12]<br />
<br />
'''Extracellular polymers''' - Many bacteria secrete a slime layer or capsule made of polysaccharides or glycoproteins.[1] The outer polysaccharide coating of bacteria helps in attachment to surfaces and the formation of biofilms.[1] Bacterial capsule secretions play a big role in soil aggregation and soil structure.[1] When the carbon to nitrogen ratio within soils is high, microbes secrete the excess carbon as extracellular polysaccharides.[1]<br />
<br />
====Reproduction==== <br />
Most bacteria reproduce by binary fission.[12] The bacterial cell expands to twice the original cell size, duplicates the bacterial DNA and pinches off, producing two daughter cells. Each resultant daughter cell is a clone of the parent cell. Prokaryotic Archaea also reproduce by binary fission.<br />
<br />
*'''Spore formation:''' Actinomycetes are a large group of filamentous bacteria, primarily found in soil.[1] Actinomycetes are morphologically similar to fungi. Actinomycetes form long filaments called hyphae. Unlike most bacteria, the majority of actinomycetes reproduce using asexual spores called conidia.[1] Though they share many characteristic with fungi, actinomycetes are still prokaryotes. They are smaller than fungi and the cell wall contains peptidoglycan.[1] Actinomycetes break down a wide variety of organic compounds and play an important role in organic matter decomposition. [1] ''Streptomyces'', a subgroup within actinomycetes, produce geosmin, which gives soil the characteristic earthy smell.[12]<br />
<br />
====Metabolism==== <br />
<br />
Along with archaea, bacteria are the most metabolically diverse and employ many different nutritional strategies.[1]<br />
*Heterotrophs - Most bacteria are heterotrophic, obtaining carbon from preformed organic substances. [1] <br />
*Autotrophs - Carbon dioxide serves as the main source of carbon. Some cyanobacteria, nitrifying and sulfur-oxidizing bacteria are autotrophs.[1]<br />
*Organotrophs - Most bacteria obtain electrons from organic substances.[1]<br />
*Lithotrophs - Some cyanobacteria, nitrifying bacteria and sulfur-oxidizing bacteria obtain electrons from inorganic substances.[1]<br />
*Phototrophs - Cyanobacteria use light as the main source of metabolic energy.[1]<br />
*Chemotrophs - All other nonphotosynthetic bacteria do not rely on light for metabolic energy.[1]<br />
<br />
====Contributions to the Cycle==== <br />
<br />
Bacteria play a significant role in the cycling of a wide range of elements.<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Carbon_cycle '''Carbon Cycle:'''] <br />
<br />
*'''Carbon Assimilation''' is the process of fixing carbon dioxide into organic forms. Carbon fixation is performed by autotrophic bacteria, such as cyanobacteria.[1] Chemoautotrophic nitrifying bacteria, such as ''Nitrobacter, Nitrosospira'' and ''Nitrosomonas'', also fix carbon.[1] Sulfur oxidizing bacteria, such as ''Thiobacillus'', fix carbon as well.<br />
<br />
*'''Carbon Mineralization''' results from microbial decomposition of organic carbon compounds into inorganic forms. As the organic carbon substances, like plant matter, are decomposed, inorganic carbon dioxide is produced. Most bacteria are heterotrophs that perform carbon mineralization. When microorganisms die, they are decomposed by successive microbial generations. Peptidoglycan, the main component of bacterial cell walls, is utilized as a polysaccharide substrate by other heterotrophic soil microbes.[1]<br />
<br />
*'''Methanogenesis''' - Methanogenic bacteria produce methane from the reduction of carbon dioxide. They are all strict anaerobes that use carbon dioxide for the carbon source.[1] They can all use hydrogen as a source of energy and electron donor. [1]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle '''Nitrogen cycle:''']<br />
<br />
*'''Nitrogen fixation:''' ''Azotobacter'' is a free living nitrogen fixing bacteria.[1] ''Rhizobium'' lives in a mutualistic relationship with plants by fixing nitrogen within root the nodules of legumes.[1] ''Anabaena'' and ''Nostoc'' have specialized heterocyte structures where nitrogen fixation occurs.[1] <br />
<br />
*'''Nitrification:''' Nitrifying bacteria, such as ''Nitrobacter, Nitrosospira,'' and ''Nitrosomonas'', oxidize ammonium to nitrate.[1] <br />
<br />
*'''Denitrification:''' ''Alcaligenes, Flavobacterium'', and ''Pseudomonas'' are common soil denitrifying bacteria.[1]<br />
<br />
===Domain Archaea===<br />
<br />
====Introduction to Archaea====<br />
<br />
Vladimir Vernadsky decided, in 1926, that only two domains of life existed on Earth, Bacteria and Eukarya.[37] About 50 years later in 1977, Carl Woese and George Fox theorized that part of the bacterial domain possed multiple dissimilarities from bacteria and recognized it to be another domain of life, now called Archaea.[38] Woese and Fox’s theory regarding the differences of archaea were confirmed in 1990’s through the use of 16S rRNA and 18S rRNA.[38] <br />
<br />
Despite the strongly held belief, in the 1990s, that archaea only inhabited extreme environments, recent discoveries have suggested their presence in abundant numbers all throughout the Earth. It is suggested that Archaea play notable roles in maintaining nutrient cycles.[37] Various methods of research, such as cultivation, culture-independent techniques and isotope-based methods, have facilitated the study of domain Archaea in carbon and nitrogen cycling. [37]<br />
<br />
The use of genomic and biochemical data has permitted the study of archaeal structure.[37] Use of these research methods has shown that domain archaea and domain bacteria differ in cell wall characteristics yet, share various ways to transfer genetic information by replication and transcription from their common ancestor, Eukarya.[37] As of 2012, 116 genera of Archaea have been observed which consists of 450 species. Most of the archaeal species in these genera remains uncultivated, known only through its gene sequences and molecular surveys.[37]<br />
<br />
====Morphology==== <br />
Archaea are characterized by various cell sizes. They are most commonly found to be small organisms ranging from “0.1 to 15 μ diameter and up to 200 μ long.”[38] The shape of many archaea are similar to bacteria, including bacillus, cocci, spirilla and “plate-like forms.” [38] Their cell membranes have ether linked lipids with no periplasmic space, similar to gram-positive bacteria, and contain no intracellular organelles.[39]<br />
<br />
'''Flagella:''' Most motile archaea inhabit a motor rotary system that allows it to move its flagella through the chemical gradient similar to bacteria.[39] Despite its similarity in function and source of energy required for motility, the flagella of both archaea and bacteria differ in structure.[39] Archaeal flagella gets the energy for its movement by ATP and is composed of dependent filaments that rotate singularly. [40] Archaeal flagella are known to be thinner than bacteria flagellin.[40] Since, the archaeal common ancestor is not bacteria but eukarya, convergent evolution is a plausible explanations for the differences between bacterial and archaeal flagellin. [40]<br />
<br />
'''Membranes:''' Archaea have a cell membrane that protects the cytoplasm and the nucleic acids from the environment. The archaeal cell membrane has a lipid bilayer with glycol-ether lipids that are more stable than ester linkages and help some archaea that live in extreme environments to withstand such conditions.[39] Most archaeal species are surrounded by a cell wall which protects the cell membrane and maintains the archaeal structure.[41]<br />
<br />
====Reproduction====<br />
Archaeal organisms reproduce by binary fission since they do not have nucleases thus, the DNA chromosome in a Archaeal organism replicate, separate and create two daughter cells.[43] The process of binary fission can be seen in Figure (3.5) process begins the parent cell duplicating the DNA. The DNA material then goes to the sides of the cell where an invagination to the cell occurs allowing the cell to become two individual cells. Binary fission is a very fast reproduction process, that allows archaeal organisms to grow at an exponential rate.[44]<br />
<br />
[[Image:WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg|frame|center|Figure 3.5 Illustration of binary fission. From[https://d2jmvrsizmvf4x.cloudfront.net/WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg]]]<br />
<br />
====Metabolism==== <br />
Archaea share similar metabolic characteristics to bacteria. The metabolic pathways taken by all archaea shown in the (Figure 3.6) demonstrates the great diversity and variation amongst archaea. [38] The kinds of archaea that are seen in the environment and the metabolic pathways taken by some can be summarized in the image. <br />
<br />
*Photoautotrophs: use light as an energy source and carbon dioxide as the carbon source with the help of the Calvin Cycle.[38]<br />
*Chemoautotrophs: use inorganic chemicals as their energy source and carbon dioxide as carbon source. <br />
*Chemoheterotrophs: take organic chemicals as energy source and organic chemicals as carbon source. The pathways taken by chemoheterotrophs varies from respiration by the Krebs Cycle to fermentation. [38]<br />
*Photoheterotrophs: use light as their energy source and organic chemicals as their carbon source. <br />
<br />
Most archaea inhabiting in the soil environment are major contributors to the biogeochemical cycles.<br />
<br />
[[Image:2000px-Troph_flowchart.svg.png|thumbnail|center|Figure 3.6 Flowchart showing different metabolic pathways. From[https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Troph_flowchart.svg/2000px-Troph_flowchart.svg.png]]]<br />
<br />
====Contributions to the Cycle====<br />
Archaea play a significant role in the nutrient cycles that take place in the ecosystem as they account for about 1-5% of all the prokaryotes present in the soil environment.[42]<br />
<br />
'''Carbon Cycle:''' Archaea have an important role in the carbon cycle that takes place specifically in methane production, carbon mineralization and carbon assimilation all of all of which contribute to the soil’s carbon sink.[42] The carbon dense soil helps to make the soil organic matter rich and helps to form extracellular polymers which creates stable aggregates. For some microbes, an electron acceptor is need to carry out metabolic functions. [42] More info on [https://microbewiki.kenyon.edu/index.php/Carbon_cycle Carbon Cycle].<br />
<br />
*'''Carbon Assimilation:''' Involves the transformation of inorganic carbon into organic carbon compounds. This process is commonly done by autotrophic phyla ''Crenarchaeota, Thaumarchaeota'', and ''Euryarchaeota'' that use carbon dioxide/ bicarbonate converting it to organic compounds.[42] Of the autotrophic lineages observed in carbon assimilation the ''Thaumarchaeota'' are strict autotrophs, the ''Euryarchaeota'' and ''Crenarchaeota'' are facultative autotrophs and the ''Halobacteriales'' and ''Thermococcales'' are obligate heterotrophs.[42] <br />
<br />
*'''Carbon Mineralization:''' The process that converts organic carbon into the oxidized inorganic carbon, carbon dioxide is commonly done by both aerobes and anaerobes.[42] The heterotrophic microbes that use organic compounds as energy to oxidize the carbon source include, methanogens and methane-oxidizing archaea belonging to the phyla ''Euryarchaetota'', and ''Crenarchaeota''.[42] <br />
<br />
*'''Methanogenesis:''' production of methane, a major greenhouse gas in the Earth’s atmosphere is commonly done by archaea upon reducing an oxidized compound.[42] The phyla ''Euryarchaeota'' is the only phyla that consists of archaea that produce methane all of which form five class: ''Methanopyri, Methanococci, Methanobacteria, Methanomicrobia'' and ''Thermoplasmata''.[42] Methanogens are commonly found in anaerobic and aerobic conditions such as bodies of water, aerated soils and oxygenated waters.[42]<br />
<br />
'''Nitrogen Cycle :''' Archaea play a pivotal role in the Nitrogen cycle and help create nitrogenous products for the plants and microbes. More info on [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle Nitrogen cycle].<br />
<br />
*'''Nitrogen Fixation:''' Fixing nitrogen from the environment and converting it to organic nitrogen in the soil or to inorganic nitrogenous form since both organic and inorganic products are in short supply in the biosphere and are fixed by many archaeal organisms.[42] N2 fixation by the environment is usually done by three major archaeal classes ''Methanobactera, Methanococci'' and ''Methanomicrobia''.[42] <br />
<br />
*'''Nitrification:''' Converting the ammonia (NH4+) in the soil to nitrite (NO2-) produces nitrate (NO3-) as an intermediate. [42] The transformation of ammonia to first nitrate then to nitrite is a two step process that is done by different microbes. [42] Most common organisms involved in nitrification include ammonia-oxidizing archaea which are lithotrophic organisms mostly, of the ''Thaumarchaeota'' phylum from the archaea domain. <br />
<br />
*'''Denitrification :''' The conversion of atmospheric N2 using the electron acceptor NO3- or NO2- creating the formation of nitric oxide, nitrous oxide and/or N2.[42] The formation of the end product N2 may not always be produced but other intermediates NO and N2O, greenhouse gases may be produced.[42] Of the archaeal organisms that have been studied in denitrification process is done by ''Pyrobaculum aerophilum'' which accepts both NO3- and NO2- as an electron acceptor producing a variety of products NO2-, NO, N20 and N2.[42]<br />
<br />
===Domain Eukarya===<br />
<br />
====Fungi====<br />
<br />
=====Introduction=====<br />
<br />
'''Introduction'''<br />
<br />
Fungi comes from the ancient Greek word “sphongos” meaning sponge in reference to the mushroom cap [47]. Fungi have the general characteristics of being eukaryotic, heterotrophic, external absorbers of nutrients, containing a hyphal thallus, reproducing via spore, and being pleomorphic (producing several forms). Fungi are generally organoheterotrophs that can survive in low pH and stay active at low moisture content[46]. Fungi reside in the domain Eukarya with an estimated species of 1.5 million, and less than five percent of them have ever been described. The general phyla included within Kingdom Fungi include Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, Chytridiomycota, and Microsporidia [48].<br />
<br />
[[Image:magical-kingdom-620.jpg|frame|center|Figure 3.7 Fungi phyla hierarchy. From.[http://www.motherjones.com/environment/2009/11/fungi-family-tree]]]<br />
<br />
=====Morphology=====<br />
<br />
'''Morphology''' <br />
<br />
Fungi can be either unicellular (yeasts) or multicellular. All multicellular fungi are made up of small, filamentous particles called hyphae. Some hyphae have cross walls called septa, while others do not- this is a large basis of fungal identification. Fungal cells generally have multiple nuclei. Fungal cell walls are generally composed of chitin, a long carbohydrate polymer that adds rigidity and structural support to fungi [49]. <br />
<br />
=====Reproduction=====<br />
<br />
'''Reproduciton'''<br />
<br />
Fungal reproduction can occur either sexually or asexually.<br />
<br />
'''Sexual reproduction''' can occur by homothallic or heterothallic mycelia.<br />
<br />
'''Asexual reproduction''' can occur by fragmentation, budding, or by producing spores (the most common method). <br />
<br />
*'''Spores:''' spores come in many different forms. One of the most well known are conidiospores, which are unicellular or multicellular spores that get released from the tip of the hyphae. <br />
<br />
'''Perfect fungi''' are those that can reproduce both sexually and asexually while imperfect fungi are those that can only reproduce asexually.<br />
<br />
*Sexual reproduction always includes the stages plasmogamy (fusion of two haploid cells), karyogamy (creation of a diploid zygote), and meiosis (gametes are created).<br />
<br />
=====Metabolism=====<br />
<br />
'''Metabolism'''<br />
<br />
Many different fungi display a myriad of metabolisms. There are primary metabolites that that help the fungi function properly, and secondary metabolites that are generally bioactive that are not the most pertinent to fungal growth (they can live without these). Secondary metabolites play a large role in chemistry today and can be manufactured into commonly used products such as new drugs. In general fungi are heterotrophic through release of extracellular enzymes into the neighboring environment to break complex molecules down into smaller ones. The materials are then absorbed and metabolized [50]. Fungi are sessile organisms that overcome their little to no movement through apical growth at the hyphal tip. Fungi are noted to grow almost everywhere on the Earth.<br />
<br />
=====Relevance to soil===== <br />
<br />
'''Relevance to soil'''<br />
<br />
Fungi include some of the most abundant biomass of microorganisms in numerous soils. They play an important role as decomposers within the soil food web through conversion of difficult to digest organic material into forms many other organisms can use [51]. Their hyphae can bind soil particles together and create aggregates that increase soil water holding capacity. They perform important functions from water dynamics to nutrient cycling and disease suppression. Soil fungi can be categorized into three different groups based on their actions: <br />
<br />
*decomposers: that convert dead organic material into fungal biomass<br />
<br />
*mutualists: which colonize plant roots and help solubilize phosphorous and bring soil nutrients<br />
<br />
*pathogens/ parasites: which help control diseases in soil via trapping organisms such as nematodes [51]. <br />
<br />
Fungi are seen common in intensively managed agricultural soils due to tillage disrupting hyphae. Fungi also play a very important role in the [https://microbewiki.kenyon.edu/index.php/Rhizosphere_Interactions rhizosphere], the region of soil that is greatly influenced by the plant root system. This area of soil which is concentrated in plant roots and fungal hyphae is known to support greater microbial activity.<br />
<br />
====Protista====<br />
<br />
Protists are mainly eukaryotic unicellular organisms. They used to belong to their own kingdom Protista, but are now known to be paraphyletic [18]. Protists are made up of protozoa, unicellular algae, and slime molds. The protozoa are divided into 4 major categories: the ciliates, the flagellates, the heliozoans, and the amoebas [10]. They are so small that they don’t need any specialized organelles in order to survive and can survive at low oxygen levels because of this. They are also known to use a contractile vacuole to remove excess water from their cells [10]. <br />
<br />
=====Protozoans=====<br />
<br />
'''Protozoans'''<br />
<br />
The microbial loop is a subsection of the microbial food web that accounts for the dissolved organic matter of systems. It’s suggested that Protozoa have an important role in the maintenance of soil nutrients, specifically nitrogen. A common known characteristic of protozoans is that they stimulate plant growth [19]. It’s hypothesized that they do this through the manipulation of nitrogen levels. In the presence of Protozoa, shoot biomass and shoot N levels are increased [20]. The protozoa is said to stimulate the mineralization of nitrogen via the microbial loop [20]. The indirect effects protozoans have on the nitrogen cycle are thought to be more important than the direct effects it has. This is because grazing stimulates microbial mineralization processes that in turn speeds up the nutrient cycles [20].<br />
<br />
In general, Protozoans range from 5 to 500 µm in diameter, making them significantly larger than bacteria [21]. They are abundantly located near the surface of the soil (15cm deep) where roots are plentiful [21]. Most protozoans have two life cycles. One is their active form where they are motile and feed on prey. The other is the cyst form where they produce a thick coating to protect them from the environment and can go dormant for years.<br />
<br />
======Ciliates======<br />
<br />
'''Cilliates:'''<br />
This group, within protozoans, is fairly diverse. A common feature shared amongst all of its members is the presence of at least one cilia at any stage of its development [10]. The cilia is used for movement and other things such as predation (tentacles). For movement, they use the massive amounts of tiny cilia to create wave like currents to propel the cell forwards. Most ciliates also have toxicysts which are used to capture prey [10]. Some ciliates even have a symbiotic relationship with algae living inside of them [10]. The algae use the CO2 produced by ciliates and turn it into O2 that can then be reused by the ciliates [10]. They are found in a wide array of habitats ranging from freshwater and soil to the rumen of Animals [22]. They are present in almost anywhere that contains water [23]. They are unicellular heterotrophs so they feed on bacteria and algae in their environment. Ciliates are one of the top predators in the microbial food web and are hypothesized to have been a major predatory group before animals evolved [23]. Parasitic ciliates exist that can cause the death of animals and are increasingly becoming dangerous in water [23].<br />
<br />
[[Image:2spiro.jpg|frame|center|Figure 3.8 Microscope image of ciliated protists. From[http://www.microscopy-uk.org.uk/mag/smallimag/2spiro.jpg]]]<br />
<br />
======Flagellates======<br />
<br />
'''Flagellates''' are one of the most commonly known protists. They are unicellular organisms that may be solitary, colonial, free living, or parasitic [24]. The hallmark feature of protists is that at some point in their life cycle, they possess a flagella. A flagellum is a long hair like structure that is used for locomotion, sensation, and sometimes predation [24]. The flagellum makes waves by whiplike lashing movements which propels the cell forwards. Flagellates also have a protective coating in the form of a thin pellicle to protect them from the environment [24]. <br />
<br />
[[Image:9703607_orig.jpg|frame|center|Figure 3.9 Illustration of flaggelates during different life cycle stages. From[http://diagnosticparasitology.weebly.com/uploads/3/9/5/4/3954522/9703607_orig.jpg]]]<br />
<br />
*'''Mastigophora:'''<br />
<br />
Mastigophora is a subphylum of flagellates. Being a member of the flagellates, their key feature is the flagellum. Their habitats include freshwater, soil, and can act as animal parasites as well [25]. They use pseudopodia, a long outward protrusion, to trap and funnel food from the environment into their cell bodies [25]. The Mastigophora are mainly known for their parasitism, which can take place in both humans and animals [25]. ''Typanosomes'' are an example of Mastigophora which causes African sleeping sickness [25]. ''Giardia lambli''a is another example that resides in the intestinal tract of warm-blooded animals and inflicts intestinal giardiases [25]. It is also a major contaminant of drinking water because it is resistant to chlorine, which is the most common water purifier [25]. Having a dormant cyst form also adds to its survival potential through filtration efforts [25].<br />
<br />
<br />
<br />
*'''Euglenids:'''<br />
<br />
Euglenids are one of the best known flagellates. They are found in freshwater and soil, as long as there are organic materials. They also participate in some symbiotic relationships with marine animals. Euglenid cells do not contain cell walls or other rigid membranes [26]. This gives the cell tremendous flexibility and allows it to change its shape to easily navigate through muddy terrain. Euglenids have two flagella, one which creates locomotion and movement for the cell [26]. The other flagellum does not protrude from the cell and is contained in the cell body [26].<br />
<br />
======Amoebas======<br />
<br />
'''Amoebas'''<br />
<br />
Amoebae are single celled eukaryotes present in many different types of environments. They are scattered throughout a variety of eukaryotic lineages and therefore are not monophyletic [27]. Amoebae range in size from 5 micrometers to 3 mm and don’t have a defined shape, commonly recognized for being polymorphic. They are motile through the use of pseudopodia, which stretch and pull the cell along with it. The pseudopodia are also used for feeding. They are able to sense prey that can be engulfed and engulf them via phagocytosis. The amoeba’s main prey consists of bacteria, algae, and other protozoa [28]. The prey is moved around within the cell via food vacuoles, a feature of amoebae [28]. Another key characteristic of amoebae are the large contractile vacuoles inside the cell. The purpose of the contractile vacuole is to osmoregulate by pumping excess water out of the cell. In times of turmoil, amoebae have an encysted form that helps them get through the tough times. This form is useful when there is low nutrient availability to limit energy consumption. There are two main forms an amoeba can be characterized as. They can either be testate or nontestate. Testate amoeba produce shells, or “tests”, that help identify their species since each species has a unique shell.<br />
<br />
[[Image:Amoeba_(PSF).png|frame|center|Figure 3.10 Amoeba morphology. From[https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Amoeba_(PSF).png/230px-Amoeba_(PSF).png]]]<br />
<br />
=====Slime Molds=====<br />
<br />
'''Slime molds''' were at once classified as fungi, but have now been placed in their own phylogenetic groups. Slime molds are single cells that can live independently, but aggregate to form multicellular reproductive structures when necessary [29]. The fruiting body releases spores which germinate into new cells. Slime molds feed off of bacteria and are most commonly found in forests. They feed off of decaying vegetation as well so they can be seen on rotting logs and leaves.<br />
<br />
[[Image:28-30-cellslimemoldlife-l.jpg|frame|center|Figure 3.11 Illustration of slime mold life cycle. From[https://lichencolony.files.wordpress.com/2006/06/28-30-cellslimemoldlife-l.jpg]]]<br />
<br />
==Current Research== <br />
<br />
'''Bacteria:''' To showcase the great diversity of soil bacterial environments, cyanobacteria have been studied in both desert and polar regions. Cyanobacteria can survive in extreme conditions likely because of their long evolutionary past.[16] Dr. Patzelt and his colleagues studied the diverse cyanobacteria residing in the Atacama desert, one of the driest parts of the world. The diverse taxa found in the Atacama desert can withstand prolonged periods of extreme desiccation.[16] The cyanobacteria dominate the soil crusts, affecting soil stability, soil structure and soil fertility.[16] Cyanobacteria inhabiting the Antarctic and Arctic regions, show similar adaptations to extreme environments as the cyanobacteria found in the desert. The polar cyanobacteria are particularly adapted to high altitudes.[17] They can withstand high ultraviolet radiation, desiccation, and repeated freeze-thaw cycles.[17] The autotrophic cyanobacteria supports heterotrophic microbes, providing an important ecosystem service in an environment with low microbial activity.[17]<br />
<br />
'''Archaea:''' In 150 soil samples acquired from North and South America, about 150,000 species were observed.[45] Of these, over 2,500 were identified as archaea based on their ssu rRNA.[45] The archaeal species were further analyzed to understand their role in the soil environment. Of the archaeal groups, ''Crenarchaeota'' and ''Euryarchaeota'' were found.[45] Bates stated that, “Across the non-experimental soils examined the soil C:N ratio was the single best predictor of archaeal relative abundances” due to their influences in the nutrient cycles.[45]<br />
<br />
'''Fungi:''' Fungi have been in the public eye for a while now due to the many different types of secondary metabolites they produce. Some produce bioactive compounds that can inhibit growth of protozoa, bacteria, parasites, insects, and even other fungi. A large area of investigation is the uses of these chemicals for human interests in use from medicine to plant and animal toxins [52].<br />
<br />
'''Protozoa:''' It’s known that Protozoa stimulate plant growth in different ways. It’s suspected that the Protozoa take part in the microbial loop which is responsible for the nutrient production for plants [19]. However, new developments have shown that the Protozoa themselves are responsible for the nitrogen mineralization and that other bacteria have no effect on the plant’s nitrogen sources [19].<br />
<br />
==References==<br />
<br />
1. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). Principles and Applications of Soil Microbiology. New Jersey: Pearson Education Inc.<br />
<br />
2. Ingham, Elaine R. Ingham R. "Chapter 4: SOIL FUNGI." Soil Biology. Natural Resources Conservation Service Illinois, n.d. Web. 9 Feb. 2016<br />
<br />
3. Reid, Greg, and Percy Wong. "SOIL BACTERIA AND FUNGI - NEW SOUTH WALES." Soil Bacteria and Fungi. New South Wales Department of Primary Industries, 2005. Web. 11 Feb. 2016.<br />
<br />
4. "Fungi." Microbiology Online. Microbiology Society, n.d. Web. 11 Feb. 2016.<br />
<br />
5. Tortora, G.J., Funke, B.R., Case, C.L. (2012). “Microbiology an Introduction.” 11th ed. Pearson Benjamin Cummings, San Francisco.<br />
<br />
6. Rizzo, D. “Intro to Fungi.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
7. Rizzo, D. “Ascomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
8. Rizzo, D. “Basidiomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
9. Pegg G.F., Brady B.L. “Verticillium Wilts.” New York, CABI Publishing 2002. Google Books. Web. 11 Feb. 2016. http://books.google.com<br />
<br />
10. Hebert, Paul. "What Is a Protist / What Are Protozoa? - Encyclopedia of Life." Encyclopedia of Life. N.p., n.d. Web. 11 Feb. 2016.http://eol.org/info/456<br />
<br />
11. "MicrobeWorld." Protista. N.p., n.d. Web. 11 Feb. 2016. http://www.microbeworld.org/types-of-microbes/protista<br />
<br />
12. Madigan, M.T., Martinko, J.M. (2006). Brock Biology of Microorganisms. New Jersey: Pearson Prentice Hall.<br />
<br />
13. Roesch, L.F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H.; Camargo, F. A. O.; Farmerie, W. G.; Triplett, E. W.(2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1(4).283-290. <br />
<br />
14. Amann, R.I, Ludwig, W., Schleifer, K.H.(1995).Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology and Molecular Biology Reviews. 59(1). 143-169. <br />
<br />
15. Geers, D., Cohan, F.M., Lawrence J.G., Spratt, B.G., Coenye, T. Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005). Opinion: Re-evaluating prokaryotic species. Nature Reviews Microbiology. 3(9). 733-739.<br />
<br />
16. Patzelt, D.J., Hodac, L., Friedl, T., Pietrasiak, N., Johansen, J.R. (2014). Biodiversity of soil cyanobacteria in the hyper-arid Atacama Desert, Chile. Journal of phycology. 50(4). 698-710. <br />
<br />
17. Makhalanyane, T. P., Valverde, A., Velázquez, D., Gunnigle, E., Van Goethem, M. W., Quesada, A., & Cowan, D. A. (2015). Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats. Biodiversity and Conservation, 24(4), 819-840.<br />
<br />
18. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist>.<br />
<br />
19. Ekelund, Flemming; Saj, Stephane; Vestergård, Mette; Bertaux, Joanne; Mikola, Juha. (2009). “The “soil microbial loop” is not always needed to explain protozoan stimulation of plants”. Soil Biology & Biochemistry. Vol. 41 Issue 11, p2336-2342, 7p.<br />
<br />
20. Bonkowski, Michael. "Protozoa and Plant Growth: The Microbial Loop in Soil Revisited." New Phytologist New Phytol 162.3 (2004): 617-31. Web.<br />
<br />
21. Hoorman, James. "The Role of Soil Protozoa and Nematodes." Fact Sheet (n.d.): n. pag. Ohio State University, 2011. Web.<br />
<br />
22. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist<br />
<br />
23. Lynn, Denis H(Apr 2012) Ciliophora. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001966.pub3]<br />
<br />
24. "flagellate". Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc., 2016. Web. 23 Feb. 2016 <http://www.britannica.com/science/flagellate>.<br />
<br />
25. "Mastigophora." World of Microbiology and Immunology. 2003. Encyclopedia.com. 23 Feb. 2016<http://www.encyclopedia.com>.<br />
<br />
26. “Plant Life." : Euglenoids. N.p., n.d. Web. 23 Feb. 2016. <http://lifeofplant.blogspot.com/2011/04/euglenoids.html><br />
<br />
27. Parales, R.E. and Martin, M. (2015) Microbial Diversity Laboratory Manual, MIC 105L, Winter 2015. Department of Microbiology and Molecular Genetics, College of Biological Sciences, The University of California, Davis.<br />
<br />
28. Arnold, Paul. "What Does an Amoeba Eat? Plus Other Ameoba Info and Questions." Bright Hub. N.p., n.d. Web. 04 Mar. 2016.<br />
<br />
29. "MicrobeWorld." Slime Molds. N.p., n.d. Web. 24 Feb. 2016. <http://www.microbeworld.org/types-of-microbes/protista/slime-molds><br />
<br />
30. Leeuwenhoek., A. V. (2009, November 18). One gram of soil: A microbial biochemical gene library. Retrieved March 13, 2016, from http://www.ncbi.nlm.nih.gov/pubmed/19921459 <br />
<br />
31. Coleman, D. C., Crossley, D. A. & Hendrix, P. F. "Soil food webs: Detritivory and microbiology in soils," in Fundamentals of Soil Ecology, 2nd ed. (Elsevier, 2004) 236-241.<br />
<br />
32. Welcome to Agriinfo.in. (n.d.). Retrieved February 21, 2016, from http://agriinfo.in/?page=topic&superid=5&topicid=172 <br />
<br />
33. Gouthro, T., & Rice, D. (1987, December 15). Interaction Terminology. Retrieved February 21, 2016, from http://www.rpi.edu/dept/chem-eng/Biotech-Environ/MixCul/ecodefn.htm <br />
<br />
34. AMENSALISM. (n.d.). Retrieved February 21, 2016, from https://biostuds.wikispaces.com/AMENSALISM <br />
<br />
35. Natural Resources Conservation Service. (n.d.). Retrieved March 10, 2016, from <br />
http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053865 <br />
<br />
36. Ecological Linkages Between Aboveground and Belowground Biota. (n.d.). Retrieved March 10, 2016, from http://science.sciencemag.org/content/304/5677/1629 <br />
<br />
37. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf<br />
<br />
38. Kingdom Archaea. (n.d.). Retrieved March 10, 2016, from http://plantphys.info/organismal/lechtml/archaea.shtml <br />
<br />
39. What are Archaea? - Encyclopedia of Life. (n.d.). Retrieved March 10, 2016, from http://eol.org/info/457 <br />
<br />
40. Flagellum. (n.d.). Retrieved March 10, 2016, from http://www.newworldencyclopedia.org/entry/Flagellum#Archaeal_flagellum <br />
<br />
41. Archaea: Morphology. (n.d.). Retrieved March 10, 2016, from http://www.ucmp.berkeley.edu/archaea/archaeamm.html <br />
<br />
42. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf <br />
<br />
43. Archaea. (n.d.). Retrieved March 10, 2016, from http://www.eoearth.org/view/article/150172/ <br />
<br />
44. Binary Fission: Cell Division & Reproduction of Prokaryotes. (n.d.). Retrieved March 10, 2016, from http://www.scienceprofonline.com/microbi <br />
<br />
45. Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2010, November 18). Examining the global distribution of dominant archaeal populations in soil. Retrieved February 21, 2016, from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105767/<br />
<br />
46. Scow, K. M. "Lecture 1 Part 1." Lecture, Davis.<br />
<br />
47. Rizzo, D. "Lecture 1." Lecture, Davis.<br />
<br />
48. Rizzo, D. "Lecture 3." Lecture, Davis.<br />
<br />
49. C.J. Alexopoulos & C. W. Mims, Introductory Mycology 3rd edition. 1979. Wiley NY. Web accessed Mar 8, 2016 from http://www.ucmp.berkeley.edu/fungi/fungimm.html<br />
<br />
50. Rizzo, D. "Lecture 2." Lecture, Davis.<br />
<br />
51. Ingham, E. “Chapter 4: Soil Fungi” (2016) Oregon State University. Retrieved Feb. 20, 2016, from http://extension.illinois.edu/soil/SoilBiology/fungi.htm<br />
<br />
52. Keller, N., Turner, G., Bennett, J. “Fungal Secondary Metabolism- from Biochemistry to Genomics.” 2005 Nature Reviews Microbiology p/ 937 to 947.</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Introduction_to_Organisms&diff=128503
Introduction to Organisms
2017-03-05T23:08:24Z
<p>Kmscow: /* Current Research */</p>
<hr />
<div>==Introduction== <br />
The soil ecosystem in an important environment that allows both plants and animals to survive, grow and reproduce. The significance of the soil as an ecosystem is at times overlooked despite its major contributions to the environment. The [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] is a complex and varied microbial habitat.[1] The plants and organisms inhabiting the soil contribute to its thriving diversity. Soil life is diverse in morphology, metabolism, size, and many other characteristics. It is believed that “there is sufficient [microbial] DNA in 1 g of soil to extend 1,598km.” [30] Soil is a heterogeneous environment with various zones of rhizosphere, aggregates, organic matter and animal residues.[31] Given each zone is a small component of the larger soil ecosystem, rhizosphere accounts for only 5 to 7 percent of the soil environments but contains over “70 percent of the bacterial- and fungal-feeding nematodes.”[31] <br />
<br />
Since, all three domains of life: archaea, bacteria and eukarya, inhabit the soil environment it is difficult to observe each microbe individually within the soil ecosystem.Only a few representative groups of each domain will be discussed to provide examples of the roles these organisms play in soil. This page attempts to outline the major microbial groups within the diverse soil environment.The interactions between soil microbes amongst the soil microbial diversity. The concept of survival of the fittest is seen in the soil food web, which allows only a selective few with the correct nutrients to thrive in a soil environment. The interactions of soil microbes is not only a part of nature but it also only selects those organisms that are fit for survival, growth and reproduction. The soil food web and symbiotic relationships are used to explain the dynamic interactions between soil organisms.<br />
<br />
==Soil Food Web and Microbial Interactions== <br />
<br />
To survive in a soil environment, an organism must be able to adapt to changing environments and organism interactions. The interactions seen between organisms allows only the fittest to survive, thrive, grow and reproduce in the soil. The only type of interaction shown in (Figure 2.1) is predation. Other common interactions in the soil environment are: <br />
<br />
:[[Image:soil_foodweb72.jpg|frame|center|Figure 2.1 Soil Food Web. From[http://www.exploringnature.org/graphics/foodwebs/soil_foodweb72.jpg]]]<br />
<br />
<br />
'''I. Commensalism:''' Organism (A) benefits from the presence of Organism (B) while (B) is unaffected by the presence of (A).[32]<br />
<br />
'''II. Mutualism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) and becomes a necessary association for each other’s survival. [32] [33]<br />
<br />
'''III. Synergism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) but the relationship is not necessary for survival.[33]<br />
<br />
'''IV. Competition:''' Depending on the organisms this interaction benefits organisms who can readily adapt to the environment and overcome any obstacles needed to survive, grow and reproduce.[33]<br />
<br />
'''V. Amensalism:''' An interaction in which Organisms (A) and (B) develop a partnership where (B) is unaffected by (A) but organism (A) is negatively affected by (B).[34]<br />
<br />
'''VI. Parasitism:''' Organism (A) benefits from Organism (B) but Organism (B) does not benefit positively from Organism (A). <br />
<br />
'''VII. Predation:''' “An interaction between organisms in which one benefits and one is harmed based on the ingestion of the smaller sized organism, the prey, by the larger organism, the predator.”[33]<br />
<br />
<br />
<br />
The soil food web consists of microbes which play an important role in maintaining the complexity of the soil environment. The interactions observed in the food web are not only based on predation, which directly affects the nutrient cycling and degradation of pollutants, but also the formation of aggregates.[35] The production of specific nutrients, such as ammonium created by microbial metabolic functions, helps to enrich the the soil for plant use.[35] Soil organism activity, along with the presence of soil organic matter, create stabilizing aggregates.[35] The hyphae within the soil environment and the microbes help form large, stable aggregates in the soil habitat.[35] The biodiversity in the soil plays a pivotal role in degrading pollutants, and also prevents pathogens from inhabiting the soil environment through competition.[35] The food web in the soil environment is necessary to maintain the soil nutrients, biological activity, and detoxifying pollutants. Thus, it directly maintains cultivation, productiveness and prosperity of the soil. <br />
<br />
In (Figure 2.1), all three domains, Archaea, Bacteria, and Eukarya, are represented in the soil food web. If one takes a closer look at the figure, the soil food web is not only dependent on small and large microbes but also dead organic matter and plant roots. Dead and living matter in the soil environment contribute to maintaining the food web. Plant residues also are apart of the soil food web. They contribute to the soil’s carbon source.[35] The plant residues either, release carbon dioxide to the environment, or contribute to the soil organic matter. Soil organic matter contributes to soil’s richness and helps to form aggregates.[35] The main focus in the image above is the diversity of organisms, both in domains and in size. The larger organisms are usually the predators. The smaller organisms eventually fall prey, due to their limited mobility, respiration, and size. The eukarya and small bacteria are apparent figures seen in the figure above, but archaea also contribute to the food cycle as they break down ammonia for plants to use. [35]<br />
<br />
The notable interactions of life that take place in the soil environment is evident both below-ground level, as seen in the figure 2.1, but also in the above-ground level.[36] Worms also impact the soil food web, acting as both drivers of the food web both belowground and aboveground.[36]<br />
<br />
==3 Domains==<br />
[[Image:Big_Tree_Bold_Letters_white.png|frame|center|Figure 3.1 Phylogenetic Tree of the 3 Domains. From[http://phylogenomics.blogspot.com/2014_02_01_archive.html]]]<br />
<br />
===Carl Woese and Phylogeny===<br />
<br />
[[Image:Carlwoese1_0565_b.jpg|frame|center|Figure 3.2 Carl Woese. From[http://ofbacteriaandmen.blogspot.com/2013/01/the-new-biology-of-carl-woese.html]]] <br />
<br />
Carl Woese (Figure 3.2) was an American microbiologist famous for pioneering the technique of phylogenetic taxonomy through use of a 16S (for prokaryotic) and 18S (for eukaryotic) ribosomal RNA, also known as small subunit ribosomal RNA [46]. This refined Linnaean classification, taking out the guesswork classification by using a gene that was present in every living organism- the small subunit ribosomal RNA. This method of classification is comprehensive because all organisms possess this form of genetic material. Ssu rRNA is sequenced because the genes are highly conserved. Due to their functional constancy, some have variable regions to differentiate organisms, and are easy to sequence. This technique also elucidated the tree of life, which shows the three domains of microbial lineage diversity: Bacteria, Archaea, and Eukarya. DNA can be compared using a sample database that allows identification of unknown organisms to a species level.<br />
<br />
===Domain Bacteria===<br />
<br />
====Introduction to Bacteria==== <br />
Bacteria are single celled prokaryotic organisms that lack membrane bound organelles. They are involved in many important processes within the soil such as decomposition, [https://microbewiki.kenyon.edu/index.php/Bioremediation bioremediation], symbiosis and biological transformation of nutrients. They are present in all terrestrial soil environments.[1] Soil is a heterogenous environment that varies in moisture content, temperature, oxygen requirements, carbon source and many other bacterial growth conditions. Those wide ranging growth factors account for the enormous diversity in soil bacteria populations. One gram of soil can contain between 26,000 to 52,000 different bacterial species.[13] In the entire microbial world, only about 1 percent of bacterial species can be cultured under laboratory conditions which leaves an immense number of bacterial species yet to be described. [14]<br />
<br />
Classification based on phenotypic characteristics, such as cellular morphology, metabolism, gram staining, oxygen requirements, carbon source and other traits, was used more readily before modern DNA sequencing. But, phenotypic classification is still used and Bergey’s Manual of Systematic Bacteriology is the most widely used source for determining species based on characteristic species traits.<br />
<br />
Traditional species definitions are not as useful in bacteria. OTUs, or operational taxonomic units, based on DNA sequencing similarity, are more applicable to bacteria. Typically, those bacteria with 97 percent similar DNA sequence are classified within the same OTU.[15] The 16S small subunit ribosomal RNA is used to substantiate phylogenetic relationships between different bacterial groups.<br />
<br />
====Morphology====<br />
<br />
Bacterial cells measure approximately 1μm wide and 1-5μm long.[12] They are smaller than eukaryotic microbes.Due to their small size, bacteria can more easily adapt to changing soil environments than larger eukaryotes.[1] Most bacteria are singled celled, but actinomycetes grow in branching filaments. There are many different bacterial cell shapes. The most common are bacilli (rods), cocci (spheres), spirilla (spirals) and actinomycete (filaments).<br />
[[Image:bacteria_sizes.jpg|frame|center|Figure 3.3 Common cell shapes cocci, bacillus, and spirilla and relative sizes. From[http://www.ppdictionary.com/gnbac.htm]]]<br />
<br />
'''Flagella''' - There are many different types and different arrangement of flagella. Movement in soil environments is dependent on soil moisture content. Though movement in soil is limited, flagellar function is important to allow bacteria to find more favorable microsites.[1]<br />
<br />
'''Cell membrane''' - The cell membrane encloses the cytoplasm. It is semi-permeable phospholipid bilayer that regulates transport of nutrients into the cell and waste products out of the cell.<br />
<br />
'''Cell wall''' - Most bacteria have a rigid cell wall surrounding the cell membrane which protects the cell from osmotic lysis. The cell wall is made of a crosslinked polysaccharide, called peptidoglycan, that is found only in bacteria.[1] The cell wall gives the cell shape and structure, but it is porous enough to permit small water soluble molecules to flow through to the cell membrane surface.[1]<br />
<br />
*'''Gram positive''' bacteria have a thick cell wall made of several layers of peptidoglycan. The cell wall is the outermost structure, as they do not have an outer membrane. The thick cell wall structure make gram positive bacteria more resilient to osmotic shock. Gram positive bacteria can tolerate 5 to 10 times more turgor pressure than gram Gram negative bacteria.[1] Teichoic acids in the cell wall may also help to bind to cationic nutrients in soil surroundings.[1] <br />
<br />
*'''Gram negative''' bacteria have a thin cell wall surrounded by an outer membrane made of phospholipids and lipopolysaccharides. Polysaccharides of the outer membrane interact with surrounding cations and are involved in attachment of bacteria to soil particles. [1] Periplasm is a gel like substance that occupies the space between the outer membrane and the cell wall of gram negative bacteria.[1] The outer membrane and periplasmic space is thought to provide protection from environmental toxins.[1] Proteins within the periplasm are thought to begin the process of catalyzing hydrolysis of organic and toxic substances.[1] <br />
<br />
[[Image:gramposnegmembrane.jpg|frame|center| Figure 3.4 Illustration of Gram positive and Gram negative cell wall structures. From[http://micro.digitalproteus.com/morphology2.php]]]<br />
<br />
'''Endospores''' are made by ''Bacillus'' and ''Clostridium'' in response to environmental stress.[1] Endospores are extremely resistant structures that can withstand extreme temperatures up to 150℃.[12] They can also withstand extreme pressure, desiccation, radiation, pH and chemicals.[12] The endospore protects the bacterial DNA until environmental conditions are more favorable and germination can proceed. Soil is the most common habitat for endospore forming bacteria.[12]<br />
<br />
'''Extracellular polymers''' - Many bacteria secrete a slime layer or capsule made of polysaccharides or glycoproteins.[1] The outer polysaccharide coating of bacteria helps in attachment to surfaces and the formation of biofilms.[1] Bacterial capsule secretions play a big role in soil aggregation and soil structure.[1] When the carbon to nitrogen ratio within soils is high, microbes secrete the excess carbon as extracellular polysaccharides.[1]<br />
<br />
====Reproduction==== <br />
Most bacteria reproduce by binary fission.[12] The bacterial cell expands to twice the original cell size, duplicates the bacterial DNA and pinches off, producing two daughter cells. Each resultant daughter cell is a clone of the parent cell. Prokaryotic Archaea also reproduce by binary fission.<br />
<br />
*'''Spore formation:''' Actinomycetes are a large group of filamentous bacteria, primarily found in soil.[1] Actinomycetes are morphologically similar to fungi. Actinomycetes form long filaments called hyphae. Unlike most bacteria, the majority of actinomycetes reproduce using asexual spores called conidia.[1] Though they share many characteristic with fungi, actinomycetes are still prokaryotes. They are smaller than fungi and the cell wall contains peptidoglycan.[1] Actinomycetes break down a wide variety of organic compounds and play an important role in organic matter decomposition. [1] ''Streptomyces'', a subgroup within actinomycetes, produce geosmin, which gives soil the characteristic earthy smell.[12]<br />
<br />
====Metabolism==== <br />
<br />
Along with archaea, bacteria are the most metabolically diverse and employ many different nutritional strategies.[1]<br />
*Heterotrophs - Most bacteria are heterotrophic, obtaining carbon from preformed organic substances. [1] <br />
*Autotrophs - Carbon dioxide serves as the main source of carbon. Some cyanobacteria, nitrifying and sulfur-oxidizing bacteria are autotrophs.[1]<br />
*Organotrophs - Most bacteria obtain electrons from organic substances.[1]<br />
*Lithotrophs - Some cyanobacteria, nitrifying bacteria and sulfur-oxidizing bacteria obtain electrons from inorganic substances.[1]<br />
*Phototrophs - Cyanobacteria use light as the main source of metabolic energy.[1]<br />
*Chemotrophs - All other nonphotosynthetic bacteria do not rely on light for metabolic energy.[1]<br />
<br />
====Contributions to the Cycle==== <br />
<br />
Bacteria play a significant role in the cycling of a wide range of elements.<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Carbon_cycle '''Carbon Cycle:'''] <br />
<br />
*'''Carbon Assimilation''' is the process of fixing carbon dioxide into organic forms. Carbon fixation is performed by autotrophic bacteria, such as cyanobacteria.[1] Chemoautotrophic nitrifying bacteria, such as ''Nitrobacter, Nitrosospira'' and ''Nitrosomonas'', also fix carbon.[1] Sulfur oxidizing bacteria, such as ''Thiobacillus'', fix carbon as well.<br />
<br />
*'''Carbon Mineralization''' results from microbial decomposition of organic carbon compounds into inorganic forms. As the organic carbon substances, like plant matter, are decomposed, inorganic carbon dioxide is produced. Most bacteria are heterotrophs that perform carbon mineralization. When microorganisms die, they are decomposed by successive microbial generations. Peptidoglycan, the main component of bacterial cell walls, is utilized as a polysaccharide substrate by other heterotrophic soil microbes.[1]<br />
<br />
*'''Methanogenesis''' - Methanogenic bacteria produce methane from the reduction of carbon dioxide. They are all strict anaerobes that use carbon dioxide for the carbon source.[1] They can all use hydrogen as a source of energy and electron donor. [1]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle '''Nitrogen cycle:''']<br />
<br />
*'''Nitrogen fixation:''' ''Azotobacter'' is a free living nitrogen fixing bacteria.[1] ''Rhizobium'' lives in a mutualistic relationship with plants by fixing nitrogen within root the nodules of legumes.[1] ''Anabaena'' and ''Nostoc'' have specialized heterocyte structures where nitrogen fixation occurs.[1] <br />
<br />
*'''Nitrification:''' Nitrifying bacteria, such as ''Nitrobacter, Nitrosospira,'' and ''Nitrosomonas'', oxidize ammonium to nitrate.[1] <br />
<br />
*'''Denitrification:''' ''Alcaligenes, Flavobacterium'', and ''Pseudomonas'' are common soil denitrifying bacteria.[1]<br />
<br />
===Domain Archaea===<br />
<br />
====Introduction to Archaea====<br />
<br />
Vladimir Vernadsky decided, in 1926, that only two domains of life existed on Earth, Bacteria and Eukarya.[37] About 50 years later in 1977, Carl Woese and George Fox theorized that part of the bacterial domain possed multiple dissimilarities from bacteria and recognized it to be another domain of life, now called Archaea.[38] Woese and Fox’s theory regarding the differences of archaea were confirmed in 1990’s through the use of 16S rRNA and 18S rRNA.[38] <br />
<br />
Despite the strongly held belief, in the 1990s, that archaea only inhabited extreme environments, recent discoveries have suggested their presence in abundant numbers all throughout the Earth. It is suggested that Archaea play notable roles in maintaining nutrient cycles.[37] Various methods of research, such as cultivation, culture-independent techniques and isotope-based methods, have facilitated the study of domain Archaea in carbon and nitrogen cycling. [37]<br />
<br />
The use of genomic and biochemical data has permitted the study of archaeal structure.[37] Use of these research methods has shown that domain archaea and domain bacteria differ in cell wall characteristics yet, share various ways to transfer genetic information by replication and transcription from their common ancestor, Eukarya.[37] As of 2012, 116 genera of Archaea have been observed which consists of 450 species. Most of the archaeal species in these genera remains uncultivated, known only through its gene sequences and molecular surveys.[37]<br />
<br />
====Morphology==== <br />
Archaea are characterized by various cell sizes. They are most commonly found to be small organisms ranging from “0.1 to 15 μ diameter and up to 200 μ long.”[38] The shape of many archaea are similar to bacteria, including bacillus, cocci, spirilla and “plate-like forms.” [38] Their cell membranes have ether linked lipids with no periplasmic space, similar to gram-positive bacteria, and contain no intracellular organelles.[39]<br />
<br />
'''Flagella:''' Most motile archaea inhabit a motor rotary system that allows it to move its flagella through the chemical gradient similar to bacteria.[39] Despite its similarity in function and source of energy required for motility, the flagella of both archaea and bacteria differ in structure.[39] Archaeal flagella gets the energy for its movement by ATP and is composed of dependent filaments that rotate singularly. [40] Archaeal flagella are known to be thinner than bacteria flagellin.[40] Since, the archaeal common ancestor is not bacteria but eukarya, convergent evolution is a plausible explanations for the differences between bacterial and archaeal flagellin. [40]<br />
<br />
'''Membranes:''' Archaea have a cell membrane that protects the cytoplasm and the nucleic acids from the environment. The archaeal cell membrane has a lipid bilayer with glycol-ether lipids that are more stable than ester linkages and help some archaea that live in extreme environments to withstand such conditions.[39] Most archaeal species are surrounded by a cell wall which protects the cell membrane and maintains the archaeal structure.[41]<br />
<br />
====Reproduction====<br />
Archaeal organisms reproduce by binary fission since they do not have nucleases thus, the DNA chromosome in a Archaeal organism replicate, separate and create two daughter cells.[43] The process of binary fission can be seen in Figure (3.5) process begins the parent cell duplicating the DNA. The DNA material then goes to the sides of the cell where an invagination to the cell occurs allowing the cell to become two individual cells. Binary fission is a very fast reproduction process, that allows archaeal organisms to grow at an exponential rate.[44]<br />
<br />
[[Image:WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg|frame|center|Figure 3.5 Illustration of binary fission. From[https://d2jmvrsizmvf4x.cloudfront.net/WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg]]]<br />
<br />
====Metabolism==== <br />
Archaea share similar metabolic characteristics to bacteria. The metabolic pathways taken by all archaea shown in the (Figure 3.6) demonstrates the great diversity and variation amongst archaea. [38] The kinds of archaea that are seen in the environment and the metabolic pathways taken by some can be summarized in the image. <br />
<br />
*Photoautotrophs: use light as an energy source and carbon dioxide as the carbon source with the help of the Calvin Cycle.[38]<br />
*Chemoautotrophs: use inorganic chemicals as their energy source and carbon dioxide as carbon source. <br />
*Chemoheterotrophs: take organic chemicals as energy source and organic chemicals as carbon source. The pathways taken by chemoheterotrophs varies from respiration by the Krebs Cycle to fermentation. [38]<br />
*Photoheterotrophs: use light as their energy source and organic chemicals as their carbon source. <br />
<br />
Most archaea inhabiting in the soil environment are major contributors to the biogeochemical cycles.<br />
<br />
[[Image:2000px-Troph_flowchart.svg.png|thumbnail|center|Figure 3.6 Flowchart showing different metabolic pathways. From[https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Troph_flowchart.svg/2000px-Troph_flowchart.svg.png]]]<br />
<br />
====Contributions to the Cycle====<br />
Archaea play a significant role in the nutrient cycles that take place in the ecosystem as they account for about 1-5% of all the prokaryotes present in the soil environment.[42]<br />
<br />
'''Carbon Cycle:''' Archaea have an important role in the carbon cycle that takes place specifically in methane production, carbon mineralization and carbon assimilation all of all of which contribute to the soil’s carbon sink.[42] The carbon dense soil helps to make the soil organic matter rich and helps to form extracellular polymers which creates stable aggregates. For some microbes, an electron acceptor is need to carry out metabolic functions. [42] More info on [https://microbewiki.kenyon.edu/index.php/Carbon_cycle Carbon Cycle].<br />
<br />
*'''Carbon Assimilation:''' Involves the transformation of inorganic carbon into organic carbon compounds. This process is commonly done by autotrophic phyla ''Crenarchaeota, Thaumarchaeota'', and ''Euryarchaeota'' that use carbon dioxide/ bicarbonate converting it to organic compounds.[42] Of the autotrophic lineages observed in carbon assimilation the ''Thaumarchaeota'' are strict autotrophs, the ''Euryarchaeota'' and ''Crenarchaeota'' are facultative autotrophs and the ''Halobacteriales'' and ''Thermococcales'' are obligate heterotrophs.[42] <br />
<br />
*'''Carbon Mineralization:''' The process that converts organic carbon into the oxidized inorganic carbon, carbon dioxide is commonly done by both aerobes and anaerobes.[42] The heterotrophic microbes that use organic compounds as energy to oxidize the carbon source include, methanogens and methane-oxidizing archaea belonging to the phyla ''Euryarchaetota'', and ''Crenarchaeota''.[42] <br />
<br />
*'''Methanogenesis:''' production of methane, a major greenhouse gas in the Earth’s atmosphere is commonly done by archaea upon reducing an oxidized compound.[42] The phyla ''Euryarchaeota'' is the only phyla that consists of archaea that produce methane all of which form five class: ''Methanopyri, Methanococci, Methanobacteria, Methanomicrobia'' and ''Thermoplasmata''.[42] Methanogens are commonly found in anaerobic and aerobic conditions such as bodies of water, aerated soils and oxygenated waters.[42]<br />
<br />
'''Nitrogen Cycle :''' Archaea play a pivotal role in the Nitrogen cycle and help create nitrogenous products for the plants and microbes. More info on [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle Nitrogen cycle].<br />
<br />
*'''Nitrogen Fixation:''' Fixing nitrogen from the environment and converting it to organic nitrogen in the soil or to inorganic nitrogenous form since both organic and inorganic products are in short supply in the biosphere and are fixed by many archaeal organisms.[42] N2 fixation by the environment is usually done by three major archaeal classes ''Methanobactera, Methanococci'' and ''Methanomicrobia''.[42] <br />
<br />
*'''Nitrification:''' Converting the ammonia (NH4+) in the soil to nitrite (NO2-) produces nitrate (NO3-) as an intermediate. [42] The transformation of ammonia to first nitrate then to nitrite is a two step process that is done by different microbes. [42] Most common organisms involved in nitrification include ammonia-oxidizing archaea which are lithotrophic organisms mostly, of the ''Thaumarchaeota'' phylum from the archaea domain. <br />
<br />
*'''Denitrification :''' The conversion of atmospheric N2 using the electron acceptor NO3- or NO2- creating the formation of nitric oxide, nitrous oxide and/or N2.[42] The formation of the end product N2 may not always be produced but other intermediates NO and N2O, greenhouse gases may be produced.[42] Of the archaeal organisms that have been studied in denitrification process is done by ''Pyrobaculum aerophilum'' which accepts both NO3- and NO2- as an electron acceptor producing a variety of products NO2-, NO, N20 and N2.[42]<br />
<br />
===Domain Eukarya===<br />
<br />
====Fungi====<br />
<br />
=====Introduction=====<br />
<br />
'''Introduction'''<br />
<br />
Fungi comes from the ancient Greek word “sphongos” meaning sponge in reference to the mushroom cap [47]. Fungi have the general characteristics of being eukaryotic, heterotrophic, external absorbers of nutrients, containing a hyphal thallus, reproducing via spore, and being pleomorphic (producing several forms). Fungi are generally organoheterotrophs that can survive in low pH and stay active at low moisture content[46]. Fungi reside in the domain Eukarya with an estimated species of 1.5 million, and less than five percent of them have ever been described. The general phyla included within Kingdom Fungi include Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, Chytridiomycota, and Microsporidia [48].<br />
<br />
[[Image:magical-kingdom-620.jpg|frame|center|Figure 3.7 Fungi phyla hierarchy. From.[http://www.motherjones.com/environment/2009/11/fungi-family-tree]]]<br />
<br />
=====Morphology=====<br />
<br />
'''Morphology''' <br />
<br />
Fungi can be either unicellular (yeasts) or multicellular. All multicellular fungi are made up of small, filamentous particles called hyphae. Some hyphae have cross walls called septa, while others do not- this is a large basis of fungal identification. Fungal cells generally have multiple nuclei. Fungal cell walls are generally composed of chitin, a long carbohydrate polymer that adds rigidity and structural support to fungi [49]. <br />
<br />
=====Reproduction=====<br />
<br />
'''Reproduciton'''<br />
<br />
Fungal reproduction can occur either sexually or asexually.<br />
<br />
'''Sexual reproduction''' can occur by homothallic or heterothallic mycelia.<br />
<br />
'''Asexual reproduction''' can occur by fragmentation, budding, or by producing spores (the most common method). <br />
<br />
*'''Spores:''' spores come in many different forms. One of the most well known are conidiospores, which are unicellular or multicellular spores that get released from the tip of the hyphae. <br />
<br />
'''Perfect fungi''' are those that can reproduce both sexually and asexually while imperfect fungi are those that can only reproduce asexually.<br />
<br />
*Sexual reproduction always includes the stages plasmogamy (fusion of two haploid cells), karyogamy (creation of a diploid zygote), and meiosis (gametes are created).<br />
<br />
=====Metabolism=====<br />
<br />
'''Metabolism'''<br />
<br />
Many different fungi display a myriad of metabolisms. There are primary metabolites that that help the fungi function properly, and secondary metabolites that are generally bioactive that are not the most pertinent to fungal growth (they can live without these). Secondary metabolites play a large role in chemistry today and can be manufactured into commonly used products such as new drugs. In general fungi are heterotrophic through release of extracellular enzymes into the neighboring environment to break complex molecules down into smaller ones. The materials are then absorbed and metabolized [50]. Fungi are sessile organisms that overcome their little to no movement through apical growth at the hyphal tip. Fungi are noted to grow almost everywhere on the Earth.<br />
<br />
=====Relevance to soil===== <br />
<br />
'''Relevance to soil'''<br />
<br />
Fungi include some of the most abundant biomass of microorganisms in numerous soils. They play an important role as decomposers within the soil food web through conversion of difficult to digest organic material into forms many other organisms can use [51]. Their hyphae can bind soil particles together and create aggregates that increase soil water holding capacity. They perform important functions from water dynamics to nutrient cycling and disease suppression. Soil fungi can be categorized into three different groups based on their actions: <br />
<br />
*decomposers: that convert dead organic material into fungal biomass<br />
<br />
*mutualists: which colonize plant roots and help solubilize phosphorous and bring soil nutrients<br />
<br />
*pathogens/ parasites: which help control diseases in soil via trapping organisms such as nematodes [51]. <br />
<br />
Fungi are seen common in intensively managed agricultural soils due to tillage disrupting hyphae. Fungi also play a very important role in the [https://microbewiki.kenyon.edu/index.php/Rhizosphere_Interactions rhizosphere], the region of soil that is greatly influenced by the plant root system. This area of soil which is concentrated in plant roots and fungal hyphae is known to support greater microbial activity.<br />
<br />
====Protista====<br />
<br />
Protists are mainly eukaryotic unicellular organisms. They used to belong to their own kingdom Protista, but are now known to be paraphyletic [18]. Protists are made up of protozoa, unicellular algae, and slime molds. The protozoa are divided into 4 major categories: the ciliates, the flagellates, the heliozoans, and the amoebas [10]. They are so small that they don’t need any specialized organelles in order to survive and can survive at low oxygen levels because of this. They are also known to use a contractile vacuole to remove excess water from their cells [10]. <br />
<br />
=====Protozoans=====<br />
<br />
'''Protozoans'''<br />
<br />
The microbial loop is a subsection of the microbial food web that accounts for the dissolved organic matter of systems. It’s suggested that Protozoa have an important role in the maintenance of soil nutrients, specifically nitrogen. A common known characteristic of protozoans is that they stimulate plant growth [19]. It’s hypothesized that they do this through the manipulation of nitrogen levels. In the presence of Protozoa, shoot biomass and shoot N levels are increased [20]. The protozoa is said to stimulate the mineralization of nitrogen via the microbial loop [20]. The indirect effects protozoans have on the nitrogen cycle are thought to be more important than the direct effects it has. This is because grazing stimulates microbial mineralization processes that in turn speeds up the nutrient cycles [20].<br />
<br />
In general, Protozoans range from 5 to 500 µm in diameter, making them significantly larger than bacteria [21]. They are abundantly located near the surface of the soil (15cm deep) where roots are plentiful [21]. Most protozoans have two life cycles. One is their active form where they are motile and feed on prey. The other is the cyst form where they produce a thick coating to protect them from the environment and can go dormant for years.<br />
<br />
======Ciliates======<br />
<br />
'''Cilliates:'''<br />
This group, within protozoans, is fairly diverse. A common feature shared amongst all of its members is the presence of at least one cilia at any stage of its development [10]. The cilia is used for movement and other things such as predation (tentacles). For movement, they use the massive amounts of tiny cilia to create wave like currents to propel the cell forwards. Most ciliates also have toxicysts which are used to capture prey [10]. Some ciliates even have a symbiotic relationship with algae living inside of them [10]. The algae use the CO2 produced by ciliates and turn it into O2 that can then be reused by the ciliates [10]. They are found in a wide array of habitats ranging from freshwater and soil to the rumen of Animals [22]. They are present in almost anywhere that contains water [23]. They are unicellular heterotrophs so they feed on bacteria and algae in their environment. Ciliates are one of the top predators in the microbial food web and are hypothesized to have been a major predatory group before animals evolved [23]. Parasitic ciliates exist that can cause the death of animals and are increasingly becoming dangerous in water [23].<br />
<br />
[[Image:2spiro.jpg|frame|center|Figure 3.8 Microscope image of ciliated protists. From[http://www.microscopy-uk.org.uk/mag/smallimag/2spiro.jpg]]]<br />
<br />
======Flagellates======<br />
<br />
'''Flagellates''' are one of the most commonly known protists. They are unicellular organisms that may be solitary, colonial, free living, or parasitic [24]. The hallmark feature of protists is that at some point in their life cycle, they possess a flagella. A flagellum is a long hair like structure that is used for locomotion, sensation, and sometimes predation [24]. The flagellum makes waves by whiplike lashing movements which propels the cell forwards. Flagellates also have a protective coating in the form of a thin pellicle to protect them from the environment [24]. <br />
<br />
[[Image:9703607_orig.jpg|frame|center|Figure 3.9 Illustration of flaggelates during different life cycle stages. From[http://diagnosticparasitology.weebly.com/uploads/3/9/5/4/3954522/9703607_orig.jpg]]]<br />
<br />
*'''Mastigophora:'''<br />
<br />
Mastigophora is a subphylum of flagellates. Being a member of the flagellates, their key feature is the flagellum. Their habitats include freshwater, soil, and can act as animal parasites as well [25]. They use pseudopodia, a long outward protrusion, to trap and funnel food from the environment into their cell bodies [25]. The Mastigophora are mainly known for their parasitism, which can take place in both humans and animals [25]. ''Typanosomes'' are an example of Mastigophora which causes African sleeping sickness [25]. ''Giardia lambli''a is another example that resides in the intestinal tract of warm-blooded animals and inflicts intestinal giardiases [25]. It is also a major contaminant of drinking water because it is resistant to chlorine, which is the most common water purifier [25]. Having a dormant cyst form also adds to its survival potential through filtration efforts [25].<br />
<br />
<br />
<br />
*'''Euglenids:'''<br />
<br />
Euglenids are one of the best known flagellates. They are found in freshwater and soil, as long as there are organic materials. They also participate in some symbiotic relationships with marine animals. Euglenid cells do not contain cell walls or other rigid membranes [26]. This gives the cell tremendous flexibility and allows it to change its shape to easily navigate through muddy terrain. Euglenids have two flagella, one which creates locomotion and movement for the cell [26]. The other flagellum does not protrude from the cell and is contained in the cell body [26].<br />
<br />
======Amoebas======<br />
<br />
'''Amoebas'''<br />
<br />
Amoebae are single celled eukaryotes present in many different types of environments. They are scattered throughout a variety of eukaryotic lineages and therefore are not monophyletic [27]. Amoebae range in size from 5 micrometers to 3 mm and don’t have a defined shape, commonly recognized for being polymorphic. They are motile through the use of pseudopodia, which stretch and pull the cell along with it. The pseudopodia are also used for feeding. They are able to sense prey that can be engulfed and engulf them via phagocytosis. The amoeba’s main prey consists of bacteria, algae, and other protozoa [28]. The prey is moved around within the cell via food vacuoles, a feature of amoebae [28]. Another key characteristic of amoebae are the large contractile vacuoles inside the cell. The purpose of the contractile vacuole is to osmoregulate by pumping excess water out of the cell. In times of turmoil, amoebae have an encysted form that helps them get through the tough times. This form is useful when there is low nutrient availability to limit energy consumption. There are two main forms an amoeba can be characterized as. They can either be testate or nontestate. Testate amoeba produce shells, or “tests”, that help identify their species since each species has a unique shell.<br />
<br />
[[Image:Amoeba_(PSF).png|frame|center|Figure 3.10 Amoeba morphology. From[https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Amoeba_(PSF).png/230px-Amoeba_(PSF).png]]]<br />
<br />
=====Slime Molds=====<br />
<br />
'''Slime molds''' are fungus like organisms that were at once classified as fungi, but have now been placed in the protozoan phylogeny. Slime molds are single cells that can live independently, but aggregate to form multicellular reproductive structures when necessary [29]. The fruiting body releases spores which germinate into new cells. Slime molds feed off of bacteria and are most commonly found in forests. They feed off of decaying vegetation as well so they can be seen on rotting logs and leaves.<br />
<br />
[[Image:28-30-cellslimemoldlife-l.jpg|frame|center|Figure 3.11 Illustration of slime mold life cycle. From[https://lichencolony.files.wordpress.com/2006/06/28-30-cellslimemoldlife-l.jpg]]]<br />
<br />
==Current Research== <br />
<br />
'''Bacteria:''' To showcase the great diversity of soil bacterial environments, cyanobacteria have been studied in both desert and polar regions. Cyanobacteria can survive in extreme conditions likely because of their long evolutionary past.[16] Dr. Patzelt and his colleagues studied the diverse cyanobacteria residing in the Atacama desert, one of the driest parts of the world. The diverse taxa found in the Atacama desert can withstand prolonged periods of extreme desiccation.[16] The cyanobacteria dominate the soil crusts, affecting soil stability, soil structure and soil fertility.[16] Cyanobacteria inhabiting the Antarctic and Arctic regions, show similar adaptations to extreme environments as the cyanobacteria found in the desert. The polar cyanobacteria are particularly adapted to high altitudes.[17] They can withstand high ultraviolet radiation, desiccation, and repeated freeze-thaw cycles.[17] The autotrophic cyanobacteria supports heterotrophic microbes, providing an important ecosystem service in an environment with low microbial activity.[17]<br />
<br />
'''Archaea:''' In 150 soil samples acquired from North and South America, about 150,000 species were observed.[45] Of these, over 2,500 were identified as archaea based on their ssu rRNA.[45] The archaeal species were further analyzed to understand their role in the soil environment. Of the archaeal groups, ''Crenarchaeota'' and ''Euryarchaeota'' were found.[45] Bates stated that, “Across the non-experimental soils examined the soil C:N ratio was the single best predictor of archaeal relative abundances” due to their influences in the nutrient cycles.[45]<br />
<br />
'''Fungi:''' Fungi have been in the public eye for a while now due to the many different types of secondary metabolites they produce. Some produce bioactive compounds that can inhibit growth of protozoa, bacteria, parasites, insects, and even other fungi. A large area of investigation is the uses of these chemicals for human interests in use from medicine to plant and animal toxins [52].<br />
<br />
'''Protozoa:''' It’s known that Protozoa stimulate plant growth in different ways. It’s suspected that the Protozoa take part in the microbial loop which is responsible for the nutrient production for plants [19]. However, new developments have shown that the Protozoa themselves are responsible for the nitrogen mineralization and that other bacteria have no effect on the plant’s nitrogen sources [19].<br />
<br />
==References==<br />
<br />
1. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). Principles and Applications of Soil Microbiology. New Jersey: Pearson Education Inc.<br />
<br />
2. Ingham, Elaine R. Ingham R. "Chapter 4: SOIL FUNGI." Soil Biology. Natural Resources Conservation Service Illinois, n.d. Web. 9 Feb. 2016<br />
<br />
3. Reid, Greg, and Percy Wong. "SOIL BACTERIA AND FUNGI - NEW SOUTH WALES." Soil Bacteria and Fungi. New South Wales Department of Primary Industries, 2005. Web. 11 Feb. 2016.<br />
<br />
4. "Fungi." Microbiology Online. Microbiology Society, n.d. Web. 11 Feb. 2016.<br />
<br />
5. Tortora, G.J., Funke, B.R., Case, C.L. (2012). “Microbiology an Introduction.” 11th ed. Pearson Benjamin Cummings, San Francisco.<br />
<br />
6. Rizzo, D. “Intro to Fungi.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
7. Rizzo, D. “Ascomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
8. Rizzo, D. “Basidiomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
9. Pegg G.F., Brady B.L. “Verticillium Wilts.” New York, CABI Publishing 2002. Google Books. Web. 11 Feb. 2016. http://books.google.com<br />
<br />
10. Hebert, Paul. "What Is a Protist / What Are Protozoa? - Encyclopedia of Life." Encyclopedia of Life. N.p., n.d. Web. 11 Feb. 2016.http://eol.org/info/456<br />
<br />
11. "MicrobeWorld." Protista. N.p., n.d. Web. 11 Feb. 2016. http://www.microbeworld.org/types-of-microbes/protista<br />
<br />
12. Madigan, M.T., Martinko, J.M. (2006). Brock Biology of Microorganisms. New Jersey: Pearson Prentice Hall.<br />
<br />
13. Roesch, L.F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H.; Camargo, F. A. O.; Farmerie, W. G.; Triplett, E. W.(2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1(4).283-290. <br />
<br />
14. Amann, R.I, Ludwig, W., Schleifer, K.H.(1995).Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology and Molecular Biology Reviews. 59(1). 143-169. <br />
<br />
15. Geers, D., Cohan, F.M., Lawrence J.G., Spratt, B.G., Coenye, T. Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005). Opinion: Re-evaluating prokaryotic species. Nature Reviews Microbiology. 3(9). 733-739.<br />
<br />
16. Patzelt, D.J., Hodac, L., Friedl, T., Pietrasiak, N., Johansen, J.R. (2014). Biodiversity of soil cyanobacteria in the hyper-arid Atacama Desert, Chile. Journal of phycology. 50(4). 698-710. <br />
<br />
17. Makhalanyane, T. P., Valverde, A., Velázquez, D., Gunnigle, E., Van Goethem, M. W., Quesada, A., & Cowan, D. A. (2015). Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats. Biodiversity and Conservation, 24(4), 819-840.<br />
<br />
18. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist>.<br />
<br />
19. Ekelund, Flemming; Saj, Stephane; Vestergård, Mette; Bertaux, Joanne; Mikola, Juha. (2009). “The “soil microbial loop” is not always needed to explain protozoan stimulation of plants”. Soil Biology & Biochemistry. Vol. 41 Issue 11, p2336-2342, 7p.<br />
<br />
20. Bonkowski, Michael. "Protozoa and Plant Growth: The Microbial Loop in Soil Revisited." New Phytologist New Phytol 162.3 (2004): 617-31. Web.<br />
<br />
21. Hoorman, James. "The Role of Soil Protozoa and Nematodes." Fact Sheet (n.d.): n. pag. Ohio State University, 2011. Web.<br />
<br />
22. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist<br />
<br />
23. Lynn, Denis H(Apr 2012) Ciliophora. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001966.pub3]<br />
<br />
24. "flagellate". Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc., 2016. Web. 23 Feb. 2016 <http://www.britannica.com/science/flagellate>.<br />
<br />
25. "Mastigophora." World of Microbiology and Immunology. 2003. Encyclopedia.com. 23 Feb. 2016<http://www.encyclopedia.com>.<br />
<br />
26. “Plant Life." : Euglenoids. N.p., n.d. Web. 23 Feb. 2016. <http://lifeofplant.blogspot.com/2011/04/euglenoids.html><br />
<br />
27. Parales, R.E. and Martin, M. (2015) Microbial Diversity Laboratory Manual, MIC 105L, Winter 2015. Department of Microbiology and Molecular Genetics, College of Biological Sciences, The University of California, Davis.<br />
<br />
28. Arnold, Paul. "What Does an Amoeba Eat? Plus Other Ameoba Info and Questions." Bright Hub. N.p., n.d. Web. 04 Mar. 2016.<br />
<br />
29. "MicrobeWorld." Slime Molds. N.p., n.d. Web. 24 Feb. 2016. <http://www.microbeworld.org/types-of-microbes/protista/slime-molds><br />
<br />
30. Leeuwenhoek., A. V. (2009, November 18). One gram of soil: A microbial biochemical gene library. Retrieved March 13, 2016, from http://www.ncbi.nlm.nih.gov/pubmed/19921459 <br />
<br />
31. Coleman, D. C., Crossley, D. A. & Hendrix, P. F. "Soil food webs: Detritivory and microbiology in soils," in Fundamentals of Soil Ecology, 2nd ed. (Elsevier, 2004) 236-241.<br />
<br />
32. Welcome to Agriinfo.in. (n.d.). Retrieved February 21, 2016, from http://agriinfo.in/?page=topic&superid=5&topicid=172 <br />
<br />
33. Gouthro, T., & Rice, D. (1987, December 15). Interaction Terminology. Retrieved February 21, 2016, from http://www.rpi.edu/dept/chem-eng/Biotech-Environ/MixCul/ecodefn.htm <br />
<br />
34. AMENSALISM. (n.d.). Retrieved February 21, 2016, from https://biostuds.wikispaces.com/AMENSALISM <br />
<br />
35. Natural Resources Conservation Service. (n.d.). Retrieved March 10, 2016, from <br />
http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053865 <br />
<br />
36. Ecological Linkages Between Aboveground and Belowground Biota. (n.d.). Retrieved March 10, 2016, from http://science.sciencemag.org/content/304/5677/1629 <br />
<br />
37. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf<br />
<br />
38. Kingdom Archaea. (n.d.). Retrieved March 10, 2016, from http://plantphys.info/organismal/lechtml/archaea.shtml <br />
<br />
39. What are Archaea? - Encyclopedia of Life. (n.d.). Retrieved March 10, 2016, from http://eol.org/info/457 <br />
<br />
40. Flagellum. (n.d.). Retrieved March 10, 2016, from http://www.newworldencyclopedia.org/entry/Flagellum#Archaeal_flagellum <br />
<br />
41. Archaea: Morphology. (n.d.). Retrieved March 10, 2016, from http://www.ucmp.berkeley.edu/archaea/archaeamm.html <br />
<br />
42. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf <br />
<br />
43. Archaea. (n.d.). Retrieved March 10, 2016, from http://www.eoearth.org/view/article/150172/ <br />
<br />
44. Binary Fission: Cell Division & Reproduction of Prokaryotes. (n.d.). Retrieved March 10, 2016, from http://www.scienceprofonline.com/microbi <br />
<br />
45. Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2010, November 18). Examining the global distribution of dominant archaeal populations in soil. Retrieved February 21, 2016, from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105767/<br />
<br />
46. Scow, K. M. "Lecture 1 Part 1." Lecture, Davis.<br />
<br />
47. Rizzo, D. "Lecture 1." Lecture, Davis.<br />
<br />
48. Rizzo, D. "Lecture 3." Lecture, Davis.<br />
<br />
49. C.J. Alexopoulos & C. W. Mims, Introductory Mycology 3rd edition. 1979. Wiley NY. Web accessed Mar 8, 2016 from http://www.ucmp.berkeley.edu/fungi/fungimm.html<br />
<br />
50. Rizzo, D. "Lecture 2." Lecture, Davis.<br />
<br />
51. Ingham, E. “Chapter 4: Soil Fungi” (2016) Oregon State University. Retrieved Feb. 20, 2016, from http://extension.illinois.edu/soil/SoilBiology/fungi.htm<br />
<br />
52. Keller, N., Turner, G., Bennett, J. “Fungal Secondary Metabolism- from Biochemistry to Genomics.” 2005 Nature Reviews Microbiology p/ 937 to 947.</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Introduction_to_Organisms&diff=128502
Introduction to Organisms
2017-03-05T23:04:59Z
<p>Kmscow: /* Soil Relevance */</p>
<hr />
<div>==Introduction== <br />
The soil ecosystem in an important environment that allows both plants and animals to survive, grow and reproduce. The significance of the soil as an ecosystem is at times overlooked despite its major contributions to the environment. The [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] is a complex and varied microbial habitat.[1] The plants and organisms inhabiting the soil contribute to its thriving diversity. Soil life is diverse in morphology, metabolism, size, and many other characteristics. It is believed that “there is sufficient [microbial] DNA in 1 g of soil to extend 1,598km.” [30] Soil is a heterogeneous environment with various zones of rhizosphere, aggregates, organic matter and animal residues.[31] Given each zone is a small component of the larger soil ecosystem, rhizosphere accounts for only 5 to 7 percent of the soil environments but contains over “70 percent of the bacterial- and fungal-feeding nematodes.”[31] <br />
<br />
Since, all three domains of life: archaea, bacteria and eukarya, inhabit the soil environment it is difficult to observe each microbe individually within the soil ecosystem.Only a few representative groups of each domain will be discussed to provide examples of the roles these organisms play in soil. This page attempts to outline the major microbial groups within the diverse soil environment.The interactions between soil microbes amongst the soil microbial diversity. The concept of survival of the fittest is seen in the soil food web, which allows only a selective few with the correct nutrients to thrive in a soil environment. The interactions of soil microbes is not only a part of nature but it also only selects those organisms that are fit for survival, growth and reproduction. The soil food web and symbiotic relationships are used to explain the dynamic interactions between soil organisms.<br />
<br />
==Soil Food Web and Microbial Interactions== <br />
<br />
To survive in a soil environment, an organism must be able to adapt to changing environments and organism interactions. The interactions seen between organisms allows only the fittest to survive, thrive, grow and reproduce in the soil. The only type of interaction shown in (Figure 2.1) is predation. Other common interactions in the soil environment are: <br />
<br />
:[[Image:soil_foodweb72.jpg|frame|center|Figure 2.1 Soil Food Web. From[http://www.exploringnature.org/graphics/foodwebs/soil_foodweb72.jpg]]]<br />
<br />
<br />
'''I. Commensalism:''' Organism (A) benefits from the presence of Organism (B) while (B) is unaffected by the presence of (A).[32]<br />
<br />
'''II. Mutualism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) and becomes a necessary association for each other’s survival. [32] [33]<br />
<br />
'''III. Synergism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) but the relationship is not necessary for survival.[33]<br />
<br />
'''IV. Competition:''' Depending on the organisms this interaction benefits organisms who can readily adapt to the environment and overcome any obstacles needed to survive, grow and reproduce.[33]<br />
<br />
'''V. Amensalism:''' An interaction in which Organisms (A) and (B) develop a partnership where (B) is unaffected by (A) but organism (A) is negatively affected by (B).[34]<br />
<br />
'''VI. Parasitism:''' Organism (A) benefits from Organism (B) but Organism (B) does not benefit positively from Organism (A). <br />
<br />
'''VII. Predation:''' “An interaction between organisms in which one benefits and one is harmed based on the ingestion of the smaller sized organism, the prey, by the larger organism, the predator.”[33]<br />
<br />
<br />
<br />
The soil food web consists of microbes which play an important role in maintaining the complexity of the soil environment. The interactions observed in the food web are not only based on predation, which directly affects the nutrient cycling and degradation of pollutants, but also the formation of aggregates.[35] The production of specific nutrients, such as ammonium created by microbial metabolic functions, helps to enrich the the soil for plant use.[35] Soil organism activity, along with the presence of soil organic matter, create stabilizing aggregates.[35] The hyphae within the soil environment and the microbes help form large, stable aggregates in the soil habitat.[35] The biodiversity in the soil plays a pivotal role in degrading pollutants, and also prevents pathogens from inhabiting the soil environment through competition.[35] The food web in the soil environment is necessary to maintain the soil nutrients, biological activity, and detoxifying pollutants. Thus, it directly maintains cultivation, productiveness and prosperity of the soil. <br />
<br />
In (Figure 2.1), all three domains, Archaea, Bacteria, and Eukarya, are represented in the soil food web. If one takes a closer look at the figure, the soil food web is not only dependent on small and large microbes but also dead organic matter and plant roots. Dead and living matter in the soil environment contribute to maintaining the food web. Plant residues also are apart of the soil food web. They contribute to the soil’s carbon source.[35] The plant residues either, release carbon dioxide to the environment, or contribute to the soil organic matter. Soil organic matter contributes to soil’s richness and helps to form aggregates.[35] The main focus in the image above is the diversity of organisms, both in domains and in size. The larger organisms are usually the predators. The smaller organisms eventually fall prey, due to their limited mobility, respiration, and size. The eukarya and small bacteria are apparent figures seen in the figure above, but archaea also contribute to the food cycle as they break down ammonia for plants to use. [35]<br />
<br />
The notable interactions of life that take place in the soil environment is evident both below-ground level, as seen in the figure 2.1, but also in the above-ground level.[36] Worms also impact the soil food web, acting as both drivers of the food web both belowground and aboveground.[36]<br />
<br />
==3 Domains==<br />
[[Image:Big_Tree_Bold_Letters_white.png|frame|center|Figure 3.1 Phylogenetic Tree of the 3 Domains. From[http://phylogenomics.blogspot.com/2014_02_01_archive.html]]]<br />
<br />
===Carl Woese and Phylogeny===<br />
<br />
[[Image:Carlwoese1_0565_b.jpg|frame|center|Figure 3.2 Carl Woese. From[http://ofbacteriaandmen.blogspot.com/2013/01/the-new-biology-of-carl-woese.html]]] <br />
<br />
Carl Woese (Figure 3.2) was an American microbiologist famous for pioneering the technique of phylogenetic taxonomy through use of a 16S (for prokaryotic) and 18S (for eukaryotic) ribosomal RNA, also known as small subunit ribosomal RNA [46]. This refined Linnaean classification, taking out the guesswork classification by using a gene that was present in every living organism- the small subunit ribosomal RNA. This method of classification is comprehensive because all organisms possess this form of genetic material. Ssu rRNA is sequenced because the genes are highly conserved. Due to their functional constancy, some have variable regions to differentiate organisms, and are easy to sequence. This technique also elucidated the tree of life, which shows the three domains of microbial lineage diversity: Bacteria, Archaea, and Eukarya. DNA can be compared using a sample database that allows identification of unknown organisms to a species level.<br />
<br />
===Domain Bacteria===<br />
<br />
====Introduction to Bacteria==== <br />
Bacteria are single celled prokaryotic organisms that lack membrane bound organelles. They are involved in many important processes within the soil such as decomposition, [https://microbewiki.kenyon.edu/index.php/Bioremediation bioremediation], symbiosis and biological transformation of nutrients. They are present in all terrestrial soil environments.[1] Soil is a heterogenous environment that varies in moisture content, temperature, oxygen requirements, carbon source and many other bacterial growth conditions. Those wide ranging growth factors account for the enormous diversity in soil bacteria populations. One gram of soil can contain between 26,000 to 52,000 different bacterial species.[13] In the entire microbial world, only about 1 percent of bacterial species can be cultured under laboratory conditions which leaves an immense number of bacterial species yet to be described. [14]<br />
<br />
Classification based on phenotypic characteristics, such as cellular morphology, metabolism, gram staining, oxygen requirements, carbon source and other traits, was used more readily before modern DNA sequencing. But, phenotypic classification is still used and Bergey’s Manual of Systematic Bacteriology is the most widely used source for determining species based on characteristic species traits.<br />
<br />
Traditional species definitions are not as useful in bacteria. OTUs, or operational taxonomic units, based on DNA sequencing similarity, are more applicable to bacteria. Typically, those bacteria with 97 percent similar DNA sequence are classified within the same OTU.[15] The 16S small subunit ribosomal RNA is used to substantiate phylogenetic relationships between different bacterial groups.<br />
<br />
====Morphology====<br />
<br />
Bacterial cells measure approximately 1μm wide and 1-5μm long.[12] They are smaller than eukaryotic microbes.Due to their small size, bacteria can more easily adapt to changing soil environments than larger eukaryotes.[1] Most bacteria are singled celled, but actinomycetes grow in branching filaments. There are many different bacterial cell shapes. The most common are bacilli (rods), cocci (spheres), spirilla (spirals) and actinomycete (filaments).<br />
[[Image:bacteria_sizes.jpg|frame|center|Figure 3.3 Common cell shapes cocci, bacillus, and spirilla and relative sizes. From[http://www.ppdictionary.com/gnbac.htm]]]<br />
<br />
'''Flagella''' - There are many different types and different arrangement of flagella. Movement in soil environments is dependent on soil moisture content. Though movement in soil is limited, flagellar function is important to allow bacteria to find more favorable microsites.[1]<br />
<br />
'''Cell membrane''' - The cell membrane encloses the cytoplasm. It is semi-permeable phospholipid bilayer that regulates transport of nutrients into the cell and waste products out of the cell.<br />
<br />
'''Cell wall''' - Most bacteria have a rigid cell wall surrounding the cell membrane which protects the cell from osmotic lysis. The cell wall is made of a crosslinked polysaccharide, called peptidoglycan, that is found only in bacteria.[1] The cell wall gives the cell shape and structure, but it is porous enough to permit small water soluble molecules to flow through to the cell membrane surface.[1]<br />
<br />
*'''Gram positive''' bacteria have a thick cell wall made of several layers of peptidoglycan. The cell wall is the outermost structure, as they do not have an outer membrane. The thick cell wall structure make gram positive bacteria more resilient to osmotic shock. Gram positive bacteria can tolerate 5 to 10 times more turgor pressure than gram Gram negative bacteria.[1] Teichoic acids in the cell wall may also help to bind to cationic nutrients in soil surroundings.[1] <br />
<br />
*'''Gram negative''' bacteria have a thin cell wall surrounded by an outer membrane made of phospholipids and lipopolysaccharides. Polysaccharides of the outer membrane interact with surrounding cations and are involved in attachment of bacteria to soil particles. [1] Periplasm is a gel like substance that occupies the space between the outer membrane and the cell wall of gram negative bacteria.[1] The outer membrane and periplasmic space is thought to provide protection from environmental toxins.[1] Proteins within the periplasm are thought to begin the process of catalyzing hydrolysis of organic and toxic substances.[1] <br />
<br />
[[Image:gramposnegmembrane.jpg|frame|center| Figure 3.4 Illustration of Gram positive and Gram negative cell wall structures. From[http://micro.digitalproteus.com/morphology2.php]]]<br />
<br />
'''Endospores''' are made by ''Bacillus'' and ''Clostridium'' in response to environmental stress.[1] Endospores are extremely resistant structures that can withstand extreme temperatures up to 150℃.[12] They can also withstand extreme pressure, desiccation, radiation, pH and chemicals.[12] The endospore protects the bacterial DNA until environmental conditions are more favorable and germination can proceed. Soil is the most common habitat for endospore forming bacteria.[12]<br />
<br />
'''Extracellular polymers''' - Many bacteria secrete a slime layer or capsule made of polysaccharides or glycoproteins.[1] The outer polysaccharide coating of bacteria helps in attachment to surfaces and the formation of biofilms.[1] Bacterial capsule secretions play a big role in soil aggregation and soil structure.[1] When the carbon to nitrogen ratio within soils is high, microbes secrete the excess carbon as extracellular polysaccharides.[1]<br />
<br />
====Reproduction==== <br />
Most bacteria reproduce by binary fission.[12] The bacterial cell expands to twice the original cell size, duplicates the bacterial DNA and pinches off, producing two daughter cells. Each resultant daughter cell is a clone of the parent cell. Prokaryotic Archaea also reproduce by binary fission.<br />
<br />
*'''Spore formation:''' Actinomycetes are a large group of filamentous bacteria, primarily found in soil.[1] Actinomycetes are morphologically similar to fungi. Actinomycetes form long filaments called hyphae. Unlike most bacteria, the majority of actinomycetes reproduce using asexual spores called conidia.[1] Though they share many characteristic with fungi, actinomycetes are still prokaryotes. They are smaller than fungi and the cell wall contains peptidoglycan.[1] Actinomycetes break down a wide variety of organic compounds and play an important role in organic matter decomposition. [1] ''Streptomyces'', a subgroup within actinomycetes, produce geosmin, which gives soil the characteristic earthy smell.[12]<br />
<br />
====Metabolism==== <br />
<br />
Along with archaea, bacteria are the most metabolically diverse and employ many different nutritional strategies.[1]<br />
*Heterotrophs - Most bacteria are heterotrophic, obtaining carbon from preformed organic substances. [1] <br />
*Autotrophs - Carbon dioxide serves as the main source of carbon. Some cyanobacteria, nitrifying and sulfur-oxidizing bacteria are autotrophs.[1]<br />
*Organotrophs - Most bacteria obtain electrons from organic substances.[1]<br />
*Lithotrophs - Some cyanobacteria, nitrifying bacteria and sulfur-oxidizing bacteria obtain electrons from inorganic substances.[1]<br />
*Phototrophs - Cyanobacteria use light as the main source of metabolic energy.[1]<br />
*Chemotrophs - All other nonphotosynthetic bacteria do not rely on light for metabolic energy.[1]<br />
<br />
====Contributions to the Cycle==== <br />
<br />
Bacteria play a significant role in the cycling of a wide range of elements.<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Carbon_cycle '''Carbon Cycle:'''] <br />
<br />
*'''Carbon Assimilation''' is the process of fixing carbon dioxide into organic forms. Carbon fixation is performed by autotrophic bacteria, such as cyanobacteria.[1] Chemoautotrophic nitrifying bacteria, such as ''Nitrobacter, Nitrosospira'' and ''Nitrosomonas'', also fix carbon.[1] Sulfur oxidizing bacteria, such as ''Thiobacillus'', fix carbon as well.<br />
<br />
*'''Carbon Mineralization''' results from microbial decomposition of organic carbon compounds into inorganic forms. As the organic carbon substances, like plant matter, are decomposed, inorganic carbon dioxide is produced. Most bacteria are heterotrophs that perform carbon mineralization. When microorganisms die, they are decomposed by successive microbial generations. Peptidoglycan, the main component of bacterial cell walls, is utilized as a polysaccharide substrate by other heterotrophic soil microbes.[1]<br />
<br />
*'''Methanogenesis''' - Methanogenic bacteria produce methane from the reduction of carbon dioxide. They are all strict anaerobes that use carbon dioxide for the carbon source.[1] They can all use hydrogen as a source of energy and electron donor. [1]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle '''Nitrogen cycle:''']<br />
<br />
*'''Nitrogen fixation:''' ''Azotobacter'' is a free living nitrogen fixing bacteria.[1] ''Rhizobium'' lives in a mutualistic relationship with plants by fixing nitrogen within root the nodules of legumes.[1] ''Anabaena'' and ''Nostoc'' have specialized heterocyte structures where nitrogen fixation occurs.[1] <br />
<br />
*'''Nitrification:''' Nitrifying bacteria, such as ''Nitrobacter, Nitrosospira,'' and ''Nitrosomonas'', oxidize ammonium to nitrate.[1] <br />
<br />
*'''Denitrification:''' ''Alcaligenes, Flavobacterium'', and ''Pseudomonas'' are common soil denitrifying bacteria.[1]<br />
<br />
===Domain Archaea===<br />
<br />
====Introduction to Archaea====<br />
<br />
Vladimir Vernadsky decided, in 1926, that only two domains of life existed on Earth, Bacteria and Eukarya.[37] About 50 years later in 1977, Carl Woese and George Fox theorized that part of the bacterial domain possed multiple dissimilarities from bacteria and recognized it to be another domain of life, now called Archaea.[38] Woese and Fox’s theory regarding the differences of archaea were confirmed in 1990’s through the use of 16S rRNA and 18S rRNA.[38] <br />
<br />
Despite the strongly held belief, in the 1990s, that archaea only inhabited extreme environments, recent discoveries have suggested their presence in abundant numbers all throughout the Earth. It is suggested that Archaea play notable roles in maintaining nutrient cycles.[37] Various methods of research, such as cultivation, culture-independent techniques and isotope-based methods, have facilitated the study of domain Archaea in carbon and nitrogen cycling. [37]<br />
<br />
The use of genomic and biochemical data has permitted the study of archaeal structure.[37] Use of these research methods has shown that domain archaea and domain bacteria differ in cell wall characteristics yet, share various ways to transfer genetic information by replication and transcription from their common ancestor, Eukarya.[37] As of 2012, 116 genera of Archaea have been observed which consists of 450 species. Most of the archaeal species in these genera remains uncultivated, known only through its gene sequences and molecular surveys.[37]<br />
<br />
====Morphology==== <br />
Archaea are characterized by various cell sizes. They are most commonly found to be small organisms ranging from “0.1 to 15 μ diameter and up to 200 μ long.”[38] The shape of many archaea are similar to bacteria, including bacillus, cocci, spirilla and “plate-like forms.” [38] Their cell membranes have ether linked lipids with no periplasmic space, similar to gram-positive bacteria, and contain no intracellular organelles.[39]<br />
<br />
'''Flagella:''' Most motile archaea inhabit a motor rotary system that allows it to move its flagella through the chemical gradient similar to bacteria.[39] Despite its similarity in function and source of energy required for motility, the flagella of both archaea and bacteria differ in structure.[39] Archaeal flagella gets the energy for its movement by ATP and is composed of dependent filaments that rotate singularly. [40] Archaeal flagella are known to be thinner than bacteria flagellin.[40] Since, the archaeal common ancestor is not bacteria but eukarya, convergent evolution is a plausible explanations for the differences between bacterial and archaeal flagellin. [40]<br />
<br />
'''Membranes:''' Archaea have a cell membrane that protects the cytoplasm and the nucleic acids from the environment. The archaeal cell membrane has a lipid bilayer with glycol-ether lipids that are more stable than ester linkages and help some archaea that live in extreme environments to withstand such conditions.[39] Most archaeal species are surrounded by a cell wall which protects the cell membrane and maintains the archaeal structure.[41]<br />
<br />
====Reproduction====<br />
Archaeal organisms reproduce by binary fission since they do not have nucleases thus, the DNA chromosome in a Archaeal organism replicate, separate and create two daughter cells.[43] The process of binary fission can be seen in Figure (3.5) process begins the parent cell duplicating the DNA. The DNA material then goes to the sides of the cell where an invagination to the cell occurs allowing the cell to become two individual cells. Binary fission is a very fast reproduction process, that allows archaeal organisms to grow at an exponential rate.[44]<br />
<br />
[[Image:WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg|frame|center|Figure 3.5 Illustration of binary fission. From[https://d2jmvrsizmvf4x.cloudfront.net/WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg]]]<br />
<br />
====Metabolism==== <br />
Archaea share similar metabolic characteristics to bacteria. The metabolic pathways taken by all archaea shown in the (Figure 3.6) demonstrates the great diversity and variation amongst archaea. [38] The kinds of archaea that are seen in the environment and the metabolic pathways taken by some can be summarized in the image. <br />
<br />
*Photoautotrophs: use light as an energy source and carbon dioxide as the carbon source with the help of the Calvin Cycle.[38]<br />
*Chemoautotrophs: use inorganic chemicals as their energy source and carbon dioxide as carbon source. <br />
*Chemoheterotrophs: take organic chemicals as energy source and organic chemicals as carbon source. The pathways taken by chemoheterotrophs varies from respiration by the Krebs Cycle to fermentation. [38]<br />
*Photoheterotrophs: use light as their energy source and organic chemicals as their carbon source. <br />
<br />
Most archaea inhabiting in the soil environment are major contributors to the biogeochemical cycles.<br />
<br />
[[Image:2000px-Troph_flowchart.svg.png|thumbnail|center|Figure 3.6 Flowchart showing different metabolic pathways. From[https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Troph_flowchart.svg/2000px-Troph_flowchart.svg.png]]]<br />
<br />
====Contributions to the Cycle====<br />
Archaea play a significant role in the nutrient cycles that take place in the ecosystem as they account for about 1-5% of all the prokaryotes present in the soil environment.[42]<br />
<br />
'''Carbon Cycle:''' Archaea have an important role in the carbon cycle that takes place specifically in methane production, carbon mineralization and carbon assimilation all of all of which contribute to the soil’s carbon sink.[42] The carbon dense soil helps to make the soil organic matter rich and helps to form extracellular polymers which creates stable aggregates. For some microbes, an electron acceptor is need to carry out metabolic functions. [42] More info on [https://microbewiki.kenyon.edu/index.php/Carbon_cycle Carbon Cycle].<br />
<br />
*'''Carbon Assimilation:''' Involves the transformation of inorganic carbon into organic carbon compounds. This process is commonly done by autotrophic phyla ''Crenarchaeota, Thaumarchaeota'', and ''Euryarchaeota'' that use carbon dioxide/ bicarbonate converting it to organic compounds.[42] Of the autotrophic lineages observed in carbon assimilation the ''Thaumarchaeota'' are strict autotrophs, the ''Euryarchaeota'' and ''Crenarchaeota'' are facultative autotrophs and the ''Halobacteriales'' and ''Thermococcales'' are obligate heterotrophs.[42] <br />
<br />
*'''Carbon Mineralization:''' The process that converts organic carbon into the oxidized inorganic carbon, carbon dioxide is commonly done by both aerobes and anaerobes.[42] The heterotrophic microbes that use organic compounds as energy to oxidize the carbon source include, methanogens and methane-oxidizing archaea belonging to the phyla ''Euryarchaetota'', and ''Crenarchaeota''.[42] <br />
<br />
*'''Methanogenesis:''' production of methane, a major greenhouse gas in the Earth’s atmosphere is commonly done by archaea upon reducing an oxidized compound.[42] The phyla ''Euryarchaeota'' is the only phyla that consists of archaea that produce methane all of which form five class: ''Methanopyri, Methanococci, Methanobacteria, Methanomicrobia'' and ''Thermoplasmata''.[42] Methanogens are commonly found in anaerobic and aerobic conditions such as bodies of water, aerated soils and oxygenated waters.[42]<br />
<br />
'''Nitrogen Cycle :''' Archaea play a pivotal role in the Nitrogen cycle and help create nitrogenous products for the plants and microbes. More info on [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle Nitrogen cycle].<br />
<br />
*'''Nitrogen Fixation:''' Fixing nitrogen from the environment and converting it to organic nitrogen in the soil or to inorganic nitrogenous form since both organic and inorganic products are in short supply in the biosphere and are fixed by many archaeal organisms.[42] N2 fixation by the environment is usually done by three major archaeal classes ''Methanobactera, Methanococci'' and ''Methanomicrobia''.[42] <br />
<br />
*'''Nitrification:''' Converting the ammonia (NH4+) in the soil to nitrite (NO2-) produces nitrate (NO3-) as an intermediate. [42] The transformation of ammonia to first nitrate then to nitrite is a two step process that is done by different microbes. [42] Most common organisms involved in nitrification include ammonia-oxidizing archaea which are lithotrophic organisms mostly, of the ''Thaumarchaeota'' phylum from the archaea domain. <br />
<br />
*'''Denitrification :''' The conversion of atmospheric N2 using the electron acceptor NO3- or NO2- creating the formation of nitric oxide, nitrous oxide and/or N2.[42] The formation of the end product N2 may not always be produced but other intermediates NO and N2O, greenhouse gases may be produced.[42] Of the archaeal organisms that have been studied in denitrification process is done by ''Pyrobaculum aerophilum'' which accepts both NO3- and NO2- as an electron acceptor producing a variety of products NO2-, NO, N20 and N2.[42]<br />
<br />
===Domain Eukarya===<br />
<br />
====Fungi====<br />
<br />
=====Introduction=====<br />
<br />
'''Introduction'''<br />
<br />
Fungi comes from the ancient Greek word “sphongos” meaning sponge in reference to the mushroom cap [47]. Fungi have the general characteristics of being eukaryotic, heterotrophic, external absorbers of nutrients, containing a hyphal thallus, reproducing via spore, and being pleomorphic (producing several forms). Fungi are generally organoheterotrophs that can survive in low pH and stay active at low moisture content[46]. Fungi reside in the domain Eukarya with an estimated species of 1.5 million, and less than five percent of them have ever been described. The general phyla included within Kingdom Fungi include Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, Chytridiomycota, and Microsporidia [48].<br />
<br />
[[Image:magical-kingdom-620.jpg|frame|center|Figure 3.7 Fungi phyla hierarchy. From.[http://www.motherjones.com/environment/2009/11/fungi-family-tree]]]<br />
<br />
=====Morphology=====<br />
<br />
'''Morphology''' <br />
<br />
Fungi can be either unicellular (yeasts) or multicellular. All multicellular fungi are made up of small, filamentous particles called hyphae. Some hyphae have cross walls called septa, while others do not- this is a large basis of fungal identification. Fungal cells generally have multiple nuclei. Fungal cell walls are generally composed of chitin, a long carbohydrate polymer that adds rigidity and structural support to fungi [49]. <br />
<br />
=====Reproduction=====<br />
<br />
'''Reproduciton'''<br />
<br />
Fungal reproduction can occur either sexually or asexually.<br />
<br />
'''Sexual reproduction''' can occur by homothallic or heterothallic mycelia.<br />
<br />
'''Asexual reproduction''' can occur by fragmentation, budding, or by producing spores (the most common method). <br />
<br />
*'''Spores:''' spores come in many different forms. One of the most well known are conidiospores, which are unicellular or multicellular spores that get released from the tip of the hyphae. <br />
<br />
'''Perfect fungi''' are those that can reproduce both sexually and asexually while imperfect fungi are those that can only reproduce asexually.<br />
<br />
*Sexual reproduction always includes the stages plasmogamy (fusion of two haploid cells), karyogamy (creation of a diploid zygote), and meiosis (gametes are created).<br />
<br />
=====Metabolism=====<br />
<br />
'''Metabolism'''<br />
<br />
Many different fungi display a myriad of metabolisms. There are primary metabolites that that help the fungi function properly, and secondary metabolites that are generally bioactive that are not the most pertinent to fungal growth (they can live without these). Secondary metabolites play a large role in chemistry today and can be manufactured into commonly used products such as new drugs. In general fungi are heterotrophic through release of extracellular enzymes into the neighboring environment to break complex molecules down into smaller ones. The materials are then absorbed and metabolized [50]. Fungi are sessile organisms that overcome their little to no movement through apical growth at the hyphal tip. Fungi are noted to grow almost everywhere on the Earth.<br />
<br />
=====Relevance to soil===== <br />
<br />
'''Relevance to soil'''<br />
<br />
Fungi include some of the most abundant biomass of microorganisms in numerous soils. They play an important role as decomposers within the soil food web through conversion of difficult to digest organic material into forms many other organisms can use [51]. Their hyphae can bind soil particles together and create aggregates that increase soil water holding capacity. They perform important functions from water dynamics to nutrient cycling and disease suppression. Soil fungi can be categorized into three different groups based on their actions: <br />
<br />
*decomposers: that convert dead organic material into fungal biomass<br />
<br />
*mutualists: which colonize plant roots and help solubilize phosphorous and bring soil nutrients<br />
<br />
*pathogens/ parasites: which help control diseases in soil via trapping organisms such as nematodes [51]. <br />
<br />
Fungi are seen common in intensively managed agricultural soils due to tillage disrupting hyphae. Fungi also play a very important role in the [https://microbewiki.kenyon.edu/index.php/Rhizosphere_Interactions rhizosphere], the region of soil that is greatly influenced by the plant root system. This area of soil which is concentrated in plant roots and fungal hyphae is known to support greater microbial activity.<br />
<br />
====Protista====<br />
<br />
Protists are mainly eukaryotic unicellular organisms. They used to belong to their own kingdom Protista, but are now known to be paraphyletic [18]. Protists are made up of protozoa, unicellular algae, and slime molds. The protozoa are divided into 4 major categories: the ciliates, the flagellates, the heliozoans, and the amoebas [10]. They are so small that they don’t need any specialized organelles in order to survive and can survive at low oxygen levels because of this. They are also known to use a contractile vacuole to remove excess water from their cells [10]. <br />
<br />
=====Protozoans=====<br />
<br />
'''Protozoans'''<br />
<br />
The microbial loop is a subsection of the microbial food web that accounts for the dissolved organic matter of systems. It’s suggested that Protozoa have an important role in the maintenance of soil nutrients, specifically nitrogen. A common known characteristic of protozoans is that they stimulate plant growth [19]. It’s hypothesized that they do this through the manipulation of nitrogen levels. In the presence of Protozoa, shoot biomass and shoot N levels are increased [20]. The protozoa is said to stimulate the mineralization of nitrogen via the microbial loop [20]. The indirect effects protozoans have on the nitrogen cycle are thought to be more important than the direct effects it has. This is because grazing stimulates microbial mineralization processes that in turn speeds up the nutrient cycles [20].<br />
<br />
In general, Protozoans range from 5 to 500 µm in diameter, making them significantly larger than bacteria [21]. They are abundantly located near the surface of the soil (15cm deep) where roots are plentiful [21]. Most protozoans have two life cycles. One is their active form where they are motile and feed on prey. The other is the cyst form where they produce a thick coating to protect them from the environment and can go dormant for years.<br />
<br />
======Ciliates======<br />
<br />
'''Cilliates:'''<br />
This group, within protozoans, is fairly diverse. A common feature shared amongst all of its members is the presence of at least one cilia at any stage of its development [10]. The cilia is used for movement and other things such as predation (tentacles). For movement, they use the massive amounts of tiny cilia to create wave like currents to propel the cell forwards. Most ciliates also have toxicysts which are used to capture prey [10]. Some ciliates even have a symbiotic relationship with algae living inside of them [10]. The algae use the CO2 produced by ciliates and turn it into O2 that can then be reused by the ciliates [10]. They are found in a wide array of habitats ranging from freshwater and soil to the rumen of Animals [22]. They are present in almost anywhere that contains water [23]. They are unicellular heterotrophs so they feed on bacteria and algae in their environment. Ciliates are one of the top predators in the microbial food web and are hypothesized to have been a major predatory group before animals evolved [23]. Parasitic ciliates exist that can cause the death of animals and are increasingly becoming dangerous in water [23].<br />
<br />
[[Image:2spiro.jpg|frame|center|Figure 3.8 Microscope image of ciliated protists. From[http://www.microscopy-uk.org.uk/mag/smallimag/2spiro.jpg]]]<br />
<br />
======Flagellates======<br />
<br />
'''Flagellates''' are one of the most commonly known protists. They are unicellular organisms that may be solitary, colonial, free living, or parasitic [24]. The hallmark feature of protists is that at some point in their life cycle, they possess a flagella. A flagellum is a long hair like structure that is used for locomotion, sensation, and sometimes predation [24]. The flagellum makes waves by whiplike lashing movements which propels the cell forwards. Flagellates also have a protective coating in the form of a thin pellicle to protect them from the environment [24]. <br />
<br />
[[Image:9703607_orig.jpg|frame|center|Figure 3.9 Illustration of flaggelates during different life cycle stages. From[http://diagnosticparasitology.weebly.com/uploads/3/9/5/4/3954522/9703607_orig.jpg]]]<br />
<br />
*'''Mastigophora:'''<br />
<br />
Mastigophora is a subphylum of flagellates. Being a member of the flagellates, their key feature is the flagellum. Their habitats include freshwater, soil, and can act as animal parasites as well [25]. They use pseudopodia, a long outward protrusion, to trap and funnel food from the environment into their cell bodies [25]. The Mastigophora are mainly known for their parasitism, which can take place in both humans and animals [25]. ''Typanosomes'' are an example of Mastigophora which causes African sleeping sickness [25]. ''Giardia lambli''a is another example that resides in the intestinal tract of warm-blooded animals and inflicts intestinal giardiases [25]. It is also a major contaminant of drinking water because it is resistant to chlorine, which is the most common water purifier [25]. Having a dormant cyst form also adds to its survival potential through filtration efforts [25].<br />
<br />
<br />
<br />
*'''Euglenids:'''<br />
<br />
Euglenids are one of the best known flagellates. They are found in freshwater and soil, as long as there are organic materials. They also participate in some symbiotic relationships with marine animals. Euglenid cells do not contain cell walls or other rigid membranes [26]. This gives the cell tremendous flexibility and allows it to change its shape to easily navigate through muddy terrain. Euglenids have two flagella, one which creates locomotion and movement for the cell [26]. The other flagellum does not protrude from the cell and is contained in the cell body [26].<br />
<br />
======Amoebas======<br />
<br />
'''Amoebas'''<br />
<br />
Amoebae are single celled eukaryotes present in many different types of environments. They are scattered throughout a variety of eukaryotic lineages and therefore are not monophyletic [27]. Amoebae range in size from 5 micrometers to 3 mm and don’t have a defined shape, commonly recognized for being polymorphic. They are motile through the use of pseudopodia, which stretch and pull the cell along with it. The pseudopodia are also used for feeding. They are able to sense prey that can be engulfed and engulf them via phagocytosis. The amoeba’s main prey consists of bacteria, algae, and other protozoa [28]. The prey is moved around within the cell via food vacuoles, a feature of amoebae [28]. Another key characteristic of amoebae are the large contractile vacuoles inside the cell. The purpose of the contractile vacuole is to osmoregulate by pumping excess water out of the cell. In times of turmoil, amoebae have an encysted form that helps them get through the tough times. This form is useful when there is low nutrient availability to limit energy consumption. There are two main forms an amoeba can be characterized as. They can either be testate or nontestate. Testate amoeba produce shells, or “tests”, that help identify their species since each species has a unique shell.<br />
<br />
[[Image:Amoeba_(PSF).png|frame|center|Figure 3.10 Amoeba morphology. From[https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Amoeba_(PSF).png/230px-Amoeba_(PSF).png]]]<br />
<br />
=====Slime Molds=====<br />
<br />
'''Slime molds''' are fungus like organisms that were at once classified as fungi, but have now been placed in the protozoan phylogeny. Slime molds are single cells that can live independently, but aggregate to form multicellular reproductive structures when necessary [29]. The fruiting body releases spores which germinate into new cells. Slime molds feed off of bacteria and are most commonly found in forests. They feed off of decaying vegetation as well so they can be seen on rotting logs and leaves.<br />
<br />
[[Image:28-30-cellslimemoldlife-l.jpg|frame|center|Figure 3.11 Illustration of slime mold life cycle. From[https://lichencolony.files.wordpress.com/2006/06/28-30-cellslimemoldlife-l.jpg]]]<br />
<br />
==Current Research== <br />
<br />
'''Bacteria:''' To showcase the great diversity of soil bacterial environments, cyanobacteria have been studied in both desert and polar regions. Cyanobacteria can survive in extreme conditions likely because of their long evolutionary past.[16] Dr. Patzelt and his colleagues studied the diverse cyanobacteria residing in the Atacama desert, one of the driest parts of the world. The diverse taxa found in the Atacama desert can withstand prolonged periods of extreme desiccation.[16] The cyanobacteria dominate the soil crusts, affecting soil stability, soil structure and soil fertility.[16] Cyanobacteria inhabiting the Antarctic and Arctic regions, show similar adaptations to extreme environments as the cyanobacteria found in the desert. The polar cyanobacteria are particularly adapted to high altitudes.[17] They can withstand high ultraviolet radiation, desiccation, and repeated freeze-thaw cycles.[17] The autotrophic cyanobacteria supports heterotrophic microbes, providing an important ecosystem service in an environment with low microbial activity.[17]<br />
<br />
'''Archaea:''' It is observed that in 150 soil samples acquired from North and South America, which inhabited only archaeal and bacterial species, about 150,000 species were observed.[45] Of the 150,000 species observed over 2,500 were identified as archaea based on their ssu rRNA.[45] In this study, the archaeal species were further analyzed to understand their role in the soil environment. Of the two common archaeal species, ''Crenarchaeota'' and ''Euryarchaeota'' were found in the soil samples.[45] Bates stated that, “Across the non-experimental soils examined the soil C:N ratio was the single best predictor of archaeal relative abundances” due to their influences in the nutrient cycles.[45]<br />
<br />
'''Fungi:''' Fungi have been in the public eye for a while now due to the many different types of secondary metabolites they produce. Many of these secondary metabolites have bioactive compounds that can inhibit any kind of growth from protozoa, bacteria, parasites, insects, and even other fungi. A large area of intrigue is currently investigating the uses of these chemicals for human interests in use from medicine to plant and animal toxins [52].<br />
<br />
'''Protozoa:''' It’s known that Protozoa stimulate plant growth in some way. It’s suspected that the Protozoa take part in the microbial loop which is responsible for the nutrient production for plants [19]. However, new developments have shown that the Protozoa themselves are responsible for the nitrogen mineralization and that other bacteria have no effect on the plant’s nitrogen sources [19]. This would mean that the stimulation of plant growth via nitrogen is solely due to the Protozoa and that the microbial loop is irrelevant [19].<br />
<br />
==References==<br />
<br />
1. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). Principles and Applications of Soil Microbiology. New Jersey: Pearson Education Inc.<br />
<br />
2. Ingham, Elaine R. Ingham R. "Chapter 4: SOIL FUNGI." Soil Biology. Natural Resources Conservation Service Illinois, n.d. Web. 9 Feb. 2016<br />
<br />
3. Reid, Greg, and Percy Wong. "SOIL BACTERIA AND FUNGI - NEW SOUTH WALES." Soil Bacteria and Fungi. New South Wales Department of Primary Industries, 2005. Web. 11 Feb. 2016.<br />
<br />
4. "Fungi." Microbiology Online. Microbiology Society, n.d. Web. 11 Feb. 2016.<br />
<br />
5. Tortora, G.J., Funke, B.R., Case, C.L. (2012). “Microbiology an Introduction.” 11th ed. Pearson Benjamin Cummings, San Francisco.<br />
<br />
6. Rizzo, D. “Intro to Fungi.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
7. Rizzo, D. “Ascomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
8. Rizzo, D. “Basidiomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
9. Pegg G.F., Brady B.L. “Verticillium Wilts.” New York, CABI Publishing 2002. Google Books. Web. 11 Feb. 2016. http://books.google.com<br />
<br />
10. Hebert, Paul. "What Is a Protist / What Are Protozoa? - Encyclopedia of Life." Encyclopedia of Life. N.p., n.d. Web. 11 Feb. 2016.http://eol.org/info/456<br />
<br />
11. "MicrobeWorld." Protista. N.p., n.d. Web. 11 Feb. 2016. http://www.microbeworld.org/types-of-microbes/protista<br />
<br />
12. Madigan, M.T., Martinko, J.M. (2006). Brock Biology of Microorganisms. New Jersey: Pearson Prentice Hall.<br />
<br />
13. Roesch, L.F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H.; Camargo, F. A. O.; Farmerie, W. G.; Triplett, E. W.(2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1(4).283-290. <br />
<br />
14. Amann, R.I, Ludwig, W., Schleifer, K.H.(1995).Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology and Molecular Biology Reviews. 59(1). 143-169. <br />
<br />
15. Geers, D., Cohan, F.M., Lawrence J.G., Spratt, B.G., Coenye, T. Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005). Opinion: Re-evaluating prokaryotic species. Nature Reviews Microbiology. 3(9). 733-739.<br />
<br />
16. Patzelt, D.J., Hodac, L., Friedl, T., Pietrasiak, N., Johansen, J.R. (2014). Biodiversity of soil cyanobacteria in the hyper-arid Atacama Desert, Chile. Journal of phycology. 50(4). 698-710. <br />
<br />
17. Makhalanyane, T. P., Valverde, A., Velázquez, D., Gunnigle, E., Van Goethem, M. W., Quesada, A., & Cowan, D. A. (2015). Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats. Biodiversity and Conservation, 24(4), 819-840.<br />
<br />
18. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist>.<br />
<br />
19. Ekelund, Flemming; Saj, Stephane; Vestergård, Mette; Bertaux, Joanne; Mikola, Juha. (2009). “The “soil microbial loop” is not always needed to explain protozoan stimulation of plants”. Soil Biology & Biochemistry. Vol. 41 Issue 11, p2336-2342, 7p.<br />
<br />
20. Bonkowski, Michael. "Protozoa and Plant Growth: The Microbial Loop in Soil Revisited." New Phytologist New Phytol 162.3 (2004): 617-31. Web.<br />
<br />
21. Hoorman, James. "The Role of Soil Protozoa and Nematodes." Fact Sheet (n.d.): n. pag. Ohio State University, 2011. Web.<br />
<br />
22. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist<br />
<br />
23. Lynn, Denis H(Apr 2012) Ciliophora. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001966.pub3]<br />
<br />
24. "flagellate". Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc., 2016. Web. 23 Feb. 2016 <http://www.britannica.com/science/flagellate>.<br />
<br />
25. "Mastigophora." World of Microbiology and Immunology. 2003. Encyclopedia.com. 23 Feb. 2016<http://www.encyclopedia.com>.<br />
<br />
26. “Plant Life." : Euglenoids. N.p., n.d. Web. 23 Feb. 2016. <http://lifeofplant.blogspot.com/2011/04/euglenoids.html><br />
<br />
27. Parales, R.E. and Martin, M. (2015) Microbial Diversity Laboratory Manual, MIC 105L, Winter 2015. Department of Microbiology and Molecular Genetics, College of Biological Sciences, The University of California, Davis.<br />
<br />
28. Arnold, Paul. "What Does an Amoeba Eat? Plus Other Ameoba Info and Questions." Bright Hub. N.p., n.d. Web. 04 Mar. 2016.<br />
<br />
29. "MicrobeWorld." Slime Molds. N.p., n.d. Web. 24 Feb. 2016. <http://www.microbeworld.org/types-of-microbes/protista/slime-molds><br />
<br />
30. Leeuwenhoek., A. V. (2009, November 18). One gram of soil: A microbial biochemical gene library. Retrieved March 13, 2016, from http://www.ncbi.nlm.nih.gov/pubmed/19921459 <br />
<br />
31. Coleman, D. C., Crossley, D. A. & Hendrix, P. F. "Soil food webs: Detritivory and microbiology in soils," in Fundamentals of Soil Ecology, 2nd ed. (Elsevier, 2004) 236-241.<br />
<br />
32. Welcome to Agriinfo.in. (n.d.). Retrieved February 21, 2016, from http://agriinfo.in/?page=topic&superid=5&topicid=172 <br />
<br />
33. Gouthro, T., & Rice, D. (1987, December 15). Interaction Terminology. Retrieved February 21, 2016, from http://www.rpi.edu/dept/chem-eng/Biotech-Environ/MixCul/ecodefn.htm <br />
<br />
34. AMENSALISM. (n.d.). Retrieved February 21, 2016, from https://biostuds.wikispaces.com/AMENSALISM <br />
<br />
35. Natural Resources Conservation Service. (n.d.). Retrieved March 10, 2016, from <br />
http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053865 <br />
<br />
36. Ecological Linkages Between Aboveground and Belowground Biota. (n.d.). Retrieved March 10, 2016, from http://science.sciencemag.org/content/304/5677/1629 <br />
<br />
37. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf<br />
<br />
38. Kingdom Archaea. (n.d.). Retrieved March 10, 2016, from http://plantphys.info/organismal/lechtml/archaea.shtml <br />
<br />
39. What are Archaea? - Encyclopedia of Life. (n.d.). Retrieved March 10, 2016, from http://eol.org/info/457 <br />
<br />
40. Flagellum. (n.d.). Retrieved March 10, 2016, from http://www.newworldencyclopedia.org/entry/Flagellum#Archaeal_flagellum <br />
<br />
41. Archaea: Morphology. (n.d.). Retrieved March 10, 2016, from http://www.ucmp.berkeley.edu/archaea/archaeamm.html <br />
<br />
42. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf <br />
<br />
43. Archaea. (n.d.). Retrieved March 10, 2016, from http://www.eoearth.org/view/article/150172/ <br />
<br />
44. Binary Fission: Cell Division & Reproduction of Prokaryotes. (n.d.). Retrieved March 10, 2016, from http://www.scienceprofonline.com/microbi <br />
<br />
45. Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2010, November 18). Examining the global distribution of dominant archaeal populations in soil. Retrieved February 21, 2016, from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105767/<br />
<br />
46. Scow, K. M. "Lecture 1 Part 1." Lecture, Davis.<br />
<br />
47. Rizzo, D. "Lecture 1." Lecture, Davis.<br />
<br />
48. Rizzo, D. "Lecture 3." Lecture, Davis.<br />
<br />
49. C.J. Alexopoulos & C. W. Mims, Introductory Mycology 3rd edition. 1979. Wiley NY. Web accessed Mar 8, 2016 from http://www.ucmp.berkeley.edu/fungi/fungimm.html<br />
<br />
50. Rizzo, D. "Lecture 2." Lecture, Davis.<br />
<br />
51. Ingham, E. “Chapter 4: Soil Fungi” (2016) Oregon State University. Retrieved Feb. 20, 2016, from http://extension.illinois.edu/soil/SoilBiology/fungi.htm<br />
<br />
52. Keller, N., Turner, G., Bennett, J. “Fungal Secondary Metabolism- from Biochemistry to Genomics.” 2005 Nature Reviews Microbiology p/ 937 to 947.</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Introduction_to_Organisms&diff=128248
Introduction to Organisms
2017-01-09T17:30:15Z
<p>Kmscow: /* Carl Woese and the ssRNA */</p>
<hr />
<div>==Introduction== <br />
The soil ecosystem in an important environment that allows both plants and animals to survive, grow and reproduce. The significance of the soil as an ecosystem is at times overlooked despite its major contributions to the environment. The [https://microbewiki.kenyon.edu/index.php/Soil_Environment soil environment] is a complex and varied microbial habitat.[1] The plants and organisms inhabiting the soil contribute to its thriving diversity. Soil life is diverse in morphology, metabolism, size, and many other characteristics. It is believed that “there is sufficient [microbial] DNA in 1 g of soil to extend 1,598km.” [30] Soil is a heterogeneous environment with various zones of rhizosphere, aggregates, organic matter and animal residues.[31] Given each zone is a small component of the larger soil ecosystem, rhizosphere accounts for only 5 to 7 percent of the soil environments but contains over “70 percent of the bacterial- and fungal-feeding nematodes.”[31] <br />
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Since, all three domains of life: archaea, bacteria and eukarya, inhabit the soil environment it is difficult to observe each microbe individually within the soil ecosystem.Only a few representative groups of each domain will be discussed to provide examples of the roles these organisms play in soil. This page attempts to outline the major microbial groups within the diverse soil environment.The interactions between soil microbes amongst the soil microbial diversity. The concept of survival of the fittest is seen in the soil food web, which allows only a selective few with the correct nutrients to thrive in a soil environment. The interactions of soil microbes is not only a part of nature but it also only selects those organisms that are fit for survival, growth and reproduction. The soil food web and symbiotic relationships are used to explain the dynamic interactions between soil organisms.<br />
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==Soil Food Web and Microbial Interactions== <br />
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To survive in a soil environment, an organism must be able to adapt to changing environments and organism interactions. The interactions seen between organisms allows only the fittest to survive, thrive, grow and reproduce in the soil. The only type of interaction shown in (Figure 2.1) is predation. Other common interactions in the soil environment are: <br />
<br />
:[[Image:soil_foodweb72.jpg|frame|center|Figure 2.1 Soil Food Web. From[http://www.exploringnature.org/graphics/foodwebs/soil_foodweb72.jpg]]]<br />
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'''I. Commensalism:''' Organism (A) benefits from the presence of Organism (B) while (B) is unaffected by the presence of (A).[32]<br />
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'''II. Mutualism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) and becomes a necessary association for each other’s survival. [32] [33]<br />
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'''III. Synergism:''' Organism (A) benefits from Organism (B) and Organism (B) benefits from Organism (A) but the relationship is not necessary for survival.[33]<br />
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'''IV. Competition:''' Depending on the organisms this interaction benefits organisms who can readily adapt to the environment and overcome any obstacles needed to survive, grow and reproduce.[33]<br />
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'''V. Amensalism:''' An interaction in which Organisms (A) and (B) develop a partnership where (B) is unaffected by (A) but organism (A) is negatively affected by (B).[34]<br />
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'''VI. Parasitism:''' Organism (A) benefits from Organism (B) but Organism (B) does not benefit positively from Organism (A). <br />
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'''VII. Predation:''' “An interaction between organisms in which one benefits and one is harmed based on the ingestion of the smaller sized organism, the prey, by the larger organism, the predator.”[33]<br />
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The soil food web consists of microbes which play an important role in maintaining the complexity of the soil environment. The interactions observed in the food web are not only based on predation, which directly affects the nutrient cycling and degradation of pollutants, but also the formation of aggregates.[35] The production of specific nutrients, such as ammonium created by microbial metabolic functions, helps to enrich the the soil for plant use.[35] Soil organism activity, along with the presence of soil organic matter, create stabilizing aggregates.[35] The hyphae within the soil environment and the microbes help form large, stable aggregates in the soil habitat.[35] The biodiversity in the soil plays a pivotal role in degrading pollutants, and also prevents pathogens from inhabiting the soil environment through competition.[35] The food web in the soil environment is necessary to maintain the soil nutrients, biological activity, and detoxifying pollutants. Thus, it directly maintains cultivation, productiveness and prosperity of the soil. <br />
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In (Figure 2.1), all three domains, Archaea, Bacteria, and Eukarya, are represented in the soil food web. If one takes a closer look at the figure, the soil food web is not only dependent on small and large microbes but also dead organic matter and plant roots. Dead and living matter in the soil environment contribute to maintaining the food web. Plant residues also are apart of the soil food web. They contribute to the soil’s carbon source.[35] The plant residues either, release carbon dioxide to the environment, or contribute to the soil organic matter. Soil organic matter contributes to soil’s richness and helps to form aggregates.[35] The main focus in the image above is the diversity of organisms, both in domains and in size. The larger organisms are usually the predators. The smaller organisms eventually fall prey, due to their limited mobility, respiration, and size. The eukarya and small bacteria are apparent figures seen in the figure above, but archaea also contribute to the food cycle as they break down ammonia for plants to use. [35]<br />
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The notable interactions of life that take place in the soil environment is evident both below-ground level, as seen in the figure 2.1, but also in the above-ground level.[36] Worms also impact the soil food web, acting as both drivers of the food web both belowground and aboveground.[36]<br />
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==3 Domains==<br />
[[Image:Big_Tree_Bold_Letters_white.png|frame|center|Figure 3.1 Phylogenetic Tree of the 3 Domains. From[http://phylogenomics.blogspot.com/2014_02_01_archive.html]]]<br />
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===Carl Woese and Phylogeny===<br />
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[[Image:Carlwoese1_0565_b.jpg|frame|center|Figure 3.2 Carl Woese. From[http://ofbacteriaandmen.blogspot.com/2013/01/the-new-biology-of-carl-woese.html]]] <br />
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Carl Woese (Figure 3.2) was an American microbiologist famous for pioneering the technique of phylogenetic taxonomy through use of a 16S (for prokaryotic) and 18S (for eukaryotic) ribosomal RNA, also known as small subunit ribosomal RNA [46]. This refined Linnaean classification, taking out the guesswork classification by using a gene that was present in every living organism- the small subunit ribosomal RNA. This method of classification is comprehensive because all organisms possess this form of genetic material. Ssu rRNA is sequenced because the genes are highly conserved. Due to their functional constancy, some have variable regions to differentiate organisms, and are easy to sequence. This technique also elucidated the tree of life, which shows the three domains of microbial lineage diversity: Bacteria, Archaea, and Eukarya. DNA can be compared using a sample database that allows identification of unknown organisms to a species level.<br />
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===Domain Bacteria===<br />
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====Introduction to Bacteria==== <br />
Bacteria are single celled prokaryotic organisms that lack membrane bound organelles. They are involved in many important processes within the soil such as decomposition, [https://microbewiki.kenyon.edu/index.php/Bioremediation bioremediation], symbiosis and biological transformation of nutrients. They are present in all terrestrial soil environments.[1] Soil is a heterogenous environment that varies in moisture content, temperature, oxygen requirements, carbon source and many other bacterial growth conditions. Those wide ranging growth factors account for the enormous diversity in soil bacteria populations. One gram of soil can contain between 26,000 to 52,000 different bacterial species.[13] In the entire microbial world, only about 1 percent of bacterial species can be cultured under laboratory conditions which leaves an immense number of bacterial species yet to be described. [14]<br />
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Classification based on phenotypic characteristics, such as cellular morphology, metabolism, gram staining, oxygen requirements, carbon source and other traits, was used more readily before modern DNA sequencing. But, phenotypic classification is still used and Bergey’s Manual of Systematic Bacteriology is the most widely used source for determining species based on characteristic species traits.<br />
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Traditional species definitions are not as useful in bacteria. OTUs, or operational taxonomic units, based on DNA sequencing similarity, are more applicable to bacteria. Typically, those bacteria with 97 percent similar DNA sequence are classified within the same OTU.[15] The 16S small subunit ribosomal RNA is used to substantiate phylogenetic relationships between different bacterial groups.<br />
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====Morphology====<br />
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Bacterial cells measure approximately 1μm wide and 1-5μm long.[12] They are smaller than eukaryotic microbes.Due to their small size, bacteria can more easily adapt to changing soil environments than larger eukaryotes.[1] Most bacteria are singled celled, but actinomycetes grow in branching filaments. There are many different bacterial cell shapes. The most common are bacilli (rods), cocci (spheres), spirilla (spirals) and actinomycete (filaments).<br />
[[Image:bacteria_sizes.jpg|frame|center|Figure 3.3 Common cell shapes cocci, bacillus, and spirilla and relative sizes. From[http://www.ppdictionary.com/gnbac.htm]]]<br />
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'''Flagella''' - There are many different types and different arrangement of flagella. Movement in soil environments is dependent on soil moisture content. Though movement in soil is limited, flagellar function is important to allow bacteria to find more favorable microsites.[1]<br />
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'''Cell membrane''' - The cell membrane encloses the cytoplasm. It is semi-permeable phospholipid bilayer that regulates transport of nutrients into the cell and waste products out of the cell.<br />
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'''Cell wall''' - Most bacteria have a rigid cell wall surrounding the cell membrane which protects the cell from osmotic lysis. The cell wall is made of a crosslinked polysaccharide, called peptidoglycan, that is found only in bacteria.[1] The cell wall gives the cell shape and structure, but it is porous enough to permit small water soluble molecules to flow through to the cell membrane surface.[1]<br />
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*'''Gram positive''' bacteria have a thick cell wall made of several layers of peptidoglycan. The cell wall is the outermost structure, as they do not have an outer membrane. The thick cell wall structure make gram positive bacteria more resilient to osmotic shock. Gram positive bacteria can tolerate 5 to 10 times more turgor pressure than gram Gram negative bacteria.[1] Teichoic acids in the cell wall may also help to bind to cationic nutrients in soil surroundings.[1] <br />
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*'''Gram negative''' bacteria have a thin cell wall surrounded by an outer membrane made of phospholipids and lipopolysaccharides. Polysaccharides of the outer membrane interact with surrounding cations and are involved in attachment of bacteria to soil particles. [1] Periplasm is a gel like substance that occupies the space between the outer membrane and the cell wall of gram negative bacteria.[1] The outer membrane and periplasmic space is thought to provide protection from environmental toxins.[1] Proteins within the periplasm are thought to begin the process of catalyzing hydrolysis of organic and toxic substances.[1] <br />
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[[Image:gramposnegmembrane.jpg|frame|center| Figure 3.4 Illustration of Gram positive and Gram negative cell wall structures. From[http://micro.digitalproteus.com/morphology2.php]]]<br />
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'''Endospores''' are made by ''Bacillus'' and ''Clostridium'' in response to environmental stress.[1] Endospores are extremely resistant structures that can withstand extreme temperatures up to 150℃.[12] They can also withstand extreme pressure, desiccation, radiation, pH and chemicals.[12] The endospore protects the bacterial DNA until environmental conditions are more favorable and germination can proceed. Soil is the most common habitat for endospore forming bacteria.[12]<br />
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'''Extracellular polymers''' - Many bacteria secrete a slime layer or capsule made of polysaccharides or glycoproteins.[1] The outer polysaccharide coating of bacteria helps in attachment to surfaces and the formation of biofilms.[1] Bacterial capsule secretions play a big role in soil aggregation and soil structure.[1] When the carbon to nitrogen ratio within soils is high, microbes secrete the excess carbon as extracellular polysaccharides.[1]<br />
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====Reproduction==== <br />
Most bacteria reproduce by binary fission.[12] The bacterial cell expands to twice the original cell size, duplicates the bacterial DNA and pinches off, producing two daughter cells. Each resultant daughter cell is a clone of the parent cell. Prokaryotic Archaea also reproduce by binary fission.<br />
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*'''Spore formation:''' Actinomycetes are a large group of filamentous bacteria, primarily found in soil.[1] Actinomycetes are morphologically similar to fungi. Actinomycetes form long filaments called hyphae. Unlike most bacteria, the majority of actinomycetes reproduce using asexual spores called conidia.[1] Though they share many characteristic with fungi, actinomycetes are still prokaryotes. They are smaller than fungi and the cell wall contains peptidoglycan.[1] Actinomycetes break down a wide variety of organic compounds and play an important role in organic matter decomposition. [1] ''Streptomyces'', a subgroup within actinomycetes, produce geosmin, which gives soil the characteristic earthy smell.[12]<br />
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====Metabolism==== <br />
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Along with archaea, bacteria are the most metabolically diverse and employ many different nutritional strategies.[1]<br />
*Heterotrophs - Most bacteria are heterotrophic, obtaining carbon from preformed organic substances. [1] <br />
*Autotrophs - Carbon dioxide serves as the main source of carbon. Some cyanobacteria, nitrifying and sulfur-oxidizing bacteria are autotrophs.[1]<br />
*Organotrophs - Most bacteria obtain electrons from organic substances.[1]<br />
*Lithotrophs - Some cyanobacteria, nitrifying bacteria and sulfur-oxidizing bacteria obtain electrons from inorganic substances.[1]<br />
*Phototrophs - Cyanobacteria use light as the main source of metabolic energy.[1]<br />
*Chemotrophs - All other nonphotosynthetic bacteria do not rely on light for metabolic energy.[1]<br />
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====Contributions to the Cycle==== <br />
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Bacteria play a significant role in the cycling of a wide range of elements.<br />
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[https://microbewiki.kenyon.edu/index.php/Carbon_cycle '''Carbon Cycle:'''] <br />
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*'''Carbon Assimilation''' is the process of fixing carbon dioxide into organic forms. Carbon fixation is performed by autotrophic bacteria, such as cyanobacteria.[1] Chemoautotrophic nitrifying bacteria, such as ''Nitrobacter, Nitrosospira'' and ''Nitrosomonas'', also fix carbon.[1] Sulfur oxidizing bacteria, such as ''Thiobacillus'', fix carbon as well.<br />
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*'''Carbon Mineralization''' results from microbial decomposition of organic carbon compounds into inorganic forms. As the organic carbon substances, like plant matter, are decomposed, inorganic carbon dioxide is produced. Most bacteria are heterotrophs that perform carbon mineralization. When microorganisms die, they are decomposed by successive microbial generations. Peptidoglycan, the main component of bacterial cell walls, is utilized as a polysaccharide substrate by other heterotrophic soil microbes.[1]<br />
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*'''Methanogenesis''' - Methanogenic bacteria produce methane from the reduction of carbon dioxide. They are all strict anaerobes that use carbon dioxide for the carbon source.[1] They can all use hydrogen as a source of energy and electron donor. [1]<br />
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[https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle '''Nitrogen cycle:''']<br />
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*'''Nitrogen fixation:''' ''Azotobacter'' is a free living nitrogen fixing bacteria.[1] ''Rhizobium'' lives in a mutualistic relationship with plants by fixing nitrogen within root the nodules of legumes.[1] ''Anabaena'' and ''Nostoc'' have specialized heterocyte structures where nitrogen fixation occurs.[1] <br />
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*'''Nitrification:''' Nitrifying bacteria, such as ''Nitrobacter, Nitrosospira,'' and ''Nitrosomonas'', oxidize ammonium to nitrate.[1] <br />
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*'''Denitrification:''' ''Alcaligenes, Flavobacterium'', and ''Pseudomonas'' are common soil denitrifying bacteria.[1]<br />
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===Domain Archaea===<br />
<br />
====Introduction to Archaea====<br />
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Vladimir Vernadsky decided, in 1926, that only two domains of life existed on Earth, Bacteria and Eukarya.[37] About 50 years later in 1977, Carl Woese and George Fox theorized that part of the bacterial domain possed multiple dissimilarities from bacteria and recognized it to be another domain of life, now called Archaea.[38] Woese and Fox’s theory regarding the differences of archaea were confirmed in 1990’s through the use of 16S rRNA and 18S rRNA.[38] <br />
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Despite the strongly held belief, in the 1990s, that archaea only inhabited extreme environments, recent discoveries have suggested their presence in abundant numbers all throughout the Earth. It is suggested that Archaea play notable roles in maintaining nutrient cycles.[37] Various methods of research, such as cultivation, culture-independent techniques and isotope-based methods, have facilitated the study of domain Archaea in carbon and nitrogen cycling. [37]<br />
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The use of genomic and biochemical data has permitted the study of archaeal structure.[37] Use of these research methods has shown that domain archaea and domain bacteria differ in cell wall characteristics yet, share various ways to transfer genetic information by replication and transcription from their common ancestor, Eukarya.[37] As of 2012, 116 genera of Archaea have been observed which consists of 450 species. Most of the archaeal species in these genera remains uncultivated, known only through its gene sequences and molecular surveys.[37]<br />
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====Morphology==== <br />
Archaea are characterized by various cell sizes. They are most commonly found to be small organisms ranging from “0.1 to 15 μ diameter and up to 200 μ long.”[38] The shape of many archaea are similar to bacteria, including bacillus, cocci, spirilla and “plate-like forms.” [38] Their cell membranes have ether linked lipids with no periplasmic space, similar to gram-positive bacteria, and contain no intracellular organelles.[39]<br />
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'''Flagella:''' Most motile archaea inhabit a motor rotary system that allows it to move its flagella through the chemical gradient similar to bacteria.[39] Despite its similarity in function and source of energy required for motility, the flagella of both archaea and bacteria differ in structure.[39] Archaeal flagella gets the energy for its movement by ATP and is composed of dependent filaments that rotate singularly. [40] Archaeal flagella are known to be thinner than bacteria flagellin.[40] Since, the archaeal common ancestor is not bacteria but eukarya, convergent evolution is a plausible explanations for the differences between bacterial and archaeal flagellin. [40]<br />
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'''Membranes:''' Archaea have a cell membrane that protects the cytoplasm and the nucleic acids from the environment. The archaeal cell membrane has a lipid bilayer with glycol-ether lipids that are more stable than ester linkages and help some archaea that live in extreme environments to withstand such conditions.[39] Most archaeal species are surrounded by a cell wall which protects the cell membrane and maintains the archaeal structure.[41]<br />
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====Reproduction====<br />
Archaeal organisms reproduce by binary fission since they do not have nucleases thus, the DNA chromosome in a Archaeal organism replicate, separate and create two daughter cells.[43] The process of binary fission can be seen in Figure (3.5) process begins the parent cell duplicating the DNA. The DNA material then goes to the sides of the cell where an invagination to the cell occurs allowing the cell to become two individual cells. Binary fission is a very fast reproduction process, that allows archaeal organisms to grow at an exponential rate.[44]<br />
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[[Image:WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg|frame|center|Figure 3.5 Illustration of binary fission. From[https://d2jmvrsizmvf4x.cloudfront.net/WLR0dWIhSZeBuAJSHwYs_11-02_BinaryFission_0_L.jpg]]]<br />
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====Metabolism==== <br />
Archaea share similar metabolic characteristics to bacteria. The metabolic pathways taken by all archaea shown in the (Figure 3.6) demonstrates the great diversity and variation amongst archaea. [38] The kinds of archaea that are seen in the environment and the metabolic pathways taken by some can be summarized in the image. <br />
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*Photoautotrophs: use light as an energy source and carbon dioxide as the carbon source with the help of the Calvin Cycle.[38]<br />
*Chemoautotrophs: use inorganic chemicals as their energy source and carbon dioxide as carbon source. <br />
*Chemoheterotrophs: take organic chemicals as energy source and organic chemicals as carbon source. The pathways taken by chemoheterotrophs varies from respiration by the Krebs Cycle to fermentation. [38]<br />
*Photoheterotrophs: use light as their energy source and organic chemicals as their carbon source. <br />
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Most archaea inhabiting in the soil environment are major contributors to the biogeochemical cycles.<br />
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[[Image:2000px-Troph_flowchart.svg.png|thumbnail|center|Figure 3.6 Flowchart showing different metabolic pathways. From[https://upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Troph_flowchart.svg/2000px-Troph_flowchart.svg.png]]]<br />
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====Contributions to the Cycle====<br />
Archaea play a significant role in the nutrient cycles that take place in the ecosystem as they account for about 1-5% of all the prokaryotes present in the soil environment.[42]<br />
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'''Carbon Cycle:''' Archaea have an important role in the carbon cycle that takes place specifically in methane production, carbon mineralization and carbon assimilation all of all of which contribute to the soil’s carbon sink.[42] The carbon dense soil helps to make the soil organic matter rich and helps to form extracellular polymers which creates stable aggregates. For some microbes, an electron acceptor is need to carry out metabolic functions. [42] More info on [https://microbewiki.kenyon.edu/index.php/Carbon_cycle Carbon Cycle].<br />
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*'''Carbon Assimilation:''' Involves the transformation of inorganic carbon into organic carbon compounds. This process is commonly done by autotrophic phyla ''Crenarchaeota, Thaumarchaeota'', and ''Euryarchaeota'' that use carbon dioxide/ bicarbonate converting it to organic compounds.[42] Of the autotrophic lineages observed in carbon assimilation the ''Thaumarchaeota'' are strict autotrophs, the ''Euryarchaeota'' and ''Crenarchaeota'' are facultative autotrophs and the ''Halobacteriales'' and ''Thermococcales'' are obligate heterotrophs.[42] <br />
<br />
*'''Carbon Mineralization:''' The process that converts organic carbon into the oxidized inorganic carbon, carbon dioxide is commonly done by both aerobes and anaerobes.[42] The heterotrophic microbes that use organic compounds as energy to oxidize the carbon source include, methanogens and methane-oxidizing archaea belonging to the phyla ''Euryarchaetota'', and ''Crenarchaeota''.[42] <br />
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*'''Methanogenesis:''' production of methane, a major greenhouse gas in the Earth’s atmosphere is commonly done by archaea upon reducing an oxidized compound.[42] The phyla ''Euryarchaeota'' is the only phyla that consists of archaea that produce methane all of which form five class: ''Methanopyri, Methanococci, Methanobacteria, Methanomicrobia'' and ''Thermoplasmata''.[42] Methanogens are commonly found in anaerobic and aerobic conditions such as bodies of water, aerated soils and oxygenated waters.[42]<br />
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'''Nitrogen Cycle :''' Archaea play a pivotal role in the Nitrogen cycle and help create nitrogenous products for the plants and microbes. More info on [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle Nitrogen cycle].<br />
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*'''Nitrogen Fixation:''' Fixing nitrogen from the environment and converting it to organic nitrogen in the soil or to inorganic nitrogenous form since both organic and inorganic products are in short supply in the biosphere and are fixed by many archaeal organisms.[42] N2 fixation by the environment is usually done by three major archaeal classes ''Methanobactera, Methanococci'' and ''Methanomicrobia''.[42] <br />
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*'''Nitrification:''' Converting the ammonia (NH4+) in the soil to nitrite (NO2-) produces nitrate (NO3-) as an intermediate. [42] The transformation of ammonia to first nitrate then to nitrite is a two step process that is done by different microbes. [42] Most common organisms involved in nitrification include ammonia-oxidizing archaea which are lithotrophic organisms mostly, of the ''Thaumarchaeota'' phylum from the archaea domain. <br />
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*'''Denitrification :''' The conversion of atmospheric N2 using the electron acceptor NO3- or NO2- creating the formation of nitric oxide, nitrous oxide and/or N2.[42] The formation of the end product N2 may not always be produced but other intermediates NO and N2O, greenhouse gases may be produced.[42] Of the archaeal organisms that have been studied in denitrification process is done by ''Pyrobaculum aerophilum'' which accepts both NO3- and NO2- as an electron acceptor producing a variety of products NO2-, NO, N20 and N2.[42]<br />
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===Domain Eukarya===<br />
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====Fungi====<br />
<br />
=====Introduction=====<br />
<br />
'''Introduction'''<br />
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Fungi comes from the ancient Greek word “sphongos” meaning sponge in reference to the mushroom cap [47]. Fungi have the general characteristics of being eukaryotic, heterotrophic, external absorbers of nutrients, containing a hyphal thallus, reproducing via spore, and being pleomorphic (producing several forms). Fungi are generally organoheterotrophs that can survive in low pH and stay active at low moisture content[46]. Fungi reside in the domain Eukarya with an estimated species of 1.5 million, and less than five percent of them have ever been described. The general phyla included within Kingdom Fungi include Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, Chytridiomycota, and Microsporidia [48].<br />
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[[Image:magical-kingdom-620.jpg|frame|center|Figure 3.7 Fungi phyla hierarchy. From.[http://www.motherjones.com/environment/2009/11/fungi-family-tree]]]<br />
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=====Morphology=====<br />
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'''Morphology''' <br />
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Fungi can be either unicellular (yeasts) or multicellular. All multicellular fungi are made up of small, filamentous particles called hyphae. Some hyphae have cross walls called septa, while others do not- this is a large basis of fungal identification. Fungal cells generally have multiple nuclei. Fungal cell walls are generally composed of chitin, a long carbohydrate polymer that adds rigidity and structural support to fungi [49]. <br />
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=====Reproduction=====<br />
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'''Reproduciton'''<br />
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Fungal reproduction can occur either sexually or asexually.<br />
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'''Sexual reproduction''' can occur by homothallic or heterothallic mycelia.<br />
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'''Asexual reproduction''' can occur by fragmentation, budding, or by producing spores (the most common method). <br />
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*'''Spores:''' spores come in many different forms. One of the most well known are conidiospores, which are unicellular or multicellular spores that get released from the tip of the hyphae. <br />
<br />
'''Perfect fungi''' are those that can reproduce both sexually and asexually while imperfect fungi are those that can only reproduce asexually.<br />
<br />
*Sexual reproduction always includes the stages plasmogamy (fusion of two haploid cells), karyogamy (creation of a diploid zygote), and meiosis (gametes are created).<br />
<br />
=====Metabolism=====<br />
<br />
'''Metabolism'''<br />
<br />
Many different fungi display a myriad of metabolisms. There are primary metabolites that that help the fungi function properly, and secondary metabolites that are generally bioactive that are not the most pertinent to fungal growth (they can live without these). Secondary metabolites play a large role in chemistry today and can be manufactured into commonly used products such as new drugs. In general fungi are heterotrophic through release of extracellular enzymes into the neighboring environment to break complex molecules down into smaller ones. The materials are then absorbed and metabolized [50]. Fungi are sessile organisms that overcome their little to no movement through apical growth at the hyphal tip. Fungi are noted to grow almost everywhere on the Earth.<br />
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=====Soil Relevance===== <br />
<br />
'''Soil Relevance'''<br />
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Fungi include some of the most abundant biomass of microorganisms in numerous soils. They play an important role as decomposers within the soil food web through conversion of difficult to digest organic material into forms many other organisms can use [51]. Their hyphae can bind soil particles together and create aggregates that increase soil water holding capacity. They perform important functions from water dynamics to nutrient cycling and disease suppression. Soil fungi can be categorized into three different groups based on their actions: <br />
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*decomposers: that convert dead organic material into fungal biomass<br />
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*mutualists: which colonize plant roots and help solubilize phosphorous and bring soil nutrients<br />
<br />
*pathogens/ parasites: which help control diseases in soil via trapping organisms such as nematodes [51]. <br />
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Fungi are seen less in agricultural soils due to tillage disrupting hyphae leading to less healthy soils. Fungi also play a very important role in the [https://microbewiki.kenyon.edu/index.php/Rhizosphere_Interactions rhizosphere], the section of soil that is greatly influenced by the plant root system. This area of soil which is saturated with plant roots and fungal hyphae is known to support greater microbial activity.<br />
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====Protista====<br />
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Protists are mainly eukaryotic unicellular organisms. They used to belong to their own kingdom Protista, but are now known to be paraphyletic [18]. Protists are made up of protozoa, unicellular algae, and slime molds. The protozoa are divided into 4 major categories: the ciliates, the flagellates, the heliozoans, and the amoebas [10]. They are so small that they don’t need any specialized organelles in order to survive and can survive at low oxygen levels because of this. They are also known to use a contractile vacuole to remove excess water from their cells [10]. <br />
<br />
=====Protozoans=====<br />
<br />
'''Protozoans'''<br />
<br />
The microbial loop is a subsection of the microbial food web that accounts for the dissolved organic matter of systems. It’s suggested that Protozoa have an important role in the maintenance of soil nutrients, specifically nitrogen. A common known characteristic of protozoans is that they stimulate plant growth [19]. It’s hypothesized that they do this through the manipulation of nitrogen levels. In the presence of Protozoa, shoot biomass and shoot N levels are increased [20]. The protozoa is said to stimulate the mineralization of nitrogen via the microbial loop [20]. The indirect effects protozoans have on the nitrogen cycle are thought to be more important than the direct effects it has. This is because grazing stimulates microbial mineralization processes that in turn speeds up the nutrient cycles [20].<br />
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In general, Protozoans range from 5 to 500 µm in diameter, making them significantly larger than bacteria [21]. They are abundantly located near the surface of the soil (15cm deep) where roots are plentiful [21]. Most protozoans have two life cycles. One is their active form where they are motile and feed on prey. The other is the cyst form where they produce a thick coating to protect them from the environment and can go dormant for years.<br />
<br />
======Ciliates======<br />
<br />
'''Cilliates:'''<br />
This group, within protozoans, is fairly diverse. A common feature shared amongst all of its members is the presence of at least one cilia at any stage of its development [10]. The cilia is used for movement and other things such as predation (tentacles). For movement, they use the massive amounts of tiny cilia to create wave like currents to propel the cell forwards. Most ciliates also have toxicysts which are used to capture prey [10]. Some ciliates even have a symbiotic relationship with algae living inside of them [10]. The algae use the CO2 produced by ciliates and turn it into O2 that can then be reused by the ciliates [10]. They are found in a wide array of habitats ranging from freshwater and soil to the rumen of Animals [22]. They are present in almost anywhere that contains water [23]. They are unicellular heterotrophs so they feed on bacteria and algae in their environment. Ciliates are one of the top predators in the microbial food web and are hypothesized to have been a major predatory group before animals evolved [23]. Parasitic ciliates exist that can cause the death of animals and are increasingly becoming dangerous in water [23].<br />
<br />
[[Image:2spiro.jpg|frame|center|Figure 3.8 Microscope image of ciliated protists. From[http://www.microscopy-uk.org.uk/mag/smallimag/2spiro.jpg]]]<br />
<br />
======Flagellates======<br />
<br />
'''Flagellates''' are one of the most commonly known protists. They are unicellular organisms that may be solitary, colonial, free living, or parasitic [24]. The hallmark feature of protists is that at some point in their life cycle, they possess a flagella. A flagellum is a long hair like structure that is used for locomotion, sensation, and sometimes predation [24]. The flagellum makes waves by whiplike lashing movements which propels the cell forwards. Flagellates also have a protective coating in the form of a thin pellicle to protect them from the environment [24]. <br />
<br />
[[Image:9703607_orig.jpg|frame|center|Figure 3.9 Illustration of flaggelates during different life cycle stages. From[http://diagnosticparasitology.weebly.com/uploads/3/9/5/4/3954522/9703607_orig.jpg]]]<br />
<br />
*'''Mastigophora:'''<br />
<br />
Mastigophora is a subphylum of flagellates. Being a member of the flagellates, their key feature is the flagellum. Their habitats include freshwater, soil, and can act as animal parasites as well [25]. They use pseudopodia, a long outward protrusion, to trap and funnel food from the environment into their cell bodies [25]. The Mastigophora are mainly known for their parasitism, which can take place in both humans and animals [25]. ''Typanosomes'' are an example of Mastigophora which causes African sleeping sickness [25]. ''Giardia lambli''a is another example that resides in the intestinal tract of warm-blooded animals and inflicts intestinal giardiases [25]. It is also a major contaminant of drinking water because it is resistant to chlorine, which is the most common water purifier [25]. Having a dormant cyst form also adds to its survival potential through filtration efforts [25].<br />
<br />
<br />
<br />
*'''Euglenids:'''<br />
<br />
Euglenids are one of the best known flagellates. They are found in freshwater and soil, as long as there are organic materials. They also participate in some symbiotic relationships with marine animals. Euglenid cells do not contain cell walls or other rigid membranes [26]. This gives the cell tremendous flexibility and allows it to change its shape to easily navigate through muddy terrain. Euglenids have two flagella, one which creates locomotion and movement for the cell [26]. The other flagellum does not protrude from the cell and is contained in the cell body [26].<br />
<br />
======Amoebas======<br />
<br />
'''Amoebas'''<br />
<br />
Amoebae are single celled eukaryotes present in many different types of environments. They are scattered throughout a variety of eukaryotic lineages and therefore are not monophyletic [27]. Amoebae range in size from 5 micrometers to 3 mm and don’t have a defined shape, commonly recognized for being polymorphic. They are motile through the use of pseudopodia, which stretch and pull the cell along with it. The pseudopodia are also used for feeding. They are able to sense prey that can be engulfed and engulf them via phagocytosis. The amoeba’s main prey consists of bacteria, algae, and other protozoa [28]. The prey is moved around within the cell via food vacuoles, a feature of amoebae [28]. Another key characteristic of amoebae are the large contractile vacuoles inside the cell. The purpose of the contractile vacuole is to osmoregulate by pumping excess water out of the cell. In times of turmoil, amoebae have an encysted form that helps them get through the tough times. This form is useful when there is low nutrient availability to limit energy consumption. There are two main forms an amoeba can be characterized as. They can either be testate or nontestate. Testate amoeba produce shells, or “tests”, that help identify their species since each species has a unique shell.<br />
<br />
[[Image:Amoeba_(PSF).png|frame|center|Figure 3.10 Amoeba morphology. From[https://upload.wikimedia.org/wikipedia/commons/thumb/5/58/Amoeba_(PSF).png/230px-Amoeba_(PSF).png]]]<br />
<br />
=====Slime Molds=====<br />
<br />
'''Slime molds''' are fungus like organisms that were at once classified as fungi, but have now been placed in the protozoan phylogeny. Slime molds are single cells that can live independently, but aggregate to form multicellular reproductive structures when necessary [29]. The fruiting body releases spores which germinate into new cells. Slime molds feed off of bacteria and are most commonly found in forests. They feed off of decaying vegetation as well so they can be seen on rotting logs and leaves.<br />
<br />
[[Image:28-30-cellslimemoldlife-l.jpg|frame|center|Figure 3.11 Illustration of slime mold life cycle. From[https://lichencolony.files.wordpress.com/2006/06/28-30-cellslimemoldlife-l.jpg]]]<br />
<br />
==Current Research== <br />
<br />
'''Bacteria:''' To showcase the great diversity of soil bacterial environments, cyanobacteria have been studied in both desert and polar regions. Cyanobacteria can survive in extreme conditions likely because of their long evolutionary past.[16] Dr. Patzelt and his colleagues studied the diverse cyanobacteria residing in the Atacama desert, one of the driest parts of the world. The diverse taxa found in the Atacama desert can withstand prolonged periods of extreme desiccation.[16] The cyanobacteria dominate the soil crusts, affecting soil stability, soil structure and soil fertility.[16] Cyanobacteria inhabiting the Antarctic and Arctic regions, show similar adaptations to extreme environments as the cyanobacteria found in the desert. The polar cyanobacteria are particularly adapted to high altitudes.[17] They can withstand high ultraviolet radiation, desiccation, and repeated freeze-thaw cycles.[17] The autotrophic cyanobacteria supports heterotrophic microbes, providing an important ecosystem service in an environment with low microbial activity.[17]<br />
<br />
'''Archaea:''' It is observed that in 150 soil samples acquired from North and South America, which inhabited only archaeal and bacterial species, about 150,000 species were observed.[45] Of the 150,000 species observed over 2,500 were identified as archaea based on their ssu rRNA.[45] In this study, the archaeal species were further analyzed to understand their role in the soil environment. Of the two common archaeal species, ''Crenarchaeota'' and ''Euryarchaeota'' were found in the soil samples.[45] Bates stated that, “Across the non-experimental soils examined the soil C:N ratio was the single best predictor of archaeal relative abundances” due to their influences in the nutrient cycles.[45]<br />
<br />
'''Fungi:''' Fungi have been in the public eye for a while now due to the many different types of secondary metabolites they produce. Many of these secondary metabolites have bioactive compounds that can inhibit any kind of growth from protozoa, bacteria, parasites, insects, and even other fungi. A large area of intrigue is currently investigating the uses of these chemicals for human interests in use from medicine to plant and animal toxins [52].<br />
<br />
'''Protozoa:''' It’s known that Protozoa stimulate plant growth in some way. It’s suspected that the Protozoa take part in the microbial loop which is responsible for the nutrient production for plants [19]. However, new developments have shown that the Protozoa themselves are responsible for the nitrogen mineralization and that other bacteria have no effect on the plant’s nitrogen sources [19]. This would mean that the stimulation of plant growth via nitrogen is solely due to the Protozoa and that the microbial loop is irrelevant [19].<br />
<br />
==References==<br />
<br />
1. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). Principles and Applications of Soil Microbiology. New Jersey: Pearson Education Inc.<br />
<br />
2. Ingham, Elaine R. Ingham R. "Chapter 4: SOIL FUNGI." Soil Biology. Natural Resources Conservation Service Illinois, n.d. Web. 9 Feb. 2016<br />
<br />
3. Reid, Greg, and Percy Wong. "SOIL BACTERIA AND FUNGI - NEW SOUTH WALES." Soil Bacteria and Fungi. New South Wales Department of Primary Industries, 2005. Web. 11 Feb. 2016.<br />
<br />
4. "Fungi." Microbiology Online. Microbiology Society, n.d. Web. 11 Feb. 2016.<br />
<br />
5. Tortora, G.J., Funke, B.R., Case, C.L. (2012). “Microbiology an Introduction.” 11th ed. Pearson Benjamin Cummings, San Francisco.<br />
<br />
6. Rizzo, D. “Intro to Fungi.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
7. Rizzo, D. “Ascomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
8. Rizzo, D. “Basidiomycota Part I.” Hutchinson Hall UC Davis, Davis. 28 Sept. 2015. Lecture.<br />
<br />
9. Pegg G.F., Brady B.L. “Verticillium Wilts.” New York, CABI Publishing 2002. Google Books. Web. 11 Feb. 2016. http://books.google.com<br />
<br />
10. Hebert, Paul. "What Is a Protist / What Are Protozoa? - Encyclopedia of Life." Encyclopedia of Life. N.p., n.d. Web. 11 Feb. 2016.http://eol.org/info/456<br />
<br />
11. "MicrobeWorld." Protista. N.p., n.d. Web. 11 Feb. 2016. http://www.microbeworld.org/types-of-microbes/protista<br />
<br />
12. Madigan, M.T., Martinko, J.M. (2006). Brock Biology of Microorganisms. New Jersey: Pearson Prentice Hall.<br />
<br />
13. Roesch, L.F., Fulthorpe, R. R., Riva, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H.; Camargo, F. A. O.; Farmerie, W. G.; Triplett, E. W.(2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME Journal, 1(4).283-290. <br />
<br />
14. Amann, R.I, Ludwig, W., Schleifer, K.H.(1995).Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiology and Molecular Biology Reviews. 59(1). 143-169. <br />
<br />
15. Geers, D., Cohan, F.M., Lawrence J.G., Spratt, B.G., Coenye, T. Feil, E.J., Stackebrandt, E., Van de Peer, Y., Vandamme, P., Thompson, F.L., Swings, J. (2005). Opinion: Re-evaluating prokaryotic species. Nature Reviews Microbiology. 3(9). 733-739.<br />
<br />
16. Patzelt, D.J., Hodac, L., Friedl, T., Pietrasiak, N., Johansen, J.R. (2014). Biodiversity of soil cyanobacteria in the hyper-arid Atacama Desert, Chile. Journal of phycology. 50(4). 698-710. <br />
<br />
17. Makhalanyane, T. P., Valverde, A., Velázquez, D., Gunnigle, E., Van Goethem, M. W., Quesada, A., & Cowan, D. A. (2015). Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats. Biodiversity and Conservation, 24(4), 819-840.<br />
<br />
18. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist>.<br />
<br />
19. Ekelund, Flemming; Saj, Stephane; Vestergård, Mette; Bertaux, Joanne; Mikola, Juha. (2009). “The “soil microbial loop” is not always needed to explain protozoan stimulation of plants”. Soil Biology & Biochemistry. Vol. 41 Issue 11, p2336-2342, 7p.<br />
<br />
20. Bonkowski, Michael. "Protozoa and Plant Growth: The Microbial Loop in Soil Revisited." New Phytologist New Phytol 162.3 (2004): 617-31. Web.<br />
<br />
21. Hoorman, James. "The Role of Soil Protozoa and Nematodes." Fact Sheet (n.d.): n. pag. Ohio State University, 2011. Web.<br />
<br />
22. Corliss, John. "Protist | Biology." Encyclopedia Britannica Online. Encyclopedia Britannica, n.d. Web. 23 Feb. 2016. <http://www.britannica.com/science/protist<br />
<br />
23. Lynn, Denis H(Apr 2012) Ciliophora. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001966.pub3]<br />
<br />
24. "flagellate". Encyclopædia Britannica. Encyclopædia Britannica Online. Encyclopædia Britannica Inc., 2016. Web. 23 Feb. 2016 <http://www.britannica.com/science/flagellate>.<br />
<br />
25. "Mastigophora." World of Microbiology and Immunology. 2003. Encyclopedia.com. 23 Feb. 2016<http://www.encyclopedia.com>.<br />
<br />
26. “Plant Life." : Euglenoids. N.p., n.d. Web. 23 Feb. 2016. <http://lifeofplant.blogspot.com/2011/04/euglenoids.html><br />
<br />
27. Parales, R.E. and Martin, M. (2015) Microbial Diversity Laboratory Manual, MIC 105L, Winter 2015. Department of Microbiology and Molecular Genetics, College of Biological Sciences, The University of California, Davis.<br />
<br />
28. Arnold, Paul. "What Does an Amoeba Eat? Plus Other Ameoba Info and Questions." Bright Hub. N.p., n.d. Web. 04 Mar. 2016.<br />
<br />
29. "MicrobeWorld." Slime Molds. N.p., n.d. Web. 24 Feb. 2016. <http://www.microbeworld.org/types-of-microbes/protista/slime-molds><br />
<br />
30. Leeuwenhoek., A. V. (2009, November 18). One gram of soil: A microbial biochemical gene library. Retrieved March 13, 2016, from http://www.ncbi.nlm.nih.gov/pubmed/19921459 <br />
<br />
31. Coleman, D. C., Crossley, D. A. & Hendrix, P. F. "Soil food webs: Detritivory and microbiology in soils," in Fundamentals of Soil Ecology, 2nd ed. (Elsevier, 2004) 236-241.<br />
<br />
32. Welcome to Agriinfo.in. (n.d.). Retrieved February 21, 2016, from http://agriinfo.in/?page=topic&superid=5&topicid=172 <br />
<br />
33. Gouthro, T., & Rice, D. (1987, December 15). Interaction Terminology. Retrieved February 21, 2016, from http://www.rpi.edu/dept/chem-eng/Biotech-Environ/MixCul/ecodefn.htm <br />
<br />
34. AMENSALISM. (n.d.). Retrieved February 21, 2016, from https://biostuds.wikispaces.com/AMENSALISM <br />
<br />
35. Natural Resources Conservation Service. (n.d.). Retrieved March 10, 2016, from <br />
http://www.nrcs.usda.gov/wps/portal/nrcs/detailfull/soils/health/biology/?cid=nrcs142p2_053865 <br />
<br />
36. Ecological Linkages Between Aboveground and Belowground Biota. (n.d.). Retrieved March 10, 2016, from http://science.sciencemag.org/content/304/5677/1629 <br />
<br />
37. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf<br />
<br />
38. Kingdom Archaea. (n.d.). Retrieved March 10, 2016, from http://plantphys.info/organismal/lechtml/archaea.shtml <br />
<br />
39. What are Archaea? - Encyclopedia of Life. (n.d.). Retrieved March 10, 2016, from http://eol.org/info/457 <br />
<br />
40. Flagellum. (n.d.). Retrieved March 10, 2016, from http://www.newworldencyclopedia.org/entry/Flagellum#Archaeal_flagellum <br />
<br />
41. Archaea: Morphology. (n.d.). Retrieved March 10, 2016, from http://www.ucmp.berkeley.edu/archaea/archaeamm.html <br />
<br />
42. Gottesman, S., Harwood, C. S., Schneewind, O., Offre, P., Spang, A., & Schleper, C. (n.d.). Annual review of microbiology. Retrieved March 9, 2016, from http://eebweb.arizona.edu/faculty/saleska/SWES.410.510/Readings/Offre_Spang_Schleper_2013_AnnRevMicro_Archaea_Biogeochemistry.pdf <br />
<br />
43. Archaea. (n.d.). Retrieved March 10, 2016, from http://www.eoearth.org/view/article/150172/ <br />
<br />
44. Binary Fission: Cell Division & Reproduction of Prokaryotes. (n.d.). Retrieved March 10, 2016, from http://www.scienceprofonline.com/microbi <br />
<br />
45. Bates, S. T., Berg-Lyons, D., Caporaso, J. G., Walters, W. A., Knight, R., & Fierer, N. (2010, November 18). Examining the global distribution of dominant archaeal populations in soil. Retrieved February 21, 2016, from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105767/<br />
<br />
46. Scow, K. M. "Lecture 1 Part 1." Lecture, Davis.<br />
<br />
47. Rizzo, D. "Lecture 1." Lecture, Davis.<br />
<br />
48. Rizzo, D. "Lecture 3." Lecture, Davis.<br />
<br />
49. C.J. Alexopoulos & C. W. Mims, Introductory Mycology 3rd edition. 1979. Wiley NY. Web accessed Mar 8, 2016 from http://www.ucmp.berkeley.edu/fungi/fungimm.html<br />
<br />
50. Rizzo, D. "Lecture 2." Lecture, Davis.<br />
<br />
51. Ingham, E. “Chapter 4: Soil Fungi” (2016) Oregon State University. Retrieved Feb. 20, 2016, from http://extension.illinois.edu/soil/SoilBiology/fungi.htm<br />
<br />
52. Keller, N., Turner, G., Bennett, J. “Fungal Secondary Metabolism- from Biochemistry to Genomics.” 2005 Nature Reviews Microbiology p/ 937 to 947.</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=121003
Bioremediation
2016-03-22T02:09:45Z
<p>Kmscow: /* Factors Affecting Rates of Biodegradation */</p>
<hr />
<div>{{Curated}}<br />
<br />
Through agriculture, industry, and daily life, harmful chemicals have been released into the earth’s air, soil, and water. Depending on their concentrations, these substances can have destructive consequences on ecosystems, as well as cause severe damage to humans and other organisms nearby. Soil pollution is of special importance because of its impact on surface, groundwater and air contamination and can easily spread and be consumed by humans. <br />
<br />
[[Image:Bioremediation_images.jpeg|upright=3|thumb|Retrieved from Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120.]]<br />
<br />
<b>Biodegradation</b> is the biologically catalyzed modification of an organic chemical's structure. However, this modification can be through different metabolic pathways and does not necessarily mean a reduction in toxicity. Mineralization, one type of biodegradation, is defined as the conversion of an organic substance to its inorganic constituents, rendering the original compound harmless. [23]. Transformation is defined as any metabolically-induced change in the chemical composition of a compound [14].<br />
<br />
<b>Bioremediation</b> refers to the use of microorganisms to degrade contaminants that pose environmental and human risks. Bioremediation processes typically involve the actions of many different microbes acting in parallel or sequence to complete the degradation process. Both in situ (in place) and ex situ (removal and treatment in another place) remediation approaches are used. The versatility of microbes to degrade a vast array of pollutants makes bioremediation a technology that can be applied in different soil conditions [3]. Though it can be inexpensive and in situ approaches can reduce disruptive engineering practices, bioremediation is still not a common practice [1].<br />
<br />
A widely used approach to bioremediation involves stimulating naturally occurring microbial communities, providing them with nutrients and other needs, to break down a contaminant. This is termed <b>biostimulation.</b> Biostimulation can be achieved through changes in pH, moisture, aeration, or additions of electron donors, electron acceptors or nutrients. Another bioremediation approach is termed <b>bioaugmentation</b>, where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously.<br />
<br />
Recent awareness of the dangers of many chemicals used in society has led to research on formulation of products that are more easily degraded in the environment.<br />
<br />
From an ecological point of view, bioremediation depends on the various interactions between three factors: substrate (pollutant), organisms, and environment, as shown in the figure at right [4]. The interactions of these factors affect biodegradability, bioavailability, and physiological requirements, which are important in assessing the feasibility of bioremediation [4]. <b>Biodegradability</b>, or whether a chemical can be degraded or not, is determined by the presence or absence of organisms that are able to degrade a chemical of interest and how widespread these organisms are in the site [4]. The substrate (pollutant) can interact with its surrounding environment to change its <b>bioavailability</b>, or availability to organisms that are capable of degrading it; for example, substrate has low bioavailability if it is tightly bound to soil organic matter or trapped inside aggregates [4]. <b>Physiological requirements</b>, or set of conditions required by organisms to carry out bioremediation in the environment, include nutrient availability, optimal pH, and availability of electron acceptors, such as oxygen and nitrate [4]. Also, the environment needs to be habitable for organisms involved in bioremediation [4].<br />
<br />
=='''Brief History'''==<br />
<br />
[[Image:Wasterwater_treatment.png|upright=2.25|thumb|First Water Treatment Facility in Japan, 1934 Image from http://www.sewerhistory.org/grfx/trtmnt/trtmnt3.htm]] <br />
<br />
Microorganisms in the environment have always broken down waste, and humans have always (knowingly or unknowingly) used them in agricultural, domestic, and industrial activities [24]. As the urbanized world shifted to a more industrial system, however, people began to take an active approach in bioremediation. In the late nineteenth century, wastewater treatment plants were formed, but even so, this was not officially called bioremediation .<br />
The project considered the initial spark of the bioremediation movement was the report “Beneficial Stimulation of Bacterial Activity in Groundwater Containing Petroleum Products” by R.L. Raymond et al. in 1975. By testing the relationship between oil presence and bacterial stimulation, Raymond found that adding nutrients to soil hastened the oil removal. This led to the development of in situ bioremediation [24].<br />
<br />
Initial bioremediation projects focused on “pump and treat” (ex situ) methods in soil around gas stations and refinery spills to get oil out of groundwater sources, but soon cleaning up chlorinated hydrocarbons became a primary concern [24]. Chlorinated compounds were commonly used in pesticides, but when people learned it was a possible carcinogen and causing ozone depletion, research into bioremediation took off [24]. This was when anaerobic bacteria started being used, as it was discovered that they dechlorinate compounds much more quickly than do aerobic bacteria, and produce fewer damaging iron compounds that precipitate from the reactions [24].<br />
<br />
=='''Overview of Pollutants'''==<br />
Pollutants found in soils present a variety of different human health risks. Soil pollutants are typically classified as organic and inorganic pollutants. The remediation of some of these pollutants will be discussed in greater depth in the following sections.<br />
Below is a link to website with a list of examples of soil pollutants and their effects on human health:<br />
<br />
[http://www.environmentalpollutioncenters.org/soil/examples/ Summary of health effects of pollutants]<br />
<br />
==='''Organic Pollutants'''===<br />
Industrialization resulted in increased use of organic compounds that build up and persist in the environment [11]. Main sources of organic pollutants are through anthropogenic activities, including use of solvents, pesticides, and fuels [11]. Some of these organic compounds are highly toxic and they are associated with variety of health issues around the world [11].<br />
<br />
Table below lists some groups of contaminants, examples, and their sources.<br />
<br />
[[Image:Pollutants_list.png|center|upright=2.5|thumb|Retrieved from Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172.]]<br />
<br />
While organic pollutants are causing both environmental and health problems, bioremediation offers an effective solution to the pollution [11]. The table below lists some of the organic pollutants and microorganisms that are found to be able to degrade them.<br />
<br />
[[Image:Pollutants_and_organisms.png|center|upright=2.5|thumb|Retrieved from Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9]]<br />
<br />
==='''Inorganic Pollutants'''=== <br />
{| border="1" style="float:right; margin-left: 10px; text-align:center"<br />
|+ Most inorganic pollutants are due to human activities.<br />
!Pollutant<br />
!Source<br />
|-<br />
| [https://en.wikipedia.org/wiki/Arsenic Arsenic] || Pesticides, wood preservatives, biosolids, ore mining and smelting<br />
|- <br />
| [https://en.wikipedia.org/wiki/Cadmium Cadmium] || Paints and pigments, plastic stabilizers, electroplating, phosphate fertilizers<br />
|-<br />
| [https://en.wikipedia.org/wiki/Chromium Chromium] || Tanneries, steel industries, fly ash<br />
|- <br />
| [https://en.wikipedia.org/wiki/Copper Copper] || Pesticides, fertilizers, biosolids, ore mining and smelting<br />
|-<br />
| [https://en.wikipedia.org/wiki/Mercury_%28element%29 Mercury] || Gold and Silver mining, coal combustion<br />
|-<br />
| [https://en.wikipedia.org/wiki/Nickel Nickel] || Effluent, kitchen appliances, surgical instruments, automobile batteries<br />
|-<br />
| [https://en.wikipedia.org/wiki/Lead Lead] || Aerial emission from combustion of leaded fuel, batteries waste, insecticide and herbicides.<br />
|}<br />
<br />
A majority of heavy metal pollutants come from human sources that accumulate over time.<br />
<br />
There are also natural forms of contamination from normal biological processes, which include:<br />
<br />
1. Weathering of minerals over time<br />
<br />
2. [https://en.wikipedia.org/wiki/Erosion Erosion] and [https://en.wikipedia.org/wiki/Volcano volcanic activities]<br />
<br />
3. [https://en.wikipedia.org/wiki/Wildfire Forest fires] and biogenic source<br />
<br />
4. Particles released by vegetation<br />
<br />
Heavy metals can be absorbed by microbes at cellular binding sites. Extracellular polymers of these microbes can complex heavy metals through various mechanisms [21]. These specialized microorganisms can mineralize the organic contaminants to metabolic intermediates, which are used as primary substrates for cell growth. The microbes prevalent in heavily metal-contaminated soil can alter the oxidation state of the heavy metals by immobilizing them [21], allowing them to be easily removed. Bioremediation of heavy metals from microbes is not heavily researched, mostly due to an incomplete understanding of the genetics of the microbes used in metal adsorption. ''[https://microbewiki.kenyon.edu/index.php/Geomicrobiology Geomicrobiology]'' takes a better look at the interactions between microbes and inorganic material.<br />
<br />
=='''Organisms'''==<br />
As stated previously, bioremediation involves various microorganisms that are able to degrade and reduce toxicity of environmental pollutants [12]. Therefore, the interactions of microbes with the environment and pollutants are significant in determining effectiveness of bioremediation [4]. Those microbes can be either naturally present in the site of bioremediation or isolated from other sites and inoculated artificially [12]. Biodegradation often occurs as part of microbial metabolism and in some cases, microbes are able to directly harvest carbon and energy by breaking down pollutants [12]. Sections below go over bacteria and fungi, the commonly used organisms in bioremediation, and archaea, the more recently discovered group of organisms with unique potential in bioremediation.<br />
<br />
==='''Bacteria'''===<br />
Bacteria are widely diverse organisms, and thus make excellent players in biodegradation and bioremediation. There are few universal toxins to bacteria, so there is likely an organism able to break down any given substrate, when provided with the right conditions (anaerobic versus aerobic environment, sufficient electron donors or acceptors, etc.). Below are several specific bacteria species known to participate in bioremediation.<br />
<br />
===='''''[[Pseudomonas putida]]'''====<br />
[[Image:Pseudomonas_putida.png|upright=1|thumb|Pseudomonas putida, Image © http://www.denniskunkel.com/DK/Bacteria/23859D.html]]<br />
<br />
''Pseudomonas putida'' is a gram-negative soil bacterium that is involved in the bioremediation of toluene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===='''''[[Dechloromonas aromatica]]''' ====<br />
''Dechloromonas aromatica'' is a rod-shaped bacterium which can oxidize aromatics including benzoate, chlorobenzoate, and toluene, coupling the reaction with the reduction of oxygen, chlorate, or nitrate. It is the only organism able to oxidize benzene anaerobically. Due to the high propensity of benzene contamination, especially in ground and surface water, ''D. aromatic'' is especially useful for in situ bioremediation of this substance. [13]<br />
<br />
===='''Nitrifiers and Denitrifiers'''==== <br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage process that involves nitrification and denitrification. During nitrification, ammonium is oxidized to nitrite by organisms like <i>Nitrosomonas europaea</i>.Then, nitrite is further oxidized to nitrate by microbes like <i>Nitrobacter hamburgensis</i>.<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like <i>Paracoccus denitrificans </i>[2]. The result is N2 gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
===='''''[[Deinococcus radiodurans]]'''====<br />
''Deinococcus radiodurans'' is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered strain of Deinococcus radiodurans has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7].<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like ''[[Paracoccus denitrificans]]'' [2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
[[Image:Alcanivorax_borkumensis.png|upright=1|thumb|Alcanivorax borkumensis, Image©https://www.biotechnologie.de/BIO/Navigation/EN/Funding/foerderbeispiele,did=44848.html?view=renderPrint [25]]]<br />
<br />
===='''''[[Methylibium petroleiphilum]]'''====<br />
''Methylibium petroleiphilum'' (formally known as PM1 strain) is a bacterium capable of [https://en.wikipedia.org/wiki/Methyl_tert-butyl_ether methyl tert-butyl ether] (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
===='''''[[Alcanivorax borkumensis]]'''====<br />
''Alcanivorax borkumensis'' is a marine rod-shaped bacterium which consumes hydrocarbons, such as the ones found in fuel, and produces carbon dioxide. It grows rapidly in environments damaged by oil, and has been used to aid in cleaning the more than 830,000 gallons of oil from the [https://en.wikipedia.org/wiki/Deepwater_Horizon_oil_spill Deepwater Horizon oil spill] in the Gulf of Mexico [25].<br />
<br />
==='''Fungi (Mycoremediation)'''===<br />
Current bioremediation applications primarily utilize bacteria, with comparatively few attempts to use fungi. Fungi have fundamentally important roles because of their participation in the cycling of elements through decomposition and transformation of organic and inorganic materials. These characteristics can be translated into applications for bioremediation which could break down organic compounds and reduce the risks of metals. In some cases, fungi have an advantage over bacteria not just in metabolic versatility but also their environmental resilience.They are able to oxidize a diverse amount of chemicals and survive in harsh environmental conditions such as low moisture and high concentrations of pollutants. Therefore, fungi are potentially an extremely powerful tool in soil bioremediation and some versatile species such as <b>[https://en.wikipedia.org/wiki/Wood-decay_fungus#White_rot White Rot Fungi]</b> have been a hot topic of research. [16,17]<br />
<br />
===='''Biodegradation Capacities of White rot fungi'''====<br />
Using fungi as potential treatment of contaminants began in 1985 when the white rot species Phanerochaete chrysosporium was discovered to metabolize multiple key environmental pollutants. The most important feature of these fungi is their enzymatic functional ability to metabolize complex chemicals such as lignin. Similar abilities were later discovered in other white rot fungal species. In addition, white rot fungi are highly advantageous because they degrade lignin extracellularly through its hyphal extension. This allows them to access soil contaminants that other organisms are incapable of and maximize surface area for enzymatic interaction. These inexpensive fungi can tolerate extreme environmental conditions, such as pH, temperature, and moisture content. While many microbial organisms that are used for bioremediation require pre-conditioning of the environment for them to survive in, white rot fungi can directly be applied into most systems because they degrade based upon nutrient deprivation. [18]<br />
<br />
[[Image:040504062021.jpg|right|thumb|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x]]<br />
<br />
===='''''[[Phanerochaete chrysosporium]]'''====<br />
<i>P. chrysosporium</i> was the first fungi linked to degradation of organic pollutants. Extensive research has show this it has strong potential for bioremediation in pesticides, PAHs, dioxins, carbon tetrachloride, and many other pollutants. Among fungal systems, <i>P. chrysosporium</i> has become the model for bioremediation. Other notable species of white rot fungi include <i>Pleurotus ostreatus</i> and <i>Trametes versicolor</i>. [18]<br />
<br />
===='''Bioremediation of Hydrocarbon Pollutants'''====<br />
<br />
Hydrocarbons are stored deep underground but are brought up to the surface to be transformed and utilized, primarily as an energy source known as fossil fuels. The majority of pollution currently comes from these byproducts in the form Polycyclic Aromatic Hydrocarbons (PAHs), which are xenobiotic environmental pollutants that form when carbon materials are incompletely combusted. Some of examples of PAHs include burning wood, fossil fuels, and cigarette smoke. [19,20]<br />
Currently, bioremediation is only effective for soils contaminated with low-molecular weight PAHs because of bacterial commercial use. However, fungi are effective at PAH degradation in comparison to bacteria for a few reasons. Firstly, they are capable degrading PAH’s that are high in molecular weight, bacteria in comparison are better at degrading smaller molecules. Secondly, fungi can function well in non-aqueous environments and low oxygen conditions, both are conditions where PAH’s can accumulate. Many fungi have evolved mechanisms that allow the to target specific PAHs. Fungi produce extracellular enzymes that degrade lignin, a process called mineralization the produces carbon dioxide as the end product. [19,20]<br />
<br />
===='''Remediating Metals'''====<br />
<br />
Toxic metals can enter the environment all life cycle stages of metal compound. For example, metal leaching can occur from the mining process till the disposal of metal wastes. However in nature, the mobility of metals comes from the geological processes that can be released into the soil and aquatic environments. The environmental largest risk from metal contamination comes from the relationship between metals and compounds that are inherently of incapable of being degraded by any natural procedures. The best solution to treating contamination is transporting the metals to location where they cannot produce negative environmental effects. Fungi have various ways of interacting with metals, some of the techniques are increasing or decreasing the mobility of metals, sorption, or even cellular uptake. After the metals have been absorbed the fungus, they can chemically altered to be stored or translocated through the hyphae and into various plants that participate in symbiosis. [17]<br />
<br />
===='''Pesticide Degradation'''====<br />
<br />
Pesticide accumulation is an issue of great concern among the public, because they are directly associated with food products and water supplies. There are number of technologies used for pesticide clean-up; however, these technologies are generally expensive and inefficient because they require contaminated soil to be excavated and sent to a separate storage location for processing. Bioremediation offers a potential solution that treats contaminated soil and groundwater without needing excavation. Studies show that White Rot Fungi has high promise for soil bioremediation application; however, most tests have been conducted in the lab rather than in the actual environment. This fungi demonstrates the ability to transform and mineralize specific pesticides in soil. [18]<br />
<br />
===='''Environmental Applications'''====<br />
<br />
Although fungi demonstrate significant biochemical and ecological useful qualities, they are hardly utilized for biotechnological purposes. Instead, bacteria are most commonly used because they usually produce superior results in their numerous advantages ranging from their highly specific biochemical reactions to their capabilities of breaking down pollutants efficiently [17]. Fungi are underused primarily because of the costs that come from providing oxygen to fungi in polluted environments. However, filamentous fungi could be highly valuable in situations where bacteria cannot perform. For example, fungi are useful in situations where contaminants are physically blockaded and bacteria cannot reach or in circumstances of environmental extremes such as high acidity or dryness prevent bacteria from functioning. [17]<br />
<br />
==='''[https://en.wikipedia.org/wiki/Archaea Archaea]'''===<br />
The role of archaea in bioremediation has not been studied as commonly as that of bacteria [10]. Nevertheless, numbers of researchers have shown their ability to degrade various pollutants and scientists began to discover more about their potential in participating in bioremediation. Below lists some important facts regarding archaea’s potential role in bioremediation.<br />
<br />
- Biodegradation by extreme [https://en.wikipedia.org/wiki/Halophile halophilic] archaea was not recognized widely in the past, but scientists have found out that extreme halophilic archaea have greater catabolic diversity than expected [9]<br />
<br />
- Hydrocarbon-contamination is observed in some extreme environments, including hypersaline (high salt concentration), high or low temperature, or extreme pH [10]. Archaea’s adaptation to extreme environment gives them the potential to participate in biodegradation and bioremediation in these environments; in fact, microorganisms naturally adapted to the cold environments are known to be important degraders of hydrocarbons in those environments [10].<br />
<br />
- Extreme halophilic archaea has potential to biodegrade pollutants in hypersaline environment, in which bacteria typically used in bioremediation cannot survive or function properly. [5]<br />
<br />
- Some archaea are known to be resistant to variety of antibiotics, including penicillin, cycloheximide, streptomycin, etc, which gives them great advantage in participating in bioremediation in the presence of antibiotics [5].<br />
<br />
===='''Examples of studies of Archaea involved in bioremediation'''====<br />
<br />
Four extreme halophilic strains of archaea (belonging to genus ''[https://en.wikipedia.org/wiki/Halobacterium Halobacterium]'', ''[https://en.wikipedia.org/wiki/Haloferax Haloferax]'', and ''[https://en.wikipedia.org/wiki/Halococcus Halococcus]'') were studied to evaluate their potential to biodegrade crude oil and hydrocarbons. [5] All four strains could use various kinds of hydrocarbons as their carbon or energy sources [5]. Two strains of Haloferax grew on n-alkanes with different lengths, ranging from C8 to C34, and also benzene, toluene, biphenyl, and naphthalene. The research demonstrated the important fact that archaea have potential to carry out biodegradation at high temperatures, in the range of 40-45 °C [5], which is advantageous because hydrocarbons have higher solubility and bioavailability at these higher temperature [10]. The four strains studied were resistant to six different antibiotics, including penicillin, streptomycin, cycloheximide [5] and this gave them the potential to carry out biodegradation in conditions unfavorable for bacteria. Research suggests other genera of archaea are also capable of biodegrading in hypersaline environments [6]<br />
<br />
''[https://en.wikipedia.org/wiki/Halococcus Archaeglobus] fulgidus'', a [https://en.wikipedia.org/wiki/Hyperthermophile hyperthermophile] which can use sulfate as an electron acceptor, can also break down various aromatic hydrocarbons (Peeples, 2014).<br />
<br />
=='''Microbial Processes'''==<br />
<br />
Microorganisms use a wide range of processes to transform chemicals in their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor. This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. Below, several steps and details of the microorganisms’ actions are described.<br />
<br />
==='''Factors Affecting Rates of Biodegradation'''===<br />
Biodegradation may be influenced by pH, temperature, moisture, carbon sources, soil texture, aerobic versus anaerobic conditions, the number of substituents, and the concentration of the pollutant. It is impossible, however, to make a generalization about the best universal conditions for biodegradation. What’s toxic to some microbes is a nutrient to others, what might be a damaging pH to some is beneficial to others, and so on.<br />
<br />
A greater amount of substituents will cause slower degradation in aerobic environments, but faster degradation in anaerobic ones. Chlorine makes a molecule less degradable due to steric hindrance preventing access to necessary enzymes, therefore molecules with higher chlorination are slower to degrade in aerobic conditions. High concentration of a pollutant generally results in faster rates of degradation. If the concentration drops below a threshold concentration, the enzymes may not detect it and will cease to degrade it [26].<br />
<br />
Soil with small pores, especially clays, may cause biodegradation to take years due to the decrease in bioavailability. Chlorine makes a molecule less degradable due to steric hindrance preventing necessary enzymes from accessing the compound, therefore molecules with higher chlorination are slower to degrade. <br />
<br />
The rate at which a compound is transformed, as well as the curves that describe its transformation, is referred to as kinetics, and is affected by all factors listed above. First order kinetics (exponential decay) often describes biodegradation when the initial substrate concentration is low, while zero-order kinetics (linear biodegradation) is often observed when the substrate concentration is very high. In some cases if the concentration of the chemical falls below a critical threshold concentration, the microbes can no longer transform it and the chemical persists. <br />
<br />
The power rate model depicting the relationship between concentration and rate of degradation (first order decay here) is as follows:<br />
<br />
-dC/dt = kC^n<br />
<br />
C is substrate concentration, t is time, k is a rate constant for the chemical in question, and n is an appropriate parameter. The values of k and n are adjusted until a line is found to match experimental data [23].<br />
<br />
==='''Primary substrate utilization'''===<br />
<b>Primary substrate utilization</b> occurs when a microbe both transforms a substrate and uses it as an energy or carbon source. [15] An electron acceptor is required for these transformations. It can be anaerobic or aerobic, although the presence of oxygen tends to speed up reactions. This form of biodegradation can be used for treating petroleum spills or the runoff of a number of pesticides. The rate of reaction follows the guidelines in the previous section, where a higher concentration leads to a higher rate. [15]<br />
<br />
==='''Cometabolism (Secondary Substrate Utilization)'''===<br />
<b>Cometabolism</b> involves the transformation of a chemical by an organism while the organism uses a different substance as its primary energy or carbon source [14]. This is a technique often used when the substrate by itself is considered non-biodegradable, and can only be transformed with another compound. During the actual reaction degrading the substance, the organism has no net carbon or energy gain, and may even result in a product with no use to the organism or which is toxic to the cell [14]. However, it is often difficult to tell whether microorganisms have a second substrate available during their transformations [23]. Cometabolism occurs in parallel with metabolism, not instead of.<br />
<br />
A key example of cometabolism is fortuitous metabolism in the degradation of trichloroethylene, shown in the diagram below. An organic growth substrate such as propane or butane is required for the enzymatic activity that transforms TCE. [14]<br />
<br />
[[Image:Cometabolism.png|center|upright=3|thumb|Image from Kate Scow lecture, 2016]]<br />
<br />
==='''Reductive and Hydrolytic Dehalogenation'''===<br />
Chloride and other halogens are common components of pesticides and hazardous industrial wastes, and by removing them the toxic chemical can often be remediated [23]. If the halogen is replaced by a hydrogen (RCl -> RH), then it is <b>reductive dehalogenation</b>. If two halogens are replaced simultaneously, then the process is called <b>dihaloelimination</b>, although it still falls under reductive dehalogenation [14]. If the halogen is replaced by OH (RCl -> ROH) then it’s <b>hydrolytic dehalogenation</b>. In both cases, the halogen is released as its inorganic form into the environment [23].<br />
<br />
==='''Acclimation'''===<br />
An <b>acclimation period</b>, also called an <b>adaptation</b> or <b>lag period</b>, occurs when no destruction of a given chemical is observed [23]. It is caused by the microbes transitioning to their altered environment and shifting their metabolism to better suit it [14]. It can last for anywhere from hours (such as aromatic compounds in warm, oxygenated soils) to months (such as halobenzoates in anaerobic sediments) depending on the chemical in question and the environment [23]. Acclimation periods can be affected by temperature, the presence of oxygen, pH, and concentration of the substance. Although they are most often faster in warm, aerated, and fairly dry environments, there are few consistencies between what shortens or lengthens the period, even if the concentration is the same [23]. Insecticides including methyl parathion and azinphosmethyl; herbicides including 2, 4-D, MCPA, Mecoprop, TCA, and amitrole; the quaternary ammonium compound dodecyltrimethylammonium chloride; polycyclic aromatic hydrocarbons including naphthalene and anthracene; and other chemicals such as phenol, chlorobenzene, PCP, diphenyl-methane, and NTA have all been reported to have acclimation periods, and this can be of severe human concern [23]. The continued presence of these toxins extends human, plant, and animal exposure, and if the chemical is in water, it can allow the substance to flow further and impact environments distant to its site of origin before being degraded.<br />
<br />
==='''Detoxification and Activation'''===<br />
<b>Detoxication</b>, sometimes called <b>detoxification</b>, has been referred to as the “most important role of microorganisms in the transformation of pollutants” [23]. The process is the changing of a molecule into something less harmful to a species in question. There are a number of ways a molecule can be transformed, including hydrolysis, hydroxylation, dehalogenation, demethylation, methylation, and ether cleavage [23]. By breaking bonds, or adding or removing groups, the organism reduces its effect on the environment. Furthermore, although sometimes the resulting chemical is simply excreted as waste, the organism may also be able to use this new compound as a carbon source or further modifies it until it is released as CO2 [23].<br />
<br />
There are instances where the initial compound is harmless, and in fact the substance produced by microorganisms, or an intermediate in the degradation process, is a toxin [23]. This process is called activation. For this reason, it is important to test all steps of a reaction when determining how a compound is degrading. The new toxins may also be more or less mobile than its predecessor, so it can either stick around one area for extended periods of time or spread to other areas and increase damage [23]. A prevalent example of this is the dechlorination of TCE, which produces DCE (50 times more hazardous than TCE) and Vinyl Chloride (a known carcinogen) [14]. Commonly used insecticides in the past, like zinophos, trichloronat, and carbofuran, were all found to increase a soil’s toxicity with extended use [23].<br />
<br />
=='''Bioremediation treatment methods'''==<br />
In order for bioremediation to be successful, it requires sufficient proof for the degradation of contaminants. However, determining the effectiveness and completeness to reach sufficient results is one of the major issues. Natural attenuation relies on natural processes to clean up or attenuate pollution in soil and groundwater [27]. This remediation is done without human interaction, and is primarily used as a monitoring technique, to make sure more aggressive cleanup strategies are not needed. [https://en.wikipedia.org/wiki/Abiotic_component Abiotic] and [https://en.wikipedia.org/wiki/Biotic_component biotic] factors play a distinguishing factor of how effective bioremediation is.<br />
<br />
Current monitoring practices determine the disappearance of contaminants and their degradation products to regulatory levels that are monitored by toxicity testing, usually on single organisms or species to ensure there are no induced changes that may result in residual toxicity. The problem with these monitoring techniques is that the assessment of contaminants may result in an inaccurate indicator of residual toxicity[28]. Rather, studying the microbial community response may be a more comprehensive indicator of residual toxicity than a single species. Once sufficient evidence is provided, human intervention may be needed for a more effective cleanup process. <br />
<br />
There are two types of remediation that are done, ex situ: which is done by removing the contaminated soil or water and treating it outside the source, and in situ: which treatment takes place within the contaminated area. There are some treatments methods that can be either ex situ or in situ. Some techniques may deal with the mobilization of pollutants, to move them out of an area, or immobilized to keep them out of an area such as a water table.<br />
<br />
<br />
[[Image:Summary_of_bioremediation_strategies.png|center|upright=3|thumb|A comparative analysis of the different types of bioremediation. It can be used to find which remediation technique may be used in certain circumstances [12]]]<br />
<br />
<br />
[[Image:Biopiling.png|right|upright=1.5|thumb|Contaminated soil is mixed with amendments and piled on top of a liner, while a pipe with a blower controls aeration. [29]]]<br />
==='''Ex-situ'''===<br />
Ex-situ techniques are those that are applied to soil and groundwater which has been removed from the site via excavation or pumping [12]. The methods used include composting, biofilters, and biopiling. Ex-situ is used for smaller projects, primarily because larger excavation of soil is not prefered. The movement of the soil can be more detrimental by destroying the preestablish horizons in the soil.<br />
<br />
[[Image:Composting.png|right|upright=3|thumb|Composting is a very versatile remediation technique that can be used for either: a very broad treatment with many contaminants, or very specific treatment that utilizes particular microbes that target specific contaminants [30]. It can also be used to augment other treatment methods.]]<br />
<br />
===='''Biopiling'''====<br />
Excavated soils are mixed with soil amendments and placed on a treatment area. Biopiles are aerated with the use of perforated pipes and blowers in order to control the progression of biodegradation more efficiently by controlling the supply of oxygen [29], which in turn may affect other factors such as pH. This system is primarily used to remediate systems with oil and hydrocarbon contamination. The remediated soil is placed in a liner to prevent further contamination of the soil, they may also be covered with plastic to control runoff, evaporation, and [https://en.wikipedia.org/wiki/Volatilisation volatilization].<br />
<br />
===='''Composting'''====<br />
Nutrients are added to soil that is mixed to increase aeration and activation of indigenous microorganisms. Composting is done in a separate container, then when composting is complete it is incorporated into the soil. Bioremediation by the utilization of compost relies on the adsorption capabilities of organic matter and the degradation capabilities of microorganisms present[30]. Composting is recognized as as one of the most cost-effective technologies for soil bioremediation and it can be done on large and small scales. The use of composting is a very versatile technique for soil polluted by a wide range of organic pollutants and heavy metals, making it great for easier remediation involving various pollutants. The utilization of organic wastes for soil remediation is also helpful in decreasing the need for their storage and treatment. Organic matter that is generated from composting offers the benefit of improving soil quality and structure. Composting is primarily used for remediation over a longer period of time, as the nutrients for the microbes are released gradually and requrire more time compared to quicker treatments such as biostimulation.<br />
<br />
==='''In-situ'''===<br />
In-situ techniques are applied to soil and groundwater at the site with minimal disturbance[12]. These methods include biostimulation, bioleaching, biosorption, and bioventing. In-situ is preferred because it is often minimally invasive to the soil structure in comparison to ex-situ, but it can be expensive due to specialized equipment.<br />
<br />
===='''Biostimulation'''====<br />
This method involves the addition of nutrients to a polluted site in order to encourage the growth of naturally occurring chemical-degrading microorganisms[31]. Biostimulation is primarily done by the addition of various nutrients that are limited in the soil as well as electron acceptors, such as phosphorus, nitrogen and oxygen, or increasing the amount of available carbon in order to increase the population or activity of naturally occurring microorganisms. Other approaches are to optimize environmental conditions such as aeration, the addition of nutrients, altering pH and temperature control [32]. The primary advantage of biostimulation is that it is done by native microorganisms that are well-suited to the environment, and are already well distributed spatially. The challenge is delivering additives so they are readily available to the subsurface microbes.<br />
<br />
===='''Metal Bioleaching'''====<br />
Metal bioleaching is the extraction of metals from soils utilizing a biological source such as microbes. This technique was first developed to extract minerals from ores. Specific microorganisms like Thiobacillus ferrooxidans and T. thiooxidans promote the metals’ solubilization. Several species of fungi are used for bioleaching. These remediation fungi can also produced in a lab. Two prevalent fungal strains ([https://microbewiki.kenyon.edu/index.php/Aspergillus_niger Aspergillus Niger], [https://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium Simplicissimum]) are capable of mobilizing metals such as copper, tin, aluminium, nickel, palladium, and zinc[33], which will make them much easier to remove from the soil.<br />
<br />
===='''Metal Biosorption'''====<br />
Adsorption of metals and other ions of an aqueous solution by the use of microbes. The biosorption process involves a solid phase and a liquid phase containing a dissolved species to be sorbed [34]. The process continues until equilibrium is established between the amount of solid-bound sorbate species and its portion remaining in the solution. The degree of affinity for the sorbate determines its distribution between the solid and liquid phases.<br />
<br />
Biosorption processes are very important in the environment, and has been utalized for conventional biotreatment processes. Biosorption is primarily aimed at the removal or recovery of organic and inorganic substances from solution [35]. The commercialization of biosorption technologies has been limited so far.<br />
<br />
[[Image:Bioventing.png|right|upright=2.5|thumb|Bioventing is primarily used for injecting air into specific remediation zones, adding oxygen as a readily available electron acceptor where it would otherwise be anaerobic. It can also be reversed to make a more anaerobic environment. Either technique can be applied depending on the remediating microbes would thrive in [36].]]<br />
<br />
===='''Bioventing'''====<br />
Bioventing is an In situ remediation technology that uses indigenous microorganisms to biodegrade organic constituents adsorbed to soils in the unsaturated zone[36]. The availability of oxygen generally controls the rate at which aerobic bioremediation proceeds. Bioventing is the coupling of soil venting and bioremediation. Bioventing can be successfully applied to compounds ranging from gasoline or diesel, to heavier hydrocarbons[36]. The addition of nutrients with the bioventing flow rates can achieve greater contaminant reductions than venting alone.<br />
<br />
==='''Ex-situ or In-situ'''===<br />
Some methods can be used by either in-situ or ex-situ methods. The soil or water can be removed from the contamination source and treated, or treated at the source, the method chosen can be based on many factors such as how expensive the project may be or how much contaminant needs to be treated. These methods include bioaugmentation, land farming and biofiltration.<br />
<br />
===='''Bioaugmentation'''====<br />
Bioaugmentation is the addition of non-native microorganisms that have the ability to degrade the contaminants that are recalcitrant to the indigenous microbiota. Bioaugmentation has been proven successful in cleaning organic pollutant, but still faces many environmental problems, such as the survival of strains introduced to soil[37]. The number of introduced microorganisms usually decreases shortly after soil inoculation, when the pollutant has been heavily removed. But the introduced species may linger for long periods of time, a wider use of non-natives runs the possible risk of creating a monoculture in the soil.<br />
<br />
Bioaugmentation is ideal for soil:<br />
<br />
1. With low number of microbes that are capable of degrading targeted pollutants<br />
<br />
2. Containing compounds requiring multi stepped remediation.<br />
<br />
Augmentation techniques have a great potential for [https://en.wikipedia.org/wiki/Category:Aromatic_compounds aromatic compound] remediation. The most important step in successful bioaugmentation is selection of proper microbial strains. The success of bioaugmentation strongly depends on the ability of inoculants to survive in contaminated soil, which may vary due to predation and an environment that does not identically mimic the lab it was grown in.<br />
<br />
===='''Land Farming'''====<br />
Contaminated soil is mixed with amendments such as nutrients, and then they are tilled into the earth, or the contaminated soil is applied into lined beds and periodically turned over or tilled to aerate the waste [38]. The topmost layer is the area of concentration for this method, so it is not ideal for deeper remediation. Land farming differs from composting because it actually incorporates contaminated soil into soil that is uncontaminated [38]. The higher zone of remediation will typically contain primarily lighter hydrocarbons that can be volatilized. The material is periodically tilled for aeration to hasten remediation of any nutrients and allow more oxygen to act as electron acceptors, as well as allowing volatilization to occur. Contaminants are degraded, transformed, and immobilized by microbiological processes and oxidation. Soil conditions are controlled to optimize the rate of contaminant degradation, moisture content, frequency of aeration, and pH are all conditions that may be controlled [38]. <br />
<br />
[[Image:Biofilter.png|right|upright=1.5|thumb|The application of a micro-algal/bacterial biofilter in the primary outflow of soil water [39]]]<br />
<br />
===='''Biofilter'''====<br />
Biofilters are primarily used for the filtration of contaminated groundwater in the soil. Biofilters can be used above soil, where the water will be pumped aboveground for treatment, or a filter can be placed in the soil near an outflow. A micro-algal/bacterial biofilter can be used for the detoxification of copper and cadmium metal wastes [22]. Biofilters have been used in larger industry environments to treat contaminated outflow of water. [https://en.wikipedia.org/wiki/Chromobacterium_violaceum Chromobacterium violaceum], is used to treat water and soil contaminated with silver nanoparticles, reducing its concentration.<br />
<br />
=='''Bioremediation Synopsis'''==<br />
<br />
==='''Advantages'''===<br />
1. Bioremediation is a publicly accepted treatment of polluted soil because it is based upon natural processes. Microbes that metabolize contaminants increase in population when the contaminant is present. The inverse is true, degradation of the contaminant causes population declines of those microbes. Usually the products from treatment are harmless; such as carbon dioxide, water, and cellular biomass. [12]<br />
<br />
2. Bioremediation is theoretically meant to completely degrade a wide range of pollutants into harmless products on site. This removes the risks involved with transportation for treatment and elimination of contaminated substances. [12]<br />
<br />
3. Bioremediation is meant to completely eliminate specific pollutants without the risks of transferring contaminants from one environmental medium to another (land, air, water). [12]<br />
<br />
4. Bioremediation can be a cheaper alternative to other technologies used for pollution mitigation. [12]<br />
<br />
==='''Disadvantages'''===<br />
1. Only biodegradable compounds are capable of undergoing bioremediation. Not every compound is capable of fully degrading quickly. [12]<br />
<br />
2. The products of biodegradation may potentially be even more persistent or toxic than the original contaminant. [12]<br />
<br />
3. Biological functions are usually extremely specific and require the presence of microbes that are capable of metabolizing the contaminants. In order for the correct microbes to be present, the appropriate environmental conditions, levels of nutrients, and contaminants need to be met. [12]<br />
<br />
4. Scaling up the size of studies from small initial studies to commercial-scale field operations is difficult.[12]<br />
<br />
5. The real environment contains contaminants that are mixed, unevenly distributed, and in different phases (solid, liquid, gas). More research needs to be completed to create technologies that can adapt. [12]<br />
<br />
6. Compared to other treatment technologies, bioremediation often takes more time. [12]<br />
<br />
7. Problems with ensuring adequate contact between the microbes and the contaminant. preferential pathway and soil structure can leave uncertainty in remediation dispersal.[12]<br />
<br />
=='''References'''== <br />
<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdf United States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120. <br />
<br />
5. Al-Mailem, D. M., Sorkhoh, N. A., Al-Awadhi, H., Eliyas, M., & Radwan, S. S. (2010). Biodegradation of crude oil and pure hydrocarbons by extreme halophilic archaea from hypersaline coasts of the Arabian Gulf. Extremophiles, 14(3), 321-328. doi: 10.1007/s00792-010-0312-9<br />
<br />
6. Fairley, D. J., Boyd, D. R., Sharma, N. D., Allen, C. C., Morgan, P., & Larkin, M. J. (2002). Aerobic metabolism of 4-hydroxybenzoic acid in Archaea via an unusual pathway involving an intramolecular migration (NIH shift). Appl Environ Microbiol, 68(12), 6246-6255.<br />
<br />
7. Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008<br />
<br />
8. Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008<br />
<br />
9. Le Borgne, S., Paniagua, D., & Vazquez-Duhalt, R. (2008). Biodegradation of organic pollutants by halophilic bacteria and archaea. J Mol Microbiol Biotechnol, 15(2-3), 74-92. doi: 10.1159/000121323<br />
<br />
10. Margesin, R., & Schinner, F. (2001). Biodegradation and biore<br />
mediation of hydrocarbons in extreme environments. Appl Microbiol Biotechnol, 56(5-6), 650-663.<br />
<br />
11. Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9<br />
<br />
12. Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172. <br />
<br />
13. "Dechloromonas Aromatica RCB." JGI Genome Portal, 16 Feb. 2016. [http://genome.jgi.doe.gov/decar/decar.home.html http://genome.jgi.doe.gov/decar/decar.home.html]<br />
<br />
14. King, R. Barry, John K. Sheldon, and GIlbert M. Long. (1998). Practical Environmental Bioremediation: The Field Guide. 2nd ed. Boca Raton: CRC, 1998.<br />
<br />
15. "Manual, Bioventing Principles and Practices." United States Environmental Protection Agency I (1995)<br />
<br />
16. Gadd, G. M. (Ed.). (2001). Fungi in bioremediation (No. 23). Cambridge University Press<br />
<br />
17. Harms, H., Schlosser, D., & Wick, L. Y. (2011). Untapped potential: exploiting fungi in bioremediation of hazardous chemicals. Nature Reviews Microbiology, 9(3), 177-192<br />
<br />
18. Fragoeiro, S. (2005). Use of fungi in bioremediation of pesticides. Applied Mycology Group Institute of Bioscience and Technology. Cranfield University<br />
<br />
19. Singh, H. (2006). Mycoremediation: fungal bioremediation. John Wiley & Sons. 283-285<br />
<br />
20. Norton, J. M. (2012). Fungi for Bioremediation of Hydrocarbon Pollutants. University of Hawai’i at Hilo. Hohonu, 10, 18-21<br />
<br />
21. Dixit, Ruchita, Emptyyn Wasiullah, Deepti Malaviya, Kuppusamy Pandiyan, Udai Singh, Asha Sahu, Renu Shukla, Bhanu Singh, Jai Rai, Pawan Sharma, Harshad Lade, and Diby Paul. "Bioremediation of Heavy Metals from Soil and Aquatic Environment: An Overview of Principles and Criteria of Fundamental Processes." Sustainability 7.2 (2015): 2189-212. Print.<br />
<br />
22. Bio-filters for Edge-of-Field Water Quality Management. (n.d.). Retrieved February 24, 2016, from [http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html]<br />
<br />
23. Alexander, Martin. (1999). Biodegradation and Bioremediation. San Diego: Academic Print. <br />
<br />
24. Litchfield, Carol. "Thirty Years and Counting: Bioremediation in Its Prime?" BioScience 55.3 (2005): 273.<br />
<br />
25. Biello, David. "Slick Solution: How Microbes Will Clean Up the Deepwater Horizon Oil Spill." Scientific American (n.d.): n. pag. 25 May 2010. <br />
<br />
26. Scow, Kate. “Lectures in Soil Microbiology.” UC Davis, Winter 2016.<br />
<br />
27 CLU-IN | Technologies Remediation About Remediation Technologies Natural Attenuation Overview. (n.d.). Retrieved February 24, 2016, from https://clu-in.org/techfocus/default.focus/sec/Natural_Attenuation/cat/Overview/<br />
<br />
28. Chauhan, Ashok K., and A. Varma. A Textbook of Molecular Biotechnology. New Delhi: I.K. International Pub. House, 2009. Print.<br />
<br />
29. Biopiles. (n.d.). Retrieved March 13, 2016, from [http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html]<br />
<br />
30. Chen, M., Xu, P., Zeng, G., Yang, C., Huang, D., & Zhang, J. (2015). Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: Applications, microbes and future research needs. Biotechnology Advances, 33(6, Part 1), 745–755.<br />
<br />
31. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. Retrieved March 13, 2016, from [http://www.sciencedirect.com/science/article/pii/S0944501309000585 http://www.sciencedirect.com/science/article/pii/S0944501309000585]<br />
<br />
32. Bioremediation, Biostimulation and Bioaugmention: A Review. (n.d.). Retrieved March 13, 2016, from http://pubs.sciepub.com/ijebb/3/1/5/<br />
<br />
33. Sulfur Oxides—Advances in Research and Application: 2013 Edition<br />
<br />
34. Fomina, M., & Gadd, G. M. (2014). Biosorption: current perspectives on concept, definition and application. Bioresource Technology, 160, 3–14. Retrieved February 24, 2016, from [https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application]<br />
<br />
35. Kotrba, Pavel, Martina Mackova, and Tomas Macek. (2011). Microbial Biosorption of Metals. Dordrecht: Springer Science Business Media Print.<br />
<br />
36. Bioventing » Water and Soil Bio-Remediation. (n.d.). Retrieved February 24, 2016, from [http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing]<br />
<br />
37. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. <br />
<br />
38. Land Farming. (n.d.). Retrieved March 13, 2016, from http://www.cpeo.org/techtree/ttdescript/lanfarm.htm<br />
<br />
<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=121002
Bioremediation
2016-03-22T02:05:39Z
<p>Kmscow: /* Examples of studies of Archaea involved in bioremediation */</p>
<hr />
<div>{{Curated}}<br />
<br />
Through agriculture, industry, and daily life, harmful chemicals have been released into the earth’s air, soil, and water. Depending on their concentrations, these substances can have destructive consequences on ecosystems, as well as cause severe damage to humans and other organisms nearby. Soil pollution is of special importance because of its impact on surface, groundwater and air contamination and can easily spread and be consumed by humans. <br />
<br />
[[Image:Bioremediation_images.jpeg|upright=3|thumb|Retrieved from Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120.]]<br />
<br />
<b>Biodegradation</b> is the biologically catalyzed modification of an organic chemical's structure. However, this modification can be through different metabolic pathways and does not necessarily mean a reduction in toxicity. Mineralization, one type of biodegradation, is defined as the conversion of an organic substance to its inorganic constituents, rendering the original compound harmless. [23]. Transformation is defined as any metabolically-induced change in the chemical composition of a compound [14].<br />
<br />
<b>Bioremediation</b> refers to the use of microorganisms to degrade contaminants that pose environmental and human risks. Bioremediation processes typically involve the actions of many different microbes acting in parallel or sequence to complete the degradation process. Both in situ (in place) and ex situ (removal and treatment in another place) remediation approaches are used. The versatility of microbes to degrade a vast array of pollutants makes bioremediation a technology that can be applied in different soil conditions [3]. Though it can be inexpensive and in situ approaches can reduce disruptive engineering practices, bioremediation is still not a common practice [1].<br />
<br />
A widely used approach to bioremediation involves stimulating naturally occurring microbial communities, providing them with nutrients and other needs, to break down a contaminant. This is termed <b>biostimulation.</b> Biostimulation can be achieved through changes in pH, moisture, aeration, or additions of electron donors, electron acceptors or nutrients. Another bioremediation approach is termed <b>bioaugmentation</b>, where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously.<br />
<br />
Recent awareness of the dangers of many chemicals used in society has led to research on formulation of products that are more easily degraded in the environment.<br />
<br />
From an ecological point of view, bioremediation depends on the various interactions between three factors: substrate (pollutant), organisms, and environment, as shown in the figure at right [4]. The interactions of these factors affect biodegradability, bioavailability, and physiological requirements, which are important in assessing the feasibility of bioremediation [4]. <b>Biodegradability</b>, or whether a chemical can be degraded or not, is determined by the presence or absence of organisms that are able to degrade a chemical of interest and how widespread these organisms are in the site [4]. The substrate (pollutant) can interact with its surrounding environment to change its <b>bioavailability</b>, or availability to organisms that are capable of degrading it; for example, substrate has low bioavailability if it is tightly bound to soil organic matter or trapped inside aggregates [4]. <b>Physiological requirements</b>, or set of conditions required by organisms to carry out bioremediation in the environment, include nutrient availability, optimal pH, and availability of electron acceptors, such as oxygen and nitrate [4]. Also, the environment needs to be habitable for organisms involved in bioremediation [4].<br />
<br />
=='''Brief History'''==<br />
<br />
[[Image:Wasterwater_treatment.png|upright=2.25|thumb|First Water Treatment Facility in Japan, 1934 Image from http://www.sewerhistory.org/grfx/trtmnt/trtmnt3.htm]] <br />
<br />
Microorganisms in the environment have always broken down waste, and humans have always (knowingly or unknowingly) used them in agricultural, domestic, and industrial activities [24]. As the urbanized world shifted to a more industrial system, however, people began to take an active approach in bioremediation. In the late nineteenth century, wastewater treatment plants were formed, but even so, this was not officially called bioremediation .<br />
The project considered the initial spark of the bioremediation movement was the report “Beneficial Stimulation of Bacterial Activity in Groundwater Containing Petroleum Products” by R.L. Raymond et al. in 1975. By testing the relationship between oil presence and bacterial stimulation, Raymond found that adding nutrients to soil hastened the oil removal. This led to the development of in situ bioremediation [24].<br />
<br />
Initial bioremediation projects focused on “pump and treat” (ex situ) methods in soil around gas stations and refinery spills to get oil out of groundwater sources, but soon cleaning up chlorinated hydrocarbons became a primary concern [24]. Chlorinated compounds were commonly used in pesticides, but when people learned it was a possible carcinogen and causing ozone depletion, research into bioremediation took off [24]. This was when anaerobic bacteria started being used, as it was discovered that they dechlorinate compounds much more quickly than do aerobic bacteria, and produce fewer damaging iron compounds that precipitate from the reactions [24].<br />
<br />
=='''Overview of Pollutants'''==<br />
Pollutants found in soils present a variety of different human health risks. Soil pollutants are typically classified as organic and inorganic pollutants. The remediation of some of these pollutants will be discussed in greater depth in the following sections.<br />
Below is a link to website with a list of examples of soil pollutants and their effects on human health:<br />
<br />
[http://www.environmentalpollutioncenters.org/soil/examples/ Summary of health effects of pollutants]<br />
<br />
==='''Organic Pollutants'''===<br />
Industrialization resulted in increased use of organic compounds that build up and persist in the environment [11]. Main sources of organic pollutants are through anthropogenic activities, including use of solvents, pesticides, and fuels [11]. Some of these organic compounds are highly toxic and they are associated with variety of health issues around the world [11].<br />
<br />
Table below lists some groups of contaminants, examples, and their sources.<br />
<br />
[[Image:Pollutants_list.png|center|upright=2.5|thumb|Retrieved from Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172.]]<br />
<br />
While organic pollutants are causing both environmental and health problems, bioremediation offers an effective solution to the pollution [11]. The table below lists some of the organic pollutants and microorganisms that are found to be able to degrade them.<br />
<br />
[[Image:Pollutants_and_organisms.png|center|upright=2.5|thumb|Retrieved from Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9]]<br />
<br />
==='''Inorganic Pollutants'''=== <br />
{| border="1" style="float:right; margin-left: 10px; text-align:center"<br />
|+ Most inorganic pollutants are due to human activities.<br />
!Pollutant<br />
!Source<br />
|-<br />
| [https://en.wikipedia.org/wiki/Arsenic Arsenic] || Pesticides, wood preservatives, biosolids, ore mining and smelting<br />
|- <br />
| [https://en.wikipedia.org/wiki/Cadmium Cadmium] || Paints and pigments, plastic stabilizers, electroplating, phosphate fertilizers<br />
|-<br />
| [https://en.wikipedia.org/wiki/Chromium Chromium] || Tanneries, steel industries, fly ash<br />
|- <br />
| [https://en.wikipedia.org/wiki/Copper Copper] || Pesticides, fertilizers, biosolids, ore mining and smelting<br />
|-<br />
| [https://en.wikipedia.org/wiki/Mercury_%28element%29 Mercury] || Gold and Silver mining, coal combustion<br />
|-<br />
| [https://en.wikipedia.org/wiki/Nickel Nickel] || Effluent, kitchen appliances, surgical instruments, automobile batteries<br />
|-<br />
| [https://en.wikipedia.org/wiki/Lead Lead] || Aerial emission from combustion of leaded fuel, batteries waste, insecticide and herbicides.<br />
|}<br />
<br />
A majority of heavy metal pollutants come from human sources that accumulate over time.<br />
<br />
There are also natural forms of contamination from normal biological processes, which include:<br />
<br />
1. Weathering of minerals over time<br />
<br />
2. [https://en.wikipedia.org/wiki/Erosion Erosion] and [https://en.wikipedia.org/wiki/Volcano volcanic activities]<br />
<br />
3. [https://en.wikipedia.org/wiki/Wildfire Forest fires] and biogenic source<br />
<br />
4. Particles released by vegetation<br />
<br />
Heavy metals can be absorbed by microbes at cellular binding sites. Extracellular polymers of these microbes can complex heavy metals through various mechanisms [21]. These specialized microorganisms can mineralize the organic contaminants to metabolic intermediates, which are used as primary substrates for cell growth. The microbes prevalent in heavily metal-contaminated soil can alter the oxidation state of the heavy metals by immobilizing them [21], allowing them to be easily removed. Bioremediation of heavy metals from microbes is not heavily researched, mostly due to an incomplete understanding of the genetics of the microbes used in metal adsorption. ''[https://microbewiki.kenyon.edu/index.php/Geomicrobiology Geomicrobiology]'' takes a better look at the interactions between microbes and inorganic material.<br />
<br />
=='''Organisms'''==<br />
As stated previously, bioremediation involves various microorganisms that are able to degrade and reduce toxicity of environmental pollutants [12]. Therefore, the interactions of microbes with the environment and pollutants are significant in determining effectiveness of bioremediation [4]. Those microbes can be either naturally present in the site of bioremediation or isolated from other sites and inoculated artificially [12]. Biodegradation often occurs as part of microbial metabolism and in some cases, microbes are able to directly harvest carbon and energy by breaking down pollutants [12]. Sections below go over bacteria and fungi, the commonly used organisms in bioremediation, and archaea, the more recently discovered group of organisms with unique potential in bioremediation.<br />
<br />
==='''Bacteria'''===<br />
Bacteria are widely diverse organisms, and thus make excellent players in biodegradation and bioremediation. There are few universal toxins to bacteria, so there is likely an organism able to break down any given substrate, when provided with the right conditions (anaerobic versus aerobic environment, sufficient electron donors or acceptors, etc.). Below are several specific bacteria species known to participate in bioremediation.<br />
<br />
===='''''[[Pseudomonas putida]]'''====<br />
[[Image:Pseudomonas_putida.png|upright=1|thumb|Pseudomonas putida, Image © http://www.denniskunkel.com/DK/Bacteria/23859D.html]]<br />
<br />
''Pseudomonas putida'' is a gram-negative soil bacterium that is involved in the bioremediation of toluene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===='''''[[Dechloromonas aromatica]]''' ====<br />
''Dechloromonas aromatica'' is a rod-shaped bacterium which can oxidize aromatics including benzoate, chlorobenzoate, and toluene, coupling the reaction with the reduction of oxygen, chlorate, or nitrate. It is the only organism able to oxidize benzene anaerobically. Due to the high propensity of benzene contamination, especially in ground and surface water, ''D. aromatic'' is especially useful for in situ bioremediation of this substance. [13]<br />
<br />
===='''Nitrifiers and Denitrifiers'''==== <br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage process that involves nitrification and denitrification. During nitrification, ammonium is oxidized to nitrite by organisms like <i>Nitrosomonas europaea</i>.Then, nitrite is further oxidized to nitrate by microbes like <i>Nitrobacter hamburgensis</i>.<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like <i>Paracoccus denitrificans </i>[2]. The result is N2 gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
===='''''[[Deinococcus radiodurans]]'''====<br />
''Deinococcus radiodurans'' is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered strain of Deinococcus radiodurans has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7].<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like ''[[Paracoccus denitrificans]]'' [2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
[[Image:Alcanivorax_borkumensis.png|upright=1|thumb|Alcanivorax borkumensis, Image©https://www.biotechnologie.de/BIO/Navigation/EN/Funding/foerderbeispiele,did=44848.html?view=renderPrint [25]]]<br />
<br />
===='''''[[Methylibium petroleiphilum]]'''====<br />
''Methylibium petroleiphilum'' (formally known as PM1 strain) is a bacterium capable of [https://en.wikipedia.org/wiki/Methyl_tert-butyl_ether methyl tert-butyl ether] (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
===='''''[[Alcanivorax borkumensis]]'''====<br />
''Alcanivorax borkumensis'' is a marine rod-shaped bacterium which consumes hydrocarbons, such as the ones found in fuel, and produces carbon dioxide. It grows rapidly in environments damaged by oil, and has been used to aid in cleaning the more than 830,000 gallons of oil from the [https://en.wikipedia.org/wiki/Deepwater_Horizon_oil_spill Deepwater Horizon oil spill] in the Gulf of Mexico [25].<br />
<br />
==='''Fungi (Mycoremediation)'''===<br />
Current bioremediation applications primarily utilize bacteria, with comparatively few attempts to use fungi. Fungi have fundamentally important roles because of their participation in the cycling of elements through decomposition and transformation of organic and inorganic materials. These characteristics can be translated into applications for bioremediation which could break down organic compounds and reduce the risks of metals. In some cases, fungi have an advantage over bacteria not just in metabolic versatility but also their environmental resilience.They are able to oxidize a diverse amount of chemicals and survive in harsh environmental conditions such as low moisture and high concentrations of pollutants. Therefore, fungi are potentially an extremely powerful tool in soil bioremediation and some versatile species such as <b>[https://en.wikipedia.org/wiki/Wood-decay_fungus#White_rot White Rot Fungi]</b> have been a hot topic of research. [16,17]<br />
<br />
===='''Biodegradation Capacities of White rot fungi'''====<br />
Using fungi as potential treatment of contaminants began in 1985 when the white rot species Phanerochaete chrysosporium was discovered to metabolize multiple key environmental pollutants. The most important feature of these fungi is their enzymatic functional ability to metabolize complex chemicals such as lignin. Similar abilities were later discovered in other white rot fungal species. In addition, white rot fungi are highly advantageous because they degrade lignin extracellularly through its hyphal extension. This allows them to access soil contaminants that other organisms are incapable of and maximize surface area for enzymatic interaction. These inexpensive fungi can tolerate extreme environmental conditions, such as pH, temperature, and moisture content. While many microbial organisms that are used for bioremediation require pre-conditioning of the environment for them to survive in, white rot fungi can directly be applied into most systems because they degrade based upon nutrient deprivation. [18]<br />
<br />
[[Image:040504062021.jpg|right|thumb|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x]]<br />
<br />
===='''''[[Phanerochaete chrysosporium]]'''====<br />
<i>P. chrysosporium</i> was the first fungi linked to degradation of organic pollutants. Extensive research has show this it has strong potential for bioremediation in pesticides, PAHs, dioxins, carbon tetrachloride, and many other pollutants. Among fungal systems, <i>P. chrysosporium</i> has become the model for bioremediation. Other notable species of white rot fungi include <i>Pleurotus ostreatus</i> and <i>Trametes versicolor</i>. [18]<br />
<br />
===='''Bioremediation of Hydrocarbon Pollutants'''====<br />
<br />
Hydrocarbons are stored deep underground but are brought up to the surface to be transformed and utilized, primarily as an energy source known as fossil fuels. The majority of pollution currently comes from these byproducts in the form Polycyclic Aromatic Hydrocarbons (PAHs), which are xenobiotic environmental pollutants that form when carbon materials are incompletely combusted. Some of examples of PAHs include burning wood, fossil fuels, and cigarette smoke. [19,20]<br />
Currently, bioremediation is only effective for soils contaminated with low-molecular weight PAHs because of bacterial commercial use. However, fungi are effective at PAH degradation in comparison to bacteria for a few reasons. Firstly, they are capable degrading PAH’s that are high in molecular weight, bacteria in comparison are better at degrading smaller molecules. Secondly, fungi can function well in non-aqueous environments and low oxygen conditions, both are conditions where PAH’s can accumulate. Many fungi have evolved mechanisms that allow the to target specific PAHs. Fungi produce extracellular enzymes that degrade lignin, a process called mineralization the produces carbon dioxide as the end product. [19,20]<br />
<br />
===='''Remediating Metals'''====<br />
<br />
Toxic metals can enter the environment all life cycle stages of metal compound. For example, metal leaching can occur from the mining process till the disposal of metal wastes. However in nature, the mobility of metals comes from the geological processes that can be released into the soil and aquatic environments. The environmental largest risk from metal contamination comes from the relationship between metals and compounds that are inherently of incapable of being degraded by any natural procedures. The best solution to treating contamination is transporting the metals to location where they cannot produce negative environmental effects. Fungi have various ways of interacting with metals, some of the techniques are increasing or decreasing the mobility of metals, sorption, or even cellular uptake. After the metals have been absorbed the fungus, they can chemically altered to be stored or translocated through the hyphae and into various plants that participate in symbiosis. [17]<br />
<br />
===='''Pesticide Degradation'''====<br />
<br />
Pesticide accumulation is an issue of great concern among the public, because they are directly associated with food products and water supplies. There are number of technologies used for pesticide clean-up; however, these technologies are generally expensive and inefficient because they require contaminated soil to be excavated and sent to a separate storage location for processing. Bioremediation offers a potential solution that treats contaminated soil and groundwater without needing excavation. Studies show that White Rot Fungi has high promise for soil bioremediation application; however, most tests have been conducted in the lab rather than in the actual environment. This fungi demonstrates the ability to transform and mineralize specific pesticides in soil. [18]<br />
<br />
===='''Environmental Applications'''====<br />
<br />
Although fungi demonstrate significant biochemical and ecological useful qualities, they are hardly utilized for biotechnological purposes. Instead, bacteria are most commonly used because they usually produce superior results in their numerous advantages ranging from their highly specific biochemical reactions to their capabilities of breaking down pollutants efficiently [17]. Fungi are underused primarily because of the costs that come from providing oxygen to fungi in polluted environments. However, filamentous fungi could be highly valuable in situations where bacteria cannot perform. For example, fungi are useful in situations where contaminants are physically blockaded and bacteria cannot reach or in circumstances of environmental extremes such as high acidity or dryness prevent bacteria from functioning. [17]<br />
<br />
==='''[https://en.wikipedia.org/wiki/Archaea Archaea]'''===<br />
The role of archaea in bioremediation has not been studied as commonly as that of bacteria [10]. Nevertheless, numbers of researchers have shown their ability to degrade various pollutants and scientists began to discover more about their potential in participating in bioremediation. Below lists some important facts regarding archaea’s potential role in bioremediation.<br />
<br />
- Biodegradation by extreme [https://en.wikipedia.org/wiki/Halophile halophilic] archaea was not recognized widely in the past, but scientists have found out that extreme halophilic archaea have greater catabolic diversity than expected [9]<br />
<br />
- Hydrocarbon-contamination is observed in some extreme environments, including hypersaline (high salt concentration), high or low temperature, or extreme pH [10]. Archaea’s adaptation to extreme environment gives them the potential to participate in biodegradation and bioremediation in these environments; in fact, microorganisms naturally adapted to the cold environments are known to be important degraders of hydrocarbons in those environments [10].<br />
<br />
- Extreme halophilic archaea has potential to biodegrade pollutants in hypersaline environment, in which bacteria typically used in bioremediation cannot survive or function properly. [5]<br />
<br />
- Some archaea are known to be resistant to variety of antibiotics, including penicillin, cycloheximide, streptomycin, etc, which gives them great advantage in participating in bioremediation in the presence of antibiotics [5].<br />
<br />
===='''Examples of studies of Archaea involved in bioremediation'''====<br />
<br />
Four extreme halophilic strains of archaea (belonging to genus ''[https://en.wikipedia.org/wiki/Halobacterium Halobacterium]'', ''[https://en.wikipedia.org/wiki/Haloferax Haloferax]'', and ''[https://en.wikipedia.org/wiki/Halococcus Halococcus]'') were studied to evaluate their potential to biodegrade crude oil and hydrocarbons. [5] All four strains could use various kinds of hydrocarbons as their carbon or energy sources [5]. Two strains of Haloferax grew on n-alkanes with different lengths, ranging from C8 to C34, and also benzene, toluene, biphenyl, and naphthalene. The research demonstrated the important fact that archaea have potential to carry out biodegradation at high temperatures, in the range of 40-45 °C [5], which is advantageous because hydrocarbons have higher solubility and bioavailability at these higher temperature [10]. The four strains studied were resistant to six different antibiotics, including penicillin, streptomycin, cycloheximide [5] and this gave them the potential to carry out biodegradation in conditions unfavorable for bacteria. Research suggests other genera of archaea are also capable of biodegrading in hypersaline environments [6]<br />
<br />
''[https://en.wikipedia.org/wiki/Halococcus Archaeglobus] fulgidus'', a [https://en.wikipedia.org/wiki/Hyperthermophile hyperthermophile] which can use sulfate as an electron acceptor, can also break down various aromatic hydrocarbons (Peeples, 2014).<br />
<br />
=='''Microbial Processes'''==<br />
<br />
Microorganisms use a wide range of processes to transform chemicals in their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor. This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. Below, several steps and details of the microorganisms’ actions are described.<br />
<br />
==='''Factors Affecting Rates of Biodegradation'''===<br />
Biodegradation may be influenced by pH, temperature, moisture, carbon sources, soil texture, aerobic versus anaerobic conditions, the number of substituents, and the concentration of the pollutant. It is impossible, however, to make a generalization about the best universal conditions for biodegradation. What’s toxic to some microbes is a nutrient to others, what might be a damaging pH to some is beneficial to others, and so on.<br />
<br />
A greater amount of substituents will cause slower degradation in aerobic environments, but faster degradation in anaerobic ones. Chlorine makes a molecule less degradable due to steric hindrance preventing access to necessary enzymes, therefore molecules with higher chlorination are slower to degrade in aerobic conditions. High concentration of a pollutant generally results in faster rates of degradation. If the concentration drops below a threshold concentration, the enzymes may not detect it and will cease to degrade it [26].<br />
<br />
The rate at which a compound is transformed, as well as the curves that describe its transformation, is referred to as kinetics, and is affected by all factors listed above. First order kinetics (logarithmic biodegradation) is often used when the substrate concentration is high enough that microbes can easily access it, while zero-order kinetics (linear biodegradation) is often observed when the substrate concentration is very small. If the concentration falls below a threshold, the microbes can no longer transform it and the concentration levels out.<br />
<br />
Soil with small pores, especially clays, may cause biodegradation to take years due to the decrease in bioavailability. Chlorine makes a molecule less degradable due to steric hindrance preventing necessary enzymes from accessing the compound, therefore molecules with higher chlorination are slower to degrade.<br />
<br />
The power rate model gives an empirical approach to the relationship between concentration and rate of degradation:<br />
<br />
-dC/dt = kC^n<br />
<br />
C is substrate concentration, t is time, k is a rate constant for the chemical in question, and n is an appropriate parameter. The values of k and n are adjusted until a line is found to match experimental data [23].<br />
<br />
==='''Primary substrate utilization'''===<br />
<b>Primary substrate utilization</b> occurs when a microbe both transforms a substrate and uses it as an energy or carbon source. [15] An electron acceptor is required for these transformations. It can be anaerobic or aerobic, although the presence of oxygen tends to speed up reactions. This form of biodegradation can be used for treating petroleum spills or the runoff of a number of pesticides. The rate of reaction follows the guidelines in the previous section, where a higher concentration leads to a higher rate. [15]<br />
<br />
==='''Cometabolism (Secondary Substrate Utilization)'''===<br />
<b>Cometabolism</b> involves the transformation of a chemical by an organism while the organism uses a different substance as its primary energy or carbon source [14]. This is a technique often used when the substrate by itself is considered non-biodegradable, and can only be transformed with another compound. During the actual reaction degrading the substance, the organism has no net carbon or energy gain, and may even result in a product with no use to the organism or which is toxic to the cell [14]. However, it is often difficult to tell whether microorganisms have a second substrate available during their transformations [23]. Cometabolism occurs in parallel with metabolism, not instead of.<br />
<br />
A key example of cometabolism is fortuitous metabolism in the degradation of trichloroethylene, shown in the diagram below. An organic growth substrate such as propane or butane is required for the enzymatic activity that transforms TCE. [14]<br />
<br />
[[Image:Cometabolism.png|center|upright=3|thumb|Image from Kate Scow lecture, 2016]]<br />
<br />
==='''Reductive and Hydrolytic Dehalogenation'''===<br />
Chloride and other halogens are common components of pesticides and hazardous industrial wastes, and by removing them the toxic chemical can often be remediated [23]. If the halogen is replaced by a hydrogen (RCl -> RH), then it is <b>reductive dehalogenation</b>. If two halogens are replaced simultaneously, then the process is called <b>dihaloelimination</b>, although it still falls under reductive dehalogenation [14]. If the halogen is replaced by OH (RCl -> ROH) then it’s <b>hydrolytic dehalogenation</b>. In both cases, the halogen is released as its inorganic form into the environment [23].<br />
<br />
==='''Acclimation'''===<br />
An <b>acclimation period</b>, also called an <b>adaptation</b> or <b>lag period</b>, occurs when no destruction of a given chemical is observed [23]. It is caused by the microbes transitioning to their altered environment and shifting their metabolism to better suit it [14]. It can last for anywhere from hours (such as aromatic compounds in warm, oxygenated soils) to months (such as halobenzoates in anaerobic sediments) depending on the chemical in question and the environment [23]. Acclimation periods can be affected by temperature, the presence of oxygen, pH, and concentration of the substance. Although they are most often faster in warm, aerated, and fairly dry environments, there are few consistencies between what shortens or lengthens the period, even if the concentration is the same [23]. Insecticides including methyl parathion and azinphosmethyl; herbicides including 2, 4-D, MCPA, Mecoprop, TCA, and amitrole; the quaternary ammonium compound dodecyltrimethylammonium chloride; polycyclic aromatic hydrocarbons including naphthalene and anthracene; and other chemicals such as phenol, chlorobenzene, PCP, diphenyl-methane, and NTA have all been reported to have acclimation periods, and this can be of severe human concern [23]. The continued presence of these toxins extends human, plant, and animal exposure, and if the chemical is in water, it can allow the substance to flow further and impact environments distant to its site of origin before being degraded.<br />
<br />
==='''Detoxification and Activation'''===<br />
<b>Detoxication</b>, sometimes called <b>detoxification</b>, has been referred to as the “most important role of microorganisms in the transformation of pollutants” [23]. The process is the changing of a molecule into something less harmful to a species in question. There are a number of ways a molecule can be transformed, including hydrolysis, hydroxylation, dehalogenation, demethylation, methylation, and ether cleavage [23]. By breaking bonds, or adding or removing groups, the organism reduces its effect on the environment. Furthermore, although sometimes the resulting chemical is simply excreted as waste, the organism may also be able to use this new compound as a carbon source or further modifies it until it is released as CO2 [23].<br />
<br />
There are instances where the initial compound is harmless, and in fact the substance produced by microorganisms, or an intermediate in the degradation process, is a toxin [23]. This process is called activation. For this reason, it is important to test all steps of a reaction when determining how a compound is degrading. The new toxins may also be more or less mobile than its predecessor, so it can either stick around one area for extended periods of time or spread to other areas and increase damage [23]. A prevalent example of this is the dechlorination of TCE, which produces DCE (50 times more hazardous than TCE) and Vinyl Chloride (a known carcinogen) [14]. Commonly used insecticides in the past, like zinophos, trichloronat, and carbofuran, were all found to increase a soil’s toxicity with extended use [23].<br />
<br />
=='''Bioremediation treatment methods'''==<br />
In order for bioremediation to be successful, it requires sufficient proof for the degradation of contaminants. However, determining the effectiveness and completeness to reach sufficient results is one of the major issues. Natural attenuation relies on natural processes to clean up or attenuate pollution in soil and groundwater [27]. This remediation is done without human interaction, and is primarily used as a monitoring technique, to make sure more aggressive cleanup strategies are not needed. [https://en.wikipedia.org/wiki/Abiotic_component Abiotic] and [https://en.wikipedia.org/wiki/Biotic_component biotic] factors play a distinguishing factor of how effective bioremediation is.<br />
<br />
Current monitoring practices determine the disappearance of contaminants and their degradation products to regulatory levels that are monitored by toxicity testing, usually on single organisms or species to ensure there are no induced changes that may result in residual toxicity. The problem with these monitoring techniques is that the assessment of contaminants may result in an inaccurate indicator of residual toxicity[28]. Rather, studying the microbial community response may be a more comprehensive indicator of residual toxicity than a single species. Once sufficient evidence is provided, human intervention may be needed for a more effective cleanup process. <br />
<br />
There are two types of remediation that are done, ex situ: which is done by removing the contaminated soil or water and treating it outside the source, and in situ: which treatment takes place within the contaminated area. There are some treatments methods that can be either ex situ or in situ. Some techniques may deal with the mobilization of pollutants, to move them out of an area, or immobilized to keep them out of an area such as a water table.<br />
<br />
<br />
[[Image:Summary_of_bioremediation_strategies.png|center|upright=3|thumb|A comparative analysis of the different types of bioremediation. It can be used to find which remediation technique may be used in certain circumstances [12]]]<br />
<br />
<br />
[[Image:Biopiling.png|right|upright=1.5|thumb|Contaminated soil is mixed with amendments and piled on top of a liner, while a pipe with a blower controls aeration. [29]]]<br />
==='''Ex-situ'''===<br />
Ex-situ techniques are those that are applied to soil and groundwater which has been removed from the site via excavation or pumping [12]. The methods used include composting, biofilters, and biopiling. Ex-situ is used for smaller projects, primarily because larger excavation of soil is not prefered. The movement of the soil can be more detrimental by destroying the preestablish horizons in the soil.<br />
<br />
[[Image:Composting.png|right|upright=3|thumb|Composting is a very versatile remediation technique that can be used for either: a very broad treatment with many contaminants, or very specific treatment that utilizes particular microbes that target specific contaminants [30]. It can also be used to augment other treatment methods.]]<br />
<br />
===='''Biopiling'''====<br />
Excavated soils are mixed with soil amendments and placed on a treatment area. Biopiles are aerated with the use of perforated pipes and blowers in order to control the progression of biodegradation more efficiently by controlling the supply of oxygen [29], which in turn may affect other factors such as pH. This system is primarily used to remediate systems with oil and hydrocarbon contamination. The remediated soil is placed in a liner to prevent further contamination of the soil, they may also be covered with plastic to control runoff, evaporation, and [https://en.wikipedia.org/wiki/Volatilisation volatilization].<br />
<br />
===='''Composting'''====<br />
Nutrients are added to soil that is mixed to increase aeration and activation of indigenous microorganisms. Composting is done in a separate container, then when composting is complete it is incorporated into the soil. Bioremediation by the utilization of compost relies on the adsorption capabilities of organic matter and the degradation capabilities of microorganisms present[30]. Composting is recognized as as one of the most cost-effective technologies for soil bioremediation and it can be done on large and small scales. The use of composting is a very versatile technique for soil polluted by a wide range of organic pollutants and heavy metals, making it great for easier remediation involving various pollutants. The utilization of organic wastes for soil remediation is also helpful in decreasing the need for their storage and treatment. Organic matter that is generated from composting offers the benefit of improving soil quality and structure. Composting is primarily used for remediation over a longer period of time, as the nutrients for the microbes are released gradually and requrire more time compared to quicker treatments such as biostimulation.<br />
<br />
==='''In-situ'''===<br />
In-situ techniques are applied to soil and groundwater at the site with minimal disturbance[12]. These methods include biostimulation, bioleaching, biosorption, and bioventing. In-situ is preferred because it is often minimally invasive to the soil structure in comparison to ex-situ, but it can be expensive due to specialized equipment.<br />
<br />
===='''Biostimulation'''====<br />
This method involves the addition of nutrients to a polluted site in order to encourage the growth of naturally occurring chemical-degrading microorganisms[31]. Biostimulation is primarily done by the addition of various nutrients that are limited in the soil as well as electron acceptors, such as phosphorus, nitrogen and oxygen, or increasing the amount of available carbon in order to increase the population or activity of naturally occurring microorganisms. Other approaches are to optimize environmental conditions such as aeration, the addition of nutrients, altering pH and temperature control [32]. The primary advantage of biostimulation is that it is done by native microorganisms that are well-suited to the environment, and are already well distributed spatially. The challenge is delivering additives so they are readily available to the subsurface microbes.<br />
<br />
===='''Metal Bioleaching'''====<br />
Metal bioleaching is the extraction of metals from soils utilizing a biological source such as microbes. This technique was first developed to extract minerals from ores. Specific microorganisms like Thiobacillus ferrooxidans and T. thiooxidans promote the metals’ solubilization. Several species of fungi are used for bioleaching. These remediation fungi can also produced in a lab. Two prevalent fungal strains ([https://microbewiki.kenyon.edu/index.php/Aspergillus_niger Aspergillus Niger], [https://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium Simplicissimum]) are capable of mobilizing metals such as copper, tin, aluminium, nickel, palladium, and zinc[33], which will make them much easier to remove from the soil.<br />
<br />
===='''Metal Biosorption'''====<br />
Adsorption of metals and other ions of an aqueous solution by the use of microbes. The biosorption process involves a solid phase and a liquid phase containing a dissolved species to be sorbed [34]. The process continues until equilibrium is established between the amount of solid-bound sorbate species and its portion remaining in the solution. The degree of affinity for the sorbate determines its distribution between the solid and liquid phases.<br />
<br />
Biosorption processes are very important in the environment, and has been utalized for conventional biotreatment processes. Biosorption is primarily aimed at the removal or recovery of organic and inorganic substances from solution [35]. The commercialization of biosorption technologies has been limited so far.<br />
<br />
[[Image:Bioventing.png|right|upright=2.5|thumb|Bioventing is primarily used for injecting air into specific remediation zones, adding oxygen as a readily available electron acceptor where it would otherwise be anaerobic. It can also be reversed to make a more anaerobic environment. Either technique can be applied depending on the remediating microbes would thrive in [36].]]<br />
<br />
===='''Bioventing'''====<br />
Bioventing is an In situ remediation technology that uses indigenous microorganisms to biodegrade organic constituents adsorbed to soils in the unsaturated zone[36]. The availability of oxygen generally controls the rate at which aerobic bioremediation proceeds. Bioventing is the coupling of soil venting and bioremediation. Bioventing can be successfully applied to compounds ranging from gasoline or diesel, to heavier hydrocarbons[36]. The addition of nutrients with the bioventing flow rates can achieve greater contaminant reductions than venting alone.<br />
<br />
==='''Ex-situ or In-situ'''===<br />
Some methods can be used by either in-situ or ex-situ methods. The soil or water can be removed from the contamination source and treated, or treated at the source, the method chosen can be based on many factors such as how expensive the project may be or how much contaminant needs to be treated. These methods include bioaugmentation, land farming and biofiltration.<br />
<br />
===='''Bioaugmentation'''====<br />
Bioaugmentation is the addition of non-native microorganisms that have the ability to degrade the contaminants that are recalcitrant to the indigenous microbiota. Bioaugmentation has been proven successful in cleaning organic pollutant, but still faces many environmental problems, such as the survival of strains introduced to soil[37]. The number of introduced microorganisms usually decreases shortly after soil inoculation, when the pollutant has been heavily removed. But the introduced species may linger for long periods of time, a wider use of non-natives runs the possible risk of creating a monoculture in the soil.<br />
<br />
Bioaugmentation is ideal for soil:<br />
<br />
1. With low number of microbes that are capable of degrading targeted pollutants<br />
<br />
2. Containing compounds requiring multi stepped remediation.<br />
<br />
Augmentation techniques have a great potential for [https://en.wikipedia.org/wiki/Category:Aromatic_compounds aromatic compound] remediation. The most important step in successful bioaugmentation is selection of proper microbial strains. The success of bioaugmentation strongly depends on the ability of inoculants to survive in contaminated soil, which may vary due to predation and an environment that does not identically mimic the lab it was grown in.<br />
<br />
===='''Land Farming'''====<br />
Contaminated soil is mixed with amendments such as nutrients, and then they are tilled into the earth, or the contaminated soil is applied into lined beds and periodically turned over or tilled to aerate the waste [38]. The topmost layer is the area of concentration for this method, so it is not ideal for deeper remediation. Land farming differs from composting because it actually incorporates contaminated soil into soil that is uncontaminated [38]. The higher zone of remediation will typically contain primarily lighter hydrocarbons that can be volatilized. The material is periodically tilled for aeration to hasten remediation of any nutrients and allow more oxygen to act as electron acceptors, as well as allowing volatilization to occur. Contaminants are degraded, transformed, and immobilized by microbiological processes and oxidation. Soil conditions are controlled to optimize the rate of contaminant degradation, moisture content, frequency of aeration, and pH are all conditions that may be controlled [38]. <br />
<br />
[[Image:Biofilter.png|right|upright=1.5|thumb|The application of a micro-algal/bacterial biofilter in the primary outflow of soil water [39]]]<br />
<br />
===='''Biofilter'''====<br />
Biofilters are primarily used for the filtration of contaminated groundwater in the soil. Biofilters can be used above soil, where the water will be pumped aboveground for treatment, or a filter can be placed in the soil near an outflow. A micro-algal/bacterial biofilter can be used for the detoxification of copper and cadmium metal wastes [22]. Biofilters have been used in larger industry environments to treat contaminated outflow of water. [https://en.wikipedia.org/wiki/Chromobacterium_violaceum Chromobacterium violaceum], is used to treat water and soil contaminated with silver nanoparticles, reducing its concentration.<br />
<br />
=='''Bioremediation Synopsis'''==<br />
<br />
==='''Advantages'''===<br />
1. Bioremediation is a publicly accepted treatment of polluted soil because it is based upon natural processes. Microbes that metabolize contaminants increase in population when the contaminant is present. The inverse is true, degradation of the contaminant causes population declines of those microbes. Usually the products from treatment are harmless; such as carbon dioxide, water, and cellular biomass. [12]<br />
<br />
2. Bioremediation is theoretically meant to completely degrade a wide range of pollutants into harmless products on site. This removes the risks involved with transportation for treatment and elimination of contaminated substances. [12]<br />
<br />
3. Bioremediation is meant to completely eliminate specific pollutants without the risks of transferring contaminants from one environmental medium to another (land, air, water). [12]<br />
<br />
4. Bioremediation can be a cheaper alternative to other technologies used for pollution mitigation. [12]<br />
<br />
==='''Disadvantages'''===<br />
1. Only biodegradable compounds are capable of undergoing bioremediation. Not every compound is capable of fully degrading quickly. [12]<br />
<br />
2. The products of biodegradation may potentially be even more persistent or toxic than the original contaminant. [12]<br />
<br />
3. Biological functions are usually extremely specific and require the presence of microbes that are capable of metabolizing the contaminants. In order for the correct microbes to be present, the appropriate environmental conditions, levels of nutrients, and contaminants need to be met. [12]<br />
<br />
4. Scaling up the size of studies from small initial studies to commercial-scale field operations is difficult.[12]<br />
<br />
5. The real environment contains contaminants that are mixed, unevenly distributed, and in different phases (solid, liquid, gas). More research needs to be completed to create technologies that can adapt. [12]<br />
<br />
6. Compared to other treatment technologies, bioremediation often takes more time. [12]<br />
<br />
7. Problems with ensuring adequate contact between the microbes and the contaminant. preferential pathway and soil structure can leave uncertainty in remediation dispersal.[12]<br />
<br />
=='''References'''== <br />
<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdf United States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120. <br />
<br />
5. Al-Mailem, D. M., Sorkhoh, N. A., Al-Awadhi, H., Eliyas, M., & Radwan, S. S. (2010). Biodegradation of crude oil and pure hydrocarbons by extreme halophilic archaea from hypersaline coasts of the Arabian Gulf. Extremophiles, 14(3), 321-328. doi: 10.1007/s00792-010-0312-9<br />
<br />
6. Fairley, D. J., Boyd, D. R., Sharma, N. D., Allen, C. C., Morgan, P., & Larkin, M. J. (2002). Aerobic metabolism of 4-hydroxybenzoic acid in Archaea via an unusual pathway involving an intramolecular migration (NIH shift). Appl Environ Microbiol, 68(12), 6246-6255.<br />
<br />
7. Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008<br />
<br />
8. Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008<br />
<br />
9. Le Borgne, S., Paniagua, D., & Vazquez-Duhalt, R. (2008). Biodegradation of organic pollutants by halophilic bacteria and archaea. J Mol Microbiol Biotechnol, 15(2-3), 74-92. doi: 10.1159/000121323<br />
<br />
10. Margesin, R., & Schinner, F. (2001). Biodegradation and biore<br />
mediation of hydrocarbons in extreme environments. Appl Microbiol Biotechnol, 56(5-6), 650-663.<br />
<br />
11. Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9<br />
<br />
12. Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172. <br />
<br />
13. "Dechloromonas Aromatica RCB." JGI Genome Portal, 16 Feb. 2016. [http://genome.jgi.doe.gov/decar/decar.home.html http://genome.jgi.doe.gov/decar/decar.home.html]<br />
<br />
14. King, R. Barry, John K. Sheldon, and GIlbert M. Long. (1998). Practical Environmental Bioremediation: The Field Guide. 2nd ed. Boca Raton: CRC, 1998.<br />
<br />
15. "Manual, Bioventing Principles and Practices." United States Environmental Protection Agency I (1995)<br />
<br />
16. Gadd, G. M. (Ed.). (2001). Fungi in bioremediation (No. 23). Cambridge University Press<br />
<br />
17. Harms, H., Schlosser, D., & Wick, L. Y. (2011). Untapped potential: exploiting fungi in bioremediation of hazardous chemicals. Nature Reviews Microbiology, 9(3), 177-192<br />
<br />
18. Fragoeiro, S. (2005). Use of fungi in bioremediation of pesticides. Applied Mycology Group Institute of Bioscience and Technology. Cranfield University<br />
<br />
19. Singh, H. (2006). Mycoremediation: fungal bioremediation. John Wiley & Sons. 283-285<br />
<br />
20. Norton, J. M. (2012). Fungi for Bioremediation of Hydrocarbon Pollutants. University of Hawai’i at Hilo. Hohonu, 10, 18-21<br />
<br />
21. Dixit, Ruchita, Emptyyn Wasiullah, Deepti Malaviya, Kuppusamy Pandiyan, Udai Singh, Asha Sahu, Renu Shukla, Bhanu Singh, Jai Rai, Pawan Sharma, Harshad Lade, and Diby Paul. "Bioremediation of Heavy Metals from Soil and Aquatic Environment: An Overview of Principles and Criteria of Fundamental Processes." Sustainability 7.2 (2015): 2189-212. Print.<br />
<br />
22. Bio-filters for Edge-of-Field Water Quality Management. (n.d.). Retrieved February 24, 2016, from [http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html]<br />
<br />
23. Alexander, Martin. (1999). Biodegradation and Bioremediation. San Diego: Academic Print. <br />
<br />
24. Litchfield, Carol. "Thirty Years and Counting: Bioremediation in Its Prime?" BioScience 55.3 (2005): 273.<br />
<br />
25. Biello, David. "Slick Solution: How Microbes Will Clean Up the Deepwater Horizon Oil Spill." Scientific American (n.d.): n. pag. 25 May 2010. <br />
<br />
26. Scow, Kate. “Lectures in Soil Microbiology.” UC Davis, Winter 2016.<br />
<br />
27 CLU-IN | Technologies Remediation About Remediation Technologies Natural Attenuation Overview. (n.d.). Retrieved February 24, 2016, from https://clu-in.org/techfocus/default.focus/sec/Natural_Attenuation/cat/Overview/<br />
<br />
28. Chauhan, Ashok K., and A. Varma. A Textbook of Molecular Biotechnology. New Delhi: I.K. International Pub. House, 2009. Print.<br />
<br />
29. Biopiles. (n.d.). Retrieved March 13, 2016, from [http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html]<br />
<br />
30. Chen, M., Xu, P., Zeng, G., Yang, C., Huang, D., & Zhang, J. (2015). Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: Applications, microbes and future research needs. Biotechnology Advances, 33(6, Part 1), 745–755.<br />
<br />
31. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. Retrieved March 13, 2016, from [http://www.sciencedirect.com/science/article/pii/S0944501309000585 http://www.sciencedirect.com/science/article/pii/S0944501309000585]<br />
<br />
32. Bioremediation, Biostimulation and Bioaugmention: A Review. (n.d.). Retrieved March 13, 2016, from http://pubs.sciepub.com/ijebb/3/1/5/<br />
<br />
33. Sulfur Oxides—Advances in Research and Application: 2013 Edition<br />
<br />
34. Fomina, M., & Gadd, G. M. (2014). Biosorption: current perspectives on concept, definition and application. Bioresource Technology, 160, 3–14. Retrieved February 24, 2016, from [https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application]<br />
<br />
35. Kotrba, Pavel, Martina Mackova, and Tomas Macek. (2011). Microbial Biosorption of Metals. Dordrecht: Springer Science Business Media Print.<br />
<br />
36. Bioventing » Water and Soil Bio-Remediation. (n.d.). Retrieved February 24, 2016, from [http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing]<br />
<br />
37. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. <br />
<br />
38. Land Farming. (n.d.). Retrieved March 13, 2016, from http://www.cpeo.org/techtree/ttdescript/lanfarm.htm<br />
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<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=121001
Bioremediation
2016-03-22T02:04:04Z
<p>Kmscow: /* Example Studies of Archaea involved in bioremediation */</p>
<hr />
<div>{{Curated}}<br />
<br />
Through agriculture, industry, and daily life, harmful chemicals have been released into the earth’s air, soil, and water. Depending on their concentrations, these substances can have destructive consequences on ecosystems, as well as cause severe damage to humans and other organisms nearby. Soil pollution is of special importance because of its impact on surface, groundwater and air contamination and can easily spread and be consumed by humans. <br />
<br />
[[Image:Bioremediation_images.jpeg|upright=3|thumb|Retrieved from Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120.]]<br />
<br />
<b>Biodegradation</b> is the biologically catalyzed modification of an organic chemical's structure. However, this modification can be through different metabolic pathways and does not necessarily mean a reduction in toxicity. Mineralization, one type of biodegradation, is defined as the conversion of an organic substance to its inorganic constituents, rendering the original compound harmless. [23]. Transformation is defined as any metabolically-induced change in the chemical composition of a compound [14].<br />
<br />
<b>Bioremediation</b> refers to the use of microorganisms to degrade contaminants that pose environmental and human risks. Bioremediation processes typically involve the actions of many different microbes acting in parallel or sequence to complete the degradation process. Both in situ (in place) and ex situ (removal and treatment in another place) remediation approaches are used. The versatility of microbes to degrade a vast array of pollutants makes bioremediation a technology that can be applied in different soil conditions [3]. Though it can be inexpensive and in situ approaches can reduce disruptive engineering practices, bioremediation is still not a common practice [1].<br />
<br />
A widely used approach to bioremediation involves stimulating naturally occurring microbial communities, providing them with nutrients and other needs, to break down a contaminant. This is termed <b>biostimulation.</b> Biostimulation can be achieved through changes in pH, moisture, aeration, or additions of electron donors, electron acceptors or nutrients. Another bioremediation approach is termed <b>bioaugmentation</b>, where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously.<br />
<br />
Recent awareness of the dangers of many chemicals used in society has led to research on formulation of products that are more easily degraded in the environment.<br />
<br />
From an ecological point of view, bioremediation depends on the various interactions between three factors: substrate (pollutant), organisms, and environment, as shown in the figure at right [4]. The interactions of these factors affect biodegradability, bioavailability, and physiological requirements, which are important in assessing the feasibility of bioremediation [4]. <b>Biodegradability</b>, or whether a chemical can be degraded or not, is determined by the presence or absence of organisms that are able to degrade a chemical of interest and how widespread these organisms are in the site [4]. The substrate (pollutant) can interact with its surrounding environment to change its <b>bioavailability</b>, or availability to organisms that are capable of degrading it; for example, substrate has low bioavailability if it is tightly bound to soil organic matter or trapped inside aggregates [4]. <b>Physiological requirements</b>, or set of conditions required by organisms to carry out bioremediation in the environment, include nutrient availability, optimal pH, and availability of electron acceptors, such as oxygen and nitrate [4]. Also, the environment needs to be habitable for organisms involved in bioremediation [4].<br />
<br />
=='''Brief History'''==<br />
<br />
[[Image:Wasterwater_treatment.png|upright=2.25|thumb|First Water Treatment Facility in Japan, 1934 Image from http://www.sewerhistory.org/grfx/trtmnt/trtmnt3.htm]] <br />
<br />
Microorganisms in the environment have always broken down waste, and humans have always (knowingly or unknowingly) used them in agricultural, domestic, and industrial activities [24]. As the urbanized world shifted to a more industrial system, however, people began to take an active approach in bioremediation. In the late nineteenth century, wastewater treatment plants were formed, but even so, this was not officially called bioremediation .<br />
The project considered the initial spark of the bioremediation movement was the report “Beneficial Stimulation of Bacterial Activity in Groundwater Containing Petroleum Products” by R.L. Raymond et al. in 1975. By testing the relationship between oil presence and bacterial stimulation, Raymond found that adding nutrients to soil hastened the oil removal. This led to the development of in situ bioremediation [24].<br />
<br />
Initial bioremediation projects focused on “pump and treat” (ex situ) methods in soil around gas stations and refinery spills to get oil out of groundwater sources, but soon cleaning up chlorinated hydrocarbons became a primary concern [24]. Chlorinated compounds were commonly used in pesticides, but when people learned it was a possible carcinogen and causing ozone depletion, research into bioremediation took off [24]. This was when anaerobic bacteria started being used, as it was discovered that they dechlorinate compounds much more quickly than do aerobic bacteria, and produce fewer damaging iron compounds that precipitate from the reactions [24].<br />
<br />
=='''Overview of Pollutants'''==<br />
Pollutants found in soils present a variety of different human health risks. Soil pollutants are typically classified as organic and inorganic pollutants. The remediation of some of these pollutants will be discussed in greater depth in the following sections.<br />
Below is a link to website with a list of examples of soil pollutants and their effects on human health:<br />
<br />
[http://www.environmentalpollutioncenters.org/soil/examples/ Summary of health effects of pollutants]<br />
<br />
==='''Organic Pollutants'''===<br />
Industrialization resulted in increased use of organic compounds that build up and persist in the environment [11]. Main sources of organic pollutants are through anthropogenic activities, including use of solvents, pesticides, and fuels [11]. Some of these organic compounds are highly toxic and they are associated with variety of health issues around the world [11].<br />
<br />
Table below lists some groups of contaminants, examples, and their sources.<br />
<br />
[[Image:Pollutants_list.png|center|upright=2.5|thumb|Retrieved from Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172.]]<br />
<br />
While organic pollutants are causing both environmental and health problems, bioremediation offers an effective solution to the pollution [11]. The table below lists some of the organic pollutants and microorganisms that are found to be able to degrade them.<br />
<br />
[[Image:Pollutants_and_organisms.png|center|upright=2.5|thumb|Retrieved from Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9]]<br />
<br />
==='''Inorganic Pollutants'''=== <br />
{| border="1" style="float:right; margin-left: 10px; text-align:center"<br />
|+ Most inorganic pollutants are due to human activities.<br />
!Pollutant<br />
!Source<br />
|-<br />
| [https://en.wikipedia.org/wiki/Arsenic Arsenic] || Pesticides, wood preservatives, biosolids, ore mining and smelting<br />
|- <br />
| [https://en.wikipedia.org/wiki/Cadmium Cadmium] || Paints and pigments, plastic stabilizers, electroplating, phosphate fertilizers<br />
|-<br />
| [https://en.wikipedia.org/wiki/Chromium Chromium] || Tanneries, steel industries, fly ash<br />
|- <br />
| [https://en.wikipedia.org/wiki/Copper Copper] || Pesticides, fertilizers, biosolids, ore mining and smelting<br />
|-<br />
| [https://en.wikipedia.org/wiki/Mercury_%28element%29 Mercury] || Gold and Silver mining, coal combustion<br />
|-<br />
| [https://en.wikipedia.org/wiki/Nickel Nickel] || Effluent, kitchen appliances, surgical instruments, automobile batteries<br />
|-<br />
| [https://en.wikipedia.org/wiki/Lead Lead] || Aerial emission from combustion of leaded fuel, batteries waste, insecticide and herbicides.<br />
|}<br />
<br />
A majority of heavy metal pollutants come from human sources that accumulate over time.<br />
<br />
There are also natural forms of contamination from normal biological processes, which include:<br />
<br />
1. Weathering of minerals over time<br />
<br />
2. [https://en.wikipedia.org/wiki/Erosion Erosion] and [https://en.wikipedia.org/wiki/Volcano volcanic activities]<br />
<br />
3. [https://en.wikipedia.org/wiki/Wildfire Forest fires] and biogenic source<br />
<br />
4. Particles released by vegetation<br />
<br />
Heavy metals can be absorbed by microbes at cellular binding sites. Extracellular polymers of these microbes can complex heavy metals through various mechanisms [21]. These specialized microorganisms can mineralize the organic contaminants to metabolic intermediates, which are used as primary substrates for cell growth. The microbes prevalent in heavily metal-contaminated soil can alter the oxidation state of the heavy metals by immobilizing them [21], allowing them to be easily removed. Bioremediation of heavy metals from microbes is not heavily researched, mostly due to an incomplete understanding of the genetics of the microbes used in metal adsorption. ''[https://microbewiki.kenyon.edu/index.php/Geomicrobiology Geomicrobiology]'' takes a better look at the interactions between microbes and inorganic material.<br />
<br />
=='''Organisms'''==<br />
As stated previously, bioremediation involves various microorganisms that are able to degrade and reduce toxicity of environmental pollutants [12]. Therefore, the interactions of microbes with the environment and pollutants are significant in determining effectiveness of bioremediation [4]. Those microbes can be either naturally present in the site of bioremediation or isolated from other sites and inoculated artificially [12]. Biodegradation often occurs as part of microbial metabolism and in some cases, microbes are able to directly harvest carbon and energy by breaking down pollutants [12]. Sections below go over bacteria and fungi, the commonly used organisms in bioremediation, and archaea, the more recently discovered group of organisms with unique potential in bioremediation.<br />
<br />
==='''Bacteria'''===<br />
Bacteria are widely diverse organisms, and thus make excellent players in biodegradation and bioremediation. There are few universal toxins to bacteria, so there is likely an organism able to break down any given substrate, when provided with the right conditions (anaerobic versus aerobic environment, sufficient electron donors or acceptors, etc.). Below are several specific bacteria species known to participate in bioremediation.<br />
<br />
===='''''[[Pseudomonas putida]]'''====<br />
[[Image:Pseudomonas_putida.png|upright=1|thumb|Pseudomonas putida, Image © http://www.denniskunkel.com/DK/Bacteria/23859D.html]]<br />
<br />
''Pseudomonas putida'' is a gram-negative soil bacterium that is involved in the bioremediation of toluene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===='''''[[Dechloromonas aromatica]]''' ====<br />
''Dechloromonas aromatica'' is a rod-shaped bacterium which can oxidize aromatics including benzoate, chlorobenzoate, and toluene, coupling the reaction with the reduction of oxygen, chlorate, or nitrate. It is the only organism able to oxidize benzene anaerobically. Due to the high propensity of benzene contamination, especially in ground and surface water, ''D. aromatic'' is especially useful for in situ bioremediation of this substance. [13]<br />
<br />
===='''Nitrifiers and Denitrifiers'''==== <br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage process that involves nitrification and denitrification. During nitrification, ammonium is oxidized to nitrite by organisms like <i>Nitrosomonas europaea</i>.Then, nitrite is further oxidized to nitrate by microbes like <i>Nitrobacter hamburgensis</i>.<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like <i>Paracoccus denitrificans </i>[2]. The result is N2 gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
===='''''[[Deinococcus radiodurans]]'''====<br />
''Deinococcus radiodurans'' is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered strain of Deinococcus radiodurans has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7].<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like ''[[Paracoccus denitrificans]]'' [2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
[[Image:Alcanivorax_borkumensis.png|upright=1|thumb|Alcanivorax borkumensis, Image©https://www.biotechnologie.de/BIO/Navigation/EN/Funding/foerderbeispiele,did=44848.html?view=renderPrint [25]]]<br />
<br />
===='''''[[Methylibium petroleiphilum]]'''====<br />
''Methylibium petroleiphilum'' (formally known as PM1 strain) is a bacterium capable of [https://en.wikipedia.org/wiki/Methyl_tert-butyl_ether methyl tert-butyl ether] (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
===='''''[[Alcanivorax borkumensis]]'''====<br />
''Alcanivorax borkumensis'' is a marine rod-shaped bacterium which consumes hydrocarbons, such as the ones found in fuel, and produces carbon dioxide. It grows rapidly in environments damaged by oil, and has been used to aid in cleaning the more than 830,000 gallons of oil from the [https://en.wikipedia.org/wiki/Deepwater_Horizon_oil_spill Deepwater Horizon oil spill] in the Gulf of Mexico [25].<br />
<br />
==='''Fungi (Mycoremediation)'''===<br />
Current bioremediation applications primarily utilize bacteria, with comparatively few attempts to use fungi. Fungi have fundamentally important roles because of their participation in the cycling of elements through decomposition and transformation of organic and inorganic materials. These characteristics can be translated into applications for bioremediation which could break down organic compounds and reduce the risks of metals. In some cases, fungi have an advantage over bacteria not just in metabolic versatility but also their environmental resilience.They are able to oxidize a diverse amount of chemicals and survive in harsh environmental conditions such as low moisture and high concentrations of pollutants. Therefore, fungi are potentially an extremely powerful tool in soil bioremediation and some versatile species such as <b>[https://en.wikipedia.org/wiki/Wood-decay_fungus#White_rot White Rot Fungi]</b> have been a hot topic of research. [16,17]<br />
<br />
===='''Biodegradation Capacities of White rot fungi'''====<br />
Using fungi as potential treatment of contaminants began in 1985 when the white rot species Phanerochaete chrysosporium was discovered to metabolize multiple key environmental pollutants. The most important feature of these fungi is their enzymatic functional ability to metabolize complex chemicals such as lignin. Similar abilities were later discovered in other white rot fungal species. In addition, white rot fungi are highly advantageous because they degrade lignin extracellularly through its hyphal extension. This allows them to access soil contaminants that other organisms are incapable of and maximize surface area for enzymatic interaction. These inexpensive fungi can tolerate extreme environmental conditions, such as pH, temperature, and moisture content. While many microbial organisms that are used for bioremediation require pre-conditioning of the environment for them to survive in, white rot fungi can directly be applied into most systems because they degrade based upon nutrient deprivation. [18]<br />
<br />
[[Image:040504062021.jpg|right|thumb|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x]]<br />
<br />
===='''''[[Phanerochaete chrysosporium]]'''====<br />
<i>P. chrysosporium</i> was the first fungi linked to degradation of organic pollutants. Extensive research has show this it has strong potential for bioremediation in pesticides, PAHs, dioxins, carbon tetrachloride, and many other pollutants. Among fungal systems, <i>P. chrysosporium</i> has become the model for bioremediation. Other notable species of white rot fungi include <i>Pleurotus ostreatus</i> and <i>Trametes versicolor</i>. [18]<br />
<br />
===='''Bioremediation of Hydrocarbon Pollutants'''====<br />
<br />
Hydrocarbons are stored deep underground but are brought up to the surface to be transformed and utilized, primarily as an energy source known as fossil fuels. The majority of pollution currently comes from these byproducts in the form Polycyclic Aromatic Hydrocarbons (PAHs), which are xenobiotic environmental pollutants that form when carbon materials are incompletely combusted. Some of examples of PAHs include burning wood, fossil fuels, and cigarette smoke. [19,20]<br />
Currently, bioremediation is only effective for soils contaminated with low-molecular weight PAHs because of bacterial commercial use. However, fungi are effective at PAH degradation in comparison to bacteria for a few reasons. Firstly, they are capable degrading PAH’s that are high in molecular weight, bacteria in comparison are better at degrading smaller molecules. Secondly, fungi can function well in non-aqueous environments and low oxygen conditions, both are conditions where PAH’s can accumulate. Many fungi have evolved mechanisms that allow the to target specific PAHs. Fungi produce extracellular enzymes that degrade lignin, a process called mineralization the produces carbon dioxide as the end product. [19,20]<br />
<br />
===='''Remediating Metals'''====<br />
<br />
Toxic metals can enter the environment all life cycle stages of metal compound. For example, metal leaching can occur from the mining process till the disposal of metal wastes. However in nature, the mobility of metals comes from the geological processes that can be released into the soil and aquatic environments. The environmental largest risk from metal contamination comes from the relationship between metals and compounds that are inherently of incapable of being degraded by any natural procedures. The best solution to treating contamination is transporting the metals to location where they cannot produce negative environmental effects. Fungi have various ways of interacting with metals, some of the techniques are increasing or decreasing the mobility of metals, sorption, or even cellular uptake. After the metals have been absorbed the fungus, they can chemically altered to be stored or translocated through the hyphae and into various plants that participate in symbiosis. [17]<br />
<br />
===='''Pesticide Degradation'''====<br />
<br />
Pesticide accumulation is an issue of great concern among the public, because they are directly associated with food products and water supplies. There are number of technologies used for pesticide clean-up; however, these technologies are generally expensive and inefficient because they require contaminated soil to be excavated and sent to a separate storage location for processing. Bioremediation offers a potential solution that treats contaminated soil and groundwater without needing excavation. Studies show that White Rot Fungi has high promise for soil bioremediation application; however, most tests have been conducted in the lab rather than in the actual environment. This fungi demonstrates the ability to transform and mineralize specific pesticides in soil. [18]<br />
<br />
===='''Environmental Applications'''====<br />
<br />
Although fungi demonstrate significant biochemical and ecological useful qualities, they are hardly utilized for biotechnological purposes. Instead, bacteria are most commonly used because they usually produce superior results in their numerous advantages ranging from their highly specific biochemical reactions to their capabilities of breaking down pollutants efficiently [17]. Fungi are underused primarily because of the costs that come from providing oxygen to fungi in polluted environments. However, filamentous fungi could be highly valuable in situations where bacteria cannot perform. For example, fungi are useful in situations where contaminants are physically blockaded and bacteria cannot reach or in circumstances of environmental extremes such as high acidity or dryness prevent bacteria from functioning. [17]<br />
<br />
==='''[https://en.wikipedia.org/wiki/Archaea Archaea]'''===<br />
The role of archaea in bioremediation has not been studied as commonly as that of bacteria [10]. Nevertheless, numbers of researchers have shown their ability to degrade various pollutants and scientists began to discover more about their potential in participating in bioremediation. Below lists some important facts regarding archaea’s potential role in bioremediation.<br />
<br />
- Biodegradation by extreme [https://en.wikipedia.org/wiki/Halophile halophilic] archaea was not recognized widely in the past, but scientists have found out that extreme halophilic archaea have greater catabolic diversity than expected [9]<br />
<br />
- Hydrocarbon-contamination is observed in some extreme environments, including hypersaline (high salt concentration), high or low temperature, or extreme pH [10]. Archaea’s adaptation to extreme environment gives them the potential to participate in biodegradation and bioremediation in these environments; in fact, microorganisms naturally adapted to the cold environments are known to be important degraders of hydrocarbons in those environments [10].<br />
<br />
- Extreme halophilic archaea has potential to biodegrade pollutants in hypersaline environment, in which bacteria typically used in bioremediation cannot survive or function properly. [5]<br />
<br />
- Some archaea are known to be resistant to variety of antibiotics, including penicillin, cycloheximide, streptomycin, etc, which gives them great advantage in participating in bioremediation in the presence of antibiotics [5].<br />
<br />
===='''Examples of studies of Archaea involved in bioremediation'''====<br />
<br />
Four extreme halophilic strains of archaea (belonging to genus ''[https://en.wikipedia.org/wiki/Halobacterium Halobacterium]'', ''[https://en.wikipedia.org/wiki/Haloferax Haloferax]'', and ''[https://en.wikipedia.org/wiki/Halococcus Halococcus]'') were studied to evaluate their potential to biodegrade crude oil and hydrocarbons. [5] All four strains could use various kinds of hydrocarbons as their carbon or energy sources [5]. Two strains of Haloferax grew on n-alkanes with different lengths, ranging from C8 to C34, and also benzene, toluene, biphenyl, and naphthalene. The research demonstrated the important fact that archaea have potential to carry out biodegradation at high temperatures, in the range of 40-45 °C [5], which is advantageous because hydrocarbons have higher solubility and bioavailability at these higher temperature [10]. The four strains studied were resistant to six different antibiotics, including penicillin, streptomycin, cycloheximide [5] and this gave them the potential to carry out biodegradation in conditions unfavorable for bacteria. Research suggests other genera of archaea are also capable of biodegrading in hypersaline environments [6]<br />
<br />
''[https://en.wikipedia.org/wiki/Halococcus Archaeglobus] fulgidus'', a [https://en.wikipedia.org/wiki/Hyperthermophile hyperthermophile] with ability to reduce sulfate, can be used to break down various aromatic hydrocarbons (Peeples, 2014).<br />
<br />
=='''Microbial Processes'''==<br />
<br />
Microorganisms use a wide range of processes to transform chemicals in their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor. This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. Below, several steps and details of the microorganisms’ actions are described.<br />
<br />
==='''Factors Affecting Rates of Biodegradation'''===<br />
Biodegradation may be influenced by pH, temperature, moisture, carbon sources, soil texture, aerobic versus anaerobic conditions, the number of substituents, and the concentration of the pollutant. It is impossible, however, to make a generalization about the best universal conditions for biodegradation. What’s toxic to some microbes is a nutrient to others, what might be a damaging pH to some is beneficial to others, and so on.<br />
<br />
A greater amount of substituents will cause slower degradation in aerobic environments, but faster degradation in anaerobic ones. Chlorine makes a molecule less degradable due to steric hindrance preventing access to necessary enzymes, therefore molecules with higher chlorination are slower to degrade in aerobic conditions. High concentration of a pollutant generally results in faster rates of degradation. If the concentration drops below a threshold concentration, the enzymes may not detect it and will cease to degrade it [26].<br />
<br />
The rate at which a compound is transformed, as well as the curves that describe its transformation, is referred to as kinetics, and is affected by all factors listed above. First order kinetics (logarithmic biodegradation) is often used when the substrate concentration is high enough that microbes can easily access it, while zero-order kinetics (linear biodegradation) is often observed when the substrate concentration is very small. If the concentration falls below a threshold, the microbes can no longer transform it and the concentration levels out.<br />
<br />
Soil with small pores, especially clays, may cause biodegradation to take years due to the decrease in bioavailability. Chlorine makes a molecule less degradable due to steric hindrance preventing necessary enzymes from accessing the compound, therefore molecules with higher chlorination are slower to degrade.<br />
<br />
The power rate model gives an empirical approach to the relationship between concentration and rate of degradation:<br />
<br />
-dC/dt = kC^n<br />
<br />
C is substrate concentration, t is time, k is a rate constant for the chemical in question, and n is an appropriate parameter. The values of k and n are adjusted until a line is found to match experimental data [23].<br />
<br />
==='''Primary substrate utilization'''===<br />
<b>Primary substrate utilization</b> occurs when a microbe both transforms a substrate and uses it as an energy or carbon source. [15] An electron acceptor is required for these transformations. It can be anaerobic or aerobic, although the presence of oxygen tends to speed up reactions. This form of biodegradation can be used for treating petroleum spills or the runoff of a number of pesticides. The rate of reaction follows the guidelines in the previous section, where a higher concentration leads to a higher rate. [15]<br />
<br />
==='''Cometabolism (Secondary Substrate Utilization)'''===<br />
<b>Cometabolism</b> involves the transformation of a chemical by an organism while the organism uses a different substance as its primary energy or carbon source [14]. This is a technique often used when the substrate by itself is considered non-biodegradable, and can only be transformed with another compound. During the actual reaction degrading the substance, the organism has no net carbon or energy gain, and may even result in a product with no use to the organism or which is toxic to the cell [14]. However, it is often difficult to tell whether microorganisms have a second substrate available during their transformations [23]. Cometabolism occurs in parallel with metabolism, not instead of.<br />
<br />
A key example of cometabolism is fortuitous metabolism in the degradation of trichloroethylene, shown in the diagram below. An organic growth substrate such as propane or butane is required for the enzymatic activity that transforms TCE. [14]<br />
<br />
[[Image:Cometabolism.png|center|upright=3|thumb|Image from Kate Scow lecture, 2016]]<br />
<br />
==='''Reductive and Hydrolytic Dehalogenation'''===<br />
Chloride and other halogens are common components of pesticides and hazardous industrial wastes, and by removing them the toxic chemical can often be remediated [23]. If the halogen is replaced by a hydrogen (RCl -> RH), then it is <b>reductive dehalogenation</b>. If two halogens are replaced simultaneously, then the process is called <b>dihaloelimination</b>, although it still falls under reductive dehalogenation [14]. If the halogen is replaced by OH (RCl -> ROH) then it’s <b>hydrolytic dehalogenation</b>. In both cases, the halogen is released as its inorganic form into the environment [23].<br />
<br />
==='''Acclimation'''===<br />
An <b>acclimation period</b>, also called an <b>adaptation</b> or <b>lag period</b>, occurs when no destruction of a given chemical is observed [23]. It is caused by the microbes transitioning to their altered environment and shifting their metabolism to better suit it [14]. It can last for anywhere from hours (such as aromatic compounds in warm, oxygenated soils) to months (such as halobenzoates in anaerobic sediments) depending on the chemical in question and the environment [23]. Acclimation periods can be affected by temperature, the presence of oxygen, pH, and concentration of the substance. Although they are most often faster in warm, aerated, and fairly dry environments, there are few consistencies between what shortens or lengthens the period, even if the concentration is the same [23]. Insecticides including methyl parathion and azinphosmethyl; herbicides including 2, 4-D, MCPA, Mecoprop, TCA, and amitrole; the quaternary ammonium compound dodecyltrimethylammonium chloride; polycyclic aromatic hydrocarbons including naphthalene and anthracene; and other chemicals such as phenol, chlorobenzene, PCP, diphenyl-methane, and NTA have all been reported to have acclimation periods, and this can be of severe human concern [23]. The continued presence of these toxins extends human, plant, and animal exposure, and if the chemical is in water, it can allow the substance to flow further and impact environments distant to its site of origin before being degraded.<br />
<br />
==='''Detoxification and Activation'''===<br />
<b>Detoxication</b>, sometimes called <b>detoxification</b>, has been referred to as the “most important role of microorganisms in the transformation of pollutants” [23]. The process is the changing of a molecule into something less harmful to a species in question. There are a number of ways a molecule can be transformed, including hydrolysis, hydroxylation, dehalogenation, demethylation, methylation, and ether cleavage [23]. By breaking bonds, or adding or removing groups, the organism reduces its effect on the environment. Furthermore, although sometimes the resulting chemical is simply excreted as waste, the organism may also be able to use this new compound as a carbon source or further modifies it until it is released as CO2 [23].<br />
<br />
There are instances where the initial compound is harmless, and in fact the substance produced by microorganisms, or an intermediate in the degradation process, is a toxin [23]. This process is called activation. For this reason, it is important to test all steps of a reaction when determining how a compound is degrading. The new toxins may also be more or less mobile than its predecessor, so it can either stick around one area for extended periods of time or spread to other areas and increase damage [23]. A prevalent example of this is the dechlorination of TCE, which produces DCE (50 times more hazardous than TCE) and Vinyl Chloride (a known carcinogen) [14]. Commonly used insecticides in the past, like zinophos, trichloronat, and carbofuran, were all found to increase a soil’s toxicity with extended use [23].<br />
<br />
=='''Bioremediation treatment methods'''==<br />
In order for bioremediation to be successful, it requires sufficient proof for the degradation of contaminants. However, determining the effectiveness and completeness to reach sufficient results is one of the major issues. Natural attenuation relies on natural processes to clean up or attenuate pollution in soil and groundwater [27]. This remediation is done without human interaction, and is primarily used as a monitoring technique, to make sure more aggressive cleanup strategies are not needed. [https://en.wikipedia.org/wiki/Abiotic_component Abiotic] and [https://en.wikipedia.org/wiki/Biotic_component biotic] factors play a distinguishing factor of how effective bioremediation is.<br />
<br />
Current monitoring practices determine the disappearance of contaminants and their degradation products to regulatory levels that are monitored by toxicity testing, usually on single organisms or species to ensure there are no induced changes that may result in residual toxicity. The problem with these monitoring techniques is that the assessment of contaminants may result in an inaccurate indicator of residual toxicity[28]. Rather, studying the microbial community response may be a more comprehensive indicator of residual toxicity than a single species. Once sufficient evidence is provided, human intervention may be needed for a more effective cleanup process. <br />
<br />
There are two types of remediation that are done, ex situ: which is done by removing the contaminated soil or water and treating it outside the source, and in situ: which treatment takes place within the contaminated area. There are some treatments methods that can be either ex situ or in situ. Some techniques may deal with the mobilization of pollutants, to move them out of an area, or immobilized to keep them out of an area such as a water table.<br />
<br />
<br />
[[Image:Summary_of_bioremediation_strategies.png|center|upright=3|thumb|A comparative analysis of the different types of bioremediation. It can be used to find which remediation technique may be used in certain circumstances [12]]]<br />
<br />
<br />
[[Image:Biopiling.png|right|upright=1.5|thumb|Contaminated soil is mixed with amendments and piled on top of a liner, while a pipe with a blower controls aeration. [29]]]<br />
==='''Ex-situ'''===<br />
Ex-situ techniques are those that are applied to soil and groundwater which has been removed from the site via excavation or pumping [12]. The methods used include composting, biofilters, and biopiling. Ex-situ is used for smaller projects, primarily because larger excavation of soil is not prefered. The movement of the soil can be more detrimental by destroying the preestablish horizons in the soil.<br />
<br />
[[Image:Composting.png|right|upright=3|thumb|Composting is a very versatile remediation technique that can be used for either: a very broad treatment with many contaminants, or very specific treatment that utilizes particular microbes that target specific contaminants [30]. It can also be used to augment other treatment methods.]]<br />
<br />
===='''Biopiling'''====<br />
Excavated soils are mixed with soil amendments and placed on a treatment area. Biopiles are aerated with the use of perforated pipes and blowers in order to control the progression of biodegradation more efficiently by controlling the supply of oxygen [29], which in turn may affect other factors such as pH. This system is primarily used to remediate systems with oil and hydrocarbon contamination. The remediated soil is placed in a liner to prevent further contamination of the soil, they may also be covered with plastic to control runoff, evaporation, and [https://en.wikipedia.org/wiki/Volatilisation volatilization].<br />
<br />
===='''Composting'''====<br />
Nutrients are added to soil that is mixed to increase aeration and activation of indigenous microorganisms. Composting is done in a separate container, then when composting is complete it is incorporated into the soil. Bioremediation by the utilization of compost relies on the adsorption capabilities of organic matter and the degradation capabilities of microorganisms present[30]. Composting is recognized as as one of the most cost-effective technologies for soil bioremediation and it can be done on large and small scales. The use of composting is a very versatile technique for soil polluted by a wide range of organic pollutants and heavy metals, making it great for easier remediation involving various pollutants. The utilization of organic wastes for soil remediation is also helpful in decreasing the need for their storage and treatment. Organic matter that is generated from composting offers the benefit of improving soil quality and structure. Composting is primarily used for remediation over a longer period of time, as the nutrients for the microbes are released gradually and requrire more time compared to quicker treatments such as biostimulation.<br />
<br />
==='''In-situ'''===<br />
In-situ techniques are applied to soil and groundwater at the site with minimal disturbance[12]. These methods include biostimulation, bioleaching, biosorption, and bioventing. In-situ is preferred because it is often minimally invasive to the soil structure in comparison to ex-situ, but it can be expensive due to specialized equipment.<br />
<br />
===='''Biostimulation'''====<br />
This method involves the addition of nutrients to a polluted site in order to encourage the growth of naturally occurring chemical-degrading microorganisms[31]. Biostimulation is primarily done by the addition of various nutrients that are limited in the soil as well as electron acceptors, such as phosphorus, nitrogen and oxygen, or increasing the amount of available carbon in order to increase the population or activity of naturally occurring microorganisms. Other approaches are to optimize environmental conditions such as aeration, the addition of nutrients, altering pH and temperature control [32]. The primary advantage of biostimulation is that it is done by native microorganisms that are well-suited to the environment, and are already well distributed spatially. The challenge is delivering additives so they are readily available to the subsurface microbes.<br />
<br />
===='''Metal Bioleaching'''====<br />
Metal bioleaching is the extraction of metals from soils utilizing a biological source such as microbes. This technique was first developed to extract minerals from ores. Specific microorganisms like Thiobacillus ferrooxidans and T. thiooxidans promote the metals’ solubilization. Several species of fungi are used for bioleaching. These remediation fungi can also produced in a lab. Two prevalent fungal strains ([https://microbewiki.kenyon.edu/index.php/Aspergillus_niger Aspergillus Niger], [https://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium Simplicissimum]) are capable of mobilizing metals such as copper, tin, aluminium, nickel, palladium, and zinc[33], which will make them much easier to remove from the soil.<br />
<br />
===='''Metal Biosorption'''====<br />
Adsorption of metals and other ions of an aqueous solution by the use of microbes. The biosorption process involves a solid phase and a liquid phase containing a dissolved species to be sorbed [34]. The process continues until equilibrium is established between the amount of solid-bound sorbate species and its portion remaining in the solution. The degree of affinity for the sorbate determines its distribution between the solid and liquid phases.<br />
<br />
Biosorption processes are very important in the environment, and has been utalized for conventional biotreatment processes. Biosorption is primarily aimed at the removal or recovery of organic and inorganic substances from solution [35]. The commercialization of biosorption technologies has been limited so far.<br />
<br />
[[Image:Bioventing.png|right|upright=2.5|thumb|Bioventing is primarily used for injecting air into specific remediation zones, adding oxygen as a readily available electron acceptor where it would otherwise be anaerobic. It can also be reversed to make a more anaerobic environment. Either technique can be applied depending on the remediating microbes would thrive in [36].]]<br />
<br />
===='''Bioventing'''====<br />
Bioventing is an In situ remediation technology that uses indigenous microorganisms to biodegrade organic constituents adsorbed to soils in the unsaturated zone[36]. The availability of oxygen generally controls the rate at which aerobic bioremediation proceeds. Bioventing is the coupling of soil venting and bioremediation. Bioventing can be successfully applied to compounds ranging from gasoline or diesel, to heavier hydrocarbons[36]. The addition of nutrients with the bioventing flow rates can achieve greater contaminant reductions than venting alone.<br />
<br />
==='''Ex-situ or In-situ'''===<br />
Some methods can be used by either in-situ or ex-situ methods. The soil or water can be removed from the contamination source and treated, or treated at the source, the method chosen can be based on many factors such as how expensive the project may be or how much contaminant needs to be treated. These methods include bioaugmentation, land farming and biofiltration.<br />
<br />
===='''Bioaugmentation'''====<br />
Bioaugmentation is the addition of non-native microorganisms that have the ability to degrade the contaminants that are recalcitrant to the indigenous microbiota. Bioaugmentation has been proven successful in cleaning organic pollutant, but still faces many environmental problems, such as the survival of strains introduced to soil[37]. The number of introduced microorganisms usually decreases shortly after soil inoculation, when the pollutant has been heavily removed. But the introduced species may linger for long periods of time, a wider use of non-natives runs the possible risk of creating a monoculture in the soil.<br />
<br />
Bioaugmentation is ideal for soil:<br />
<br />
1. With low number of microbes that are capable of degrading targeted pollutants<br />
<br />
2. Containing compounds requiring multi stepped remediation.<br />
<br />
Augmentation techniques have a great potential for [https://en.wikipedia.org/wiki/Category:Aromatic_compounds aromatic compound] remediation. The most important step in successful bioaugmentation is selection of proper microbial strains. The success of bioaugmentation strongly depends on the ability of inoculants to survive in contaminated soil, which may vary due to predation and an environment that does not identically mimic the lab it was grown in.<br />
<br />
===='''Land Farming'''====<br />
Contaminated soil is mixed with amendments such as nutrients, and then they are tilled into the earth, or the contaminated soil is applied into lined beds and periodically turned over or tilled to aerate the waste [38]. The topmost layer is the area of concentration for this method, so it is not ideal for deeper remediation. Land farming differs from composting because it actually incorporates contaminated soil into soil that is uncontaminated [38]. The higher zone of remediation will typically contain primarily lighter hydrocarbons that can be volatilized. The material is periodically tilled for aeration to hasten remediation of any nutrients and allow more oxygen to act as electron acceptors, as well as allowing volatilization to occur. Contaminants are degraded, transformed, and immobilized by microbiological processes and oxidation. Soil conditions are controlled to optimize the rate of contaminant degradation, moisture content, frequency of aeration, and pH are all conditions that may be controlled [38]. <br />
<br />
[[Image:Biofilter.png|right|upright=1.5|thumb|The application of a micro-algal/bacterial biofilter in the primary outflow of soil water [39]]]<br />
<br />
===='''Biofilter'''====<br />
Biofilters are primarily used for the filtration of contaminated groundwater in the soil. Biofilters can be used above soil, where the water will be pumped aboveground for treatment, or a filter can be placed in the soil near an outflow. A micro-algal/bacterial biofilter can be used for the detoxification of copper and cadmium metal wastes [22]. Biofilters have been used in larger industry environments to treat contaminated outflow of water. [https://en.wikipedia.org/wiki/Chromobacterium_violaceum Chromobacterium violaceum], is used to treat water and soil contaminated with silver nanoparticles, reducing its concentration.<br />
<br />
=='''Bioremediation Synopsis'''==<br />
<br />
==='''Advantages'''===<br />
1. Bioremediation is a publicly accepted treatment of polluted soil because it is based upon natural processes. Microbes that metabolize contaminants increase in population when the contaminant is present. The inverse is true, degradation of the contaminant causes population declines of those microbes. Usually the products from treatment are harmless; such as carbon dioxide, water, and cellular biomass. [12]<br />
<br />
2. Bioremediation is theoretically meant to completely degrade a wide range of pollutants into harmless products on site. This removes the risks involved with transportation for treatment and elimination of contaminated substances. [12]<br />
<br />
3. Bioremediation is meant to completely eliminate specific pollutants without the risks of transferring contaminants from one environmental medium to another (land, air, water). [12]<br />
<br />
4. Bioremediation can be a cheaper alternative to other technologies used for pollution mitigation. [12]<br />
<br />
==='''Disadvantages'''===<br />
1. Only biodegradable compounds are capable of undergoing bioremediation. Not every compound is capable of fully degrading quickly. [12]<br />
<br />
2. The products of biodegradation may potentially be even more persistent or toxic than the original contaminant. [12]<br />
<br />
3. Biological functions are usually extremely specific and require the presence of microbes that are capable of metabolizing the contaminants. In order for the correct microbes to be present, the appropriate environmental conditions, levels of nutrients, and contaminants need to be met. [12]<br />
<br />
4. Scaling up the size of studies from small initial studies to commercial-scale field operations is difficult.[12]<br />
<br />
5. The real environment contains contaminants that are mixed, unevenly distributed, and in different phases (solid, liquid, gas). More research needs to be completed to create technologies that can adapt. [12]<br />
<br />
6. Compared to other treatment technologies, bioremediation often takes more time. [12]<br />
<br />
7. Problems with ensuring adequate contact between the microbes and the contaminant. preferential pathway and soil structure can leave uncertainty in remediation dispersal.[12]<br />
<br />
=='''References'''== <br />
<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdf United States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120. <br />
<br />
5. Al-Mailem, D. M., Sorkhoh, N. A., Al-Awadhi, H., Eliyas, M., & Radwan, S. S. (2010). Biodegradation of crude oil and pure hydrocarbons by extreme halophilic archaea from hypersaline coasts of the Arabian Gulf. Extremophiles, 14(3), 321-328. doi: 10.1007/s00792-010-0312-9<br />
<br />
6. Fairley, D. J., Boyd, D. R., Sharma, N. D., Allen, C. C., Morgan, P., & Larkin, M. J. (2002). Aerobic metabolism of 4-hydroxybenzoic acid in Archaea via an unusual pathway involving an intramolecular migration (NIH shift). Appl Environ Microbiol, 68(12), 6246-6255.<br />
<br />
7. Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008<br />
<br />
8. Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008<br />
<br />
9. Le Borgne, S., Paniagua, D., & Vazquez-Duhalt, R. (2008). Biodegradation of organic pollutants by halophilic bacteria and archaea. J Mol Microbiol Biotechnol, 15(2-3), 74-92. doi: 10.1159/000121323<br />
<br />
10. Margesin, R., & Schinner, F. (2001). Biodegradation and biore<br />
mediation of hydrocarbons in extreme environments. Appl Microbiol Biotechnol, 56(5-6), 650-663.<br />
<br />
11. Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9<br />
<br />
12. Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172. <br />
<br />
13. "Dechloromonas Aromatica RCB." JGI Genome Portal, 16 Feb. 2016. [http://genome.jgi.doe.gov/decar/decar.home.html http://genome.jgi.doe.gov/decar/decar.home.html]<br />
<br />
14. King, R. Barry, John K. Sheldon, and GIlbert M. Long. (1998). Practical Environmental Bioremediation: The Field Guide. 2nd ed. Boca Raton: CRC, 1998.<br />
<br />
15. "Manual, Bioventing Principles and Practices." United States Environmental Protection Agency I (1995)<br />
<br />
16. Gadd, G. M. (Ed.). (2001). Fungi in bioremediation (No. 23). Cambridge University Press<br />
<br />
17. Harms, H., Schlosser, D., & Wick, L. Y. (2011). Untapped potential: exploiting fungi in bioremediation of hazardous chemicals. Nature Reviews Microbiology, 9(3), 177-192<br />
<br />
18. Fragoeiro, S. (2005). Use of fungi in bioremediation of pesticides. Applied Mycology Group Institute of Bioscience and Technology. Cranfield University<br />
<br />
19. Singh, H. (2006). Mycoremediation: fungal bioremediation. John Wiley & Sons. 283-285<br />
<br />
20. Norton, J. M. (2012). Fungi for Bioremediation of Hydrocarbon Pollutants. University of Hawai’i at Hilo. Hohonu, 10, 18-21<br />
<br />
21. Dixit, Ruchita, Emptyyn Wasiullah, Deepti Malaviya, Kuppusamy Pandiyan, Udai Singh, Asha Sahu, Renu Shukla, Bhanu Singh, Jai Rai, Pawan Sharma, Harshad Lade, and Diby Paul. "Bioremediation of Heavy Metals from Soil and Aquatic Environment: An Overview of Principles and Criteria of Fundamental Processes." Sustainability 7.2 (2015): 2189-212. Print.<br />
<br />
22. Bio-filters for Edge-of-Field Water Quality Management. (n.d.). Retrieved February 24, 2016, from [http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html]<br />
<br />
23. Alexander, Martin. (1999). Biodegradation and Bioremediation. San Diego: Academic Print. <br />
<br />
24. Litchfield, Carol. "Thirty Years and Counting: Bioremediation in Its Prime?" BioScience 55.3 (2005): 273.<br />
<br />
25. Biello, David. "Slick Solution: How Microbes Will Clean Up the Deepwater Horizon Oil Spill." Scientific American (n.d.): n. pag. 25 May 2010. <br />
<br />
26. Scow, Kate. “Lectures in Soil Microbiology.” UC Davis, Winter 2016.<br />
<br />
27 CLU-IN | Technologies Remediation About Remediation Technologies Natural Attenuation Overview. (n.d.). Retrieved February 24, 2016, from https://clu-in.org/techfocus/default.focus/sec/Natural_Attenuation/cat/Overview/<br />
<br />
28. Chauhan, Ashok K., and A. Varma. A Textbook of Molecular Biotechnology. New Delhi: I.K. International Pub. House, 2009. Print.<br />
<br />
29. Biopiles. (n.d.). Retrieved March 13, 2016, from [http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html]<br />
<br />
30. Chen, M., Xu, P., Zeng, G., Yang, C., Huang, D., & Zhang, J. (2015). Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: Applications, microbes and future research needs. Biotechnology Advances, 33(6, Part 1), 745–755.<br />
<br />
31. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. Retrieved March 13, 2016, from [http://www.sciencedirect.com/science/article/pii/S0944501309000585 http://www.sciencedirect.com/science/article/pii/S0944501309000585]<br />
<br />
32. Bioremediation, Biostimulation and Bioaugmention: A Review. (n.d.). Retrieved March 13, 2016, from http://pubs.sciepub.com/ijebb/3/1/5/<br />
<br />
33. Sulfur Oxides—Advances in Research and Application: 2013 Edition<br />
<br />
34. Fomina, M., & Gadd, G. M. (2014). Biosorption: current perspectives on concept, definition and application. Bioresource Technology, 160, 3–14. Retrieved February 24, 2016, from [https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application]<br />
<br />
35. Kotrba, Pavel, Martina Mackova, and Tomas Macek. (2011). Microbial Biosorption of Metals. Dordrecht: Springer Science Business Media Print.<br />
<br />
36. Bioventing » Water and Soil Bio-Remediation. (n.d.). Retrieved February 24, 2016, from [http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing]<br />
<br />
37. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. <br />
<br />
38. Land Farming. (n.d.). Retrieved March 13, 2016, from http://www.cpeo.org/techtree/ttdescript/lanfarm.htm<br />
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<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Bioremediation&diff=121000
Bioremediation
2016-03-22T01:58:36Z
<p>Kmscow: </p>
<hr />
<div>{{Curated}}<br />
<br />
Through agriculture, industry, and daily life, harmful chemicals have been released into the earth’s air, soil, and water. Depending on their concentrations, these substances can have destructive consequences on ecosystems, as well as cause severe damage to humans and other organisms nearby. Soil pollution is of special importance because of its impact on surface, groundwater and air contamination and can easily spread and be consumed by humans. <br />
<br />
[[Image:Bioremediation_images.jpeg|upright=3|thumb|Retrieved from Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120.]]<br />
<br />
<b>Biodegradation</b> is the biologically catalyzed modification of an organic chemical's structure. However, this modification can be through different metabolic pathways and does not necessarily mean a reduction in toxicity. Mineralization, one type of biodegradation, is defined as the conversion of an organic substance to its inorganic constituents, rendering the original compound harmless. [23]. Transformation is defined as any metabolically-induced change in the chemical composition of a compound [14].<br />
<br />
<b>Bioremediation</b> refers to the use of microorganisms to degrade contaminants that pose environmental and human risks. Bioremediation processes typically involve the actions of many different microbes acting in parallel or sequence to complete the degradation process. Both in situ (in place) and ex situ (removal and treatment in another place) remediation approaches are used. The versatility of microbes to degrade a vast array of pollutants makes bioremediation a technology that can be applied in different soil conditions [3]. Though it can be inexpensive and in situ approaches can reduce disruptive engineering practices, bioremediation is still not a common practice [1].<br />
<br />
A widely used approach to bioremediation involves stimulating naturally occurring microbial communities, providing them with nutrients and other needs, to break down a contaminant. This is termed <b>biostimulation.</b> Biostimulation can be achieved through changes in pH, moisture, aeration, or additions of electron donors, electron acceptors or nutrients. Another bioremediation approach is termed <b>bioaugmentation</b>, where organisms selected for high degradation abilities are used to inoculate the contaminated site [3]. These two approaches are not mutually exclusive- they can be used simultaneously.<br />
<br />
Recent awareness of the dangers of many chemicals used in society has led to research on formulation of products that are more easily degraded in the environment.<br />
<br />
From an ecological point of view, bioremediation depends on the various interactions between three factors: substrate (pollutant), organisms, and environment, as shown in the figure at right [4]. The interactions of these factors affect biodegradability, bioavailability, and physiological requirements, which are important in assessing the feasibility of bioremediation [4]. <b>Biodegradability</b>, or whether a chemical can be degraded or not, is determined by the presence or absence of organisms that are able to degrade a chemical of interest and how widespread these organisms are in the site [4]. The substrate (pollutant) can interact with its surrounding environment to change its <b>bioavailability</b>, or availability to organisms that are capable of degrading it; for example, substrate has low bioavailability if it is tightly bound to soil organic matter or trapped inside aggregates [4]. <b>Physiological requirements</b>, or set of conditions required by organisms to carry out bioremediation in the environment, include nutrient availability, optimal pH, and availability of electron acceptors, such as oxygen and nitrate [4]. Also, the environment needs to be habitable for organisms involved in bioremediation [4].<br />
<br />
=='''Brief History'''==<br />
<br />
[[Image:Wasterwater_treatment.png|upright=2.25|thumb|First Water Treatment Facility in Japan, 1934 Image from http://www.sewerhistory.org/grfx/trtmnt/trtmnt3.htm]] <br />
<br />
Microorganisms in the environment have always broken down waste, and humans have always (knowingly or unknowingly) used them in agricultural, domestic, and industrial activities [24]. As the urbanized world shifted to a more industrial system, however, people began to take an active approach in bioremediation. In the late nineteenth century, wastewater treatment plants were formed, but even so, this was not officially called bioremediation .<br />
The project considered the initial spark of the bioremediation movement was the report “Beneficial Stimulation of Bacterial Activity in Groundwater Containing Petroleum Products” by R.L. Raymond et al. in 1975. By testing the relationship between oil presence and bacterial stimulation, Raymond found that adding nutrients to soil hastened the oil removal. This led to the development of in situ bioremediation [24].<br />
<br />
Initial bioremediation projects focused on “pump and treat” (ex situ) methods in soil around gas stations and refinery spills to get oil out of groundwater sources, but soon cleaning up chlorinated hydrocarbons became a primary concern [24]. Chlorinated compounds were commonly used in pesticides, but when people learned it was a possible carcinogen and causing ozone depletion, research into bioremediation took off [24]. This was when anaerobic bacteria started being used, as it was discovered that they dechlorinate compounds much more quickly than do aerobic bacteria, and produce fewer damaging iron compounds that precipitate from the reactions [24].<br />
<br />
=='''Overview of Pollutants'''==<br />
Pollutants found in soils present a variety of different human health risks. Soil pollutants are typically classified as organic and inorganic pollutants. The remediation of some of these pollutants will be discussed in greater depth in the following sections.<br />
Below is a link to website with a list of examples of soil pollutants and their effects on human health:<br />
<br />
[http://www.environmentalpollutioncenters.org/soil/examples/ Summary of health effects of pollutants]<br />
<br />
==='''Organic Pollutants'''===<br />
Industrialization resulted in increased use of organic compounds that build up and persist in the environment [11]. Main sources of organic pollutants are through anthropogenic activities, including use of solvents, pesticides, and fuels [11]. Some of these organic compounds are highly toxic and they are associated with variety of health issues around the world [11].<br />
<br />
Table below lists some groups of contaminants, examples, and their sources.<br />
<br />
[[Image:Pollutants_list.png|center|upright=2.5|thumb|Retrieved from Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172.]]<br />
<br />
While organic pollutants are causing both environmental and health problems, bioremediation offers an effective solution to the pollution [11]. The table below lists some of the organic pollutants and microorganisms that are found to be able to degrade them.<br />
<br />
[[Image:Pollutants_and_organisms.png|center|upright=2.5|thumb|Retrieved from Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9]]<br />
<br />
==='''Inorganic Pollutants'''=== <br />
{| border="1" style="float:right; margin-left: 10px; text-align:center"<br />
|+ Most inorganic pollutants are due to human activities.<br />
!Pollutant<br />
!Source<br />
|-<br />
| [https://en.wikipedia.org/wiki/Arsenic Arsenic] || Pesticides, wood preservatives, biosolids, ore mining and smelting<br />
|- <br />
| [https://en.wikipedia.org/wiki/Cadmium Cadmium] || Paints and pigments, plastic stabilizers, electroplating, phosphate fertilizers<br />
|-<br />
| [https://en.wikipedia.org/wiki/Chromium Chromium] || Tanneries, steel industries, fly ash<br />
|- <br />
| [https://en.wikipedia.org/wiki/Copper Copper] || Pesticides, fertilizers, biosolids, ore mining and smelting<br />
|-<br />
| [https://en.wikipedia.org/wiki/Mercury_%28element%29 Mercury] || Gold and Silver mining, coal combustion<br />
|-<br />
| [https://en.wikipedia.org/wiki/Nickel Nickel] || Effluent, kitchen appliances, surgical instruments, automobile batteries<br />
|-<br />
| [https://en.wikipedia.org/wiki/Lead Lead] || Aerial emission from combustion of leaded fuel, batteries waste, insecticide and herbicides.<br />
|}<br />
<br />
A majority of heavy metal pollutants come from human sources that accumulate over time.<br />
<br />
There are also natural forms of contamination from normal biological processes, which include:<br />
<br />
1. Weathering of minerals over time<br />
<br />
2. [https://en.wikipedia.org/wiki/Erosion Erosion] and [https://en.wikipedia.org/wiki/Volcano volcanic activities]<br />
<br />
3. [https://en.wikipedia.org/wiki/Wildfire Forest fires] and biogenic source<br />
<br />
4. Particles released by vegetation<br />
<br />
Heavy metals can be absorbed by microbes at cellular binding sites. Extracellular polymers of these microbes can complex heavy metals through various mechanisms [21]. These specialized microorganisms can mineralize the organic contaminants to metabolic intermediates, which are used as primary substrates for cell growth. The microbes prevalent in heavily metal-contaminated soil can alter the oxidation state of the heavy metals by immobilizing them [21], allowing them to be easily removed. Bioremediation of heavy metals from microbes is not heavily researched, mostly due to an incomplete understanding of the genetics of the microbes used in metal adsorption. ''[https://microbewiki.kenyon.edu/index.php/Geomicrobiology Geomicrobiology]'' takes a better look at the interactions between microbes and inorganic material.<br />
<br />
=='''Organisms'''==<br />
As stated previously, bioremediation involves various microorganisms that are able to degrade and reduce toxicity of environmental pollutants [12]. Therefore, the interactions of microbes with the environment and pollutants are significant in determining effectiveness of bioremediation [4]. Those microbes can be either naturally present in the site of bioremediation or isolated from other sites and inoculated artificially [12]. Biodegradation often occurs as part of microbial metabolism and in some cases, microbes are able to directly harvest carbon and energy by breaking down pollutants [12]. Sections below go over bacteria and fungi, the commonly used organisms in bioremediation, and archaea, the more recently discovered group of organisms with unique potential in bioremediation.<br />
<br />
==='''Bacteria'''===<br />
Bacteria are widely diverse organisms, and thus make excellent players in biodegradation and bioremediation. There are few universal toxins to bacteria, so there is likely an organism able to break down any given substrate, when provided with the right conditions (anaerobic versus aerobic environment, sufficient electron donors or acceptors, etc.). Below are several specific bacteria species known to participate in bioremediation.<br />
<br />
===='''''[[Pseudomonas putida]]'''====<br />
[[Image:Pseudomonas_putida.png|upright=1|thumb|Pseudomonas putida, Image © http://www.denniskunkel.com/DK/Bacteria/23859D.html]]<br />
<br />
''Pseudomonas putida'' is a gram-negative soil bacterium that is involved in the bioremediation of toluene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. [2]<br />
<br />
===='''''[[Dechloromonas aromatica]]''' ====<br />
''Dechloromonas aromatica'' is a rod-shaped bacterium which can oxidize aromatics including benzoate, chlorobenzoate, and toluene, coupling the reaction with the reduction of oxygen, chlorate, or nitrate. It is the only organism able to oxidize benzene anaerobically. Due to the high propensity of benzene contamination, especially in ground and surface water, ''D. aromatic'' is especially useful for in situ bioremediation of this substance. [13]<br />
<br />
===='''Nitrifiers and Denitrifiers'''==== <br />
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage process that involves nitrification and denitrification. During nitrification, ammonium is oxidized to nitrite by organisms like <i>Nitrosomonas europaea</i>.Then, nitrite is further oxidized to nitrate by microbes like <i>Nitrobacter hamburgensis</i>.<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like <i>Paracoccus denitrificans </i>[2]. The result is N2 gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
===='''''[[Deinococcus radiodurans]]'''====<br />
''Deinococcus radiodurans'' is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered strain of Deinococcus radiodurans has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments [7].<br />
<br />
In anaerobic conditions, nitrate produced during ammonium oxidation is used as a terminal electron acceptor by microbes like ''[[Paracoccus denitrificans]]'' [2]. The result is dinitrogen gas. Through this process, ammonium and nitrate, two pollutants responsible for eutrophication in natural waters, are remediated.<br />
<br />
[[Image:Alcanivorax_borkumensis.png|upright=1|thumb|Alcanivorax borkumensis, Image©https://www.biotechnologie.de/BIO/Navigation/EN/Funding/foerderbeispiele,did=44848.html?view=renderPrint [25]]]<br />
<br />
===='''''[[Methylibium petroleiphilum]]'''====<br />
''Methylibium petroleiphilum'' (formally known as PM1 strain) is a bacterium capable of [https://en.wikipedia.org/wiki/Methyl_tert-butyl_ether methyl tert-butyl ether] (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source [8].<br />
<br />
===='''''[[Alcanivorax borkumensis]]'''====<br />
''Alcanivorax borkumensis'' is a marine rod-shaped bacterium which consumes hydrocarbons, such as the ones found in fuel, and produces carbon dioxide. It grows rapidly in environments damaged by oil, and has been used to aid in cleaning the more than 830,000 gallons of oil from the [https://en.wikipedia.org/wiki/Deepwater_Horizon_oil_spill Deepwater Horizon oil spill] in the Gulf of Mexico [25].<br />
<br />
==='''Fungi (Mycoremediation)'''===<br />
Current bioremediation applications primarily utilize bacteria, with comparatively few attempts to use fungi. Fungi have fundamentally important roles because of their participation in the cycling of elements through decomposition and transformation of organic and inorganic materials. These characteristics can be translated into applications for bioremediation which could break down organic compounds and reduce the risks of metals. In some cases, fungi have an advantage over bacteria not just in metabolic versatility but also their environmental resilience.They are able to oxidize a diverse amount of chemicals and survive in harsh environmental conditions such as low moisture and high concentrations of pollutants. Therefore, fungi are potentially an extremely powerful tool in soil bioremediation and some versatile species such as <b>[https://en.wikipedia.org/wiki/Wood-decay_fungus#White_rot White Rot Fungi]</b> have been a hot topic of research. [16,17]<br />
<br />
===='''Biodegradation Capacities of White rot fungi'''====<br />
Using fungi as potential treatment of contaminants began in 1985 when the white rot species Phanerochaete chrysosporium was discovered to metabolize multiple key environmental pollutants. The most important feature of these fungi is their enzymatic functional ability to metabolize complex chemicals such as lignin. Similar abilities were later discovered in other white rot fungal species. In addition, white rot fungi are highly advantageous because they degrade lignin extracellularly through its hyphal extension. This allows them to access soil contaminants that other organisms are incapable of and maximize surface area for enzymatic interaction. These inexpensive fungi can tolerate extreme environmental conditions, such as pH, temperature, and moisture content. While many microbial organisms that are used for bioremediation require pre-conditioning of the environment for them to survive in, white rot fungi can directly be applied into most systems because they degrade based upon nutrient deprivation. [18]<br />
<br />
[[Image:040504062021.jpg|right|thumb|Scanning electron micrograph (SEM) depicts ''Phanerochaete chrysosporium'' fungi; Mag. .5x]]<br />
<br />
===='''''[[Phanerochaete chrysosporium]]'''====<br />
<i>P. chrysosporium</i> was the first fungi linked to degradation of organic pollutants. Extensive research has show this it has strong potential for bioremediation in pesticides, PAHs, dioxins, carbon tetrachloride, and many other pollutants. Among fungal systems, <i>P. chrysosporium</i> has become the model for bioremediation. Other notable species of white rot fungi include <i>Pleurotus ostreatus</i> and <i>Trametes versicolor</i>. [18]<br />
<br />
===='''Bioremediation of Hydrocarbon Pollutants'''====<br />
<br />
Hydrocarbons are stored deep underground but are brought up to the surface to be transformed and utilized, primarily as an energy source known as fossil fuels. The majority of pollution currently comes from these byproducts in the form Polycyclic Aromatic Hydrocarbons (PAHs), which are xenobiotic environmental pollutants that form when carbon materials are incompletely combusted. Some of examples of PAHs include burning wood, fossil fuels, and cigarette smoke. [19,20]<br />
Currently, bioremediation is only effective for soils contaminated with low-molecular weight PAHs because of bacterial commercial use. However, fungi are effective at PAH degradation in comparison to bacteria for a few reasons. Firstly, they are capable degrading PAH’s that are high in molecular weight, bacteria in comparison are better at degrading smaller molecules. Secondly, fungi can function well in non-aqueous environments and low oxygen conditions, both are conditions where PAH’s can accumulate. Many fungi have evolved mechanisms that allow the to target specific PAHs. Fungi produce extracellular enzymes that degrade lignin, a process called mineralization the produces carbon dioxide as the end product. [19,20]<br />
<br />
===='''Remediating Metals'''====<br />
<br />
Toxic metals can enter the environment all life cycle stages of metal compound. For example, metal leaching can occur from the mining process till the disposal of metal wastes. However in nature, the mobility of metals comes from the geological processes that can be released into the soil and aquatic environments. The environmental largest risk from metal contamination comes from the relationship between metals and compounds that are inherently of incapable of being degraded by any natural procedures. The best solution to treating contamination is transporting the metals to location where they cannot produce negative environmental effects. Fungi have various ways of interacting with metals, some of the techniques are increasing or decreasing the mobility of metals, sorption, or even cellular uptake. After the metals have been absorbed the fungus, they can chemically altered to be stored or translocated through the hyphae and into various plants that participate in symbiosis. [17]<br />
<br />
===='''Pesticide Degradation'''====<br />
<br />
Pesticide accumulation is an issue of great concern among the public, because they are directly associated with food products and water supplies. There are number of technologies used for pesticide clean-up; however, these technologies are generally expensive and inefficient because they require contaminated soil to be excavated and sent to a separate storage location for processing. Bioremediation offers a potential solution that treats contaminated soil and groundwater without needing excavation. Studies show that White Rot Fungi has high promise for soil bioremediation application; however, most tests have been conducted in the lab rather than in the actual environment. This fungi demonstrates the ability to transform and mineralize specific pesticides in soil. [18]<br />
<br />
===='''Environmental Applications'''====<br />
<br />
Although fungi demonstrate significant biochemical and ecological useful qualities, they are hardly utilized for biotechnological purposes. Instead, bacteria are most commonly used because they usually produce superior results in their numerous advantages ranging from their highly specific biochemical reactions to their capabilities of breaking down pollutants efficiently [17]. Fungi are underused primarily because of the costs that come from providing oxygen to fungi in polluted environments. However, filamentous fungi could be highly valuable in situations where bacteria cannot perform. For example, fungi are useful in situations where contaminants are physically blockaded and bacteria cannot reach or in circumstances of environmental extremes such as high acidity or dryness prevent bacteria from functioning. [17]<br />
<br />
==='''[https://en.wikipedia.org/wiki/Archaea Archaea]'''===<br />
The role of archaea in bioremediation has not been studied as commonly as that of bacteria [10]. Nevertheless, numbers of researchers have shown their ability to degrade various pollutants and scientists began to discover more about their potential in participating in bioremediation. Below lists some important facts regarding archaea’s potential role in bioremediation.<br />
<br />
- Biodegradation by extreme [https://en.wikipedia.org/wiki/Halophile halophilic] archaea was not recognized widely in the past, but scientists have found out that extreme halophilic archaea have greater catabolic diversity than expected [9]<br />
<br />
- Hydrocarbon-contamination is observed in some extreme environments, including hypersaline (high salt concentration), high or low temperature, or extreme pH [10]. Archaea’s adaptation to extreme environment gives them the potential to participate in biodegradation and bioremediation in these environments; in fact, microorganisms naturally adapted to the cold environments are known to be important degraders of hydrocarbons in those environments [10].<br />
<br />
- Extreme halophilic archaea has potential to biodegrade pollutants in hypersaline environment, in which bacteria typically used in bioremediation cannot survive or function properly. [5]<br />
<br />
- Some archaea are known to be resistant to variety of antibiotics, including penicillin, cycloheximide, streptomycin, etc, which gives them great advantage in participating in bioremediation in the presence of antibiotics [5].<br />
<br />
===='''Example Studies of Archaea involved in bioremediation'''====<br />
<br />
Al-Mailem et al. examined the ability of four extreme halophilic strains (belonging to genus ''[https://en.wikipedia.org/wiki/Halobacterium Halobacterium]'', ''[https://en.wikipedia.org/wiki/Haloferax Haloferax]'', and ''[https://en.wikipedia.org/wiki/Halococcus Halococcus]'') collected from Arabian Gulf (two from soils and two from water) to biodegrade crude oil and hydrocarbons. [5]<br />
<br />
The results indicated that all four strains have ability to use various kinds of hydrocarbons as their carbon or energy source [5]. Two strains of Haloferax grew on n-alkanes with different lengths, ranging from C8 to C34, and also the aromatics including benzene, toluene, biphenyl, and naphthalene. Although Halobacterium and Halococcus strains used less variety of hydrocarbons for growth compared to the two Haloferax strains, they could still utilize short to medium length n-alkanes and aromatics including benzene, toluene, naphthalene, and p-Hydroxybenzoic acid.<br />
<br />
The research also points out the important fact that archaea has potential to carry out biodegradation in high temperature, in the range of 40-45 °C [5], which is advantageous because hydrocarbons have higher solubility and bioavailability at higher temperature [10]. The four strains studied were resistant to six different antibiotics, including penicillin, streptomycin, cycloheximide [5]. Their resistance to these antibiotics give them potential to carry out biodegradation in conditions unfavorable for bacteria.<br />
<br />
Research suggests that there are other genus of archaea also capable of biodegrading in hypersaline environments. For example, it was found that Genus ''[https://en.wikipedia.org/wiki/Halococcus Haloarcula]'' strain D1 can grow using 4-hydroxybenzoic acid as both carbon and energy source. [6]<br />
<br />
''[https://en.wikipedia.org/wiki/Halococcus Archaeglobus] fulgidus'', a [https://en.wikipedia.org/wiki/Hyperthermophile hyperthermophile] with ability to reduce sulfate, can be used to break down various aromatic hydrocarbons (Peeples, 2014).<br />
<br />
=='''Microbial Processes'''==<br />
<br />
Microorganisms use a wide range of processes to transform chemicals in their environment. In some cases, pollutants serve as the carbon and energy source for microbial growth, while in other cases, pollutants serve as the terminal electron acceptor. This manifests itself in the diverse ability of microbes to transform and degrade toxic molecules. Below, several steps and details of the microorganisms’ actions are described.<br />
<br />
==='''Factors Affecting Rates of Biodegradation'''===<br />
Biodegradation may be influenced by pH, temperature, moisture, carbon sources, soil texture, aerobic versus anaerobic conditions, the number of substituents, and the concentration of the pollutant. It is impossible, however, to make a generalization about the best universal conditions for biodegradation. What’s toxic to some microbes is a nutrient to others, what might be a damaging pH to some is beneficial to others, and so on.<br />
<br />
A greater amount of substituents will cause slower degradation in aerobic environments, but faster degradation in anaerobic ones. Chlorine makes a molecule less degradable due to steric hindrance preventing access to necessary enzymes, therefore molecules with higher chlorination are slower to degrade in aerobic conditions. High concentration of a pollutant generally results in faster rates of degradation. If the concentration drops below a threshold concentration, the enzymes may not detect it and will cease to degrade it [26].<br />
<br />
The rate at which a compound is transformed, as well as the curves that describe its transformation, is referred to as kinetics, and is affected by all factors listed above. First order kinetics (logarithmic biodegradation) is often used when the substrate concentration is high enough that microbes can easily access it, while zero-order kinetics (linear biodegradation) is often observed when the substrate concentration is very small. If the concentration falls below a threshold, the microbes can no longer transform it and the concentration levels out.<br />
<br />
Soil with small pores, especially clays, may cause biodegradation to take years due to the decrease in bioavailability. Chlorine makes a molecule less degradable due to steric hindrance preventing necessary enzymes from accessing the compound, therefore molecules with higher chlorination are slower to degrade.<br />
<br />
The power rate model gives an empirical approach to the relationship between concentration and rate of degradation:<br />
<br />
-dC/dt = kC^n<br />
<br />
C is substrate concentration, t is time, k is a rate constant for the chemical in question, and n is an appropriate parameter. The values of k and n are adjusted until a line is found to match experimental data [23].<br />
<br />
==='''Primary substrate utilization'''===<br />
<b>Primary substrate utilization</b> occurs when a microbe both transforms a substrate and uses it as an energy or carbon source. [15] An electron acceptor is required for these transformations. It can be anaerobic or aerobic, although the presence of oxygen tends to speed up reactions. This form of biodegradation can be used for treating petroleum spills or the runoff of a number of pesticides. The rate of reaction follows the guidelines in the previous section, where a higher concentration leads to a higher rate. [15]<br />
<br />
==='''Cometabolism (Secondary Substrate Utilization)'''===<br />
<b>Cometabolism</b> involves the transformation of a chemical by an organism while the organism uses a different substance as its primary energy or carbon source [14]. This is a technique often used when the substrate by itself is considered non-biodegradable, and can only be transformed with another compound. During the actual reaction degrading the substance, the organism has no net carbon or energy gain, and may even result in a product with no use to the organism or which is toxic to the cell [14]. However, it is often difficult to tell whether microorganisms have a second substrate available during their transformations [23]. Cometabolism occurs in parallel with metabolism, not instead of.<br />
<br />
A key example of cometabolism is fortuitous metabolism in the degradation of trichloroethylene, shown in the diagram below. An organic growth substrate such as propane or butane is required for the enzymatic activity that transforms TCE. [14]<br />
<br />
[[Image:Cometabolism.png|center|upright=3|thumb|Image from Kate Scow lecture, 2016]]<br />
<br />
==='''Reductive and Hydrolytic Dehalogenation'''===<br />
Chloride and other halogens are common components of pesticides and hazardous industrial wastes, and by removing them the toxic chemical can often be remediated [23]. If the halogen is replaced by a hydrogen (RCl -> RH), then it is <b>reductive dehalogenation</b>. If two halogens are replaced simultaneously, then the process is called <b>dihaloelimination</b>, although it still falls under reductive dehalogenation [14]. If the halogen is replaced by OH (RCl -> ROH) then it’s <b>hydrolytic dehalogenation</b>. In both cases, the halogen is released as its inorganic form into the environment [23].<br />
<br />
==='''Acclimation'''===<br />
An <b>acclimation period</b>, also called an <b>adaptation</b> or <b>lag period</b>, occurs when no destruction of a given chemical is observed [23]. It is caused by the microbes transitioning to their altered environment and shifting their metabolism to better suit it [14]. It can last for anywhere from hours (such as aromatic compounds in warm, oxygenated soils) to months (such as halobenzoates in anaerobic sediments) depending on the chemical in question and the environment [23]. Acclimation periods can be affected by temperature, the presence of oxygen, pH, and concentration of the substance. Although they are most often faster in warm, aerated, and fairly dry environments, there are few consistencies between what shortens or lengthens the period, even if the concentration is the same [23]. Insecticides including methyl parathion and azinphosmethyl; herbicides including 2, 4-D, MCPA, Mecoprop, TCA, and amitrole; the quaternary ammonium compound dodecyltrimethylammonium chloride; polycyclic aromatic hydrocarbons including naphthalene and anthracene; and other chemicals such as phenol, chlorobenzene, PCP, diphenyl-methane, and NTA have all been reported to have acclimation periods, and this can be of severe human concern [23]. The continued presence of these toxins extends human, plant, and animal exposure, and if the chemical is in water, it can allow the substance to flow further and impact environments distant to its site of origin before being degraded.<br />
<br />
==='''Detoxification and Activation'''===<br />
<b>Detoxication</b>, sometimes called <b>detoxification</b>, has been referred to as the “most important role of microorganisms in the transformation of pollutants” [23]. The process is the changing of a molecule into something less harmful to a species in question. There are a number of ways a molecule can be transformed, including hydrolysis, hydroxylation, dehalogenation, demethylation, methylation, and ether cleavage [23]. By breaking bonds, or adding or removing groups, the organism reduces its effect on the environment. Furthermore, although sometimes the resulting chemical is simply excreted as waste, the organism may also be able to use this new compound as a carbon source or further modifies it until it is released as CO2 [23].<br />
<br />
There are instances where the initial compound is harmless, and in fact the substance produced by microorganisms, or an intermediate in the degradation process, is a toxin [23]. This process is called activation. For this reason, it is important to test all steps of a reaction when determining how a compound is degrading. The new toxins may also be more or less mobile than its predecessor, so it can either stick around one area for extended periods of time or spread to other areas and increase damage [23]. A prevalent example of this is the dechlorination of TCE, which produces DCE (50 times more hazardous than TCE) and Vinyl Chloride (a known carcinogen) [14]. Commonly used insecticides in the past, like zinophos, trichloronat, and carbofuran, were all found to increase a soil’s toxicity with extended use [23].<br />
<br />
=='''Bioremediation treatment methods'''==<br />
In order for bioremediation to be successful, it requires sufficient proof for the degradation of contaminants. However, determining the effectiveness and completeness to reach sufficient results is one of the major issues. Natural attenuation relies on natural processes to clean up or attenuate pollution in soil and groundwater [27]. This remediation is done without human interaction, and is primarily used as a monitoring technique, to make sure more aggressive cleanup strategies are not needed. [https://en.wikipedia.org/wiki/Abiotic_component Abiotic] and [https://en.wikipedia.org/wiki/Biotic_component biotic] factors play a distinguishing factor of how effective bioremediation is.<br />
<br />
Current monitoring practices determine the disappearance of contaminants and their degradation products to regulatory levels that are monitored by toxicity testing, usually on single organisms or species to ensure there are no induced changes that may result in residual toxicity. The problem with these monitoring techniques is that the assessment of contaminants may result in an inaccurate indicator of residual toxicity[28]. Rather, studying the microbial community response may be a more comprehensive indicator of residual toxicity than a single species. Once sufficient evidence is provided, human intervention may be needed for a more effective cleanup process. <br />
<br />
There are two types of remediation that are done, ex situ: which is done by removing the contaminated soil or water and treating it outside the source, and in situ: which treatment takes place within the contaminated area. There are some treatments methods that can be either ex situ or in situ. Some techniques may deal with the mobilization of pollutants, to move them out of an area, or immobilized to keep them out of an area such as a water table.<br />
<br />
<br />
[[Image:Summary_of_bioremediation_strategies.png|center|upright=3|thumb|A comparative analysis of the different types of bioremediation. It can be used to find which remediation technique may be used in certain circumstances [12]]]<br />
<br />
<br />
[[Image:Biopiling.png|right|upright=1.5|thumb|Contaminated soil is mixed with amendments and piled on top of a liner, while a pipe with a blower controls aeration. [29]]]<br />
==='''Ex-situ'''===<br />
Ex-situ techniques are those that are applied to soil and groundwater which has been removed from the site via excavation or pumping [12]. The methods used include composting, biofilters, and biopiling. Ex-situ is used for smaller projects, primarily because larger excavation of soil is not prefered. The movement of the soil can be more detrimental by destroying the preestablish horizons in the soil.<br />
<br />
[[Image:Composting.png|right|upright=3|thumb|Composting is a very versatile remediation technique that can be used for either: a very broad treatment with many contaminants, or very specific treatment that utilizes particular microbes that target specific contaminants [30]. It can also be used to augment other treatment methods.]]<br />
<br />
===='''Biopiling'''====<br />
Excavated soils are mixed with soil amendments and placed on a treatment area. Biopiles are aerated with the use of perforated pipes and blowers in order to control the progression of biodegradation more efficiently by controlling the supply of oxygen [29], which in turn may affect other factors such as pH. This system is primarily used to remediate systems with oil and hydrocarbon contamination. The remediated soil is placed in a liner to prevent further contamination of the soil, they may also be covered with plastic to control runoff, evaporation, and [https://en.wikipedia.org/wiki/Volatilisation volatilization].<br />
<br />
===='''Composting'''====<br />
Nutrients are added to soil that is mixed to increase aeration and activation of indigenous microorganisms. Composting is done in a separate container, then when composting is complete it is incorporated into the soil. Bioremediation by the utilization of compost relies on the adsorption capabilities of organic matter and the degradation capabilities of microorganisms present[30]. Composting is recognized as as one of the most cost-effective technologies for soil bioremediation and it can be done on large and small scales. The use of composting is a very versatile technique for soil polluted by a wide range of organic pollutants and heavy metals, making it great for easier remediation involving various pollutants. The utilization of organic wastes for soil remediation is also helpful in decreasing the need for their storage and treatment. Organic matter that is generated from composting offers the benefit of improving soil quality and structure. Composting is primarily used for remediation over a longer period of time, as the nutrients for the microbes are released gradually and requrire more time compared to quicker treatments such as biostimulation.<br />
<br />
==='''In-situ'''===<br />
In-situ techniques are applied to soil and groundwater at the site with minimal disturbance[12]. These methods include biostimulation, bioleaching, biosorption, and bioventing. In-situ is preferred because it is often minimally invasive to the soil structure in comparison to ex-situ, but it can be expensive due to specialized equipment.<br />
<br />
===='''Biostimulation'''====<br />
This method involves the addition of nutrients to a polluted site in order to encourage the growth of naturally occurring chemical-degrading microorganisms[31]. Biostimulation is primarily done by the addition of various nutrients that are limited in the soil as well as electron acceptors, such as phosphorus, nitrogen and oxygen, or increasing the amount of available carbon in order to increase the population or activity of naturally occurring microorganisms. Other approaches are to optimize environmental conditions such as aeration, the addition of nutrients, altering pH and temperature control [32]. The primary advantage of biostimulation is that it is done by native microorganisms that are well-suited to the environment, and are already well distributed spatially. The challenge is delivering additives so they are readily available to the subsurface microbes.<br />
<br />
===='''Metal Bioleaching'''====<br />
Metal bioleaching is the extraction of metals from soils utilizing a biological source such as microbes. This technique was first developed to extract minerals from ores. Specific microorganisms like Thiobacillus ferrooxidans and T. thiooxidans promote the metals’ solubilization. Several species of fungi are used for bioleaching. These remediation fungi can also produced in a lab. Two prevalent fungal strains ([https://microbewiki.kenyon.edu/index.php/Aspergillus_niger Aspergillus Niger], [https://en.wikipedia.org/wiki/Penicillium_simplicissimum Penicillium Simplicissimum]) are capable of mobilizing metals such as copper, tin, aluminium, nickel, palladium, and zinc[33], which will make them much easier to remove from the soil.<br />
<br />
===='''Metal Biosorption'''====<br />
Adsorption of metals and other ions of an aqueous solution by the use of microbes. The biosorption process involves a solid phase and a liquid phase containing a dissolved species to be sorbed [34]. The process continues until equilibrium is established between the amount of solid-bound sorbate species and its portion remaining in the solution. The degree of affinity for the sorbate determines its distribution between the solid and liquid phases.<br />
<br />
Biosorption processes are very important in the environment, and has been utalized for conventional biotreatment processes. Biosorption is primarily aimed at the removal or recovery of organic and inorganic substances from solution [35]. The commercialization of biosorption technologies has been limited so far.<br />
<br />
[[Image:Bioventing.png|right|upright=2.5|thumb|Bioventing is primarily used for injecting air into specific remediation zones, adding oxygen as a readily available electron acceptor where it would otherwise be anaerobic. It can also be reversed to make a more anaerobic environment. Either technique can be applied depending on the remediating microbes would thrive in [36].]]<br />
<br />
===='''Bioventing'''====<br />
Bioventing is an In situ remediation technology that uses indigenous microorganisms to biodegrade organic constituents adsorbed to soils in the unsaturated zone[36]. The availability of oxygen generally controls the rate at which aerobic bioremediation proceeds. Bioventing is the coupling of soil venting and bioremediation. Bioventing can be successfully applied to compounds ranging from gasoline or diesel, to heavier hydrocarbons[36]. The addition of nutrients with the bioventing flow rates can achieve greater contaminant reductions than venting alone.<br />
<br />
==='''Ex-situ or In-situ'''===<br />
Some methods can be used by either in-situ or ex-situ methods. The soil or water can be removed from the contamination source and treated, or treated at the source, the method chosen can be based on many factors such as how expensive the project may be or how much contaminant needs to be treated. These methods include bioaugmentation, land farming and biofiltration.<br />
<br />
===='''Bioaugmentation'''====<br />
Bioaugmentation is the addition of non-native microorganisms that have the ability to degrade the contaminants that are recalcitrant to the indigenous microbiota. Bioaugmentation has been proven successful in cleaning organic pollutant, but still faces many environmental problems, such as the survival of strains introduced to soil[37]. The number of introduced microorganisms usually decreases shortly after soil inoculation, when the pollutant has been heavily removed. But the introduced species may linger for long periods of time, a wider use of non-natives runs the possible risk of creating a monoculture in the soil.<br />
<br />
Bioaugmentation is ideal for soil:<br />
<br />
1. With low number of microbes that are capable of degrading targeted pollutants<br />
<br />
2. Containing compounds requiring multi stepped remediation.<br />
<br />
Augmentation techniques have a great potential for [https://en.wikipedia.org/wiki/Category:Aromatic_compounds aromatic compound] remediation. The most important step in successful bioaugmentation is selection of proper microbial strains. The success of bioaugmentation strongly depends on the ability of inoculants to survive in contaminated soil, which may vary due to predation and an environment that does not identically mimic the lab it was grown in.<br />
<br />
===='''Land Farming'''====<br />
Contaminated soil is mixed with amendments such as nutrients, and then they are tilled into the earth, or the contaminated soil is applied into lined beds and periodically turned over or tilled to aerate the waste [38]. The topmost layer is the area of concentration for this method, so it is not ideal for deeper remediation. Land farming differs from composting because it actually incorporates contaminated soil into soil that is uncontaminated [38]. The higher zone of remediation will typically contain primarily lighter hydrocarbons that can be volatilized. The material is periodically tilled for aeration to hasten remediation of any nutrients and allow more oxygen to act as electron acceptors, as well as allowing volatilization to occur. Contaminants are degraded, transformed, and immobilized by microbiological processes and oxidation. Soil conditions are controlled to optimize the rate of contaminant degradation, moisture content, frequency of aeration, and pH are all conditions that may be controlled [38]. <br />
<br />
[[Image:Biofilter.png|right|upright=1.5|thumb|The application of a micro-algal/bacterial biofilter in the primary outflow of soil water [39]]]<br />
<br />
===='''Biofilter'''====<br />
Biofilters are primarily used for the filtration of contaminated groundwater in the soil. Biofilters can be used above soil, where the water will be pumped aboveground for treatment, or a filter can be placed in the soil near an outflow. A micro-algal/bacterial biofilter can be used for the detoxification of copper and cadmium metal wastes [22]. Biofilters have been used in larger industry environments to treat contaminated outflow of water. [https://en.wikipedia.org/wiki/Chromobacterium_violaceum Chromobacterium violaceum], is used to treat water and soil contaminated with silver nanoparticles, reducing its concentration.<br />
<br />
=='''Bioremediation Synopsis'''==<br />
<br />
==='''Advantages'''===<br />
1. Bioremediation is a publicly accepted treatment of polluted soil because it is based upon natural processes. Microbes that metabolize contaminants increase in population when the contaminant is present. The inverse is true, degradation of the contaminant causes population declines of those microbes. Usually the products from treatment are harmless; such as carbon dioxide, water, and cellular biomass. [12]<br />
<br />
2. Bioremediation is theoretically meant to completely degrade a wide range of pollutants into harmless products on site. This removes the risks involved with transportation for treatment and elimination of contaminated substances. [12]<br />
<br />
3. Bioremediation is meant to completely eliminate specific pollutants without the risks of transferring contaminants from one environmental medium to another (land, air, water). [12]<br />
<br />
4. Bioremediation can be a cheaper alternative to other technologies used for pollution mitigation. [12]<br />
<br />
==='''Disadvantages'''===<br />
1. Only biodegradable compounds are capable of undergoing bioremediation. Not every compound is capable of fully degrading quickly. [12]<br />
<br />
2. The products of biodegradation may potentially be even more persistent or toxic than the original contaminant. [12]<br />
<br />
3. Biological functions are usually extremely specific and require the presence of microbes that are capable of metabolizing the contaminants. In order for the correct microbes to be present, the appropriate environmental conditions, levels of nutrients, and contaminants need to be met. [12]<br />
<br />
4. Scaling up the size of studies from small initial studies to commercial-scale field operations is difficult.[12]<br />
<br />
5. The real environment contains contaminants that are mixed, unevenly distributed, and in different phases (solid, liquid, gas). More research needs to be completed to create technologies that can adapt. [12]<br />
<br />
6. Compared to other treatment technologies, bioremediation often takes more time. [12]<br />
<br />
7. Problems with ensuring adequate contact between the microbes and the contaminant. preferential pathway and soil structure can leave uncertainty in remediation dispersal.[12]<br />
<br />
=='''References'''== <br />
<br />
1. [http://www.epa.gov/tio/download/citizens/bioremediation.pdf United States Environmental Protection Agency, "A Citizen's Guide to Bioremediation" 2001.]<br />
<br />
2. [http://www.google.com/patents?id=F9UZAAAAEBAJ Nitrification and Denitrification Wastewater Treatment. No. 5536407. 16 July 1996.]<br />
<br />
3. Sylvia, D. M., Fuhrmann, J.F., Hartel, P.G., and D.A Zuberer (2005). "Principles and Applications of Soil Microbiology." New Jersey, Pearson Education Inc.<br />
<br />
4. Tiedje, J. M. (1993). Bioremediation from an ecological perspective. In situ bioremediation: When does it work, 110-120. <br />
<br />
5. Al-Mailem, D. M., Sorkhoh, N. A., Al-Awadhi, H., Eliyas, M., & Radwan, S. S. (2010). Biodegradation of crude oil and pure hydrocarbons by extreme halophilic archaea from hypersaline coasts of the Arabian Gulf. Extremophiles, 14(3), 321-328. doi: 10.1007/s00792-010-0312-9<br />
<br />
6. Fairley, D. J., Boyd, D. R., Sharma, N. D., Allen, C. C., Morgan, P., & Larkin, M. J. (2002). Aerobic metabolism of 4-hydroxybenzoic acid in Archaea via an unusual pathway involving an intramolecular migration (NIH shift). Appl Environ Microbiol, 68(12), 6246-6255.<br />
<br />
7. Hassam, Sara C. McFarlan, James K. Fredrickson, Kenneth W. Minton, Min Zhai, Lawrence P. Wackett, and Michael J. Daly. "Engineering Deinococcus radiodurans for metal remediation in radioactive mixed waste environments ." biotech.nature.com 18 (2000): 85-90. 2 Mar. 2008<br />
<br />
8. Jessica R., Corinne E. Ackerman, and Kate M. Scow. "Biodegradation of Methyl Tert-Butyl Ether by a Bacterial Pure Culture." Appl Environ Microbiol. 11 (1999): 4788-4792. 2 Mar. 2008<br />
<br />
9. Le Borgne, S., Paniagua, D., & Vazquez-Duhalt, R. (2008). Biodegradation of organic pollutants by halophilic bacteria and archaea. J Mol Microbiol Biotechnol, 15(2-3), 74-92. doi: 10.1159/000121323<br />
<br />
10. Margesin, R., & Schinner, F. (2001). Biodegradation and biore<br />
mediation of hydrocarbons in extreme environments. Appl Microbiol Biotechnol, 56(5-6), 650-663.<br />
<br />
11. Kang, J. W. (2014). Removing environmental organic pollutants with bioremediation and phytoremediation. Biotechnol Lett, 36(6), 1129-1139. doi: 10.1007/s10529-014-1466-9<br />
<br />
12. Vidali, M. (2001). Bioremediation. an overview. Pure and Applied Chemistry, 73(7), 1163-1172. <br />
<br />
13. "Dechloromonas Aromatica RCB." JGI Genome Portal, 16 Feb. 2016. [http://genome.jgi.doe.gov/decar/decar.home.html http://genome.jgi.doe.gov/decar/decar.home.html]<br />
<br />
14. King, R. Barry, John K. Sheldon, and GIlbert M. Long. (1998). Practical Environmental Bioremediation: The Field Guide. 2nd ed. Boca Raton: CRC, 1998.<br />
<br />
15. "Manual, Bioventing Principles and Practices." United States Environmental Protection Agency I (1995)<br />
<br />
16. Gadd, G. M. (Ed.). (2001). Fungi in bioremediation (No. 23). Cambridge University Press<br />
<br />
17. Harms, H., Schlosser, D., & Wick, L. Y. (2011). Untapped potential: exploiting fungi in bioremediation of hazardous chemicals. Nature Reviews Microbiology, 9(3), 177-192<br />
<br />
18. Fragoeiro, S. (2005). Use of fungi in bioremediation of pesticides. Applied Mycology Group Institute of Bioscience and Technology. Cranfield University<br />
<br />
19. Singh, H. (2006). Mycoremediation: fungal bioremediation. John Wiley & Sons. 283-285<br />
<br />
20. Norton, J. M. (2012). Fungi for Bioremediation of Hydrocarbon Pollutants. University of Hawai’i at Hilo. Hohonu, 10, 18-21<br />
<br />
21. Dixit, Ruchita, Emptyyn Wasiullah, Deepti Malaviya, Kuppusamy Pandiyan, Udai Singh, Asha Sahu, Renu Shukla, Bhanu Singh, Jai Rai, Pawan Sharma, Harshad Lade, and Diby Paul. "Bioremediation of Heavy Metals from Soil and Aquatic Environment: An Overview of Principles and Criteria of Fundamental Processes." Sustainability 7.2 (2015): 2189-212. Print.<br />
<br />
22. Bio-filters for Edge-of-Field Water Quality Management. (n.d.). Retrieved February 24, 2016, from [http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html http://agronomyday.cropsci.illinois.edu/2000/bio-filters/index.html]<br />
<br />
23. Alexander, Martin. (1999). Biodegradation and Bioremediation. San Diego: Academic Print. <br />
<br />
24. Litchfield, Carol. "Thirty Years and Counting: Bioremediation in Its Prime?" BioScience 55.3 (2005): 273.<br />
<br />
25. Biello, David. "Slick Solution: How Microbes Will Clean Up the Deepwater Horizon Oil Spill." Scientific American (n.d.): n. pag. 25 May 2010. <br />
<br />
26. Scow, Kate. “Lectures in Soil Microbiology.” UC Davis, Winter 2016.<br />
<br />
27 CLU-IN | Technologies Remediation About Remediation Technologies Natural Attenuation Overview. (n.d.). Retrieved February 24, 2016, from https://clu-in.org/techfocus/default.focus/sec/Natural_Attenuation/cat/Overview/<br />
<br />
28. Chauhan, Ashok K., and A. Varma. A Textbook of Molecular Biotechnology. New Delhi: I.K. International Pub. House, 2009. Print.<br />
<br />
29. Biopiles. (n.d.). Retrieved March 13, 2016, from [http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html http://www.navfac.navy.mil/navfac_worldwide/specialty_centers/exwc/products_and_services/ev/erb/tech/rem/biopiles.html]<br />
<br />
30. Chen, M., Xu, P., Zeng, G., Yang, C., Huang, D., & Zhang, J. (2015). Bioremediation of soils contaminated with polycyclic aromatic hydrocarbons, petroleum, pesticides, chlorophenols and heavy metals by composting: Applications, microbes and future research needs. Biotechnology Advances, 33(6, Part 1), 745–755.<br />
<br />
31. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. Retrieved March 13, 2016, from [http://www.sciencedirect.com/science/article/pii/S0944501309000585 http://www.sciencedirect.com/science/article/pii/S0944501309000585]<br />
<br />
32. Bioremediation, Biostimulation and Bioaugmention: A Review. (n.d.). Retrieved March 13, 2016, from http://pubs.sciepub.com/ijebb/3/1/5/<br />
<br />
33. Sulfur Oxides—Advances in Research and Application: 2013 Edition<br />
<br />
34. Fomina, M., & Gadd, G. M. (2014). Biosorption: current perspectives on concept, definition and application. Bioresource Technology, 160, 3–14. Retrieved February 24, 2016, from [https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application https://www.researchgate.net/publication/259955406_Biosorption_Current_perspectives_on_concept_definition_and_application]<br />
<br />
35. Kotrba, Pavel, Martina Mackova, and Tomas Macek. (2011). Microbial Biosorption of Metals. Dordrecht: Springer Science Business Media Print.<br />
<br />
36. Bioventing » Water and Soil Bio-Remediation. (n.d.). Retrieved February 24, 2016, from [http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing http://waterandsoilbioremediation.com/index.php/in-situ-remediation-methods/bioventing]<br />
<br />
37. Mrozik, A., & Piotrowska-Seget, Z. (2010). Bioaugmentation as a strategy for cleaning up of soils contaminated with aromatic compounds. Microbiological Research, 165(5), 363–375. <br />
<br />
38. Land Farming. (n.d.). Retrieved March 13, 2016, from http://www.cpeo.org/techtree/ttdescript/lanfarm.htm<br />
<br />
<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Geomicrobiology&diff=120999
Geomicrobiology
2016-03-22T01:39:57Z
<p>Kmscow: /* Key processes of geomicrobiology */</p>
<hr />
<div>{{Curated}}<br />
[[File:Desulfovibrio_desulfuricans.jpeg|300px|thumb|right|Scanning electron micrograph of <i>Desulfovibrio desulfricans</i>, a Gram-negative sulfate-reducing bacteria. [http://www.lbl.gov/Publications/Currents/Archive/Apr-30-2004.html Image Source]]]Geomicrobiology is the interdisciplinary study of the interactions of microorganisms with earth materials. It concerns the role of microbes in geological and geochemical processes. The field of geomicrobiology has revealed new insights into the intersection of life with the physical and chemical composition of Earth’s surface. Soil microbes play a large role in the transformations of elements and minerals <ref name=USGS>U.S. Geological Survey http://microbiology.usgs.gov/geomicrobiology.html</ref>. The interactions between microbes and elements and minerals is especially important in the near surface environment known as Earth’s Critical Zone, where biotic and abiotic factors regulate the conditions for life-sustaining resources. Virtually all elements can be transformed by microbes and many elemental cycles depend on soil microbes <ref name=Gadd>Gadd, G. M. 2010. Metals, minerals and microbes: geomicrobiology and bioremediation. Microbiology, 156(3), 609-643.</ref>. The relationships between microorganisms and these inorganic compounds have important implications for both the surrounding natural environment and human use. Soil microbes can be used by humans in mineral resource extraction and bioremediation. <!-- Introduction. Maybe add image here --><br />
<br />
==Key processes of geomicrobiology==<br />
Geomicrobiological processes are relevant in many natural environments including aquifers, geological and geochemical processes, extreme environments (acidic, extreme temperatures and saline conditions) and metal ion reduction.<br />
<br />
Changes in the mobility and availability of metal is governed by redox reactions, complexation by metabolites and siderophores, and methylation. Immobilization transforms metals and other inorganic substances into microbial biomass. [http://chemwiki.ucdavis.edu/Core/Organic_Chemistry/Reactions/Oxidation_and_Reduction_Reactions Oxidation and reduction] reactions are used by microbes to gain energy during respiration and photosynthesis, resulting in the immobilization and mineralization of metals and nutrients. Redox reactions also drive the nitrogen cycle, and reduce toxic compounds <ref name=Gadd /> Conjugation reactions are another process by which toxic chemicals are converted to polar components. These conjugated substances are then made unavailable by immobilization or they become recalcitrant and accumulate in the food web <ref name=Hall>Hall , J.C., Wickenden ,J.S., Kerrm Y. F. Yau. 2009. Biochemical Conjugation of Pesticides in Plants and Microorganisms: An Overview of Similarities and Divergences. Pesticide Biotransformation in Plants and Microorganisms. 5, 89-118.</ref><br />
===Weathering===<br />
<br />
Weathering plays an important role on Earth ecosystems and is important for the release of nutrients into the biosphere as a result of rock dissolution or the regulation of long-term climate by the consumption of atmospheric carbon dioxide from silicate alterations. Weathering has been considered a strictly physical and chemical process. Nonetheless, many weathering processes can be affected by the presence of microbial communities. All types of rocks are susceptible to microbial weathering, including siliceous and calcareous rocks. In general microbial weathering is due to the formation of organic acids or the production of metal-chelating siderophores on the surface of rock or minerals. Other processes include oxidative or reductive conditions of metals on rocks or minerals <ref name=Herrera>Herrera, A., Cockell, C. S., Self, S., Blaxter, M., Reitner, J., Arp, G., Drose, W., Thorsteinsson, T. , Tindle, A. G. 2008. Bacterial Colonization and Weathering of Terrestrial Obsidian in Iceland. Geomicro. J. 25: 25-37.</ref>.<br />
<br />
===Precipitation of carbonates and phosphates===<br />
<br />
The influence of bacteria in mineral precipitation has been described in different natural habitats including aquatic environments and terrestrial systems. Carbonate precipitation is controlled by bacterial processes and one of the mechanisms proposed is the oxidation of ammonium by ammonium oxidizers which decreases environment pH. Other authors report that the matrix of extracellular polymeric secretions (EPS) affects mineral precipitation Simultaneous precipitation of struvite (MgNH4PO4•6H2O) associated with bacterial activity has been described in vitro carbonate precipitation experiments as well as carbonate and phosphate precipitation by bacteria from saline soils <ref name=Delgado>Delgado, G. Delgado, R., Parraga, J., Rivadeneyra, M. A., Aranda, V. 2008. Precipitation of Carbonates and Phosphates by Bacteria in Extract Solutions from a Semi-arid Saline Soil. Influence of Ca2+ and Mg2+ Concentrations and Mg2+/Ca2+ Molar Ratio in Biomineralization. Geomicro. J. 25:1–13.</ref>.<br />
<br />
==Examples of microbial metabolism of Minerals and inorganic substances==<br />
[[File:Mineral_Metabolism.gif|thumb|300px|right|A comprehensive depiction of the effects of microbial mineral metabolism [http://mic.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.037143-0 Image Source]]]<br />
{| class="wikitable" border="1" <br />
!colspan="2"|Table of Microbial Roles for Representative Elements (Taken from Gadd 2010)[2]<br />
|- style="text-align:center"<br />
|<b>Elements</b> || <b>Microbial roles in elemental cycles</b><br />
|-<br />
|Phosphorus (P) || Dissolution of inorganic phosphate minerals in soils; Decomposition of organic phosphorus; Release of organically bound phosphorus by use of phosphatase enzymes; Assimilation and transformation of inorganic phosphorus species; Transformations of soil organic phosphorus; Phosphorus transfer to plants by mycorrhizae<br />
|-<br />
|Sulfur (S) || Degradation of organic sulfur compounds; Sulfur transformations; Assimilation of organic and inorganic sulfur; Sulfidogenesis, Sulfur accumulation, SO<sub>4</sub><sup>2-</sup> reduction and assimilation; Oxidation of H2S to S(0) and reduction of S(0) to H<sub>2</sub>S<br />
|-<br />
|Iron (Fe) || Bioweathering of iron-containing minerals in soil; Iron solubilization by siderophores; Fe(III) reduction to Fe(II); Fe(II) oxidation to Fe(III); Iron biomineralization to oxides, hydroxides, carbonates, sulfides, etc. Metal sorption to iron oxides<br />
|-<br />
|Manganese (Mn) || Mn(II) oxidation and immobilization as Mn(IV) oxides; Bioaccumulation of Manganese oxides to surfaces and exopolymers; contribution to desert varnish formation; biosorption; accumulation; intracellular precipitation; biomineralization; metal sorption to manganese oxides<br />
|-<br />
|Magnesium (Mg), Calcium (Ca), Nickel (Ni), Zinc (Zn), Cadmium (Cd), and Strontium (Sr) || Bioweathering of minerals in soil; biosorption; uptake and accumulation; bioprecipitation of oxalates, sulfides, carbonate, phosphates, etc. <br />
|-<br />
|Copper (Cu) || Mobilization from copper containing minerals in soils; CuS formation; biosorption; uptake and accumulation; bioprecipitation<br />
|-<br />
|Mercury (Hg) || Biomethylation; Reduction of Hg(III) to Hg(0); Oxidation of Hg(0) to Hg(II). Mercury volatilization as Hg(0); degradation of organomercurials; biosorption; accumulation<br />
|-<br />
|Selenium (Se) || Reductive transformation of Se (VI) to Se(IV) to Se(0); Se(0) oxidation; Biomethylation and demethylation; assimilation of organic and inorganic Se compounds<br />
|}<br />
<br />
===Manganese===<br />
In soil, Mn typically exists as bound to metal or as an oxide, and is most abundant as MnO2.[2] Of the several oxidation states Mn has in nature, only three (II, III, and IV) are biologically important. Other than as a component of enzymes in living organisms, Mn also serves as a source of energy (i.e. as an electron acceptor and donor). Furthermore, of the three biologically important oxidation states, only Mn (II) is soluble, Mn-reduction may also serve to extract mineral Mn from soil to fulfill nutritional needs <ref name=Das>Das, A. P., Sukla, L. B., Pradhan, N., & Nayak, S. 2011. Manganese biomining: a review.Bioresource technology, 102(16), 7381-7387.</ref> <br />
<br />
Mn(II)-oxidizing bacteria are a diverse group found in almost all environments. These bacteria are up to 5 orders of magnitude faster than abiotic reactions in the production of Mn oxides which have an amorphous structure with a high surface area. The mechanism of Mn(II) oxidation by these bacteria is not clear, although recent outcomes from studies with Bacillus sp. strain SG-1 have shown that a Mn(III) is an intermediate in the final oxidation of Mn(II) through enzymatic activity <ref name=Murray>Murray, K.J., Tebo, B.M. 2007. Cr(III) Is Indirectly Oxidized by the Mn(II)-Oxidizing Bacterium Bacillus sp. Strain SG-1. Environ. Sci. Technol., 41, 528-533.</ref><br />
<br />
===Uranium-Nitrate relationship===<br />
Uranium occurs naturally in soils, and is mined for use in energy and weapon production. Contamination of aquifers by Uranium produced from nuclear weapons and fuel is becoming a real problem in different parts of the world. These aquifers are generally oxidized, therefore uranium predominantly exists in the reactive state U(VI). The U(VI) is often coupled with carbonate making the compound quite soluble and easy to leach.<br />
Uranium reduction occurs under anaerobic conditions with Fe(III) and/or sulfate reduction. The biogeochemical processes that occur after uranium reduction are poorly understood. Recent research has shown that the addition of nitrate (a common co-contaminant with uranium) to U(IV)-containing sediments leads to the oxidation and remobilization of U(IV). Microorganisms responsible in this process are believed to be associated with nitrate dependent Fe(II)-oxidizing microorganisms <ref name=Senko>Senko, J. M., Suflita, J. M., Krumholz, L. R. 2005. Geochemical Controls on Microbial Nitrate-Dependent U(IV) Oxidation. Geomicro. J. 22:371-378.</ref><br />
<br />
===Mineral Cycles Involving Microbes===<br />
Microbes are involved in and drive many geochemical cycles. Among them, [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle the nitrogen cycle], the phosphorus cycle, the sulfur cycle, and the iron cycle.<br />
<br />
====Phosphorus Cycle====<br />
[[Image:Phosphorus_Cycle.jpeg|thumb|350px|right|The Phosphorus Cycle, from a soil perspective. [https://en.wikipedia.org/wiki/File:Phosphorus_Cycle_copy.jpg Image Source]]]<br />
Phosphorus is an important nutrient for all living organisms. Most phosphorus found in living systems are in the form of inorganic phosphate. On Earth virtually all known phosphorus exists in the +5 oxidation state. Nonetheless, there are also two additional known forms: phosphonates (+3) and phosphonates (+1). Microbes immobilize, mineralize, and solubilize phosphorus <ref name=EnvLitPhosphorus>The Environmental Literacy Council. Phosphorus cycle. http://enviroliteracy.org/air-climate-weather/biogeochemical-cycles/phosphorus-cycle/</ref>.<br />
<br />
The phosphorus cycle does not include a gas phase, and thus very little phosphorus makes its way into the atmosphere (small amounts of phosphoric acid can make their way into the atmosphere to contribute to acid rain). The phosphorus cycle begins in sedimentary rock and is released into the soil and water through weathering. Microbes (and plants, as well) assist in the solubilization of mineral phosphorus in soil through the production of acids to lower the soil pH, as well as the secretion of chelating agents to bind the metal ions that would bind to the phosphate. These soluble phosphates are immobilized by living organisms, and can be produced through mineralization reactions <ref name=Sylvia>Sylvia, D. M., Hartel, P. G., Fuhrmann, J. J., Zuberer, D. A. Principles of Applications of Soil Microbiology. 2nd edition. 2005. Pearson Prentice Hall.</ref>.<br />
<br />
<i>Actinomycetes</i>, <i>Pseudomonas</i>, and <i>Bacillus</i> species are among the bacteria that solubilize inorganic phosphorus. <i>Aspergillus</i> and <i>Penicillium</i> are among the fungi that solubilize phosphorus. Additionally in the rhizosphere, mycorrhizal symbioses between fungi and plants greatly increase phosphorus uptake by plants. Some of the fungi involved are <i>Zygomycetes</i> in the order of <i>Mucorales</i> and <i>Ascomycetes</i> <ref name=Rosling />.<br />
<br />
Microbes also increase the mineralization process of phosphorous in soil by using phosphatase enzymes to hydrolyze organic phosphorus and convert it back to its inorganic form <ref name=Sylvia />.<br />
<br />
====Sulfur Cycle====<br />
[[File:Sulfur.jpg|thumb|350px|left|The sulfur cycle. This example show sulfur cycling in the Everglades. [http://pubs.usgs.gov/fs/fs109-03/fs109-03.html Image Source]]]<br />
Most sulfur is contained in rock, with small amounts in the atmosphere and water. In soil, however, most sulfur is organic, as part of an organism; the addition of new sulfur into the ecosystem is through the weathering of sulfur-containing stone. Thus, the sulfur cycle in soil is driven by microorganisms. Some of the microbially-induced transformations sulfur undergoes are: reduction and oxidation, mineralization and immobilization, and volatilization. In short, sulfur bacteria convert mineral sulfur into soluble forms, which are then taken up into microbial biomass, or converted into other mineral forms. Sulfur exits the soil through leaching or volatilization of sulfur <ref name=Klotz>Klotz, M. G. (2011). BryantDA and Hanson TE (2011) The microbial sulfurcycle. The microbial sulfur cycle, 5.</ref>.<br />
<br />
As an elemental substance, sulfur is important in that it has a wide range of stable redox states. Inorganic sulfur can be used as a terminal electron acceptor for energy. Sulfate-reducing bacteria are comprised of several groups of bacteria that use sulfate as an oxidizing agent, reducing it to sulfide. Most sulfate-reducing bacteria can also use other oxidized sulfur compounds such as sulfite and thiosulfate, or elemental sulfur. This type of metabolism is called dissimilation, since sulfur is not incorporated or assimilated into any organic compounds <ref name=Campbell>Campbell, B. J., Engel, A. S., Porter, M. L., & Takai, K. (2006). The versatile &epsi;-proteobacteria: key players in sulphidic habitats. Nature Reviews Microbiology, 4(6), 458-468.</ref>.<br />
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Anaerobic sulfur reducing bacteria reduce sulfate ions to hydrogen sulfide. These sulfur reducing bacteria are heterotrophic organisms that use sulfur ions as terminal electron acceptors in their metabolism. These organisms include bacteria of the genera <i>Desulfovibrio</i> and <i>Desulfotomaculum</i>.<br />
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The bacterial genera <i>Thiobacillus</i>, <i>Sulfolobus</i>, and <i>Thiomicrospira</i> oxidize sulfur to produce sulfuric acid as a byproduct. These bacteria accelerate the generation of [http://technology.infomine.com/enviromine/ard/Microorganisms/roleof.htm acid rock drainage] (ARD) from pyritic and pyrrhotitic rocks. <i>Acidithiobacillus thiooxidans</i> also produces sulfuric acid and, in conjunction with others of the same genus, is currently used in a mining technique called bioleaching whereby metals are extracted from their ores through oxidation. The bacteria are used as catalysts in the oxidation reaction. Sulfate-reducing bacteria have been considered for remediating water contamination produced by other bacteria from acid mine tailings.<br />
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====Iron Cycle====<br />
[[File:Mineral_Cycle.jpg|thumb|300px|right|A representation of the general metal cycle. The iron cycle, in specific, is known as the ferrous wheel -- a cycle where Fe(III) is microbially reduced into Fe(II), which is then chemically or microbially oxidized back into Fe(III). The reduction of Fe(III) occurs through anaerobic respiration, where iron is used as a terminal electron acceptor. The oxidation of Fe(II) occurs through several pathways, and can occur in both aerobic and anaerobic conditions. [http://www.lifesci.dundee.ac.uk/people/geoff-gadd Image Source]]]<br />
After oxygen, iron is the most abundant redox-active element in the Earth’s crust. However, it is not easily available in its preferred state <ref name=Emerson>Emerson, D., Roden, E., Twining, B.S. 2012. The microbial ferrous wheel: iron cycling in terrestrial, freshwater, and marine environments. Frontiers in Microbiolog</ref>. The availability of iron depends on the aerobic condition and pH level of the soil. Under aerobic conditions, iron readily binds with oxygen, forming insoluble (and therefore non-bioavailable) iron oxides. However, at low pH, both common forms of Fe (II, III) are readily soluble. In terms of mineralization and solubilization, microbes accomplish both through redox reactions <ref name=Colombo>Colombo, C., Palumbo, G., He, J. Z., Pinton, R., & Cesco, S. (2014). Review on iron availability in soil: interaction of Fe minerals, plants, and microbes.Journal of soils and sediments, 14(3), 538-548.</ref>. Iron can be mineralized, immobilized, oxidized, and reduced.<br />
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Fe(III) is an important electron acceptor in organic matter decomposition in saturated soil. As this form of iron is soluble, the iron leaves the soil; this causes gleying of the soil (the color of the soil becomes grey or blue), as the color of the sand’s sand content becomes dominant. Fe(III) reduction also corrodes steel which causes many industrial problems. One of the most common iron redox reactions in anaerobic soils is the mineralization of iron through binding sulfur to iron, producing pyrite <ref name=Colombo />. Furthermore, in these flooded conditions, iron is also used as an energy source; anaerobic iron-reducing bacteria use iron as an terminal electron acceptor in respiration <ref name=Lovley>Lovley, D. R., Holmes, D. E., & Nevin, K. P. (2004). Dissimilatory fe (iii) and mn (iv) reduction.Advances in microbial physiology, 49, 219-286.</ref>.<br />
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Siderophores are iron transporting ligands that are produced by bacteria and fungi that reduce Fe(III) to Fe(II). When microbes experience iron deficiency, siderophores are secreted into the environment to capture iron. The solubilized iron is then taken up by the microbe through a siderophore receptor protein on the outer cell membrane. Iron is the only known essential element for which these specific organic shuttles operate.<br />
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==Examples of Geomicrobiology Interactions in nature==<br />
===Rhizosphere===<br />
In terms of geobiology, microbes in the rhizosphere serve to alter soil concentration of metals and other minerals In terms of geobiology, microbes in the rhizosphere serve to alter soil concentration of metals and other minerals to assist plants in a symbiotic manner, both indirectly and directly. Low concentrations of bioavailable minerals activate and stimulate the activity of these microorganisms in these biogeochemical processes. Microbes capable of generating these processes, altering the mineral concentration and composition of the rhizosphere soil, include those part of [https://microbewiki.kenyon.edu/index.php/Nitrogen_Cycle the nitrogen cycle], siderophore-producing microbes, and phosphorus-solubilizing microorganisms. <br />
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Iron, as an element, is relatively abundant in soil; however, most of that iron is sequestered in various inorganic iron compounds inaccessible to both plants and microbes <ref name="Colombo" />. Iron deficiency stimulates the production and secretion of siderophores <ref name="Saha">Saha, R., Saha, N., Donofrio, R. S., & Bestervelt, L. L. (2013). Microbial siderophores: a mini review. Journal of basic microbiology, 53(4), 303-317.</ref>. Microbial siderophores are chelating agents (organic compounds that can bind to metal ions) secreted by bacteria and fungi, used to capture free iron ions in the soil and, as highly soluble substances, transport that iron to the microorganisms. More importantly from a geochemical point of view, siderophores can also increase the concentration of iron ions in the soil through stimulating the release of inorganic iron (usually from iron oxide crystals, which trap most of the inaccessible iron in the soil). There are three general categories of methods used to promote this release: direct reaction at the surface of the iron oxide crystal; ligand-promoted exchange of iron ions; and the protonation of coordinating partners of iron ions to free the ions <ref name=Kraemer>Kraemer, S. M. (2004). Iron oxide dissolution and solubility in the presence of siderophores. Aquatic sciences, 66(1), 3-18.</ref>. <br />
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Inorganic phosphorus in soil is usually complexed with metal ions, a reaction that happens very fast. For example, the spike in concentration of soluble (bioavailable) phosphorus from addition of chemical fertilizers decreases to normal levels in a few days <ref name="Sindhu">Sindhu, S. S., Phour, M., Choudhary, S. R., & Chaudhary, D. (2014). Phosphorus Cycling: prospects of using rhizosphere microorganisms for improving phosphorus nutrition of plants. In Geomicrobiology and biogeochemistry (pp. 199-237). Springer Berlin Heidelberg.</ref>. This complexation is dependent on many factors, among them, the pH of the soil. Thus, the commonly accepted method for microbial-caused dissolution of phosphorus is through the activity of low molecular weight (i.e. highly soluble) organic acids <ref name=Khan>Khan, M. S., Zaidi, A., & Ahmad, E. (2014). Mechanism of phosphate solubilization and physiological functions of phosphate-solubilizing microorganisms. In Phosphate Solubilizing Microorganisms (pp. 31-62). Springer International Publishing.</ref>. Though the exact mechanisms are still unknown, the accepted theory is that carboxylic acids act as chelating agents for the metal ions complexed with phosphorus, preventing precipitation of the free phosphorus ions released with a drop of pH <ref name=Sindhu />. That is, the metal phosphorus complexes were disrupted by a drop in pH induced by the organic acids, the carboxylic acids caught the released metal ions, and therefore phosphorus ions was released into solution, where plants and microbes can uptake the phosphorus.<br />
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====Volcanic Hot Springs====<br />
[[File:Sulfur_Rocks.jpg|thumb|200px|right| Sulfur deposits by microbes at a hot spring. [http://www.lpi.usra.edu/science/treiman/greatdesert/workshop/sulphursprings/ Image Source]]]<br />
Thermophilic Microbes occur in volcanic hot springs around the world. Sulfur is an element commonly found in and around hot springs. The spring water is rich in sulfides that leach out of the rocks and soil, which is then oxidized by the microbes. The microbes strip electrons from the sulfide to use in their metabolic pathways, leaving behind sulfur. Other kinds of bacteria can oxidize sulfide or sulfur to sulfate, and form sulfuric acid. This is why many hot springs are acidic. <br />
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Different kinds of metabolic lifestyles can be found in different volcanic environments. For example, in the Kamchatka Hot Springs, lithotrophic methanogenesis was found to occur at alkaline conditions with a neutral pH. Sulfidogenesis occurred at neutral and acidic pH, and lithotrophic acetogenesis occurred over the entire range of pH. Lithotrophic reduction of Fe(III) also occurred over the entire range of pH. In these conditions, the only source of metabolic substrate comes from volcanic gases and methanogenesis is the process most commonly associated with hot spring microbial activity <ref name="Bonch">Bonch-Osmolovskaya, E. A., Miroshnichenko, M. L., Slobodkin, A. I., Sokolova, T. G., Karpov, G. A., Kostrikina, N. A., ... & Pimenov, N. V. (1999). Biodiversity of anaerobic lithotrophic prokaryotes in terrestrial hot springs of Kamchatka. MICROBIOLOGY-AIBS-C/C OF MIKROBIOLOGIIA, 68, 343-351.</ref>.<br />
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==Examples of Applied Geomicrobiology==<br />
Geomicrobiology has many useful applications for humans. Many microbes are involved with breaking down toxic compounds (see [https://microbewiki.kenyon.edu/index.php/Bioremediation Bioremediation]), mineral extraction, and the manufacturing of valuable minerals and compounds.<br />
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===Space exploration===<br />
Geomicrobiology is being considered an important tool in the exploration and settlement of space because microorganisms can be used for a variety of uses, such as life support and waste management, energy production, extraction of industrially useful minerals, and the search for life using microbe-mineral interactions. Below are a couple of examples of how humans can use processes that are studied on earth to help explore and colonize space.<br />
====Life Support and Waste Management====<br />
[[Image:Melissaloop.jpeg|thumb|300px|right|General concept of the MELISSA loop for advanced life support [http://ecls.esa.int/ecls/?p=newmelissaloop Image Source]]]<br />
The biggest use of microbes in space exploration and settlement would be the use of photosynthetic organisms to convert water and carbon dioxide into oxygen and food in what is known as a biological life support system. Additionally the waste from these processes could be used to make more carbon dioxide, recycling the nutrients, water and carbon. The Micro Ecological Life Support System Alternative (MELiSSA), designed by European Space Agency, is a model system of an advance biological life support system that would be based on different species of microbes and plants. Consisting of many bioreactors and plant chambers, MELiSSA would break down the organic waste from the crew and non-edible parts of the higher plants <ref name="Godia">Godia, F., Albiol, J., Montesinos, J. L., Pérez, J., Creus, N., Cabello, F., ... & Lasseur, C. (2002). MELISSA: a loop of interconnected bioreactors to develop life support in space. Journal of biotechnology, 99(3), 319-330.</ref>. We can learn a lot about how MELiSSA works by looking at soil systems and processes here on Earth. <br />
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The MELiSSA loop is the basis of the life support system created by the ESA and uses processes we see all the time on earth. For example, the transformations of nitrogen (mineralization, nitrification, immobilization and denitrification) show the different ways nitrogen is transformed in soil and in the atmosphere. From studying how microbes interact in soil has helped us create MELiSSA, which combines multiple systems to produce food, water and oxygen for space explorers.<br />
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====Energy Production====<br />
One example of the use of microbes in in the production of energy and additional waste management is the use of a MFC, or microbial fuel cell. MFCs can be used to generate electricity and process waste, but they currently produce low amounts of energy and depend on microbes processing organic matter in an anaerobic anode chamber <ref name=Cockell>Cockell, C. S. (2010). Geomicrobiology beyond Earth: microbe–mineral interactions in space exploration and settlement. Trends in microbiology, 18(7), 308-314.</ref>. On earth MFCs can be made using the soil found all around us because soil contains a diverse population of microbes, along with the nutrients needed by those microbes to generate energy.<br />
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===Microbial Mineral Resource Extraction===<br />
====Gold Production, Detection, and Transformation by Microbes====<br />
[[File:Gold_bacteria.jpg|thumb|150px|left|<i>Cupriavidus metallidurans</i> bacteria metabolize toxic gold chloride into gold nanoparticles (white). Photo from Frank Reith and caption from Gwynne. [http://www.nature.com/nature/journal/v495/n7440_supp/full/495S12a.html Image Source]]]<br />
Some bacteria are capable of reducing toxic gold chloride into pure gold. Cupriavidus metallidurans is one of the few bacteria that can survive in high concentrations of heavy metal in mines throughout the world <ref name=Gywnne>Gwynne, P. (2013). Microbiology: There's gold in them there bugs. Nature, 495(7440), S12-S13.</ref>. Although the bacteria only produce small amounts of gold nanoparticles too small to be profitable, they can be used by miners as biosensors to detect the concentrations of gold in environmental samples. Additionally, the gold nanoparticles synthesized by the bacteria could have potential in applications for many kinds of technology, such as optoelectronics, imaging technology, and drug delivery. Transcriptomic microarrays and DNA sequencing can detect bacterial genes that are associated with gold transformation, and thus pinpoint where significant gold deposits are present. There is great interest for the application of microbes in transforming toxic salts into gold, and scientists are studying both marine and terrestrial species to look for new insights into this area of geomicrobiology.<br />
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====Role of Geomicrobiology in Bioleaching====<br />
Bioleaching can use microbes to extract metal from ore and remove metal impurities without the use of cyanide, mercury, or other chemicals. Biological forms of extraction can be cleaner than chemical methods because less toxins are released by the process, and detoxification can occur on site during processing. Chemolithotrophic bacteria reduce metal sulfides to metal sulfates, and heterotrophic bacteria or fungi exude organic acids, chelating, and complexing compounds to extract other ores and minerals. Although chemical extraction is still used when it is cheaper or another process is unknown, the field of bioleaching has high potential for further development.<br />
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The most active bacteria used in bioleaching are from genus Thiobacillus, gram negative bacteria that perform aerobic oxidation of sulfur compounds in acidic conditions. Other bioleaching genus’ include iron- oxidizing Leptospirillum and Thermophilic bacteria <ref name=Bosecker>Bosecker, Klaus (1997). Bioleaching: metal solubilization by microorganisms. FEMS Microbiology Review 20 (pp. 591-604)</ref>.<br />
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===Role of Geomicrobiology in Removal and Disposal of Heavy Metals and Pollutants===<br />
[[File:Cr_Spill_Durango.jpg|thumb|right|300px|A plume from a mine waste spill in Durango, Colorado, with high Cromium (VI) content has spread to northwestern New Mexico, carried on the San Juan river (Jerry McBride, The Durango Herald, AP, 2015)]]<br />
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Geomicrobiology can be applied to [https://microbewiki.kenyon.edu/index.php/Bioremediation soil bioremediation], watershed reclamation, and to remove plumes of industrial contamination or radiation from the environment. Microbes in the soil and watertable are able to degrade contaminants that have no other practical source of removal and may be toxic to plants and other organisms. Inoculation of multiple target microbes can be used to remove multi-chemical pollutants from a site simultaneously<ref name=Sobolewski>Sobolewski, A. 2006. A Review of Processes Responsible for Metal Removal in Wetlands Treating Contaminated Mine Drainage, International Journal of Phytoremediation, 1:1, 19-51.</ref>. Selection and application of species must take into consideration the reactions that will take place at each step, to ensure the target compound is cleaned from the soil; for example, the desired reactions may require anaerobic or aerobic conditions in the soil and thus the introduced microbes must survive and thrive in such conditions.<br />
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Extraction processes bring heavy metals and other deep subsurface compounds to the surface soil or to the watershed resulting in contamination. Processing metal ore and other resources for production with heavy metals, like mercury, also contribute to the pollution. Microbes found within these layers have evolved to breakdown, reduce, or remove these compounds in their natural settings to extract energy and nutrients through use of precipitation, redox, sorption, and metabolic processes. Target microbes are inoculated at contaminated sites and/or the conditions are changed to select for the desired native microbial community that will transform the pollutant<ref name=Parmar />. Heavy metals including arsenic, zinc and sulfur can be precipitated out of acid mine wastewaters by sulfate-reducing bacteria, producing highly insoluble metal sulfides that are retained by wetland sediments<ref name=Sobolewski />.<br />
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Bacteria can reduce heavy metals from the soil in the rhizosphere for plant uptake and removal<ref name=Dimitroula>Dimitroula, H., Syranidou, E., Manousaki, E., Nikolaidis, N. P., Karatzas, G. P., & Kalogerakis, N. (2015). Mitigation measures for chromium-VI contaminated groundwater–The role of endophytic bacteria in rhizofiltration. Journal of hazardous materials, 281, 114-120.</ref>. Toxins can be converted to nontoxic forms and remain in the soil or be removed by translocation from the roots up into the plant, which can then be harvested to remove the metal from the site. For example, by providing anoxic conditions, high concentrations of toxic chromium (VI) are reduced by rhizospheric bacteria Arthrobacter and Pseudomonas to form immobile, nontoxic Cr(III)<ref name=Gutierrez>Gutiérrez, A. M., Cabriales, J. J. P., & Vega, M. M. (2010). Isolation and characterization of hexavalent chromium-reducing rhizospheric bacteria from a wetland. International journal of phytoremediation, 12(4), 317-334.</ref>. Chromium can be reduced from toxic Cr(VI) to nontoxic Cr(III) by endophytic bacteria within their cells; these Cr compounds are absorbed into the plant for easy removal from the soil and groundwater through harvesting. Some examples of endophytic bacteria species capable of Cr reduction include Ralstonia pickettii and Ochrobactrum intermedium (both gram -), and other non-endophytic examples of Cr-reducing bacteria include Bacillus cereus and Streptomyces (both gram +)<ref name=Dimitroula />.<br />
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===Role of Geomicrobiology in Radiation Contaminated Soils and Groundwater===<br />
[https://microbewiki.kenyon.edu/index.php/Radiotrophic_Fungi Radiotrophic fungi] can survive and colonize water and substrates (i.e. concrete barriers) in sites contaminated by severe radioactivity by using melanin pigment to transfer electrons and gain energy from the radioactive material. More study is needed to confirm if the radioactive material is then transformed to lower energy, safer products as the extra electrons are transferred by reduction. The fungal hyphae also deteriorate the concrete barriers by colonization and mineral weathering processes, which could result in release of radioactive material. A famous case is Chernobyl: after ten years of the catastrophe of Chernobyl in 1986 extensive fungal growth was observed on the walls and other building structures constructed in the inner part of the “Shelter” built over the fourth Unit of the Chernobyl nuclear power plant. Safe long-term storage of both existing and future nuclear waste is of vital importance in protecting the environment, therefore the study of these fungi has been key for future construction of nuclear waste repositories. Some of the microorganisms isolated from these extreme environments include modified strains from the genera Alternaria, Cladosporium, and Aureobasidium<ref name=Formina>Fomina, M., Podgorsky, V. S., Olishevska, V., Kadoshnikov, V. M., Pisanska, I. R., Hillier, S., Gadd, G. M. 2007. Fungal Deterioration of Barrier Concrete used in Nuclear Waste Disposal. Geomicro. J. 24:643-653.</ref>.<br />
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===Role of Geomicrobiology in Agriculture===<br />
As agriculture enters the 21st century, new innovations are being discovered using microbes to increase production, yield, and sustainability in cropping systems. Soil quality and conservation are also becoming priorities on the agricultural forefront to combat the unintended consequences of conventional cropping systems. Metal and sulfate-reducing bacteria are responsible for precipitation and immobilization of metals like iron or manganese, and sulfate in the soil, determining the availability of these plant limiting nutrients<ref name=Parmar>N. Parmar and A. Singh (eds.), Geomicrobiology and Biogeochemistry, Soil Biology 39, DOI 10.1007/978-3-642-41837-2_11. Springer-Verlag Berlin Heidelberg 2014</ref>.<br />
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For example, Phosphate solubilizing microorganisms (PSMs) use organic acids to dissociate phosphorus in small amounts from metal-phosphate compounds, making it available for plant uptake. PSM activity can result in reduced need for P fertilizer use and is being researched for use in biofertilizers. Some examples of PSMs include Chromobacterium, Azotobacter, and Bradyrhizobium<ref name=Parmar />. Rhizobia have been used for some time to help increase Nitrogen fixation in soils, however increasing knowledge of microbial control of nutrient availability are broadening sustainable approaches to improved crop and soil health and quality.<br />
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Microorganisms can be used in integrated pest management systems to fend off pests. The bacterium Thiobacillus, a genus of 'Hydrogenophilaceae', are thermophilic Proteobacteria growing in temperatures up to 50 °C. They obtain their energy from hydrogen oxidation and are used as pest control in potato fields to control scabs<ref name="Rosling">Rosling, A., Suttle, K B., Johansson, E., Van Hees, P. A. W., Banfield, J. F. 2007. Phosphorous availability influences the dissolution of apatite by soil fungi. Geobiology 5 (3): 265–280.<br />
</ref>. Microbes are also used in less toxic insecticides called [http://www.ipm.ucdavis.edu/QT/lesstoxicinsecticidescard.html Microbials].<br />
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==Current Research==<br />
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===Magnetotactic Bacteria===<br />
Magnetotactic bacteria produce small magnetite crystals to form microbial compasses. These materials are used in building microchips and electronics. <br />
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For example, a number of magnetic nanomaterials are being synthesized with biomimetic techniques, which were inspired by the mineralization processes of iron these magnetotactic bacteria did, and are used in, to name a few, "high-density data storage and ferrofluidic devices, electromagnetic shielding, spintronics, and quantum computing, and applications in diagnostic medicine and targeted drug delivery"<ref name=Prozorov>Prozorov, T., Bazylinski, D. A., Mallapragada, S. K., & Prozorov, R. (2013). Novel magnetic nanomaterials inspired by magnetotactic bacteria: Topical review. Materials Science and Engineering: R: Reports, 74(5), 133-172.</ref>.<br />
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===Advances in Removal of Heavy Metals and Radioactivity===<br />
Research of microbial activities using radioactive and toxic metal waste in bedrock groundwater for safe long-term disposal is showing great potential for nuclear waste management. Corrosion of steel, copper, and other compounds is induced deep within the bedrock at greater rates than abiotic processes. The groundwater microbes bind the metal surfaces, forming biofilms resulting in corrosion of the metals<ref name=Carpen>L. Carpén, P. Rajala, M. Bomberg, "Microbially Induced Corrosion in Deep Bedrock", Advanced Materials Research, Vol. 1130, pp. 75-78, Nov. 2015</ref>.<br />
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==References==<br />
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Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]<br />
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<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Soil_Health&diff=120996
Soil Health
2016-03-17T06:52:04Z
<p>Kmscow: </p>
<hr />
<div>==Introduction==<br />
“Essentially, all life depends upon the soil...There can be no life without soil and no soil without life; they have evolved together."<ref>USDA Yearbook of Agriculture. (1938). 75th Congress, 2d session. House Document No. 398. Retrieved from http://naldc.nal.usda.gov/download/IND50000140/PDF<ref/</ref><br />
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===The Living Soil===<br />
[[File:11 living soil.jpg|frame|border|right|top|upright|alt=Alt|The physical, chemical, and biological interactions driven by soil microorganisms in a healthy soil support a complex food web, including human beings.<ref>Fresh, Organic Produce & Mushrooms for Sale in Porter County IN | Living Earth Farms. (n.d.). Retrieved from http://www.livingearthfarms.net/</ref>]] <br />
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Much like the success of the human body is measured by its health, soil health is a measure of a complex set of biological, chemical and physical interactions, which are driven by microbial processes. The soil supports and sustains most life forms on earth, but it is the work of microorganisms that give soil its unique life giving properties. <br />
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It is estimated that between 1-5% of all organic matter in the soil comes from microorganism. <ref>The Living Soil. (n.d.). Retrieved March 13, 2016, from http://www.ext.colostate.edu/mg/gardennotes/212.html</ref> In just one teaspoon of healthy soil more microbial life exists than the current global population.<ref>USDA NRCS. (n.d.). Soil Health Nuggets. Retrieved March 13, 2016, from http://www.nrcs.usda.gov/Internet/FSE_DOCUMENTS/stelprdb1101660.pdf</ref> Today, less than 1% of the bacteria, fungi and protozoa that help support our global population are identified as well as the crucial roles they play in supporting soil health.<br />
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Healthy soils are being lost at alarming rates through degradation, salinization, acidification, desertification, erosion, nutrient depletion and microbial species extermination. We have less and less healthy land available, yet we are being pressured to feed a growing population. Having an understanding of the processes microbes undergo which support the formation and maintenance of healthy soils is essential for facing the global food security challenges of the present and future.<ref>Foley, J. A., DeFries, R., Asner, G. P., Barford, C., Bonan, G., Carpenter, S. R., … Snyder, P. K. (2005). Global Consequences of Land Use. Science, 309(5734), 570–574. http://doi.org/10.1126/science.1111772</ref><br />
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This page will explore ideas and research relating soil health and microbiology to the agricultural context.<br />
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===Soil Quality vs. Soil Health===<br />
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Soil quality and soil health are two related but distinguishable terms. Delineating between soil quality and soil health is useful for clarifying the complex and somewhat amorphous definition of soil health. <br />
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'''Soil quality''', generally speaking, refers to how functional a soil is as defined by human goals. Within the agricultural context, soil quality refers to the quality or quantity of crop yield that a soil can produce within a given production system. <br />
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'''Soil health''', in contrast to soil quality, takes into account other ecosystem functions and services that go beyond immediate human use goals for a particular soil. The term soil health was introduced in order to integrate a more holistic lens to the understanding of the complex network of relationships that exist within soils, including the roles of microbes. Additionally, it focuses on the mitigation and reversal of soil degradation globally. <br />
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A healthy agricultural soil, for example, is not simply a soil that acts as a substrate for high quality crop production; it will also support a diversity of organisms, which will perform functions such as nutrient cycling, carbon sequestration, degradation of toxins, and improving soil structure for water retention and aeration. All of these functions support healthy plant growth; therefore the human functionality of the soil is incorporated into the term “soil health.”<br />
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==Definitions and Indicators==<br />
If soil health is a measure of a complex set of biological, chemical and physical interactions, then it must be measured by an assessment of many indicators taken together, rather than by a single parameter. Indicators can fall into the above-mentioned categories (biological, chemical, physical). Most of the indicators of soil health that exist today (e.g. FAO, NRCS) can either be directly linked to microbial processes or are affected by them.<br />
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[[File:20 indicator venn.png|thumb|border|left|top|upright=2.0|alt=Alt|Soil health indicators can be divided into three categories: Physical, Biological, and Chemical.]] <br />
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===FAO===<br />
The FAO takes a global approach to soil health and maintains databases of soil health assessments for soils worldwide.<ref>FAO. (2016b). Global Soil Health Indicators and Assessment. Retrieved February 21, 2016, from http://www.fao.org/soils-portal/soil-degradation-restoration/global-soil-health-indicators-and-assessment/en/</ref> Soils can be assessed using either an absolute framework or a relative framework. The absolute definition of soil health compares a given soil to a set of ideal properties, whereas the relative definition takes into account the current use of that soil. A degraded soil under sparse vegetation might have low soil health on the absolute scale, but may score well on the relative scale since the soil properties support the existing ecosystem.<ref>FAO. (2016a). Global Soil Health. Retrieved February 21, 2016, from http://www.fao.org/soils-portal/soil-degradation-restoration/global-soil-health-indicators-and-assessment/global-soil-health/en/</ref> <br />
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FAO indicators are divided into two distinct categories, “Physical” and “Biological and Chemical.” Although the FAO divides physical from biological indicators, many physical indicators of soil health have a biological component. According to the FAO, the three most important '''physical indicators''' of soil health are:<br />
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(1)“the absence of sealing and crusting” <br />
(2)“the absence of erosion both by water and by wind” <br />
(3)“the absence of compaction”<ref>FAO. (2016c). Management and Natural Processes affecting the biological and chemical aspects of soils. Retrieved February 21, 2016, from http://www.fao.org/soils-portal/soil-degradation-restoration/global-soil-health-indicators-and-assessment/soil-heath-biological-and-chemical/en/</ref><br />
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Sealing occurs mainly in soils covered by infrastructure. Crusting however, depends in part, on aggregate stability, and therefore microbiological processes in the soil. Erosion by wind and water could be influenced by microbial activity as well, since soils with well-formed aggregates are less likely to erode.<ref>LeBissonnais, Y. (1996). Aggregate stability and assessment of soil crustability and erodibility .1. Theory and methodology. European Journal of Soil Science, 47(4), 425–437.</ref> Compaction results primarily from heavy livestock grazing and machinery and could alter microbial activity by decreasing gas diffusion and water infiltration).<ref>Arias, M. E., Gonzalez-Perez, J. A., Gonzalez-Vila, F. J., & Ball, A. S. (2005). Soil health - a new challenge for microbiologists and chemists. International Microbiology, 8(1), 13–21.</ref> <br />
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'''Biological and chemical indicators''' of soil health described by the FAO include:<br />
(1) “soil nutrient mining” <br />
(2) “salinization” <br />
(3) “pollution”<ref>FAO. (2016b). Global Soil Health Indicators and Assessment. Retrieved February 21, 2016, from http://www.fao.org/soils-portal/soil-degradation-restoration/global-soil-health-indicators-and-assessment/en/</ref> <br />
<br />
Nutrient depletion is only considered applicable in agricultural contexts and results from management practices that do not restore nutrients removed by crops. Limitation of key soil nutrients such as nitrogen or phosphorus may restrict microbial growth.<ref>Sylvia, D. M., Fuhrmann, J. J., Hartel, P. G., & Zuberer, D. A. (2005). Principles and Applications of Soil Microbiology (2nd ed.). Upper Saddle River, NJ: Pearson Prentice Hall. Retrieved from http://www.pearsonhighered.com/educator/product/Principles-and-Applications-of-Soil-Microbiology/9780130941176.page</ref> Salinization can be a consequence of poor irrigation management, and can have detrimental effects on microbial biomass and activity.<ref>Wichern, J., Wichern, F., & Joergensen, R. G. (2006). Impact of salinity on soil microbial communities and the decomposition of maize in acidic soils. Geoderma, 137(1-2), 100–108. http://doi.org/10.1016/j.geoderma.2006.08.001</ref> Pollution resulting from inputs of heavy metals, industrial chemicals, or excessive fertilization, for example, could harm microbial communities<ref>Brookes, P. C. (1995). The use of microbial parameters in monitoring soil pollution by heavy metals. Biology and Fertility of Soils, 19(4), 269–279. http://doi.org/10.1007/BF00336094</ref> but could also represent an opportunity for bioremediation using microbes capable of metabolizing the pollutants.<ref>Samanta, S. K., Singh, O. V., & Jain, R. K. (2002). Polycyclic aromatic hydrocarbons: environmental pollution and bioremediation. Trends in Biotechnology, 20(6), 243–248. http://doi.org/10.1016/S0167-7799(02)01943-1</ref><br />
<br />
===NRCS===<br />
[[File:22 aggregate.png|frame|border|right|top|upright|alt=Alt|An example distribution of extracellular polysaccharides, humus, fungal hyphae, and bacterial cells in a soil aggregate.]]<br />
<br />
The NRCS “Guidelines for Soil Quality Assessment in Conservation and Planning”<ref>USDA NRCS. (2001). Guidelines for Soil Quality Assessment in Conservation Planning. Retrieved from http://www.nrcs.usda.gov/Internet/FSE_DOCUMENTS/nrcs142p2_051259.pdf</ref> provides an outline for a nine-step planning process for incorporating soil quality and health indicators into the conservation planning process. In these guidelines, a healthy soil is defined as one that should perform the following functions: <br />
<br />
# sustain biological activity, diversity, and productivity;<br />
# regulate and partition water and solute flow;<br />
# filter and buffer, degrade, immobilize, and detoxify organic and inorganic materials, including industrial and municipal by-products and atmospheric deposition;<br />
# store and cycle nutrients and other elements within the earth’s biosphere; and<br />
# provide support of socioeconomic structures and protection for archaeological treasures associated with human habitation.<br />
<br />
The NRCS has created a list of clearly delineated, measurable properties (or indicators) that, taken together, can be used to assess the healthy functioning of a soil according to the definition above. Many, if not all, of the NRCS indicators can be directly linked to microbial activity in the soil. "Indicator sheets" define each indicator, its significance, and standardized measurement methods. Examples of some key indicators are featured below with links to their indicator sheets, to illustrate how microbial processes are drivers of these soil health indicators.<br />
<br />
====Physical Properties====<br />
<br />
'''Aggregate stability''' (PDF, 380KB[http://www.nrcs.usda.gov/wps/PA_NRCSConsumption/download?cid=nrcs142p2_051276&ext=pdf]) is enhanced and accelerated by the activity of many different groups of soil microorganisms. Fungal hyphae bind strongly to inorganic soil particles (like clays) and thus physically connect soil particles that were not previously grouped into an aggregate.<ref>Sylvia, D. M., Fuhrmann, J. J., Hartel, P. G., & Zuberer, D. A. (2005). Principles and Applications of Soil Microbiology (2nd ed.). Upper Saddle River, NJ: Pearson Prentice Hall. Retrieved from http://www.pearsonhighered.com/educator/product/Principles-and-Applications-of-Soil-Microbiology/9780130941176.page</ref> Mycorrhizal fungi produce glycoproteins (such as glomalin) that bind soil particles together and are thus highly correlated with aggregate stability.<ref>Wright, S. F., & Upadhyaya, A. (n.d.). A survey of soils for aggregate stability and glomalin, a glycoprotein produced by the hyphae of arbuscular mycorrhizal fungi. Plant and Soil, 198, 97–107.</ref><ref>Wu, Q., Cao, M., Zou, Y., & He, X. (2014). Direct and indirect effects of glomalin, mycorrhizal hyphae, and roots on aggregate stability in rhizosphere of trifoliate orange. Scientific Reports, 4, 5823.</ref> Bacteria also contribute to aggregate stability; many bacteria either actively excrete extracellular polymeric substances or release them during cell lysis and death.<ref>Sylvia, D. M., Fuhrmann, J. J., Hartel, P. G., & Zuberer, D. A. (2005). Principles and Applications of Soil Microbiology (2nd ed.). Upper Saddle River, NJ: Pearson Prentice Hall. Retrieved from http://www.pearsonhighered.com/educator/product/Principles-and-Applications-of-Soil-Microbiology/9780130941176.page</ref> The glucose content of these polymeric substances is correlated with soil aggregation.<ref>Martens, D. A., & Frankenburger Jr., W. T. (1992). Decomposition of bacterial polymers in soil and their influence on soil structure. Biology and Fertility of Soils, 13, 65–73.</ref> Interestingly, the addition of these compounds alone to sterilized soil does not generally increase soil aggregation, suggesting that other microbial processes and transformations are necessary for these polymeric substances to contribute to aggregate stability and soil structure.<ref>Martens, D. A., & Frankenburger Jr., W. T. (1992). Decomposition of bacterial polymers in soil and their influence on soil structure. Biology and Fertility of Soils, 13, 65–73.</ref> <br />
<br />
'''Soil Structure and Macropores''' (PDF, 480KB[http://www.nrcs.usda.gov/wps/PA_NRCSConsumption/download?cid=nrcs142p2_052819&ext=pdf]) are established by soil macroaggregates and are thus influenced by microorganisms in the same way as aggregate stability.<ref>Sylvia, D. M., Fuhrmann, J. J., Hartel, P. G., & Zuberer, D. A. (2005). Principles and Applications of Soil Microbiology (2nd ed.). Upper Saddle River, NJ: Pearson Prentice Hall. Retrieved from http://www.pearsonhighered.com/educator/product/Principles-and-Applications-of-Soil-Microbiology/9780130941176.</ref> Many types of microorganisms excrete substances that contribute to aggregate formation or release them during the turnover of microbial biomass. This in turn affects the development of soil structure and macropores.<ref>Sylvia, D. M., Fuhrmann, J. J., Hartel, P. G., & Zuberer, D. A. (2005). Principles and Applications of Soil Microbiology (2nd ed.). Upper Saddle River, NJ: Pearson Prentice Hall. Retrieved from http://www.pearsonhighered.com/educator/product/Principles-and-Applications-of-Soil-Microbiology/9780130941176.</ref><ref>Wright, S. F., & Upadhyaya, A. (n.d.). A survey of soils for aggregate stability and glomalin, a glycoprotein produced by the hyphae of arbuscular mycorrhizal fungi. Plant and Soil, 198, 97–107.</ref> Macropores can also be created by soil macrofauna, such as earthworms and arthropods, as they move through the soil.<ref>Sylvia, D. M., Fuhrmann, J. J., Hartel, P. G., & Zuberer, D. A. (2005). Principles and Applications of Soil Microbiology (2nd ed.). Upper Saddle River, NJ: Pearson Prentice Hall. Retrieved from http://www.pearsonhighered.com/educator/product/Principles-and-Applications-of-Soil-Microbiology/9780130941176.</ref><br />
<br />
====Chemical Properties====<br />
'''Soil pH''' (PDF, 265KB[http://www.nrcs.usda.gov/wps/PA_NRCSConsumption/download?cid=nrcs142p2_052474&ext=pdf]) both impacts and is impacted by biological, chemical, plant, and microbial activity thresholds, all of which will critically affect plant available nutrients and N and P loss/retention. Microorganisms can alter pH by producing organic acids as a byproduct of fermentation or through any number of oxidation-reduction (redox) reactions.<ref>Soil Quality Indicator Sheets | NRCS Soils. (n.d.). Retrieved March 13, 2016, from http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/health/assessment/?cid=stelprdb1237387</ref> For example, the oxidation of both ammonium (to nitrate) and sulfur (to sulfate) produces protons (H+) and thus acidifies the soil.<ref>Sylvia, D. M., Fuhrmann, J. J., Hartel, P. G., & Zuberer, D. A. (2005). Principles and Applications of Soil Microbiology (2nd ed.). Upper Saddle River, NJ: Pearson Prentice Hall. Retrieved from http://www.pearsonhighered.com/educator/product/Principles-and-Applications-of-Soil-Microbiology/9780130941176.</ref> This in turn affects the distribution of microorganisms - fungi in particular are quite tolerant of acid soils.<ref>Sylvia, D. M., Fuhrmann, J. J., Hartel, P. G., & Zuberer, D. A. (2005). Principles and Applications of Soil Microbiology (2nd ed.). Upper Saddle River, NJ: Pearson Prentice Hall. Retrieved from http://www.pearsonhighered.com/educator/product/Principles-and-Applications-of-Soil-Microbiology/9780130941176.</ref><br />
<br />
[[File:22 pH distribution.png|frame|border|left|top|upright=0.3|alt=Alt|The effect of soil pH on the composition of fungal and bacterial communities. Each band color represents a different taxonomic class.]]<br />
<br />
'''Soil Nitrate''' (PDF, 673KB[[http://www.nrcs.usda.gov/wps/PA_NRCSConsumption/download?cid=stelprdb1243373&ext=pdf]]) is one inorganic pool of nitrogen (N). Nitrogen represents a critical (and often limiting) nutrient for both plants and soil microbes. Nitrate (NO3) is introduced into the soil through plant residues, fertilizer inputs, and sometimes lightning. Microbial processes drive the [[Nitrogen Cycle|nitrogen cycle]] and both produce NO3 (through nitrification) and consume it (through denitrification and immobilization).<ref>Soil Quality Indicator Sheets | NRCS Soils. (n.d.). Retrieved March 13, 2016, from http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/health/assessment/?cid=stelprdb1237387</ref><br />
<br />
====Biological Properties====<br />
'''Particulate Organic Matter''' (PDF, 1.8MB[[http://www.nrcs.usda.gov/wps/PA_NRCSConsumption/download?cid=nrcs142p2_053138&ext=pdf]]) can boost nutrient retention, improve soil structure, increase water infiltration, and help prevent soil erosion. Leaf litter and other large scale organic inputs (dead trees, manure, dead animals, etc.) are integrated into the particulate organic matter pool as they are degraded by a large consortium of soil microbes(“Soil Quality Indicator Sheets | NRCS Soils,” n.d.)<br />
<br />
'''Potentially Mineralizable Nitrogen''' (PDF, 611KB[[http://www.nrcs.usda.gov/wps/PA_NRCSConsumption/download?cid=stelprdb1243371&ext=pdf]]), or PMN, indicates soil productivity and N supplying potential, and also directly enhances soil microbial activity.<ref>Soil Quality Indicator Sheets | NRCS Soils. (n.d.). Retrieved March 13, 2016, from http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/health/assessment/?cid=stelprdb1237387</ref> Mineralization is the conversion of organic N to inorganic N, often as a result of microbes secreting N that is in excess of their own requirements.<ref>Sylvia, D. M., Fuhrmann, J. J., Hartel, P. G., & Zuberer, D. A. (2005). Principles and Applications of Soil Microbiology (2nd ed.). Upper Saddle River, NJ: Pearson Prentice Hall. Retrieved from http://www.pearsonhighered.com/educator/product/Principles-and-Applications-of-Soil-Microbiology/9780130941176.</ref> As mineralized nitrogen is subsequently nitrified by bacteria and archaea, determination of PMN requires flooded anaerobic conditions in order to inhibit the aerobic process of nitrification.<ref>Waring, S. A., & Bremner, J. M. (1964). Ammonium production in soil under waterlogged conditions as an index of nitrogen availability. Nature, 201, 951–952.</ref><br />
<br />
'''Soil Enzymes''' (PDF, 220KB[[http://www.nrcs.usda.gov/wps/PA_NRCSConsumption/download?cid=nrcs142p2_053139&ext=pdf]]) are produced by all the plants and microbes that live in the soil. These enzymes work to break down plant residues and other organic inputs and release nutrients back into the soil environment.<ref>Soil Quality Indicator Sheets | NRCS Soils. (n.d.). Retrieved March 13, 2016, from http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/health/assessment/?cid=stelprdb1237387</ref><br />
<br />
'''Soil Respiration''' (PDF, 329KB[[http://www.nrcs.usda.gov/wps/PA_NRCSConsumption/download?cid=nrcs142p2_052801&ext=pdf]]) refers to the CO2 released from the bulk soil and is mainly the product of aerobic soil microorganisms decomposing soil organic matter and contributing to soil organic carbon.<ref>Soil Quality Indicator Sheets | NRCS Soils. (n.d.). Retrieved March 13, 2016, from http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/health/assessment/?cid=stelprdb1237387</ref><br />
<br />
'''Total Organic Carbon''' (PDF, 210KB[[http://www.nrcs.usda.gov/wps/PA_NRCSConsumption/download?cid=nrcs142p2_051877&ext=pdf]]) is essentially the carbon stored in soil organic matter and it is released from those stores primarily by the activity of microorganisms that decompose organic matter. Carbon stores in the soil provide the main source of energy to both plants and soil microbes.<ref>Soil Quality Indicator Sheets | NRCS Soils. (n.d.). Retrieved March 13, 2016, from http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/health/assessment/?cid=stelprdb1237387</ref><br />
<br />
===Beyond Existing Indicators: Incorporating Soil Biology=== <br />
One of the major limitations of existing indicators is that they pay relatively little attention to the key role of soil microorganisms in soil health. The FAO, for example, does not have any microbe-focused indicators in its “Biological and Chemical Indicators,” even though its definition of soil health emphasizes the importance of soil biology. The latest draft of “Biological Indicators and Soil Functions” published by the NRCS is more comprehensive, including parameters such as soil enzyme activity, particulate organic matter (POM), potentially mineralizable nitrogen (PMN), phospholipid fatty acid (PLFA) analysis, and respiration. Β-glucosidase activity may be particularly important among soil enzymes measured because of its role in plant residue degradation.<ref>Lehman, R. M., Cambardella, C. A., Stott, D. E., Acosta-Martinez, V., Manter, D. K., Buyer, J. S., … Karlen, D. L. (2015). Understanding and Enhancing Soil Biological Health: The Solution for Reversing Soil Degradation. Sustainability, 7(1), 988–1027. http://doi.org/10.3390/su7010988</ref><br />
<br />
[[File:23 micro biomass.png|frame|border|right|top|upright|alt=Alt|Measuring microbial biomass a biologically-focused indicator of soil health integrates physical, chemical, and biological indicators.]]<br />
<br />
'''What could additional indicators of soil health look like?''' <br />
Soil microbial biomass has been suggested as one alternative.<ref>Gonzalez-Quinones, V., Stockdale, E. A., Banning, N. C., Hoyle, F. C., Sawada, Y., Wherrett, A. D., … Murphy, D. V. (2011). Soil microbial biomass-Interpretation and consideration for soil monitoring. Soil Research, 49(4), 287–304. http://doi.org/10.1071/SR10203<br />
H</ref> Because microorganisms are involved in complex, interrelated processes that drive soil health, measuring total microbial biomass gives a more complete picture of soil health than measuring individual enzymes or particular species. However, care should be taken to measure changes from a baseline for a given soil rather than total microbial biomass, since comparing totals across soils could be misleading.<br />
<br />
A large number of currently available potential biological indicators were analyzed based on input from experts and stakeholders and ranked them according to a number of criteria. Their ranked list can be found in Table 6 in Ritz et al. (2009).<ref>Ritz, K., Black, H. I. J., Campbell, C. D., Harris, J. A., & Wood, C. (2009). Selecting biological indicators for monitoring soils: A framework for balancing scientific and technical opinion to assist policy development. Ecological Indicators, 9(6), 1212–1221. http://doi.org/10.1016/j.ecolind.2009.02.009</ref> Top-ranked indicators included: (1) terminal restriction fragment length polymorphism (TRFLP) characterization of ammonia oxidizers/denitrifiers, (2) PLFA profiles of the entire soil microbial community, (3) TRFLP of the intergenic spacer (ITS) region of fungal rRNA, and many more. Some of the indicators were most useful for one specific function such as nitrogen or carbon cycling, whereas others could be used as a proxy for multiple functions.<ref>Ritz, K., Black, H. I. J., Campbell, C. D., Harris, J. A., & Wood, C. (2009). Selecting biological indicators for monitoring soils: A framework for balancing scientific and technical opinion to assist policy development. Ecological Indicators, 9(6), 1212–1221. http://doi.org/10.1016/j.ecolind.2009.02.009</ref><br />
<br />
New possible evaluation techniques for soil biological health might also one day include genetic tools. Since the 1980’s, when microbiologists began to acknowledge that organisms identified by pure-culture techniques represented only a tiny fraction of the metabolic and organismal diversity existing in the world, many new technologies have been developed in order to address the pressing question of not only “who is there” in the microbial community (which can be addressed using techniques like PLFA), but also, “what are they doing”.<ref>Handelsman, J. (2004). Metagenomics: Application of Genomics to Uncultured Microorganisms. Microbiology and Molecular Biology Reviews, 68(4), 669–685. http://doi.org/10.1128/MMBR.68.4.669-685.2004</ref> <br />
<br />
Metagenomics is one such method for genomic analysis of communities of organisms. The word itself was meant to convey its usefulness in analyzing a collection of similar, but not identical items. Metagenomics involves isolating DNA from a particular environmental sample, cloning the DNA into a suitable vector, generating a host bacterium from cloned DNA, and finally screening the resulting transformants. Using diverse methods to analyze gene expression in the generated hosts, it has been possible to establish the function of certain genes. These new insights, however, taken out of specific biological context, cannot truly be used to make any conclusions at the ecological scale. The current state of the technology still requires some technical advances in order to move the field forward from concluded inferences to a true mechanistic analysis and understanding of functional genes.<ref>Handelsman, J. (2004). Metagenomics: Application of Genomics to Uncultured Microorganisms. Microbiology and Molecular Biology Reviews, 68(4), 669–685. http://doi.org/10.1128/MMBR.68.4.669-685.2004</ref><ref>Rondon, M. R., August, P. R., Bettermann, A. D., Brady, S. F., Grossman, T. H., Liles, M. R., … Goodman, R. M. (2000). Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and Functional Diversity of Uncultured Microorganisms. Applied and Environmental Microbiology, 66(6), 2541–2547. http://doi.org/10.1128/AEM.66.6.2541-2547.2000</ref><br />
<br />
==Soil Health and Agriculture==<br />
[[File:33 soils and ag.jpg|thumb|border|left|top|upright=2.0|alt=Alt|A UN-FAO infographic illustrating the importance of soil health to agricultural and natural ecosystems.]]<br />
<br />
Soil is an interconnected system with high levels of exchange of energy between organisms and physical-chemicals components, which leads to the concept that soil is a self-organized system. However, despite having the unique and incredible capacity of adapting to environmental change, described as resistance and resilience, microbes are sensitive to land management and climate change. Resistance is the capacity of the soil to maintain its health despite the magnitude of the change caused by any kind of perturbation. Resilience is the capacity of the system to return to its original state after a disturbance, which is also known as the self-healing capacity of the system.<ref>Geisseler, D., & Scow, K. M. (2014). Long-term effects of mineral fertilizers on soil microorganisms – A review. Soil Biology and Biochemistry, 75, 54–63. http://doi.org/10.1016/j.soilbio.2014.03.023</ref> Some impacts of soil management in soil health are described below:<br />
<br />
===Physical Disturbances===<br />
====Tillage====<br />
Disturbance of the soil through tillage breaks aggregates and destroys soil structure. Additionally, the use of heavy machinery for tillage can compact the soil, reducing infiltration of water and gases. Compacted soils can, in some cases, form a crust on the surface, which seals the soil, prevents plant and microbial growth, and increases runoff.<ref>Geisseler, D., & Scow, K. M. (2014). Long-term effects of mineral fertilizers on soil microorganisms – A review. Soil Biology and Biochemistry, 75, 54–63. http://doi.org/10.1016/j.soilbio.2014.03.023</ref><br />
<br />
====Overgrazing====<br />
The intense biological disturbance of soil caused by overgrazing cattle can be equally detrimental to soil. In an overgrazed pasture, the most palatable species are consumed first, which favors the growth of weedy species. An exposed and compacted soil will have a higher temperature and diminished habitat for the soil microbes. As a result, there is a higher necessity of synthetic inputs, such as fertilizers and pesticides to control those weeds.<ref>Bot, A., & Benites, J. (2005). The importance of soil organic matter: key to drought-resistant soil and sustained food production. Food & Agriculture Org. Retrieved from https://books.google.com/books?hl=en&lr=&id=dJe5-pmmjaAC&oi=fnd&pg=PP10&dq=Bot,+A.,+%26+Benites,+J.+(2005).+The+importance+of+soil+organic+matter.+FAO+Soils+Bulletin.+doi:10.1080/03650340214162&ots=FvzYW77rvl&sig=2pWepjUk315bvm-fx55R-_kcfYM</ref><br />
<br />
===Inputs===<br />
====Fertilizers====<br />
The addition of inorganic fertilizers to increase productivity impacts microbial activity in the short-term by reducing its biomass, as high application rates increase the soil's osmotic potential, which can be toxic for microbes. However, when applied in a well-managed agroecosystem (where crop residues are kept in the soil as a carbon source), mineral fertilizers can supply microbes with nutrients (N, P and K) and stimulate microbial activity in the long-term.<ref>Geisseler, D., & Scow, K. M. (2014). Long-term effects of mineral fertilizers on soil microorganisms – A review. Soil Biology and Biochemistry, 75, 54–63. http://doi.org/10.1016/j.soilbio.2014.03.023</ref> Additionally, excess application of fertilizers can lead to leaching and eutrophication in water bodies.<ref>Ongley, E. D. (1996). Control of water pollution from agriculture. Food & Agriculture Org. Retrieved from https://books.google.com/books?hl=en&lr=&id=LxJsTnFoGagC&oi=fnd&pg=PA3&dq=Ongley,+E.+D.+(1996).+Chapter+3.+Fertilizers+as+water+pollutants.+Control+of+Water+Pollution+from+Agriculture.+FAO+Irrigation+and+Drainage+Paper+55,+37%E2%80%9352&ots=AS4mBIzA69&sig=IddpgpuSM8GgbvwXPdb-Yhko4Aw</ref><br />
<br />
====Fumigation====<br />
The use of biocides for pest control is highly effective in the short-term, but in the long term pathogens can recolonize. Fumigation destroys predator-prey relationships which exist within the natural food web, allowing pathogens to grow without predator control.<br />
<br />
===Water Availability===<br />
<br />
====Exposed soil====<br />
An exposed soil has high level of water evaporation. Without water, the microbial population dies. Plant productivity and the symbiotic relationship between plants and microbes, such as those found in the [[Rhizosphere Interactions|rhizosphere]], are also diminished. An exposed soil is also subject to increased temperature and a loss in water retention, both of which increase erosion by runoff. <br />
<br />
[[File:33 irrigation salinity.gif|thumb|border|right|top|upright=2.0|alt=Alt|An illustration of how poor irrigation practices can lead to soil salinization]]<br />
<br />
====Irrigation Practices====<br />
Irrigation allows plants to keep stomata open and maximize transpiration, which increases productivity and thus C inputs into the soil, while also providing moisture that is essential for microbial activity. It is estimated that 17% of land that is irrigated produces 40% of the global food.<ref>THE STATE OF FOOD AND AGRICULTURE 2002. (n.d.). Retrieved March 14, 2016, from http://www.fao.org/docrep/004/y6000e/y6000e00.htm</ref> Irrigation affects the distribution of water in the soil profile, which in turn affects the distribution of oxygen, and can create anaerobic micro-environments. The use of low quality irrigation water, failure to add enough water to leach salts from the soil profile, and the presence of a shallow groundwater table can all lead to salinization in arid and semi-arid environments.<ref>Ongley, E. D. (1996). Control of water pollution from agriculture. Food & Agriculture Org. Retrieved from https://books.google.com/books?hl=en&lr=&id=LxJsTnFoGagC&oi=fnd&pg=PA3&dq=Ongley,+E.+D.+(1996).+Chapter+3.+Fertilizers+as+water+pollutants.+Control+of+Water+Pollution+from+Agriculture.+FAO+Irrigation+and+Drainage+Paper+55,+37%E2%80%9352&ots=AS4mBIzA69&sig=IddpgpuSM8GgbvwXPdb-Yhko4Aw</ref><ref>Podmore, C. (2009). Irrigation salinity–causes and impacts. Primefact, 937(1), 1–4.</ref> Salinization affects microbes directly by increasing the osmotic potential of the soil solution, as well as indirectly by affecting plant growth and C cycling.<br />
<br />
===Crop Rotation===<br />
====Monoculture====<br />
Planting a homogeneous stand of a single crop can select a narrow set of microbial species, which can be more vulnerable for pest cycles. High microbial abundance within few trophic groups does not guarantee soil health unless it includes key groups that provide certain functions.<ref>Geisseler, D., & Scow, K. M. (2014). Long-term effects of mineral fertilizers on soil microorganisms – A review. Soil Biology and Biochemistry, 75, 54–63. http://doi.org/10.1016/j.soilbio.2014.03.023</ref> However, even when crops are rotated, some nutrients (such as nitrogen) and organic matter are exhausted, demanding more fertilizer inputs. Rotating crops does, however, provides windows where the farmer can incorporate organic inputs which would contribute to soil organism diversity.<br />
<br />
===Mitigation===<br />
Unfortunately, approximately 40% of the world’s cropland has become unproductive due to erosion, which has reduced food production and contributed to the undernourishment of more than 3 billion people.<ref>Foley, J. A., DeFries, R., Asner, G. P., Barford, C., Bonan, G., Carpenter, S. R., … Snyder, P. K. (2005). Global Consequences of Land Use. Science, 309(5734), 570–574. http://doi.org/10.1126/science.1111772</ref> This degradation process may be exacerbated by climate change, creating a positive feedback loop, where climate change accelerates soil degradation and soil degradation stimulates climate change. For example, when a soil system is disturbed by tillage, enhanced microbial degradation of organic matter may lead to increased losses of mineralized N through leaching or volatilization, especially when the supply of mineralized nitrogen exceeds biological demand. These processes increase greenhouse gas emissions leading to higher temperatures, subsequently, greater temperatures promulgate faster chemical reactions.<ref>Geisseler, D., & Scow, K. M. (2014). Long-term effects of mineral fertilizers on soil microorganisms – A review. Soil Biology and Biochemistry, 75, 54–63. http://doi.org/10.1016/j.soilbio.2014.03.023</ref><br />
<br />
New approaches, such as climate-smart agriculture and agroecological practices, focus on making agriculture more adaptive and resilient to environmental pressures, while simultaneously reducing its negative impacts on ecosystem services. Studies have shown that sustainable soil management could produce up to 58% more food.<ref>FAO. (2016a). Global Soil Health. Retrieved February 21, 2016, from http://www.fao.org/soils-portal/soil-degradation-restoration/global-soil-health-indicators-and-assessment/global-soil-health/en/</ref> Soil management practices that promote soil health include: <br />
<br />
* cover crops<br />
* no-till farming <br />
* compost and other organic fertilizers which include C in addition to other macro and micro nutrients. <br />
* diversified cropping systems <br />
* biological pathogen control<ref>FAO. (2016b). Global Soil Health Indicators and Assessment. Retrieved February 21, 2016, from http://www.fao.org/soils-portal/soil-degradation-restoration/global-soil-health-indicators-and-assessment/en/</ref><br />
<br />
[[File:36 plant disease supp.jpg|thumb|border|left|top|upright=1.0|alt=Alt|A conceptual diagram of relationships in soil that lead to microbial suppression of plant diseases.]]<br />
<br />
===Microbes and Soil Disease Suppression: A Case for Soil Health===<br />
Soil health in agricultural systems must take into account plant health. The [[Rhizosphere Interactions|rhizosphere]] is the soil zone around plant roots where microbially mediated soil-plant interaction occurs. Plants live in close association with rhizosphere microbes, which are referred to as the plant’s “second genome”, similar to the human gut.<ref>Berendsen, R. L., Pieterse, C. M. J., & Bakker, P. A. H. M. (2012). The rhizosphere microbiome and plant health. Trends in Plant Science, 17(8), 478–486. http://doi.org/10.1016/j.tplants.2012.04.001</ref> Through long-term adaptation and coevolution, plant roots and their soil microbiome have developed complex interrelationships and symbioses. One of these processes is the suppression of soil plant pathogens by microbial populations. <br />
<br />
The microbial population in the rhizosphere is abundant and highly diverse. Such diversity contributes to “niche overlap”; in effect, the native microbes leave no empty niche for pathogens to colonize plant roots. Furthermore, fierce competition for a limited resource base ensures that no single microbial group can dominate.<ref>Ghorbani, R., Wilcockson, S., Koocheki, A., & Leifert, C. (2008). Soil management for sustainable crop disease control: a review. Environmental Chemistry Letters, 6(3), 149–162. http://doi.org/10.1007/s10311-008-0147-0</ref> Through these mechanisms, microbes inhibit plant pathogens and create natural soil disease suppression. <br />
<br />
Application of pesticides, fungicides, and inorganic fertilizers applies selective pressure to the root microbiome, reducing abundance and diversity of soil microorganisms. This creates space for newcomers that can be harmful or beneficial to plants. For example, when a mycorrhizal fungi population is inhibited by fungicide, pathogenic invaders enter the “empty” rhizosphere niche and infect plant roots. Evidence suggests that plants select for beneficial microbes through secretion of root exudates.<ref>Berendsen, R. L., Pieterse, C. M. J., & Bakker, P. A. H. M. (2012). The rhizosphere microbiome and plant health. Trends in Plant Science, 17(8), 478–486. http://doi.org/10.1016/j.tplants.2012.04.001</ref> In this case, a less diverse root microbiome increases soil disease suppression. Ongoing research is being done on the effect of intentionally disrupting plant-microbe associations to treat pathogen-infected soils.<br />
In one study,<ref>Rondon, M. R., August, P. R., Bettermann, A. D., Brady, S. F., Grossman, T. H., Liles, M. R., … Goodman, R. M. (2000). Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and Functional Diversity of Uncultured Microorganisms. Applied and Environmental Microbiology, 66(6), 2541–2547. http://doi.org/10.1128/AEM.66.6.2541-2547.2000</ref> diseased agricultural soils due to successive monocrops were inoculated with a microbe pathogen antagonist. Recruiting microbes to attack soil pathogens as a means facilitating soil disease suppression and plant health is at the forefront of research advances.<br />
<br />
==Current Research==<br />
The study of soil health represents an exciting and rapidly growing body of science. Many major universities and agencies have dedicated significant time and resources to further understand the role microorganisms play in creating and maintaining soil health. Explore these pages to see some of the work being done by some of the top labs in the country:<br />
<br />
* [https://enst.umd.edu/research/research-labs/biogeochemistry_lab|Stephanie Yarwood Microbial Ecology and Biogeochemistry Lab, University of Maryland]<br />
* [http://scowlab.lawr.ucdavis.edu/|Kate Scow Microbial Ecology Lab, University of California Davis]<br />
* [http://fiererlab.org/|Noah Fierer Lab, University of Colorado]<br />
* [http://www.fao.org/home/en/|Food and Agriculture Organization of the United Nations (UN-FAO)]<br />
* [http://www.fao.org/soils-2015/en/|2015, International Year of Soils (UN-FAO)]<br />
* [http://www.usda.gov/|United States Department of Agriculture (USDA)]<br />
* [http://www.nrcs.usda.gov/|Natural Resources Conservation Service (NRCS)]<br />
* [https://www.soils.org/|Soil Science Society of America (SSSA)]<br />
<br />
==References==<br />
<references/></div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Talk:Nitrogen_Cycle&diff=28576
Talk:Nitrogen Cycle
2008-03-11T15:18:56Z
<p>Kmscow: </p>
<hr />
<div>I suggested putting 2.4 as a subheading under 2.3 though now I see it is about both mineralization and immobilization. I still think it is a little odd to have it called out as its own heading after these 2 processes. Perhaps you could include it within mineralization section and not as heading. Or you could combine mineral/immob and have C/N as first subsection. It is up to you folks, though.<br />
<br />
[[User:Kmscow|Kate Scow]] 15:18, 11 March 2008 (UTC)<br />
---<br />
It is really an issue assocdo you really mean, under environmental concerns, that nitrificatoin has POSITIVE impacts on groundwater pollution. Seems like negative impact to me.<br />
[[User:Kmscow|Kate Scow]] 07:22, 11 March 2008 (UTC)<br />
----<br />
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----<br />
Good start. A couple of comments. N cycle is biogeochemical not just chemical cycle. Also add that nitrate is then converted to N2 gas and then everything repeats itself. <br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
<br />
Great start! See if you can find some key nitrogen cycle organisms on the microbewiki and create links to their pages. Then start a page for a new microbe by using the code of an existing page as a template and editing the content. Remember to cite your sources!<br />
<br />
[[User:Irina.chakraborty|Irina C]] 21:45, 10 February 2008 (UTC)<br />
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I would suggest putting the microbes involved under each subheading. you can have nitrosomonas/nitrobacter and archaea under nitrification. Facultative anaerobes under denitr. Just mention breadth of organisms involved in immob/mineralization and why there is that breadth.<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
For global warming, you can find lots of good links for greenhouse gases. One good one would be good.<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
Remember to cite references for your information, especially for somewhat unique info (like alternative nitrogenases)<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
----<br />
hi, you really know your N! <br />
looks real good. I was going to suggest considering "Introduction" for #1. -Paul W<br />
----<br />
<br />
I would suggest putting C/N ratio under the category of immobilization as it is a subtopic of this process.<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
Most of nitrogen cycle related microbes are popular and already created in wiki.However,I create a new microbe page at http://microbewiki.kenyon.edu/index.php/Thiomicrospira_denitrificans. Let check it. [[User:Tantayotai|Tantayotai]] 00:39, 11 March 2008 (UTC)<br />
<br />
Wow, good job Tee. Make sure to add the new page to your watchlist so you get notified on comments. [[User:Irina.chakraborty|Irina C]] 01:03, 11 March 2008 (UTC)<br />
<br />
----</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Talk:Nitrogen_Cycle&diff=28575
Talk:Nitrogen Cycle
2008-03-11T07:22:01Z
<p>Kmscow: </p>
<hr />
<div>do you really mean, under environmental concerns, that nitrificatoin has POSITIVE impacts on groundwater pollution. Seems like negative impact to me.<br />
[[User:Kmscow|Kate Scow]] 07:22, 11 March 2008 (UTC)<br />
----<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
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----<br />
Good start. A couple of comments. N cycle is biogeochemical not just chemical cycle. Also add that nitrate is then converted to N2 gas and then everything repeats itself. <br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
<br />
Great start! See if you can find some key nitrogen cycle organisms on the microbewiki and create links to their pages. Then start a page for a new microbe by using the code of an existing page as a template and editing the content. Remember to cite your sources!<br />
<br />
[[User:Irina.chakraborty|Irina C]] 21:45, 10 February 2008 (UTC)<br />
----<br />
I would suggest putting the microbes involved under each subheading. you can have nitrosomonas/nitrobacter and archaea under nitrification. Facultative anaerobes under denitr. Just mention breadth of organisms involved in immob/mineralization and why there is that breadth.<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
For global warming, you can find lots of good links for greenhouse gases. One good one would be good.<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
Remember to cite references for your information, especially for somewhat unique info (like alternative nitrogenases)<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
----<br />
hi, you really know your N! <br />
looks real good. I was going to suggest considering "Introduction" for #1. -Paul W<br />
----<br />
<br />
I would suggest putting C/N ratio under the category of immobilization as it is a subtopic of this process.<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
Most of nitrogen cycle related microbes are popular and already created in wiki.However,I create a new microbe page at http://microbewiki.kenyon.edu/index.php/Thiomicrospira_denitrificans. Let check it. [[User:Tantayotai|Tantayotai]] 00:39, 11 March 2008 (UTC)<br />
<br />
Wow, good job Tee. Make sure to add the new page to your watchlist so you get notified on comments. [[User:Irina.chakraborty|Irina C]] 01:03, 11 March 2008 (UTC)<br />
<br />
----</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Talk:Flooded_Soils&diff=28317
Talk:Flooded Soils
2008-03-10T02:09:00Z
<p>Kmscow: </p>
<hr />
<div>I would remove section 2.3.2. Move that material (renamed microbial activity) as part of the intro to microorganisms involved. I would rename that section something like key microbial processes and organisms involved.<br />
<br />
[[User:Kmscow|Kate Scow]] 02:09, 10 March 2008 (UTC)<br />
----<br />
<br />
wow this is looking nice!<br />
Methaneous organisms needs to be changes to methanogens. You also need to add the fermenting organisms as a category. <br />
Also include some of the broader changes with flooding: gleying, and what happens when oxygen becomes available again.<br />
[[User:Kmscow|Kate Scow]] 02:04, 10 March 2008 (UTC)<br />
----<br />
<br />
---- <br />
are the plants linked to microbes now?-david [[User:Dtla|Dtla]] 01:07, 10 March 2008 (UTC)<br />
<br />
It's better, bur organize the information (one main idea per paragraph). [[User:Irina.chakraborty|Irina C]] 01:12, 10 March 2008 (UTC)<br />
<br />
----<br />
im doing effects on life, plants, microorganisms? -david ````[[User:Dtla|Dtla]] 00:10, 10 March 2008 (UTC)<br />
<br />
<br />
The section called "Effects on life" seems out of place. Also, if you want to talk about effects on plants, you need to link it to microbes (i.e. what do microbes to in flooded soils that would effect plants). As it is now, there is no connection to plants. Make sure you site your sources and do not just copy and paste text as you did with at least some of the phrases in your section. You have to paraphrase AND cite the source of the information. Your section on microorganisms is ok but seems try to make it more clear and make sure it doesn't contain info that is covered elsewhere on the page (compare to "electron tower" section) [[User:Irina.chakraborty|Irina C]] 00:29, 10 March 2008 (UTC)<br />
ok-david<br />
----<br />
<br />
is what im doing ok? a i supposed to make my own page? -david ````[[User:Dtla|Dtla]] 06:00, 9 March 2008 (UTC)<br />
<br />
It looks good. You guys need more detail in some sections. Have you decided among yourselves how to split up the work? [[User:Irina.chakraborty|Irina C]] 06:42, 9 March 2008 (UTC)<br />
----<br />
I erased your "edits and dates" section. We don't need this since we can see who did what and when in the history tab.<br />
<br />
[[User:Irina.chakraborty|Irina C]] 23:37, 6 March 2008 (UTC)<br />
----<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
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----<br />
<br />
is what im doing ok? a i supposed to make my own page? -david ````[[User:Dtla|Dtla]] 06:00, 9 March 2008 (UTC)<br />
----<br />
<br />
I would suggest slightly different organization.<br />
<br />
Maybe under flooded soils could be....<br />
#Overall definition and description of phenomenon of flooded soils. You can put a figure here. You can also say that this type of phenomenon can also be observed in other types of situations.....aggregates and pollutant plumes in groundwater<br />
#Chemical changes : Make sure you focus this on redox. organize these by changes in dominant electron acceptors being used and make the connection to electron tower. ALso include fate of products generated during electron acceptor untilization. e.g. methane migrates up. Sulfides.....<br />
#Changes in microbial community composition<br />
#Changes when the flooded soil is unflooded and oxygen comes in<br />
<br />
Maybe something else??<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
<br />
----<br />
* You don't need to have a list of topics because that is automatically created for you at the top of the page.<br />
* Please put back the text that says "crated by the students of Kate Scow" at the bottom of the template page<br />
* You don't need to sign your names at the end. We can see who did what by looking at the history of the page. Also, Laleh's name is mentioned but it doesn't look like she's logged in. Please make sure you log in and make edits through your own account, since otherwise we can't tell who did what.<br />
[[User:Irina.chakraborty|Irina C]] 19:05, 8 February 2008 (UTC)</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Talk:Flooded_Soils&diff=28316
Talk:Flooded Soils
2008-03-10T02:04:51Z
<p>Kmscow: </p>
<hr />
<div>wow this is looking nice!<br />
Methaneous organisms needs to be changes to methanogens. You also need to add the fermenting organisms as a category. <br />
Also include some of the broader changes with flooding: gleying, and what happens when oxygen becomes available again.<br />
[[User:Kmscow|Kate Scow]] 02:04, 10 March 2008 (UTC)<br />
----<br />
<br />
---- <br />
are the plants linked to microbes now?-david [[User:Dtla|Dtla]] 01:07, 10 March 2008 (UTC)<br />
<br />
It's better, bur organize the information (one main idea per paragraph). [[User:Irina.chakraborty|Irina C]] 01:12, 10 March 2008 (UTC)<br />
<br />
----<br />
im doing effects on life, plants, microorganisms? -david ````[[User:Dtla|Dtla]] 00:10, 10 March 2008 (UTC)<br />
<br />
<br />
The section called "Effects on life" seems out of place. Also, if you want to talk about effects on plants, you need to link it to microbes (i.e. what do microbes to in flooded soils that would effect plants). As it is now, there is no connection to plants. Make sure you site your sources and do not just copy and paste text as you did with at least some of the phrases in your section. You have to paraphrase AND cite the source of the information. Your section on microorganisms is ok but seems try to make it more clear and make sure it doesn't contain info that is covered elsewhere on the page (compare to "electron tower" section) [[User:Irina.chakraborty|Irina C]] 00:29, 10 March 2008 (UTC)<br />
ok-david<br />
----<br />
<br />
is what im doing ok? a i supposed to make my own page? -david ````[[User:Dtla|Dtla]] 06:00, 9 March 2008 (UTC)<br />
<br />
It looks good. You guys need more detail in some sections. Have you decided among yourselves how to split up the work? [[User:Irina.chakraborty|Irina C]] 06:42, 9 March 2008 (UTC)<br />
----<br />
I erased your "edits and dates" section. We don't need this since we can see who did what and when in the history tab.<br />
<br />
[[User:Irina.chakraborty|Irina C]] 23:37, 6 March 2008 (UTC)<br />
----<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
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----<br />
<br />
is what im doing ok? a i supposed to make my own page? -david ````[[User:Dtla|Dtla]] 06:00, 9 March 2008 (UTC)<br />
----<br />
<br />
I would suggest slightly different organization.<br />
<br />
Maybe under flooded soils could be....<br />
#Overall definition and description of phenomenon of flooded soils. You can put a figure here. You can also say that this type of phenomenon can also be observed in other types of situations.....aggregates and pollutant plumes in groundwater<br />
#Chemical changes : Make sure you focus this on redox. organize these by changes in dominant electron acceptors being used and make the connection to electron tower. ALso include fate of products generated during electron acceptor untilization. e.g. methane migrates up. Sulfides.....<br />
#Changes in microbial community composition<br />
#Changes when the flooded soil is unflooded and oxygen comes in<br />
<br />
Maybe something else??<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
<br />
----<br />
* You don't need to have a list of topics because that is automatically created for you at the top of the page.<br />
* Please put back the text that says "crated by the students of Kate Scow" at the bottom of the template page<br />
* You don't need to sign your names at the end. We can see who did what by looking at the history of the page. Also, Laleh's name is mentioned but it doesn't look like she's logged in. Please make sure you log in and make edits through your own account, since otherwise we can't tell who did what.<br />
[[User:Irina.chakraborty|Irina C]] 19:05, 8 February 2008 (UTC)</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Talk:Soil_Environment&diff=28315
Talk:Soil Environment
2008-03-10T01:59:56Z
<p>Kmscow: </p>
<hr />
<div>A suggestion: since you are looking at soil environ/physic factors, rather than a specific cycle or special environment, you get to be more creative with your relevant organisms. Some that I can think of, though, are ones that build soil structure (e.g. make polysaccharides, hyphae formers), as well as those extemophiles that tolerate really low and high pH, low and high temperature, osmotic extemists. Should be fun.<br />
[[User:Kmscow|Kate Scow]] 01:59, 10 March 2008 (UTC)<br />
----<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
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----<br />
I suggest replacing microflora with "interactions with other microorganisms".----Kate Scow<br />
----<br />
Bioavailability :<br />
<br />
Definition of bioavailability is not quite right. You can go to book and lecture notes, or other sites, and develop better definition.---Kate<br />
----<br />
<br />
It seems your section on relevant microorganisms has disappeared. Please add it back and complete that part of the assignment. [[User:Irina.chakraborty|Irina C]] 02:42, 25 February 2008 (UTC)<br />
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<br />
Another thing, make sure to note down the sources of your information on the page as you write. You can format and link them as proper references later, but don't add any information without a citation to the source.<br />
<br />
To get subheadings, use various numbers of equal signs before and after the word (see template code).<br />
<br />
To actually create numbered lists, use the pound sign '#'. Different numbers of pound signs will create different levels of numbered text (click on Edit tab of this page to see):<br />
#Topic 1<br />
##Subtopic 1a<br />
##Subtopic 1b<br />
#Topic 2<br />
###etc<br />
####etc<br />
#####etc<br />
<br />
[[User:Irina.chakraborty|Irina C]] 18:48, 28 January 2008 (UTC)<br />
----<br />
<br />
Hi soil environment group. Please use section formats as in the template. You're the first group to start! great!!<br />
<br />
[[User:Irina.chakraborty|Irina C]] 04:58, 28 January 2008 (UTC)</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Talk:Carbon_cycle&diff=28312
Talk:Carbon cycle
2008-03-10T01:55:24Z
<p>Kmscow: </p>
<hr />
<div>I would modify the heading of Decomposition of organic..... to include "and the microorganisms involved" Then you can include some info on the players in each category if there is specific info available AND make nice links to the existing microbe pages. There should be a lot of these pages.<br />
<br />
This way you can eliminate the section on just microbes and integrate it into each important process. If there are no really specific organisms, e.g. with the sugars section, you can just say that metabolism of these compounds is by a broad group of microorganisms.<br />
<br />
[[User:Kmscow|Kate Scow]] 01:55, 10 March 2008 (UTC) ----<br />
<br />
[[User:Kmscow|Kate Scow]] 01:45, 10 March 2008 (UTC)<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
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----<br />
Ok, guys: we need to do this wiki. I'm sorry that I haven't gotten to it until today, but I don't any other effort here either. I'm going to work through some of it, but what I leave undone had better get done by tomorrow.<br />
[[User:Njblackburn|Njblackburn]] 19:37, 9 March 2008 (UTC)<br />
----<br />
I would suggest not breaking out geo/bio/hydro/atmosphere unless you really want to go into detail about this. Please include the 2 main sections in the lecture:<br />
# Decomposition of organic matter--<br />
and then cover all the different chemical components of plant materials e.g. monomers, cellulose, hemicellulose, lignin, etc<br />
# Formation of humic substances<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
You might want to link the microbial types directly to the processes rather than split it out alone.<br />
<br />
E.g. cellulose decomposition is where you would discuss a little about the organisms involved and you can link this to the organisms already listed in the wiki. A lot of these organisms start with "cellu"<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
<br />
You don't need to have an Edits and Dates section at the end either - all this information is collected under "History". I noticed you wrote "Jaime and Alex". I can see that Jaime made edits but not Alex. So please make sure you log in yourselves when editing, so that we can attribute work - [[User:Irina.chakraborty|Irina C]] 22:52, 10 February 2008 (UTC)<br />
<br />
Good start - You don't need to have a list of your sections at the start of your page because a content list is automatically generated if you use heading formats for the title of each section. Also you used internal link formatting for the items in "List of Topics". You only need to do this if you are creating new pages for each item - this would make sense if we were going to add a lot of detail. Instead each item is just a section within your page, so does not require a link to its own page.<br />
<br />
[[User:Irina.chakraborty|Irina C]] 22:22, 10 February 2008 (UTC)<br />
<br />
----<br />
Has anyone seen the template for our page we need to write about a microbe? Jess and I have gone through and put in a bunch of links, but I'm not sure how to create an entirely new page. (~Jaime)<br />
----</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Talk:Carbon_cycle&diff=28311
Talk:Carbon cycle
2008-03-10T01:45:59Z
<p>Kmscow: </p>
<hr />
<div>I would modify the heading of Decomposition of organic..... to include "and the microorganisms involved" Then you can include some info on the players in each category if there is specific info available AND make nice links to the existing microbe pages. There should be a lot of these pages.<br />
<br />
<br />
[[User:Kmscow|Kate Scow]] 01:45, 10 March 2008 (UTC)<br />
<br />
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----<br />
Ok, guys: we need to do this wiki. I'm sorry that I haven't gotten to it until today, but I don't any other effort here either. I'm going to work through some of it, but what I leave undone had better get done by tomorrow.<br />
[[User:Njblackburn|Njblackburn]] 19:37, 9 March 2008 (UTC)<br />
----<br />
I would suggest not breaking out geo/bio/hydro/atmosphere unless you really want to go into detail about this. Please include the 2 main sections in the lecture:<br />
# Decomposition of organic matter--<br />
and then cover all the different chemical components of plant materials e.g. monomers, cellulose, hemicellulose, lignin, etc<br />
# Formation of humic substances<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
You might want to link the microbial types directly to the processes rather than split it out alone.<br />
<br />
E.g. cellulose decomposition is where you would discuss a little about the organisms involved and you can link this to the organisms already listed in the wiki. A lot of these organisms start with "cellu"<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
<br />
You don't need to have an Edits and Dates section at the end either - all this information is collected under "History". I noticed you wrote "Jaime and Alex". I can see that Jaime made edits but not Alex. So please make sure you log in yourselves when editing, so that we can attribute work - [[User:Irina.chakraborty|Irina C]] 22:52, 10 February 2008 (UTC)<br />
<br />
Good start - You don't need to have a list of your sections at the start of your page because a content list is automatically generated if you use heading formats for the title of each section. Also you used internal link formatting for the items in "List of Topics". You only need to do this if you are creating new pages for each item - this would make sense if we were going to add a lot of detail. Instead each item is just a section within your page, so does not require a link to its own page.<br />
<br />
[[User:Irina.chakraborty|Irina C]] 22:22, 10 February 2008 (UTC)<br />
<br />
----<br />
Has anyone seen the template for our page we need to write about a microbe? Jess and I have gone through and put in a bunch of links, but I'm not sure how to create an entirely new page. (~Jaime)<br />
----</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Talk:Rhizosphere_Interactions&diff=28310
Talk:Rhizosphere Interactions
2008-03-10T01:42:15Z
<p>Kmscow: </p>
<hr />
<div>Looking good. It would be good to include the N fixers under symbiotic organisms. You may not need so much detail under the root exudates: all that could be included under just one major heading.<br />
<br />
[[User:Kmscow|Kate Scow]] 01:42, 10 March 2008 (UTC)<br />
<br />
The Rhizoplane, Rhizosphere, and Physical Environment Sections I was planning on doing have been completed by Amber. Therefore, I have changed my topics to Plant Exudates, Microbial Communities, and Mycorrhizal Fungi. Please let me know if you intend to take these topics so I do not do anymore unnecessary work. Thanks. [[User:Metotman|Metotman]] 22:28, 9 March 2008 (UTC)<br />
----<br />
<br />
<br />
I edited the outline to better match the recommendations of Prof. Scow (see below). I will be responsible for the following topics: Introduction, Rhizoplane, Physical Environment (under Rhizosphere), Fungi (under Microbial Communities), and Mycorrhizal Fungi (under Symbiotic Relationships). I will assume the rest of you are OK with this unless I hear otherwise from you. [[User:Metotman|Metotman]] 20:17, 8 March 2008 (UTC)<br />
----<br />
<br />
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----<br />
[http://www.physorg.com/news123945390.html Interesting article on mycorrhizae] that you could look into for your current research sections (you would need to find the original paper if you want to use this) [[User:Irina.chakraborty|Irina C]] 22:41, 6 March 2008 (UTC)<br />
----<br />
<br />
And of course include the inoculants as its own subheading.<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
<br />
I would suggest a modification to your outline something along these lines......<br />
# The soil environment associated with plants (?)<br />
## rhizoplane<br />
## rhizosphere (this would be bulk of your effort; under rhizosphere heading you could have..)<br />
### physical environment<br />
### plant exudates<br />
### microbial communities<br />
## other ? not really necessary<br />
# Biotic interactions in the rhizosphere<br />
## General impacts on plants of rhizosphere microorganisms<br />
## General impacts on rhizosphere microorganisms of plant<br />
## Symbiotic relationships<br />
### mycorrhizal fungi<br />
### etc.<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
-----<br />
<br />
Other members of my group- I just chose three topics because I lost the list or never wrote it down. I'm not trying to set this in stone, I can reserach whatever, just let me know) 14:52, 9 February 2008 [[user:Metotman]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Talk:Bioremediation&diff=28308
Talk:Bioremediation
2008-03-10T01:38:59Z
<p>Kmscow: </p>
<hr />
<div>would be good in intro to define in situ vs ex situ remediation. Ex situ then cover the use of bioreactors and other such systems.<br />
<br />
[[User:Kmscow|Kate Scow]] 01:38, 10 March 2008 (UTC)<br />
<br />
looking very good. Make sure you use proper scientific nomenclature for naming organisms: genus starting with caps and species name starting with lower case.<br />
<br />
Also I think it flows better to start with pollutants and put the organisms second. <br />
[[User:Kmscow|Kate Scow]] 01:36, 10 March 2008 (UTC) <br />
<br />
<br />
<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
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----<br />
<br />
Looking good! Is your source on-line? You can create an external link like [http://ucdavis.edu this]. <br />
- [[User:Irina.chakraborty|Irina C]] 22:49, 10 February 2008 (UTC)</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Talk:Bioremediation&diff=28306
Talk:Bioremediation
2008-03-10T01:36:49Z
<p>Kmscow: </p>
<hr />
<div>looking very good. Make sure you use proper scientific nomenclature for naming organisms: genus starting with caps and species name starting with lower case.<br />
<br />
Also I think it flows better to start with pollutants and put the organisms second. <br />
[[User:Kmscow|Kate Scow]] 01:36, 10 March 2008 (UTC) <br />
<br />
<br />
<br />
<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
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----<br />
<br />
Looking good! Is your source on-line? You can create an external link like [http://ucdavis.edu this]. <br />
- [[User:Irina.chakraborty|Irina C]] 22:49, 10 February 2008 (UTC)</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Talk:Geomicrobiology&diff=28302
Talk:Geomicrobiology
2008-03-10T01:29:36Z
<p>Kmscow: </p>
<hr />
<div>You don't need to geomicrobiology methods section because those methods are common to all the sections in the wiki, unless you can justify some very specific methods for geomicrobiology itself.<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
<br />
Also I don't know that the category "geomicrobiology habitats" will work well in your section unless you want to do some special environments like hot springs or volcanic soils.<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
I would suggest organizing the category process by the different elements: e.g. iron, manganese, mercury, selenium sulfur (you don't have to go too far with this, just focus on main ones)<br />
<br />
You might want to maintain that type of organization then when you talk about specific organisms OR you can have the organisms as a subcategory under each element.<br />
[[User:Kmscow|Kate Scow]]<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
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----<br />
<br />
Good start - did you look around to see if any microbes that are important to different geomicrobiology processes have pages already?<br />
<br />
[[User:Irina.chakraborty|Irina C]] 21:42, 10 February 2008 (UTC)</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Talk:Geomicrobiology&diff=28301
Talk:Geomicrobiology
2008-03-10T01:27:42Z
<p>Kmscow: </p>
<hr />
<div>Also I don't know that the category "geomicrobiology habitats" will work well in your section unless you want to do some special environments like hot springs or volcanic soils.<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
I would suggest organizing the category process by the different elements: e.g. iron, manganese, mercury, selenium sulfur (you don't have to go too far with this, just focus on main ones)<br />
<br />
You might want to maintain that type of organization then when you talk about specific organisms OR you can have the organisms as a subcategory under each element.<br />
[[User:Kmscow|Kate Scow]]<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
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----<br />
<br />
Good start - did you look around to see if any microbes that are important to different geomicrobiology processes have pages already?<br />
<br />
[[User:Irina.chakraborty|Irina C]] 21:42, 10 February 2008 (UTC)</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Talk:Geomicrobiology&diff=28299
Talk:Geomicrobiology
2008-03-10T01:25:47Z
<p>Kmscow: /* IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE */</p>
<hr />
<div>I would suggest organizing the category process by the different elements: e.g. iron, manganese, mercury, selenium sulfur (you don't have to go too far with this, just focus on main ones)<br />
<br />
You might want to maintain that type of organization then when you talk about specific organisms OR you can have the organisms as a subcategory under each element.<br />
[[User:Kmscow|Kate Scow]]<br />
=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
* Add new comments to the TOP of the discussion page, so that we have newest comments first.<br />
* After your comment, type four tilde marks ( &#126;&#126;&#126;&#126; ). This displays the time and your user name, so that we can tell who left the comment and when.<br />
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----<br />
<br />
Good start - did you look around to see if any microbes that are important to different geomicrobiology processes have pages already?<br />
<br />
[[User:Irina.chakraborty|Irina C]] 21:42, 10 February 2008 (UTC)</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Talk:Nitrogen_Cycle&diff=28295
Talk:Nitrogen Cycle
2008-03-10T01:19:32Z
<p>Kmscow: </p>
<hr />
<div>=== IMPORTANT NOTE ON ADDING COMMENTS TO DISCUSSION PAGE ===<br />
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----<br />
Good start. A couple of comments. N cycle is biogeochemical not just chemical cycle. Also add that nitrate is then converted to N2 gas and then everything repeats itself. <br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
<br />
Great start! See if you can find some key nitrogen cycle organisms on the microbewiki and create links to their pages. Then start a page for a new microbe by using the code of an existing page as a template and editing the content. Remember to cite your sources!<br />
<br />
[[User:Irina.chakraborty|Irina C]] 21:45, 10 February 2008 (UTC)<br />
----<br />
I would suggest putting the microbes involved under each subheading. you can have nitrosomonas/nitrobacter and archaea under nitrification. Facultative anaerobes under denitr. Just mention breadth of organisms involved in immob/mineralization and why there is that breadth.<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
For global warming, you can find lots of good links for greenhouse gases. One good one would be good.<br />
[[User:Kmscow|Kate Scow]]<br />
----<br />
Remember to cite references for your information, especially for somewhat unique info (like alternative nitrogenases)<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
----<br />
hi, you really know your N! <br />
looks real good. I was going to suggest considering "Introduction" for #1. -Paul W<br />
----<br />
<br />
I would suggest putting C/N ratio under the category of immobilization as it is a subtopic of this process.<br />
[[User:Kmscow|Kate Scow]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Talk:Flooded_Soils&diff=27502
Talk:Flooded Soils
2008-02-26T18:16:39Z
<p>Kmscow: </p>
<hr />
<div>* You don't need to have a list of topics because that is automatically created for you at the top of the page.<br />
* Please put back the text that says "crated by the students of Kate Scow" at the bottom of the template page<br />
* You don't need to sign your names at the end. We can see who did what by looking at the history of the page. Also, Laleh's name is mentioned but it doesn't look like she's logged in. Please make sure you log in and make edits through your own account, since otherwise we can't tell who did what.<br />
[[User:Irina.chakraborty|Irina C]] 19:05, 8 February 2008 (UTC)<br />
<br />
I would suggest slightly different organization.<br />
<br />
Maybe under flooded soils could be....<br />
<br />
1. Overall definition and description of phenomenon of flooded soils. You can put a figure here. You can also say that this type of phenomenon can also be observed in other types of situations.....aggregates and pollutant plumes in groundwater<br />
<br />
2. Chemical changes<br />
<br />
Make sure you focus this on redox. organize these by changes in dominant electron acceptors being used and make the connection to electron tower<br />
ALso include fate of products generated during electron acceptor untilization. e.g. methane migrates up. Sulfides.....<br />
<br />
3. Changes in microbial community composition<br />
<br />
4. Changes when the flooded soil is unflooded and oxygen comes in<br />
<br />
Maybe something else??<br />
<br />
[[User:Kmscow|Kate Scow]]</div>
Kmscow
https://microbewiki.kenyon.edu/index.php?title=Talk:Carbon_cycle&diff=27501
Talk:Carbon cycle
2008-02-26T17:40:03Z
<p>Kmscow: </p>
<hr />
<div>You don't need to have an Edits and Dates section at the end either - all this information is collected under "History". I noticed you wrote "Jaime and Alex". I can see that Jaime made edits but not Alex. So please make sure you log in yourselves when editing, so that we can attribute work - [[User:Irina.chakraborty|Irina C]] 22:52, 10 February 2008 (UTC)<br />
<br />
Good start - You don't need to have a list of your sections at the start of your page because a content list is automatically generated if you use heading formats for the title of each section. Also you used internal link formatting for the items in "List of Topics". You only need to do this if you are creating new pages for each item - this would make sense if we were going to add a lot of detail. Instead each item is just a section within your page, so does not require a link to its own page.<br />
<br />
[[User:Irina.chakraborty|Irina C]] 22:22, 10 February 2008 (UTC)<br />
<br />
<br />
Has anyone seen the template for our page we need to write about a microbe? Jess and I have gone through and put in a bunch of links, but I'm not sure how to create an entirely new page. (~Jaime)<br />
<br />
I would suggest not breaking out geo/bio/hydro/atmosphere unless you really want to go into detail about this. Please include the 2 main sections in the lecture:<br />
<br />
1. Decomposition of organic matter--<br />
and then cover all the different chemical components of plant materials e.g. monomers, cellulose, hemicellulose, lignin, etc<br />
2. Formation of humic substances<br />
<br />
[[User:Kmscow|Kate Scow]]<br />
<br />
You might want to link the microbial types directly to the processes rather than split it out alone.<br />
<br />
E.g. cellulose decomposition is where you would discuss a little about the organisms involved and you can link this to the organisms already listed in the wiki. A lot of these organisms start with "cellu"<br />
<br />
[[User:Kmscow|Kate Scow]]</div>
Kmscow