Soil Environment: Difference between revisions

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==I. Introduction==
==Introduction==


The soil environment consists of a variety of physical, biological and chemical factors that affect the abundance and diversity of microbes found in the soil. [4] At its basic level, the soil environment consists of a solid  and porous fraction. Within these fractions, a variety of chemical and physical factors are affected by and and affect microbes. These include, but are not limited to texture, temperature, pH, oxygen, cation exchange capacity and redox reactions.  
The soil environment consists of a variety of physical, biological and chemical factors that affect the abundance and diversity of microbes found in the soil. [4] At its basic level, the soil environment consists of a solid  and porous fraction. Within these fractions, a variety of chemical and physical factors are affected by and and affect microbes. These include, but are not limited to texture, temperature, pH, oxygen, cation exchange capacity and redox reactions.  
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The soil environment directly affects the types of microbes, as well as the rates of processes they perform. For example, microbial activity increases with temperature, which in turn affects rates of decomposition. On the other hand, microbial processes directly affect their environments as well, contributing to the carbon and nitrogen cycles, which are important for microbial and plant health. [5] At the micro scale, bacteria and other microbes participate in a variety of reactions that affect nutrient cycling, pH, as well as oxygen and CO2 content. At the macro scale, these processes can change the landscape in drastic ways, assisting in weathering of the soil and development of soil layers.
The soil environment directly affects the types of microbes, as well as the rates of processes they perform. For example, microbial activity increases with temperature, which in turn affects rates of decomposition. On the other hand, microbial processes directly affect their environments as well, contributing to the carbon and nitrogen cycles, which are important for microbial and plant health. [5] At the micro scale, bacteria and other microbes participate in a variety of reactions that affect nutrient cycling, pH, as well as oxygen and CO2 content. At the macro scale, these processes can change the landscape in drastic ways, assisting in weathering of the soil and development of soil layers.


==II. Soil Environment Overview==
==Soil Environment Overview==
===Solid Fraction===
===Solid Fraction===
The solid fraction of the soil consists of mineral and organic matter, which is typically about 50% of the soil by volume (see figure 1), and it has a dominant influence on heat, water, and chemical transport and retention process. [4] Most of the solid particles are derived from mineral sources such as decomposed rocks or sediments. [13] Soil organic matter (SOM) consists of all of the organic components of a soil, including living biomass, decomposing tissue, and fully decomposed tissue called humus. [5] The rate and pathway of carbon decomposition and SOM formation directly affects the carbon cycle . Texture can also influence chemical properties such as cation exchange capacity (CEC). Finer textured soils with high clay content will have great CEC than soils with low clay content.
The solid fraction of the soil consists of mineral and organic matter, which is typically about 50% of the soil by volume (see figure 1), and it has a dominant influence on heat, water, and chemical transport and retention process. [4] Most of the solid particles are derived from mineral sources such as decomposed rocks or sediments. [13] Soil organic matter (SOM) consists of all of the organic components of a soil, including living biomass, decomposing tissue, and fully decomposed tissue called humus. [5] The rate and pathway of carbon decomposition and SOM formation directly affects the carbon cycle . Texture can also influence chemical properties such as cation exchange capacity (CEC). Finer textured soils with high clay content will have great CEC than soils with low clay content.
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===Soil Pores===
===Soil Pores===
Soil pores consist of the air and water filled fractions of the soil, and together they make up about 50% of the soil by volume. Pore space is largely determined by size and arrangement of aggregates and affects the movement of water, air, and organisms in soil. Soil pores are typically classified based on size: Macropores ( >75um) Mesopores ( 30-70um) Micropores ( 5-30um) Ultramicropores (0.1-5um) Cryptoporus ( <0.1um). [5]
Soil pores consist of the air and water filled fractions of the soil, and together they make up about 50% of the soil by volume. Pore space is largely determined by size and arrangement of aggregates and affects the movement of water, air, and organisms in soil. Soil pores are typically classified based on size: Macropores ( >75µm) Mesopores ( 30-70µm) Micropores ( 5-30µm) Ultramicropores (0.1-5µm) Cryptoporus ( <0.1µm). [5]


The air filled pores of the soil typically have a similar distribution of gases as the atmosphere above the soil, with slightly lower oxygen and slightly more CO2. The soil atmosphere consists of about 18-20% oxygen near the surface, which decreases with depth. CO2 is around 1%, and N2 is about 78% of the soil air filled pore space. [5] Oxygen (O2) content will be lower when available carbon is high (high O2 demand). Soil that is high in clay content and/or compacted may have trouble exchanging gases to the atmosphere. Soil air generally has a very high moisture content when compared to the atmosphere (~100% unless the soil is very dry). The amount and composition of air in a soil is largely determined by the water content in the soil. [4]
The air filled pores of the soil typically have a similar distribution of gases as the atmosphere above the soil, with slightly lower oxygen and slightly more CO2 due to the respiration of microorganisms. The soil atmosphere consists of about 18-20% oxygen near the surface, which decreases with depth. CO2 is around 1%, and N2 is about 78% of the soil air filled pore space. [5] Oxygen content will be lower when available carbon is high (demand for high O2 to utilize carbon). Soil that is high in clay content and/or compacted may have trouble exchanging gases to the atmosphere. Soil air generally has a very high moisture content when compared to the atmosphere (~100% unless the soil is very dry). The amount and composition of air in a soil is largely determined by the water content in the soil. [4]


The main source of soil water is rainfall and overland flow. The amount of water that enters the soil is a function of soil structure and texture.  Water moves in soil through mass flow and capillary action. The water in soil is often called the soil solution, which can move nutrients from the surface through the soil column. The water fraction of the pores is typically between 20 to 30% but can vary depending on precipitation, soil texture, and soil structure. The water content of a soil influences gas exchange, controls movement and concentrations of nutrients, and buffers the temperature of the soil. [5]
The main source of soil water is rainfall and overland flow. The amount of water that enters the soil is a function of soil structure and texture.  Water moves in soil through mass flow and capillary action. The water in soil is often called the soil solution, which can move nutrients from the surface through the soil column. The water fraction of the pores is typically between 20% to 30% but can vary depending on precipitation, soil texture, and soil structure. The water content of a soil influences gas exchange, nutrient movement and concentrations of nutrients, and buffers the temperature of the soil. [5]


===Soil Aggregates & Structure===
===Soil Aggregates & Structure===
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Soil structure is the arrangement of primary soil particles into aggregates which describes the arrangement of the solid parts of the soil and the pore spaces between them. Soil structure has a major influence on water movement, SOM leaching, and gas exchanges of the soils. The water movement, affected by structure can bring SOM in the surface to deep inside the soil. Soil with high clay content and/or poor structure, may have reduced infiltration and will cause runoff, erosion and surface crusting. [11] This can cause nutrient loss and increase the potential of desertification.
Soil structure is the arrangement of primary soil particles into aggregates which describes the arrangement of the solid parts of the soil and the pore spaces between them. Soil structure has a major influence on water movement, SOM leaching, and gas exchanges of the soils. The water movement, affected by structure can bring SOM in the surface to deep inside the soil. Soil with high clay content and/or poor structure, may have reduced infiltration and will cause runoff, erosion and surface crusting. [11] This can cause nutrient loss and increase the potential of desertification.


==III. Physical & Chemical Factors that Control Biological Activity in the Soil==
==Physical & Chemical Factors that Control Biological Activity in the Soil==




===Soil Texture===  
===Texture===  


Soil texture is defined as the distribution of sand (0.05-2.0 mm), silt (0.002-0.05mm), and clay ( < 0.002mm) in soil. Soil texture indirectly influences  properties such as: water holding capacity, porosity, aeration and nutrient availability. Clay particles have a very high surface to volume ratio, which makes them very chemically active and have high nutrient availability. Due to the adhesion of water, soils high in clay will also have a high water holding capacity. Soils with a high clay content will often have a very active microbial community, especially in areas  the rhizosphere. [5]
Soil texture is defined as the distribution of sand (0.05-2.0 mm), silt (0.002-0.05mm), and clay ( < 0.002mm) in soil. Soil texture indirectly influences  properties such as: water holding capacity, porosity, aeration and nutrient availability. Clay particles have a very high surface to volume ratio, which makes them very chemically active and have high nutrient availability. Due to the adhesion of water, soils high in clay will also have a high water holding capacity. Soils with a high clay content will often have a very active microbial community, especially in areas  of the rhizosphere. [5]


One study by Hamarshid 2010 found that CO2 production rates were greatest in fine textured soil compared to coarse textured soil. [6] This was due to finer textured soils’ greater ability to hold nutrients and water, allowing microbial populations to thrive. However, this is not always the case, as other chemical or physical properties may affect the ability of microbes to perform processes such as carbon decomposition. (e.g. temperature, pH and quality of substrate).
One study by Hamarshid found that CO2 production rates were greatest in fine textured soil compared to coarse textured soil. [6] This was due to finer textured soils’ greater ability to hold nutrients and water, allowing microbial populations to thrive. However, this is not always the case, as other chemical or physical properties may affect the ability of microbes to perform processes such as carbon decomposition. (e.g. temperature, pH and quality of substrate).


===Temperature===  
===Temperature===  
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===pH===
===pH===
pH changes in soils is due to both biotic and abiotic processes. Microbes consume and release H+ through redox reactions and fermentation. Abiotic processes such as rainfall can also affect the pH of the soil. In areas of high rainfall, acidic soils can be created through leaching of bases from the soil, while more basic soils are typically located in arid environments. One study by Fierer et al. found that pH was the single most important factor influencing microbial diversity at the continental scale. [10] The study used 98 samples from across North and South America, and found that the greatest microbial diversity coincided with a neutral pH, even between two soil from the same forest.
pH change in soils is due to both biotic and abiotic processes. Microbes consume and release H+ through redox reactions and fermentation. Abiotic processes such as rainfall can also affect the pH of the soil. In areas of high rainfall, acidic soils can be created through leaching of bases from the soil, while more basic soils are typically located in arid environments. One study by Fierer et al, found that pH was the single most important factor influencing microbial diversity at the continental scale. [10] The study used 98 samples from across North and South America, and found that the greatest microbial diversity coincided with a neutral pH, even between two soil from the same forest.


pH affects microbial diversity because many microbial species cannot tolerate extreme levels of pH (high or low). Alterations in pH can render essential microbe enzymes inactive and/or denature proteins within the cells and prevent microbial activity from occurring. [4] However, there are microbes that can withstand extreme pH environments. At pH below 5, fungi and acidophilic bacteria have a competitive advantage over other bacteria that thrive at a more neutral pH.
pH affects microbial diversity because many microbial species cannot tolerate extreme levels of pH (high or low). Alterations in pH can render essential microbe enzymes inactive and/or denature proteins within the cells and prevent microbial activity from occurring. [4] However, there are microbes that can withstand extreme pH environments. At pH below 5, fungi and acidophilic bacteria have a competitive advantage over other bacteria that thrive at a more neutral pH.
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The amount of oxygen available in a soil depends on a number of factors, including soil porosity, water content, and consumption by respiring organisms. If soil pores are large and interconnected, oxygen can flow easily. However, even in a well aerated soil, micro-aggregates may contain anaerobic zones in which oxygen flow is very limited. In a flooded soil environment oxygen content will be very limited because oxygen diffuses about 10,000 times more slowly through water than through air. [4]
The amount of oxygen available in a soil depends on a number of factors, including soil porosity, water content, and consumption by respiring organisms. If soil pores are large and interconnected, oxygen can flow easily. However, even in a well aerated soil, micro-aggregates may contain anaerobic zones in which oxygen flow is very limited. In a flooded soil environment oxygen content will be very limited because oxygen diffuses about 10,000 times more slowly through water than through air. [4]


In areas where oxygen is not present, soil microbes may use alternative electron acceptors such as nitrate, manganese, iron, sulfate, and carbon dioxide. An example of the result of the use of an alternative electron acceptor can be seen in figure 8.
In areas where oxygen is not present, soil microbes may use alternative electron acceptors such as nitrate, manganese, iron, sulfate, and carbon dioxide. An example of the result of the use of an alternative electron acceptor can be seen in figure 7.


[[Image:Soilenv_fig7.jpeg‎‎|250px|thumb|right|Figure 7. Without oxygen, bacteria can potentially use iron as an electron acceptor, reducing it, and creating the blue/gray soil in the photo. The mottled red areas are the result of oxygen getting in (perhaps through root canals) and oxidizing the iron. [3]
[[Image:Soilenv_fig7.jpeg‎‎|250px|thumb|right|Figure 7. Without oxygen, bacteria can potentially use iron as an electron acceptor, reducing it, and creating the blue/gray soil in the photo. The mottled red areas are the result of oxygen getting in (perhaps through root canals) and oxidizing the iron. [3]
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[[Image:Soilenv_fig8.jpeg‎‎|250px|thumb|left|Figure 8. Figure 9 : Cation exchange capacity and anion exchange capacity of a soil as function of soil pH. [9]]]
[[Image:Soilenv_fig8.jpeg‎‎|250px|thumb|left|Figure 8. Figure 9 : Cation exchange capacity and anion exchange capacity of a soil as function of soil pH. [9]]]


==Biological Factors==
===Redox Reactions===


===Soil Fauna===
Reduction-oxidation (redox) reactions are chemical reactions in which reactants experience a change in oxidation number (which means these reactants either gain or lose electrons) . Many reactions in the soil involve the gain or loss of electrons, obtaining or releasing energy. Redox reactions are important in the soil, because microbes obtain energy through redox reactions for their metabolism, and the redox state can also determine the microbial processes that will occur.  
Soil animals are divided into macrofauna (>2 mm, earthworms), mesofauna (0.1-0.2 mm, mites and nematodes), and microfauna (<0.1 mm, protozoa). These eukaryotes have a range of effects on microbial communities:
:*Grazing: Grazing increases decomposition rates, freeing nutrients. Grazing also includes direct consumption of other organisms. 
:*Nutrient cycling: Soil fauna is responsible for up to 30% of the total soil mineralizable nitrogen. Additionally, soil fauna can remobilize nutrients as waste products. This allows for increases in microbial growth.
:*Microbial community composition: Other organisms in the community are directly effected through consumption. Some soil fauna feed selectively, consuming certain organisms instead of others. This changes the makeup of the microbial community.


In addition to these direct effects, soil fauna has several indirect effects on microbes. One of these effects is habitat alteration. Earthworms especially alter the soil habitat through the formation of burroughs, which changes gas exchange, water movement, and resource locations. Microorganisms are sensitive to the presence of oxygen in their enviroment, and water is essential for microbial existence. Changes in resource locations may allow for microorganisms to colonize another area. [1]
Redox reactions include anabolism and catabolism process, both of which play important roles in microbial metabolism. Anabolism is the biosynthesis of cellular components, linked to energy requirements, while catabolism is the the biochemical processes leading to breakdown of organic substances, linked to energy production. For example, the photosynthesis and respiration processes are the coupled reactions in the soil, where plants required energy from light and reduce carbon dioxide to glucose, which then be used by microbes in the soil as the energy for their metabolism.  


===Organism Interactions===
The tendency of compounds to accept or donate electrons is expressed as “redox potential”. Redox potential (Eh), determined from the concentration of oxidants and reductants in the environment, is to measure the oxidation-reduction status and electron availability within this system. Electrons are essential to all inorganic and organic chemical reactions. Redox potential measurements allow for rapid characterization of the degree of reduction and for predicting stability of various compounds that regulate nutrients and metal availability in soil and sediment. The inorganic oxidants include oxygen, nitrate, nitrite, manganese, sulfate, and CO2, while the reductants include various organic substrates and reduced inorganic compounds (NH4+, Fe2+, Mn2+, S2-, CH4, and H2). [15]
There are several types of interactions between organisms. The table below outlines the positive, negative, and neutral aspects that each organism receives as a result of the interaction. These interactions can create environments that promote or discourage specific microbial growth.
{|
!-
Interaction Type 
!-
Population 1
!-
Population 2
!-
Example 
|-
| Mutualism (symbiosis)
|align="center" | + 
|align="center" | +
|align="left" | Rhizobia/legumes, [[Rhizosphere: environment and mycorrhizal fungi| mycorrhizal fungi/most plants]] ([[Bradyrhizobium]]), fungi/green algae, fungi/cyanobacteria ([[Anabaena]])
|-
| Commensalism              
|align="center" | +   
|align="center" | 0
|align="left" | Aerobic oxygen consumption creates an anaerobic environment to support anaerobes
|-
|Synergism              
|align="center" | +          
|align="center" | + or 0
|align="left" | [[Flooded soils]]: fermenters provide carbon and hydrogen gas for [methanogens]] and sulfate reducers ([[Desulfosarcina]]), which in turn reduce toxic effects of acetate and hydrogen gas to fermenters
|-
|Amensalism
|align="center" | -          
|align="center" | + or 0
|align="left" | Production of acidic or toxic chemicals
|-
|Predation
|align="center" | -
|align="center" | +
|align="left"  | Protozoa, nematodes, and slime molds are all major soil predators that consume bacteria
|-
|Competition (antagonism)    
|align="center" | -            
|align="center" | +
|align="left"  | Growth rates that allow for utilization of a resource before a competitor
|-
|Parasitism              
|align="center" | -            
|align="center" | +
|align="left"  | Viruses
|}
[1, 2]


===Bioavailability===
The redox potential of a substance depends on Affinity of molecules for electrons and Concentration of reductants and oxidants (referred to as  redox pair)
Bioavailability is a term that refers to the availability of a soil substrate (both nutrients and toxins) to an organism. The EPA lists this definition of bioavailability:
Anaerobic environments such as wetland soils and flooded soils are usually limited by electron acceptors and have an abundant supply of electron donors. In this case, most microbes’ activity is limited, and facultative and obligate microbes reduce the minerals following the electron tower. Aerated soils are usually limited by electron donors and have an abundant supply of electron acceptors (primarily O2). [15]
: “The term bioavailability designates the state of that fraction of a chemical that is available for uptake and/or transformation by living organisms. Although associated primarily with ecotoxicology, and usually in reference to organic and metallic pollutants, the term bioavailability is also relevant to native organic material. Thus, the “problem” of bioavailability, has existed for microorganisms far longer than has the presence of xenobiotic chemicals in the environment. Sorption, insolubility, and related processes are largely responsible for controlling bioavailability of many pollutants to microorganisms in soils and sediments” [3].


Bioavailability is of special interest to environmental groups because of it's correlation with [[bioremediation]]. A common assumption made when discussing bioavailability is that only what is in solution can be metabolized. There are three major factors that effect bioavailability:
===Salinity===
:*Sorption: how a substrate bonds to surfaces, especially charged surfaces such as clay and organic matter.
:*Solubility: the capacity for a substance to dissolve in solution. (Insolubility refers to a substance that is unable to dissolve.)
:*Chemical speciation: some substrates may be less available at certain pH or are less available because of charge [2]


===Plant Growth-Promoting Rhizobacteria (PGPR)===
Soil salinity refers to the salt content in the soil. The concentrations and types of ions in solution in the soil can cause modifications in the dispersion of the clay fraction, degrading the original soil fraction. The sodium ion, being monovalent, increases the width of the diffuse double layer on the surface of the clays, reducing the attractive forces between them with a consequent increase in particle dispersion. [16] The consequence of this dispersion of the clay is also shown by a reduction in stability of the soil aggregates, which are thus easily transported by rain or irrigation.  
Rhizobacteria colonize roots. PGPR bacteria colonization promotes plant growth and seed germination and helps plants resist environmental stresses and diseases. Harmful root colonization is caused by deleterious [[Rhizosphere: environment and mycorrhizal fungi| rhizosphere]] microorganisms (DRMO). DRMO bacteria remove water and nutrients from the plant supply. PGPR bacteria are able to promote plant growth by colonizing before and thus preventing the colonization of DRMO. [[Pseudomonas]] is a genus containing many PGPR bacteria. [[Azotobacter]] and Azospirillum are also PGPR bacteria because of their production of gibberellic and indoleacetic acid, which are plant growth-stimulating hormones. [1]


==Relevant Organisms==
Soil salinization is a big problem for soils in arid or semi-arid regions and agricultural soils throughout the world. [5] Salts can adversely affect plant and microbial growth, due to destruction of the soil structure and its consequent compacting. The stress of high salt concentration can be detrimental for sensitive microorganisms and decrease the activity of surviving cells, due to the metabolic load imposed by the need for stress tolerance mechanisms.
Acidobacterium capsulatum - it was found in acid mine drainage (AMD)
[[Image:acidobacteria.jpg|thumb|500px|right|Acidobacterium capsulatum picture [13]]]  


[[Sinorhizobium meliloti]] is isolated from soil, which synthesizes an extracellular polymer that facilitates the transport of such hydrophobic pollutants as polynuclear aromatic hydrocarbons, as well as the toxic metals lead and cadmium in soil.[9]
===Bioavailability===
 
Some microbial environments are extreme for life. Organisms inhabiting extreme environments are called extremophiles. Extremophilic microorganisms could be found in the harsh environment, such as hot springs, ice-covered lakes, salty water, and in soils or waters with pH lower than 0 or as high as 12. Those microorganisms cannot live without the extreme environment.[10] One of recent discovery is [[Spirochaeta Americana]].
{| class="wikitable"
 
|-
 
! Extreme condition                       
 
! Descriptive term
 
! Genus/ species
 
! Domain
 
|-
 
| High temperature                     
 
| Hyperthermophile
 
| Pyrolobus fumarii
 
| Archaea
|-
 
| Low temperature                       
 
| Psychophile
 
| olaromonas vacuolata
 
| Bacteria
|-
 
| Low pH                                   
| Acidophile
 
| [[Picrophilus]] oshimae
 
| Archaea
|-
 
| High pH                                 
 
| Alkaliphile 
 
| Natronobacterium
 
| Archaea
|-
 
| Pressure                             
| Barophile 


| Moritella yayanosii
Bioavailability assesses what proportion of a contaminant present at a contaminated site is available for uptake by organisms. Bioavailability processes are the biological, chemical and physical processes that result in an organism being exposed to a contaminant present in the soil. These processes are: release of
the contaminant from the solid phase, transport of the contaminant to and across a biological
membrane and, incorporation into a living organism. [18]


| Bacteria
Bioavailable molecules must cross a biological membrane, which means the molecules have to interact with the aqueous phase. Therefore, soil properties which control partitioning between the solid phase in soil and the pore water, such as pH, organic matter content, Eh, cation exchange capacity (CEC), and the concentration of clay minerals, have a significant impact on bioavailability. Increasing exchange sites aids the retention of molecules in the pore water in a bioavailable form, but molecules sorbed strongly to surfaces or in solid form are generally not bioavailable. [18]
|-
 
| Salt                                         
   
| Halophile
 
| [[Halobacterium]]  
 
| Archaea
 
|}


==Current Research==
==Current Research==


To find out what is new in the according to the American Academy of Microbiology (AAM) click: http://www.asm.org/Academy/index.asp
Soil functions are hugely influenced by soil aggregate properties like strength and porosity. The effect of soil management on soil aggregation can assist in determining best management practices. One study sought to quantify the long-term effect of rotation and tillage on aggregate shape , strength and pore characteristics. [8] Soil samples were taken from a long-term rotation and tillage trial with both continuous and diverse rotations. The size of these soil samples were determined by X-ray micro-CT, and the study concluded several findings :


An Overview of Extremophiles:
- Rotation and tillage effect on aggregate and bulk soil    properties


" Prokaryotic extremophiles were the first representatives of life on Earth and they are responsible for the genesis of geological structures during the evolution and creation of all currently known ecosystems. Flexibility of the genome probably allowed life to adapt to a wide spectrum of extreme environments. As a result, modern prokaryotic diversity formed in a framework of physico-chemical factors, and it is composed of: thermophilic, psychrophilic, acidophilic, alkaliphilic, halophilic, barophilic, and radioresistant species. This artificial systematics cannot reflect the multiple actions of different environmental factors since one organism could unite characteristics of several extreme-groups. In this review we show the current status of studies in all fields of extremophiles and summarize the limits of life for different species of microbial extremophiles. We also discuss the finding of extremophiles from unusual places such as soils, and briefly review recent studies of microfossils in meteorites in the context of the significance of microbial extremophiles to Astrobiology." [11]
- Rotation affected soil aggregate properties more than tillage.


 
- Tillage have a stronger effect on bulk soil porosity
Molecular Genetics from Michigan State University:
 
" Bacteria in the phylum Acidobacteria are widely distributed and abundant in soils, but their ecological roles are poorly understood, owing in part to a paucity of cultured representatives. In a molecular survey of acidobacterial diversity at the Michigan State University Kellogg Biological Station Long-Term Ecological Research site, 27% of acidobacterial 16S rRNA gene clones in a never-tilled, successional plant community belonged to subdivision 1, whose relative abundance varied inversely with soil pH. Strains of subdivision 1 were isolated from these never-tilled soils using low-nutrient medium incubated for 3 to 4 weeks under elevated levels of carbon dioxide, which resulted in a slightly acidified medium that matched the pH optima of the strains (between 5 and 6). Colonies were approximately 1 mm in diameter and either white or pink, the latter due to a carotenoid(s) that was synthesized preferentially under 20% instead of 2% oxygen. Strains were gram-negative, aerobic, chemo-organotrophic, nonmotile rods that produced an extracellular matrix. All strains contained either one or two copies of the 16S rRNA encoding gene, which along with a relatively slow doubling time (10 to 15 h at ca. 23°C) is suggestive of an oligotrophic lifestyle. Six of the strains are sufficiently similar to one another, but distinct from previously named Acidobacteria, to warrant creation of a new genus, Terriglobus, with Terriglobus roseus defined as the type species. The physiological and nutritional characteristics of Terriglobus are consistent with its potential widespread distribution in soil." [12]
 
 
 
Andrew D. Cartmill, Luis A. Valdez-Aguilar, Donita L. Bryan and Alejandro Alarcon, Arbuscular mycorrhizal fungi enhance tolerance of vinca to high alkalinity in irrigation water, Scientia HorticulturaeVolume 115, Issue 3, , 1 February 2008, Pages 275-284.
(http://www.sciencedirect.com/science/article/B6TC3-4PYRKM2-1/2/64bcf8c9a8286c08606ec95ada501b97)
 
==Apendix==
[[Image:Soilenv_figure3.jpeg‎|350px|thumb|middle|Figure 3. Diagram that is used to determine soil texture class if percent sand, silt and clay are known. [11]]]


==References==
==References==
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<http://www.cmg.colostate.edu/>
<http://www.cmg.colostate.edu/>


14.
14. “BIO 212 Study Guide”. Iowa State University.
<https://www.studyblue.com/notes/note/n/bio-212-study-guide-2012-13-yin/deck/9716305>
 
15. Delaune, R. D., and Reddy, K, R., Encyclopedia of Soils in the Environment. 2005, Elsevier Ltd.
 
16. Maganhotto, C. M.,and Francisconi Fay,E., (2012). Effect of Salinity on Soil Microorganisms, Soil Health and Land Use Management, Dr. Maria C. Hernandez Soriano (Ed.), InTech, Available from: http://www.intechopen.com/books/soil-health-and-land-usemanagement/Effect-of-salinity-on-soil-microorganisms


17. Provin, T., and Pitt, J. L. “Managing Soil Salinity”. Texas AgriLife Extension Service. March, 2012.
<http://soiltesting.tamu.edu/publications>
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]
18. Hodson, M. E., Vijver, M. G. and Peijnenberg, W. J. G. M. (2011) Bioavailability in soils. In: Swartjes, F. A. (ed.) Dealing  with contaminated sites: from theory towards practical application. Springer, pp. 721-746. ISBN 9789048197569 doi:  10.1007/978-90-481-9757-6 Available at http://centaur.reading.ac.uk/20839/


<!-- Do not edit or remove this line --> [[Category:Pages edited by students of Kate Scow at UC Davis]]
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Soil env title.jpeg

Introduction

The soil environment consists of a variety of physical, biological and chemical factors that affect the abundance and diversity of microbes found in the soil. [4] At its basic level, the soil environment consists of a solid and porous fraction. Within these fractions, a variety of chemical and physical factors are affected by and and affect microbes. These include, but are not limited to texture, temperature, pH, oxygen, cation exchange capacity and redox reactions.

The soil environment directly affects the types of microbes, as well as the rates of processes they perform. For example, microbial activity increases with temperature, which in turn affects rates of decomposition. On the other hand, microbial processes directly affect their environments as well, contributing to the carbon and nitrogen cycles, which are important for microbial and plant health. [5] At the micro scale, bacteria and other microbes participate in a variety of reactions that affect nutrient cycling, pH, as well as oxygen and CO2 content. At the macro scale, these processes can change the landscape in drastic ways, assisting in weathering of the soil and development of soil layers.

Soil Environment Overview

Solid Fraction

The solid fraction of the soil consists of mineral and organic matter, which is typically about 50% of the soil by volume (see figure 1), and it has a dominant influence on heat, water, and chemical transport and retention process. [4] Most of the solid particles are derived from mineral sources such as decomposed rocks or sediments. [13] Soil organic matter (SOM) consists of all of the organic components of a soil, including living biomass, decomposing tissue, and fully decomposed tissue called humus. [5] The rate and pathway of carbon decomposition and SOM formation directly affects the carbon cycle . Texture can also influence chemical properties such as cation exchange capacity (CEC). Finer textured soils with high clay content will have great CEC than soils with low clay content.

Figure 1. Volume composition of the solid and porous fractions of a typical loam surface soil. [5]

Soil Pores

Soil pores consist of the air and water filled fractions of the soil, and together they make up about 50% of the soil by volume. Pore space is largely determined by size and arrangement of aggregates and affects the movement of water, air, and organisms in soil. Soil pores are typically classified based on size: Macropores ( >75µm) Mesopores ( 30-70µm) Micropores ( 5-30µm) Ultramicropores (0.1-5µm) Cryptoporus ( <0.1µm). [5]

The air filled pores of the soil typically have a similar distribution of gases as the atmosphere above the soil, with slightly lower oxygen and slightly more CO2 due to the respiration of microorganisms. The soil atmosphere consists of about 18-20% oxygen near the surface, which decreases with depth. CO2 is around 1%, and N2 is about 78% of the soil air filled pore space. [5] Oxygen content will be lower when available carbon is high (demand for high O2 to utilize carbon). Soil that is high in clay content and/or compacted may have trouble exchanging gases to the atmosphere. Soil air generally has a very high moisture content when compared to the atmosphere (~100% unless the soil is very dry). The amount and composition of air in a soil is largely determined by the water content in the soil. [4]

The main source of soil water is rainfall and overland flow. The amount of water that enters the soil is a function of soil structure and texture. Water moves in soil through mass flow and capillary action. The water in soil is often called the soil solution, which can move nutrients from the surface through the soil column. The water fraction of the pores is typically between 20% to 30% but can vary depending on precipitation, soil texture, and soil structure. The water content of a soil influences gas exchange, nutrient movement and concentrations of nutrients, and buffers the temperature of the soil. [5]

Soil Aggregates & Structure

Soil aggregates are groups of soil particles that bind to each other more strongly than to adjacent particles. The space between the aggregates provide pore space for retention and exchange of air and water. Aggregation affects erosion, movement of water, and plant root growth. [7] Polysaccharides produced by soil bacteria, and humic substances and hyphae produced by fungi improve aggregation.

Figure 2. A soil aggregate at the micro and macro scale. [11]

Soil structure is the arrangement of primary soil particles into aggregates which describes the arrangement of the solid parts of the soil and the pore spaces between them. Soil structure has a major influence on water movement, SOM leaching, and gas exchanges of the soils. The water movement, affected by structure can bring SOM in the surface to deep inside the soil. Soil with high clay content and/or poor structure, may have reduced infiltration and will cause runoff, erosion and surface crusting. [11] This can cause nutrient loss and increase the potential of desertification.

Physical & Chemical Factors that Control Biological Activity in the Soil

Texture

Soil texture is defined as the distribution of sand (0.05-2.0 mm), silt (0.002-0.05mm), and clay ( < 0.002mm) in soil. Soil texture indirectly influences properties such as: water holding capacity, porosity, aeration and nutrient availability. Clay particles have a very high surface to volume ratio, which makes them very chemically active and have high nutrient availability. Due to the adhesion of water, soils high in clay will also have a high water holding capacity. Soils with a high clay content will often have a very active microbial community, especially in areas of the rhizosphere. [5]

One study by Hamarshid found that CO2 production rates were greatest in fine textured soil compared to coarse textured soil. [6] This was due to finer textured soils’ greater ability to hold nutrients and water, allowing microbial populations to thrive. However, this is not always the case, as other chemical or physical properties may affect the ability of microbes to perform processes such as carbon decomposition. (e.g. temperature, pH and quality of substrate).

Temperature

Soil temperature changes with depth: the surface soil (~0-20cm) is highly affected by the solar radiation. Moving deeper (~below 27cm) temperatures are very stable over time (see figure 5). This is because heat moves in soil mainly by conduction, which does not allow much heat to reach deep in the soil profile. Soil temperature is also affected by the soil color, soil cover, and the water content of the soil. A darker soil can absorb more heat compared to lighter color soil. A dry soil is more easily heated than a wet one due to the higher heat capacity of water. Heat moving in soil is analogous to the movement of water. [5] Generally, the higher the temperature, the more active microbes are, with microbial activity typically doubling with a 10° rise in temperature. However, some bacteria thrive at very low temperatures (psychrophiles) and very high temperatures (extremophiles), which can be seen in figure 6. [4]

Figure 4. Soil temperature fluctuation as a function of depth. [5]
Figure 5. Microbial growth rate as a function of temperature for different types of bacteria. [7]

pH

pH change in soils is due to both biotic and abiotic processes. Microbes consume and release H+ through redox reactions and fermentation. Abiotic processes such as rainfall can also affect the pH of the soil. In areas of high rainfall, acidic soils can be created through leaching of bases from the soil, while more basic soils are typically located in arid environments. One study by Fierer et al, found that pH was the single most important factor influencing microbial diversity at the continental scale. [10] The study used 98 samples from across North and South America, and found that the greatest microbial diversity coincided with a neutral pH, even between two soil from the same forest.

pH affects microbial diversity because many microbial species cannot tolerate extreme levels of pH (high or low). Alterations in pH can render essential microbe enzymes inactive and/or denature proteins within the cells and prevent microbial activity from occurring. [4] However, there are microbes that can withstand extreme pH environments. At pH below 5, fungi and acidophilic bacteria have a competitive advantage over other bacteria that thrive at a more neutral pH.

pH can also affect the availability of nutrients in this soil. Below a pH of 5, essential plant nutrients such as phosphorous, calcium and magnesium are not available. Low pH can also cause aluminum (Al3+) to be released from soil minerals. Al3+ in soil solution is not only toxic to plants and microbes, it can combine with OH- ions causing the free H+ ions to lower the pH further. [5] The effect of pH on nutrient availability and microbe survivability can be seen in figure 7.

Figure 6. Nutrient availability and microbial diversity as a function of pH. [2]

Oxygen

Oxygen (O2) is a very important component of the productivity of both microbes and plant roots. Oxygen has a very high electrical potential (Eh), meaning that it has a lot of potential to produce energy when used as an electron acceptor in an oxidation-reduction reaction. [5] An example oxidation-reduction reaction can be seen in equation 1, where glucose is being oxidized, and oxygen is being reduced. 

                                              6O2+C6H12O6→6CO2+6H2O		[eq.1]

The amount of oxygen available in a soil depends on a number of factors, including soil porosity, water content, and consumption by respiring organisms. If soil pores are large and interconnected, oxygen can flow easily. However, even in a well aerated soil, micro-aggregates may contain anaerobic zones in which oxygen flow is very limited. In a flooded soil environment oxygen content will be very limited because oxygen diffuses about 10,000 times more slowly through water than through air. [4]

In areas where oxygen is not present, soil microbes may use alternative electron acceptors such as nitrate, manganese, iron, sulfate, and carbon dioxide. An example of the result of the use of an alternative electron acceptor can be seen in figure 7.

Figure 7. Without oxygen, bacteria can potentially use iron as an electron acceptor, reducing it, and creating the blue/gray soil in the photo. The mottled red areas are the result of oxygen getting in (perhaps through root canals) and oxidizing the iron. [3]

Cation Exchange Capacity

Cation exchange capacity (CEC) is the ability of a soil to hold and exchange cations. The amount of CEC in soil is highly dependent on the texture and organic matter of the soil. The high surface area and negative charge of clay allows it to bind and exchange with soil solution, which contains cations that are important for plant and microbial health. [4]

For many soils, especially those with low clay and organic carbon content , CEC is dependant upon soil pH (see figure 9). As pH decreases , an increasing amount of H+ ions are attracted to negatively charged clay particles and functional groups in SOM. This causes other cations, that were attached to these surfaces to fall off into the soil solution. CEC will increase as pH increases as less cations are being pushed out by H+ ions. [5]

At typical soil pH values (5-8), microbes and clay particles are both negatively charged, but microbes still to bind to clay. This binding could be due van der waals, hydrogen bonding, sharing electrons and ion exchange.

Figure 8. Figure 9 : Cation exchange capacity and anion exchange capacity of a soil as function of soil pH. [9]

Redox Reactions

Reduction-oxidation (redox) reactions are chemical reactions in which reactants experience a change in oxidation number (which means these reactants either gain or lose electrons) . Many reactions in the soil involve the gain or loss of electrons, obtaining or releasing energy. Redox reactions are important in the soil, because microbes obtain energy through redox reactions for their metabolism, and the redox state can also determine the microbial processes that will occur.

Redox reactions include anabolism and catabolism process, both of which play important roles in microbial metabolism. Anabolism is the biosynthesis of cellular components, linked to energy requirements, while catabolism is the the biochemical processes leading to breakdown of organic substances, linked to energy production. For example, the photosynthesis and respiration processes are the coupled reactions in the soil, where plants required energy from light and reduce carbon dioxide to glucose, which then be used by microbes in the soil as the energy for their metabolism.

The tendency of compounds to accept or donate electrons is expressed as “redox potential”. Redox potential (Eh), determined from the concentration of oxidants and reductants in the environment, is to measure the oxidation-reduction status and electron availability within this system. Electrons are essential to all inorganic and organic chemical reactions. Redox potential measurements allow for rapid characterization of the degree of reduction and for predicting stability of various compounds that regulate nutrients and metal availability in soil and sediment. The inorganic oxidants include oxygen, nitrate, nitrite, manganese, sulfate, and CO2, while the reductants include various organic substrates and reduced inorganic compounds (NH4+, Fe2+, Mn2+, S2-, CH4, and H2). [15]

The redox potential of a substance depends on Affinity of molecules for electrons and Concentration of reductants and oxidants (referred to as redox pair) Anaerobic environments such as wetland soils and flooded soils are usually limited by electron acceptors and have an abundant supply of electron donors. In this case, most microbes’ activity is limited, and facultative and obligate microbes reduce the minerals following the electron tower. Aerated soils are usually limited by electron donors and have an abundant supply of electron acceptors (primarily O2). [15]

Salinity

Soil salinity refers to the salt content in the soil. The concentrations and types of ions in solution in the soil can cause modifications in the dispersion of the clay fraction, degrading the original soil fraction. The sodium ion, being monovalent, increases the width of the diffuse double layer on the surface of the clays, reducing the attractive forces between them with a consequent increase in particle dispersion. [16] The consequence of this dispersion of the clay is also shown by a reduction in stability of the soil aggregates, which are thus easily transported by rain or irrigation.

Soil salinization is a big problem for soils in arid or semi-arid regions and agricultural soils throughout the world. [5] Salts can adversely affect plant and microbial growth, due to destruction of the soil structure and its consequent compacting. The stress of high salt concentration can be detrimental for sensitive microorganisms and decrease the activity of surviving cells, due to the metabolic load imposed by the need for stress tolerance mechanisms.

Bioavailability

Bioavailability assesses what proportion of a contaminant present at a contaminated site is available for uptake by organisms. Bioavailability processes are the biological, chemical and physical processes that result in an organism being exposed to a contaminant present in the soil. These processes are: release of the contaminant from the solid phase, transport of the contaminant to and across a biological membrane and, incorporation into a living organism. [18]

Bioavailable molecules must cross a biological membrane, which means the molecules have to interact with the aqueous phase. Therefore, soil properties which control partitioning between the solid phase in soil and the pore water, such as pH, organic matter content, Eh, cation exchange capacity (CEC), and the concentration of clay minerals, have a significant impact on bioavailability. Increasing exchange sites aids the retention of molecules in the pore water in a bioavailable form, but molecules sorbed strongly to surfaces or in solid form are generally not bioavailable. [18]

Current Research

Soil functions are hugely influenced by soil aggregate properties like strength and porosity. The effect of soil management on soil aggregation can assist in determining best management practices. One study sought to quantify the long-term effect of rotation and tillage on aggregate shape , strength and pore characteristics. [8] Soil samples were taken from a long-term rotation and tillage trial with both continuous and diverse rotations. The size of these soil samples were determined by X-ray micro-CT, and the study concluded several findings :

- Rotation and tillage effect on aggregate and bulk soil properties

- Rotation affected soil aggregate properties more than tillage.

- Tillage have a stronger effect on bulk soil porosity

References

1. "Soil_Microaggregate_and_bacteria." UC Berkeley, n.d. Web. 25 Feb. 2016. <http://em-lab.berkeley.edu/EML/images/TEM-Gallery1/pages/Soil_Microaggregate_and_bacteria.htm>.

2. " Soil Reaction (pH)." University of New South Wales, n.d. Web. 25 Feb. 2016. <http://www.terragis.bees.unsw.edu.au/terraGIS_soil/sp_soil_reaction_ph.html>.

3. "Soil Images - Redoximorphic Features." New England Soil, n.d. Web. 25 Feb. 2016. <http://nesoil.com/images/redox.htm>.

4. Sylvia, D. M. Principles and Applications of Soil Microbiology. Upper Saddle River, NJ: Pearson Prentice Hall, 2005. Print.

5. Brady, Nyle C., and Ray R. Weil. Elements of the Nature and Properties of Soils. Upper Saddle River, NJ: Pearson Prentice Hall, 2010. Print.

6. Hamarshid N.H., Othman M.A., and Hussain M.-A.H., 2010. Effects of soil texture on chemical compositions, microbial populations and carbon mineralization in soil. Egypt. J. Exp. Biol. (Bot.), 6(1), 59-64. Kabala C. and Zapart J., 2012.

7. Todar, Kenneth. "Nutrition and Growth of Bacteria." N.p., n.d. Web. 13 Mar. 2016. <http://textbookofbacteriology.net/nutgro_5.html>.

8. Munkholm, L. J., Heck, R. J., Deen, B., & Zidar, T. (2016). Relationship between soil aggregate strength, shape and porosity for soils under different long-term management. Geoderma, 26852-59. doi:10.1016/j.geoderma.2016.01.005

9. "PH and Organic Substrate Nutrients." N.p., n.d. Web. 13 Mar. 2016. <http://organicsoiltechnology.com/ph-and-organic-substrate-nutrients.html>.

10. Fierer, N., and R. B. Jackson. "The Diversity and Biogeography of Soil Bacterial Communities." Proceedings of the National Academy of Sciences 103.3 (2006): 626-31. Web.

11. "Soil Structure and Macropores." Soil Quality: Indicators:. NRCS, n.d. Web. 13 Mar. 2016. <http://soilquality.org/indicators/soil_structure.html>.

12. "Electron Tower Theory." Bioremediation Specialists, n.d. Web. 14 Mar. 2016. <http://bioremediation-specialists.com/Electron-Tower-Theory.php>.

13. Moravec, C., Whiting, D., and Reeder, J. “Introduction to Soils.” CMG GardenNotes. Colorado State University Extension. Oct. 2015. <http://www.cmg.colostate.edu/>

14. “BIO 212 Study Guide”. Iowa State University. <https://www.studyblue.com/notes/note/n/bio-212-study-guide-2012-13-yin/deck/9716305>

15. Delaune, R. D., and Reddy, K, R., Encyclopedia of Soils in the Environment. 2005, Elsevier Ltd.

16. Maganhotto, C. M.,and Francisconi Fay,E., (2012). Effect of Salinity on Soil Microorganisms, Soil Health and Land Use Management, Dr. Maria C. Hernandez Soriano (Ed.), InTech, Available from: http://www.intechopen.com/books/soil-health-and-land-usemanagement/Effect-of-salinity-on-soil-microorganisms

17. Provin, T., and Pitt, J. L. “Managing Soil Salinity”. Texas AgriLife Extension Service. March, 2012. <http://soiltesting.tamu.edu/publications> Edited by students of Kate Scow

18. Hodson, M. E., Vijver, M. G. and Peijnenberg, W. J. G. M. (2011) Bioavailability in soils. In: Swartjes, F. A. (ed.) Dealing with contaminated sites: from theory towards practical application. Springer, pp. 721-746. ISBN 9789048197569 doi: 10.1007/978-90-481-9757-6 Available at http://centaur.reading.ac.uk/20839/

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