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Rhizosphere Interactions
2008-03-22T07:03:37Z
<p>Alorloff: /* Nitrogen Fixing Bacteria */</p>
<hr />
<div>==Rhizosphere==<br />
<br />
[[Image:rhizobact.jpg|thumb|250px|right|Rhizosphere [http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/rhizobact.jpg Source]]]<br />
<br />
The rhizosphere is a microecological zone in direct proximity of plant roots. It is functionally defined as the particulate matter and microorganisms that cling to roots after being gently shaken in water. The theoretical extent of the rhizosphere is dependent on the zone of influence of the plant roots and associated microorganisms. The rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane is the root epidermis and outer cortex where soil particles, bacteria and fungal hyphae adhere (Singer, 2006; Sylvia, 2005). The functional definition is the remaining microorganisms and soil particles after the roots have been shaken vigorously in water. There are more microbes in the rhizoplane than in the more loosely assoicated rhizosphere. This is determined by counting the number of colony forming units (CFUs) which are determined by spreading extracted soil microorganisms across an agar and counting the number of independent clusters of microorganisms. Microbes are most abundant where the integrety of the root is compromised. For this reason, rhizoplane microorganisms tend to be found on older rather than younger roots. Bacteria and fungi that live within the cells of the root are not considered a part of the rhizoplane, but instead called endophytes (Sylvia, 2005).<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Soil Texture====<br />
Movement of organic matter away from the root as well as bacteria colonizing new locations occurs more readily in sandy soils than clayey soils. Sand has larger pores between each granule allowing microorganisms and exudates can travel. Therefore, the larger the granule size, the further the rhizosphere and microorganisms associated with it will extend into the surrounding soil. (Sylvia, 2005)<br />
<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous.<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
[[Image:rhizospherebacteria.jpg|thumb|250px|right|Rhizosphere Bacteria [https://www.soils.org/divisions/s03/images/rhizospherebacteria.jpg source]]]<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [http://en.wikipedia.org/wiki/Actinomycete acetinomycetes] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced [http://genome.jgi-psf.org/Lacbi1/Lacbi1.home.html genome of ''Laccaria Bicolor]'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
[[Image:ectomycorrhizae.gif|thumb|200px|right|Ectomycorrhizae [http://www-mykopat.slu.se/Newwebsite/mycorrhiza/kantarellfiler/bilder/C.GIF Reference to Source of Image]]]<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
[[Image:arbuscular.jpg|thumb|200px|right|Image of Arbuscular Mycorrhizae[http://biology.kenyon.edu/fennessy/SrexMarx/arbgood.jpg Reference to Source of Image]]]<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
[[Image:nodes.jpg|thumb|300px|left|Image of N cycle [http://academic.reed.edu/biology/Nitrogen/images/part1/bigFL1.jpg Reference to Source of Image]]]<br />
Due to the high energetic cost of fixing dinitrogen, a significant part of nitrogen fixation occurs near the plant roots, where there is an influx of sugar to power the process. Some nitrogen fixation occurs in the rizosphere by free-living bacteria (the ability is found only in prokaryotes). When these otherwise free living bacteria form a close association with a plant they’re called “associative symbiotes”. An example of a free living nitrogen fixer is ''[[Bradyrhizobium]]''. <br />
<br />
There are several drawbacks to this lifestyle: 1. Nitrogen fixing bacteria are sensitive to fluxuations in oxygen. Many are aerobes who use oxygen as a terminal electron acceptor, but on the other hand, oxygen can poison the [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase enzyme]. Hence free-living bacteria need to take energetically costly steps such as having extremely fast respiration or producing large amounts slime to protect nitrogenase. Another disadvantage Associative symbiotes have do deal with is that they are in direct competition with the rest of the rizosphere for the available carbon. Experiments indicate that carbon is a limiting factor in rhizosphere nitrogen fixation. <br />
<br />
An alternate form of nitrogen-fixing lifestyle is to actually live in the plant root cells themselves. Bacteria who do this are called ”symbiotes” or “mutualistic symbiotes”, and an example of one such bacteria is ''[[Rhizobia]]''. These bacteria form “nodules” on plants, which are huge masses of bacteria living inside plant cells which have been modified for the purpose. The process of forming a nodule requires recognition between bacteria and plant (usually very specific), and gene expression changes in both players. The plant provides carbon to the bacteria and the bacteria provide fixed nitrogen to the plant. The masses of bacteria produce leghemoglobin to protect nitrogenase from oxygen, and do not have to compete with other rhizosphere microbes for carbon (Sylvia, 2005).<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==Current Research==<br />
<br />
*In the article, [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TC3-4PYRKM2-1&_user=4421&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059598&_version=1&_urlVersion=0&_userid=4421&md5=d5dc6db07423535c2d31eedc48131fed ''Arbuscular mycorrhizal fungi enhance tolerance of vinca to high alkalinity in irrigation water,''] Cartmill and collegues found that arbuscular mycorrhizal fungi are capable of increasing the salt tolerance of plants. Applications for this finding include increasing the tolerance of crops to irrigation water of high alkalinity.<br />
<br />
==References==<br />
*Martin F., A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rodriguez, Rusty J, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
*Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
*Singer, Michael J and Donald N. Munns. 2006 ''Soils: an Introduction''. Pearson Education Inc. New Jersey.<br />
<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29502
Rhizosphere Interactions
2008-03-22T07:01:56Z
<p>Alorloff: /* Nitrogen Fixing Bacteria */</p>
<hr />
<div>==Rhizosphere==<br />
<br />
[[Image:rhizobact.jpg|thumb|250px|right|Rhizosphere [http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/rhizobact.jpg Source]]]<br />
<br />
The rhizosphere is a microecological zone in direct proximity of plant roots. It is functionally defined as the particulate matter and microorganisms that cling to roots after being gently shaken in water. The theoretical extent of the rhizosphere is dependent on the zone of influence of the plant roots and associated microorganisms. The rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane is the root epidermis and outer cortex where soil particles, bacteria and fungal hyphae adhere (Singer, 2006; Sylvia, 2005). The functional definition is the remaining microorganisms and soil particles after the roots have been shaken vigorously in water. There are more microbes in the rhizoplane than in the more loosely assoicated rhizosphere. This is determined by counting the number of colony forming units (CFUs) which are determined by spreading extracted soil microorganisms across an agar and counting the number of independent clusters of microorganisms. Microbes are most abundant where the integrety of the root is compromised. For this reason, rhizoplane microorganisms tend to be found on older rather than younger roots. Bacteria and fungi that live within the cells of the root are not considered a part of the rhizoplane, but instead called endophytes (Sylvia, 2005).<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Soil Texture====<br />
Movement of organic matter away from the root as well as bacteria colonizing new locations occurs more readily in sandy soils than clayey soils. Sand has larger pores between each granule allowing microorganisms and exudates can travel. Therefore, the larger the granule size, the further the rhizosphere and microorganisms associated with it will extend into the surrounding soil. (Sylvia, 2005)<br />
<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous.<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
[[Image:rhizospherebacteria.jpg|thumb|250px|right|Rhizosphere Bacteria [https://www.soils.org/divisions/s03/images/rhizospherebacteria.jpg source]]]<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [http://en.wikipedia.org/wiki/Actinomycete acetinomycetes] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced [http://genome.jgi-psf.org/Lacbi1/Lacbi1.home.html genome of ''Laccaria Bicolor]'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
[[Image:ectomycorrhizae.gif|thumb|200px|right|Ectomycorrhizae [http://www-mykopat.slu.se/Newwebsite/mycorrhiza/kantarellfiler/bilder/C.GIF Reference to Source of Image]]]<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
[[Image:arbuscular.jpg|thumb|200px|right|Image of Arbuscular Mycorrhizae[http://biology.kenyon.edu/fennessy/SrexMarx/arbgood.jpg Reference to Source of Image]]]<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
[[Image:nodes.jpg|thumb|300px|left|Image of N cycle [http://academic.reed.edu/biology/Nitrogen/images/part1/bigFL1.jpg Reference to Source of Image]]]<br />
Due to the high energetic cost of fixing dinitrogen, a significant part of nitrogen fixation occurs near the plant roots, where there is an influx of sugar to power the process. Some nitrogen fixation occurs in the rizosphere by free-living bacteria (the ability is found only in prokaryotes). When these otherwise free living bacteria form a close association with a plant they’re called “associative symbiotes”. An example of a free living nitrogen fixer is ''[[Azotobacter]]''. <br />
<br />
There are several drawbacks to this lifestyle: 1. Nitrogen fixing bacteria are sensitive to fluxuations in oxygen. Many are aerobes who use oxygen as a terminal electron acceptor, but on the other hand, oxygen can poison the [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase enzyme]. Hence free-living bacteria need to take energetically costly steps such as having extremely fast respiration or producing large amounts slime to protect nitrogenase. Another disadvantage Associative symbiotes have do deal with is that they are in direct competition with the rest of the rizosphere for the available carbon. Experiments indicate that carbon is a limiting factor in rhizosphere nitrogen fixation. <br />
<br />
An alternate form of nitrogen-fixing lifestyle is to actually live in the plant root cells themselves. Bacteria who do this are called ”symbiotes” or “mutualistic symbiotes”, and an example of one such bacteria is ''[[Rhizobia]]''. These bacteria form “nodules” on plants, which are huge masses of bacteria living inside plant cells which have been modified for the purpose. The process of forming a nodule requires recognition between bacteria and plant (usually very specific), and gene expression changes in both players. The plant provides carbon to the bacteria and the bacteria provide fixed nitrogen to the plant. The masses of bacteria produce leghemoglobin to protect nitrogenase from oxygen, and do not have to compete with other rhizosphere microbes for carbon (Sylvia, 2005).<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==Current Research==<br />
<br />
*In the article, [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TC3-4PYRKM2-1&_user=4421&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059598&_version=1&_urlVersion=0&_userid=4421&md5=d5dc6db07423535c2d31eedc48131fed ''Arbuscular mycorrhizal fungi enhance tolerance of vinca to high alkalinity in irrigation water,''] Cartmill and collegues found that arbuscular mycorrhizal fungi are capable of increasing the salt tolerance of plants. Applications for this finding include increasing the tolerance of crops to irrigation water of high alkalinity.<br />
<br />
==References==<br />
*Martin F., A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rodriguez, Rusty J, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
*Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
*Singer, Michael J and Donald N. Munns. 2006 ''Soils: an Introduction''. Pearson Education Inc. New Jersey.<br />
<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29501
Rhizosphere Interactions
2008-03-22T07:01:24Z
<p>Alorloff: /* Nitrogen Fixing Bacteria */</p>
<hr />
<div>==Rhizosphere==<br />
<br />
[[Image:rhizobact.jpg|thumb|250px|right|Rhizosphere [http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/rhizobact.jpg Source]]]<br />
<br />
The rhizosphere is a microecological zone in direct proximity of plant roots. It is functionally defined as the particulate matter and microorganisms that cling to roots after being gently shaken in water. The theoretical extent of the rhizosphere is dependent on the zone of influence of the plant roots and associated microorganisms. The rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane is the root epidermis and outer cortex where soil particles, bacteria and fungal hyphae adhere (Singer, 2006; Sylvia, 2005). The functional definition is the remaining microorganisms and soil particles after the roots have been shaken vigorously in water. There are more microbes in the rhizoplane than in the more loosely assoicated rhizosphere. This is determined by counting the number of colony forming units (CFUs) which are determined by spreading extracted soil microorganisms across an agar and counting the number of independent clusters of microorganisms. Microbes are most abundant where the integrety of the root is compromised. For this reason, rhizoplane microorganisms tend to be found on older rather than younger roots. Bacteria and fungi that live within the cells of the root are not considered a part of the rhizoplane, but instead called endophytes (Sylvia, 2005).<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Soil Texture====<br />
Movement of organic matter away from the root as well as bacteria colonizing new locations occurs more readily in sandy soils than clayey soils. Sand has larger pores between each granule allowing microorganisms and exudates can travel. Therefore, the larger the granule size, the further the rhizosphere and microorganisms associated with it will extend into the surrounding soil. (Sylvia, 2005)<br />
<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous.<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
[[Image:rhizospherebacteria.jpg|thumb|250px|right|Rhizosphere Bacteria [https://www.soils.org/divisions/s03/images/rhizospherebacteria.jpg source]]]<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [http://en.wikipedia.org/wiki/Actinomycete acetinomycetes] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced [http://genome.jgi-psf.org/Lacbi1/Lacbi1.home.html genome of ''Laccaria Bicolor]'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
[[Image:ectomycorrhizae.gif|thumb|200px|right|Ectomycorrhizae [http://www-mykopat.slu.se/Newwebsite/mycorrhiza/kantarellfiler/bilder/C.GIF Reference to Source of Image]]]<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
[[Image:arbuscular.jpg|thumb|200px|right|Image of Arbuscular Mycorrhizae[http://biology.kenyon.edu/fennessy/SrexMarx/arbgood.jpg Reference to Source of Image]]]<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
[[Image:nodes.jpg|thumb|300px|left|Image of N cycle [http://academic.reed.edu/biology/Nitrogen/images/part1/bigFL1.jpg Reference to Source of Image]]]<br />
Due to the high energetic cost of fixing dinitrogen, a significant part of nitrogen fixation occurs near the plant roots, where there is an influx of sugar to power the process. Some nitrogen fixation occurs in the rizosphere by free-living bacteria (the ability is found only in prokaryotes). When these otherwise free living bacteria form a close association with a plant they’re called “associative symbiotes”. An example of a free living nitrogen fixer is ''[[Azotobacter]]''. <br />
<br />
There are several drawbacks to this lifestyle: 1. Nitrogen fixing bacteria are sensitive to fluxuations in oxygen. Many are aerobes who use oxygen as a terminal electron acceptor, but on the other hand, oxygen can poison the [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase enzyme]. Hence free-living bacteria need to take energetically costly steps such as having extremely fast respiration or producing large amounts slime to protect nitrogenase. Another disadvantage Associative symbiotes have do deal with is that they are in direct competition with the rest of the rizosphere for the available carbon. Experiments indicate that carbon is a limiting factor in rhizosphere nitrogen fixation. <br />
<br />
An alternate form of nitrogen-fixing lifestyle is to actually live in the plant root cells themselves. Bacteria who do this are called ”symbiotes” or “mutualistic symbiotes”, and an example of one such bacteria is [[''Rhizobia'']]. These bacteria form “nodules” on plants, which are huge masses of bacteria living inside plant cells which have been modified for the purpose. The process of forming a nodule requires recognition between bacteria and plant (usually very specific), and gene expression changes in both players. The plant provides carbon to the bacteria and the bacteria provide fixed nitrogen to the plant. The masses of bacteria produce leghemoglobin to protect nitrogenase from oxygen, and do not have to compete with other rhizosphere microbes for carbon (Sylvia, 2005).<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==Current Research==<br />
<br />
*In the article, [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TC3-4PYRKM2-1&_user=4421&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059598&_version=1&_urlVersion=0&_userid=4421&md5=d5dc6db07423535c2d31eedc48131fed ''Arbuscular mycorrhizal fungi enhance tolerance of vinca to high alkalinity in irrigation water,''] Cartmill and collegues found that arbuscular mycorrhizal fungi are capable of increasing the salt tolerance of plants. Applications for this finding include increasing the tolerance of crops to irrigation water of high alkalinity.<br />
<br />
==References==<br />
*Martin F., A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rodriguez, Rusty J, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
*Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
*Singer, Michael J and Donald N. Munns. 2006 ''Soils: an Introduction''. Pearson Education Inc. New Jersey.<br />
<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29500
Rhizosphere Interactions
2008-03-22T06:59:19Z
<p>Alorloff: /* Symbiotic or Mutualistic Relationships */</p>
<hr />
<div>==Rhizosphere==<br />
<br />
[[Image:rhizobact.jpg|thumb|250px|right|Rhizosphere [http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/rhizobact.jpg Source]]]<br />
<br />
The rhizosphere is a microecological zone in direct proximity of plant roots. It is functionally defined as the particulate matter and microorganisms that cling to roots after being gently shaken in water. The theoretical extent of the rhizosphere is dependent on the zone of influence of the plant roots and associated microorganisms. The rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane is the root epidermis and outer cortex where soil particles, bacteria and fungal hyphae adhere (Singer, 2006; Sylvia, 2005). The functional definition is the remaining microorganisms and soil particles after the roots have been shaken vigorously in water. There are more microbes in the rhizoplane than in the more loosely assoicated rhizosphere. This is determined by counting the number of colony forming units (CFUs) which are determined by spreading extracted soil microorganisms across an agar and counting the number of independent clusters of microorganisms. Microbes are most abundant where the integrety of the root is compromised. For this reason, rhizoplane microorganisms tend to be found on older rather than younger roots. Bacteria and fungi that live within the cells of the root are not considered a part of the rhizoplane, but instead called endophytes (Sylvia, 2005).<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Soil Texture====<br />
Movement of organic matter away from the root as well as bacteria colonizing new locations occurs more readily in sandy soils than clayey soils. Sand has larger pores between each granule allowing microorganisms and exudates can travel. Therefore, the larger the granule size, the further the rhizosphere and microorganisms associated with it will extend into the surrounding soil. (Sylvia, 2005)<br />
<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous.<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
[[Image:rhizospherebacteria.jpg|thumb|250px|right|Rhizosphere Bacteria [https://www.soils.org/divisions/s03/images/rhizospherebacteria.jpg source]]]<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [http://en.wikipedia.org/wiki/Actinomycete acetinomycetes] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced [http://genome.jgi-psf.org/Lacbi1/Lacbi1.home.html genome of ''Laccaria Bicolor]'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
[[Image:ectomycorrhizae.gif|thumb|200px|right|Ectomycorrhizae [http://www-mykopat.slu.se/Newwebsite/mycorrhiza/kantarellfiler/bilder/C.GIF Reference to Source of Image]]]<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
[[Image:arbuscular.jpg|thumb|200px|right|Image of Arbuscular Mycorrhizae[http://biology.kenyon.edu/fennessy/SrexMarx/arbgood.jpg Reference to Source of Image]]]<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
[[Image:nodes.jpg|thumb|300px|left|Image of N cycle [http://academic.reed.edu/biology/Nitrogen/images/part1/bigFL1.jpg Reference to Source of Image]]]<br />
Due to the high energetic cost of fixing dinitrogen, a significant part of nitrogen fixation occurs near the plant roots, where there is an influx of sugar to power the process. Some nitrogen fixation occurs in the rizosphere by free-living bacteria (the ability is found only in prokaryotes). When these otherwise free living bacteria form a close association with a plant they’re called “associative symbiotes”. An example of a free living nitrogen fixer is [[Azotobacter]]. <br />
<br />
There are several drawbacks to this lifestyle: 1. Nitrogen fixing bacteria are sensitive to fluxuations in oxygen. Many are aerobes who use oxygen as a terminal electron acceptor, but on the other hand, oxygen can poison the [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase enzyme]. Hence free-living bacteria need to take energetically costly steps such as having extremely fast respiration or producing large amounts slime to protect nitrogenase. Another disadvantage Associative symbiotes have do deal with is that they are in direct competition with the rest of the rizosphere for the available carbon. Experiments indicate that carbon is a limiting factor in rhizosphere nitrogen fixation. <br />
<br />
An alternate form of nitrogen-fixing lifestyle is to actually live in the plant root cells themselves. Bacteria who do this are called ”symbiotes” or “mutualistic symbiotes”, and an example of one such bacteria is Rhizobia. These bacteria form “nodules” on plants, which are huge masses of bacteria living inside plant cells which have been modified for the purpose. The process of forming a nodule requires recognition between bacteria and plant (usually very specific), and gene expression changes in both players. The plant provides carbon to the bacteria and the bacteria provide fixed nitrogen to the plant. The masses of bacteria produce leghemoglobin to protect nitrogenase from oxygen, and do not have to compete with other rhizosphere microbes for carbon (Sylvia, 2005).<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==Current Research==<br />
<br />
*In the article, [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TC3-4PYRKM2-1&_user=4421&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059598&_version=1&_urlVersion=0&_userid=4421&md5=d5dc6db07423535c2d31eedc48131fed ''Arbuscular mycorrhizal fungi enhance tolerance of vinca to high alkalinity in irrigation water,''] Cartmill and collegues found that arbuscular mycorrhizal fungi are capable of increasing the salt tolerance of plants. Applications for this finding include increasing the tolerance of crops to irrigation water of high alkalinity.<br />
<br />
==References==<br />
*Martin F., A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rodriguez, Rusty J, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
*Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
*Singer, Michael J and Donald N. Munns. 2006 ''Soils: an Introduction''. Pearson Education Inc. New Jersey.<br />
<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29499
Rhizosphere Interactions
2008-03-22T06:57:49Z
<p>Alorloff: /* Symbiotic or Mutualistic Relationships */</p>
<hr />
<div>==Rhizosphere==<br />
<br />
[[Image:rhizobact.jpg|thumb|250px|right|Rhizosphere [http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/rhizobact.jpg Source]]]<br />
<br />
The rhizosphere is a microecological zone in direct proximity of plant roots. It is functionally defined as the particulate matter and microorganisms that cling to roots after being gently shaken in water. The theoretical extent of the rhizosphere is dependent on the zone of influence of the plant roots and associated microorganisms. The rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane is the root epidermis and outer cortex where soil particles, bacteria and fungal hyphae adhere (Singer, 2006; Sylvia, 2005). The functional definition is the remaining microorganisms and soil particles after the roots have been shaken vigorously in water. There are more microbes in the rhizoplane than in the more loosely assoicated rhizosphere. This is determined by counting the number of colony forming units (CFUs) which are determined by spreading extracted soil microorganisms across an agar and counting the number of independent clusters of microorganisms. Microbes are most abundant where the integrety of the root is compromised. For this reason, rhizoplane microorganisms tend to be found on older rather than younger roots. Bacteria and fungi that live within the cells of the root are not considered a part of the rhizoplane, but instead called endophytes (Sylvia, 2005).<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Soil Texture====<br />
Movement of organic matter away from the root as well as bacteria colonizing new locations occurs more readily in sandy soils than clayey soils. Sand has larger pores between each granule allowing microorganisms and exudates can travel. Therefore, the larger the granule size, the further the rhizosphere and microorganisms associated with it will extend into the surrounding soil. (Sylvia, 2005)<br />
<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous.<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
[[Image:rhizospherebacteria.jpg|thumb|250px|right|Rhizosphere Bacteria [https://www.soils.org/divisions/s03/images/rhizospherebacteria.jpg source]]]<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [http://en.wikipedia.org/wiki/Actinomycete acetinomycetes] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''[http://genome.jgi-psf.org/Lacbi1/Lacbi1.home.html Laccaria Bicolor]'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
[[Image:ectomycorrhizae.gif|thumb|200px|right|Ectomycorrhizae [http://www-mykopat.slu.se/Newwebsite/mycorrhiza/kantarellfiler/bilder/C.GIF Reference to Source of Image]]]<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
[[Image:arbuscular.jpg|thumb|200px|right|Image of Arbuscular Mycorrhizae[http://biology.kenyon.edu/fennessy/SrexMarx/arbgood.jpg Reference to Source of Image]]]<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
[[Image:nodes.jpg|thumb|300px|left|Image of N cycle [http://academic.reed.edu/biology/Nitrogen/images/part1/bigFL1.jpg Reference to Source of Image]]]<br />
Due to the high energetic cost of fixing dinitrogen, a significant part of nitrogen fixation occurs near the plant roots, where there is an influx of sugar to power the process. Some nitrogen fixation occurs in the rizosphere by free-living bacteria (the ability is found only in prokaryotes). When these otherwise free living bacteria form a close association with a plant they’re called “associative symbiotes”. An example of a free living nitrogen fixer is [[Azotobacter]]. <br />
<br />
There are several drawbacks to this lifestyle: 1. Nitrogen fixing bacteria are sensitive to fluxuations in oxygen. Many are aerobes who use oxygen as a terminal electron acceptor, but on the other hand, oxygen can poison the [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase enzyme]. Hence free-living bacteria need to take energetically costly steps such as having extremely fast respiration or producing large amounts slime to protect nitrogenase. Another disadvantage Associative symbiotes have do deal with is that they are in direct competition with the rest of the rizosphere for the available carbon. Experiments indicate that carbon is a limiting factor in rhizosphere nitrogen fixation. <br />
<br />
An alternate form of nitrogen-fixing lifestyle is to actually live in the plant root cells themselves. Bacteria who do this are called ”symbiotes” or “mutualistic symbiotes”, and an example of one such bacteria is Rhizobia. These bacteria form “nodules” on plants, which are huge masses of bacteria living inside plant cells which have been modified for the purpose. The process of forming a nodule requires recognition between bacteria and plant (usually very specific), and gene expression changes in both players. The plant provides carbon to the bacteria and the bacteria provide fixed nitrogen to the plant. The masses of bacteria produce leghemoglobin to protect nitrogenase from oxygen, and do not have to compete with other rhizosphere microbes for carbon (Sylvia, 2005).<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==Current Research==<br />
<br />
*In the article, [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TC3-4PYRKM2-1&_user=4421&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059598&_version=1&_urlVersion=0&_userid=4421&md5=d5dc6db07423535c2d31eedc48131fed ''Arbuscular mycorrhizal fungi enhance tolerance of vinca to high alkalinity in irrigation water,''] Cartmill and collegues found that arbuscular mycorrhizal fungi are capable of increasing the salt tolerance of plants. Applications for this finding include increasing the tolerance of crops to irrigation water of high alkalinity.<br />
<br />
==References==<br />
*Martin F., A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rodriguez, Rusty J, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
*Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
*Singer, Michael J and Donald N. Munns. 2006 ''Soils: an Introduction''. Pearson Education Inc. New Jersey.<br />
<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29498
Rhizosphere Interactions
2008-03-22T06:55:55Z
<p>Alorloff: /* Soil Texture */</p>
<hr />
<div>==Rhizosphere==<br />
<br />
[[Image:rhizobact.jpg|thumb|250px|right|Rhizosphere [http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/rhizobact.jpg Source]]]<br />
<br />
The rhizosphere is a microecological zone in direct proximity of plant roots. It is functionally defined as the particulate matter and microorganisms that cling to roots after being gently shaken in water. The theoretical extent of the rhizosphere is dependent on the zone of influence of the plant roots and associated microorganisms. The rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane is the root epidermis and outer cortex where soil particles, bacteria and fungal hyphae adhere (Singer, 2006; Sylvia, 2005). The functional definition is the remaining microorganisms and soil particles after the roots have been shaken vigorously in water. There are more microbes in the rhizoplane than in the more loosely assoicated rhizosphere. This is determined by counting the number of colony forming units (CFUs) which are determined by spreading extracted soil microorganisms across an agar and counting the number of independent clusters of microorganisms. Microbes are most abundant where the integrety of the root is compromised. For this reason, rhizoplane microorganisms tend to be found on older rather than younger roots. Bacteria and fungi that live within the cells of the root are not considered a part of the rhizoplane, but instead called endophytes (Sylvia, 2005).<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Soil Texture====<br />
Movement of organic matter away from the root as well as bacteria colonizing new locations occurs more readily in sandy soils than clayey soils. Sand has larger pores between each granule allowing microorganisms and exudates can travel. Therefore, the larger the granule size, the further the rhizosphere and microorganisms associated with it will extend into the surrounding soil. (Sylvia, 2005)<br />
<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous.<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
[[Image:rhizospherebacteria.jpg|thumb|250px|right|Rhizosphere Bacteria [https://www.soils.org/divisions/s03/images/rhizospherebacteria.jpg source]]]<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [http://en.wikipedia.org/wiki/Actinomycete acetinomycetes] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
[[Image:ectomycorrhizae.gif|thumb|200px|right|Ectomycorrhizae [http://www-mykopat.slu.se/Newwebsite/mycorrhiza/kantarellfiler/bilder/C.GIF Reference to Source of Image]]]<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
[[Image:arbuscular.jpg|thumb|200px|right|Image of Arbuscular Mycorrhizae[http://biology.kenyon.edu/fennessy/SrexMarx/arbgood.jpg Reference to Source of Image]]]<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
[[Image:nodes.jpg|thumb|300px|left|Image of N cycle [http://academic.reed.edu/biology/Nitrogen/images/part1/bigFL1.jpg Reference to Source of Image]]]<br />
Due to the high energetic cost of fixing dinitrogen, a significant part of nitrogen fixation occurs near the plant roots, where there is an influx of sugar to power the process. Some nitrogen fixation occurs in the rizosphere by free-living bacteria (the ability is found only in prokaryotes). When these otherwise free living bacteria form a close association with a plant they’re called “associative symbiotes”. An example of a free living nitrogen fixer is [[Azotobacter]]. <br />
<br />
There are several drawbacks to this lifestyle: 1. Nitrogen fixing bacteria are sensitive to fluxuations in oxygen. Many are aerobes who use oxygen as a terminal electron acceptor, but on the other hand, oxygen can poison the [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase enzyme]. Hence free-living bacteria need to take energetically costly steps such as having extremely fast respiration or producing large amounts slime to protect nitrogenase. Another disadvantage Associative symbiotes have do deal with is that they are in direct competition with the rest of the rizosphere for the available carbon. Experiments indicate that carbon is a limiting factor in rhizosphere nitrogen fixation. <br />
<br />
An alternate form of nitrogen-fixing lifestyle is to actually live in the plant root cells themselves. Bacteria who do this are called ”symbiotes” or “mutualistic symbiotes”, and an example of one such bacteria is Rhizobia. These bacteria form “nodules” on plants, which are huge masses of bacteria living inside plant cells which have been modified for the purpose. The process of forming a nodule requires recognition between bacteria and plant (usually very specific), and gene expression changes in both players. The plant provides carbon to the bacteria and the bacteria provide fixed nitrogen to the plant. The masses of bacteria produce leghemoglobin to protect nitrogenase from oxygen, and do not have to compete with other rhizosphere microbes for carbon (Sylvia, 2005).<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==Current Research==<br />
<br />
*In the article, [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TC3-4PYRKM2-1&_user=4421&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059598&_version=1&_urlVersion=0&_userid=4421&md5=d5dc6db07423535c2d31eedc48131fed ''Arbuscular mycorrhizal fungi enhance tolerance of vinca to high alkalinity in irrigation water,''] Cartmill and collegues found that arbuscular mycorrhizal fungi are capable of increasing the salt tolerance of plants. Applications for this finding include increasing the tolerance of crops to irrigation water of high alkalinity.<br />
<br />
==References==<br />
*Martin F., A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rodriguez, Rusty J, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
*Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
*Singer, Michael J and Donald N. Munns. 2006 ''Soils: an Introduction''. Pearson Education Inc. New Jersey.<br />
<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29497
Rhizosphere Interactions
2008-03-22T06:54:45Z
<p>Alorloff: /* Rhizoplane */</p>
<hr />
<div>==Rhizosphere==<br />
<br />
[[Image:rhizobact.jpg|thumb|250px|right|Rhizosphere [http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/rhizobact.jpg Source]]]<br />
<br />
The rhizosphere is a microecological zone in direct proximity of plant roots. It is functionally defined as the particulate matter and microorganisms that cling to roots after being gently shaken in water. The theoretical extent of the rhizosphere is dependent on the zone of influence of the plant roots and associated microorganisms. The rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane is the root epidermis and outer cortex where soil particles, bacteria and fungal hyphae adhere (Singer, 2006; Sylvia, 2005). The functional definition is the remaining microorganisms and soil particles after the roots have been shaken vigorously in water. There are more microbes in the rhizoplane than in the more loosely assoicated rhizosphere. This is determined by counting the number of colony forming units (CFUs) which are determined by spreading extracted soil microorganisms across an agar and counting the number of independent clusters of microorganisms. Microbes are most abundant where the integrety of the root is compromised. For this reason, rhizoplane microorganisms tend to be found on older rather than younger roots. Bacteria and fungi that live within the cells of the root are not considered a part of the rhizoplane, but instead called endophytes (Sylvia, 2005).<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Soil Texture====<br />
Movement of organic matter away from the root as well as bacteria colonizing new locations occurs more readily in sandy soils than clayey soils. Sand has larger pores between each grenule allowing microorganisms and exudates can travel. Therefore, the larger the granule size, the further the rhizosphere and microorganisms associated with it will extend into the surrounding soil. (Sylvia, 2005)<br />
<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous.<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
[[Image:rhizospherebacteria.jpg|thumb|250px|right|Rhizosphere Bacteria [https://www.soils.org/divisions/s03/images/rhizospherebacteria.jpg source]]]<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [http://en.wikipedia.org/wiki/Actinomycete acetinomycetes] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
[[Image:ectomycorrhizae.gif|thumb|200px|right|Ectomycorrhizae [http://www-mykopat.slu.se/Newwebsite/mycorrhiza/kantarellfiler/bilder/C.GIF Reference to Source of Image]]]<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
[[Image:arbuscular.jpg|thumb|200px|right|Image of Arbuscular Mycorrhizae[http://biology.kenyon.edu/fennessy/SrexMarx/arbgood.jpg Reference to Source of Image]]]<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
[[Image:nodes.jpg|thumb|300px|left|Image of N cycle [http://academic.reed.edu/biology/Nitrogen/images/part1/bigFL1.jpg Reference to Source of Image]]]<br />
Due to the high energetic cost of fixing dinitrogen, a significant part of nitrogen fixation occurs near the plant roots, where there is an influx of sugar to power the process. Some nitrogen fixation occurs in the rizosphere by free-living bacteria (the ability is found only in prokaryotes). When these otherwise free living bacteria form a close association with a plant they’re called “associative symbiotes”. An example of a free living nitrogen fixer is [[Azotobacter]]. <br />
<br />
There are several drawbacks to this lifestyle: 1. Nitrogen fixing bacteria are sensitive to fluxuations in oxygen. Many are aerobes who use oxygen as a terminal electron acceptor, but on the other hand, oxygen can poison the [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase enzyme]. Hence free-living bacteria need to take energetically costly steps such as having extremely fast respiration or producing large amounts slime to protect nitrogenase. Another disadvantage Associative symbiotes have do deal with is that they are in direct competition with the rest of the rizosphere for the available carbon. Experiments indicate that carbon is a limiting factor in rhizosphere nitrogen fixation. <br />
<br />
An alternate form of nitrogen-fixing lifestyle is to actually live in the plant root cells themselves. Bacteria who do this are called ”symbiotes” or “mutualistic symbiotes”, and an example of one such bacteria is Rhizobia. These bacteria form “nodules” on plants, which are huge masses of bacteria living inside plant cells which have been modified for the purpose. The process of forming a nodule requires recognition between bacteria and plant (usually very specific), and gene expression changes in both players. The plant provides carbon to the bacteria and the bacteria provide fixed nitrogen to the plant. The masses of bacteria produce leghemoglobin to protect nitrogenase from oxygen, and do not have to compete with other rhizosphere microbes for carbon (Sylvia, 2005).<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==Current Research==<br />
<br />
*In the article, [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TC3-4PYRKM2-1&_user=4421&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059598&_version=1&_urlVersion=0&_userid=4421&md5=d5dc6db07423535c2d31eedc48131fed ''Arbuscular mycorrhizal fungi enhance tolerance of vinca to high alkalinity in irrigation water,''] Cartmill and collegues found that arbuscular mycorrhizal fungi are capable of increasing the salt tolerance of plants. Applications for this finding include increasing the tolerance of crops to irrigation water of high alkalinity.<br />
<br />
==References==<br />
*Martin F., A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rodriguez, Rusty J, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
*Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
*Singer, Michael J and Donald N. Munns. 2006 ''Soils: an Introduction''. Pearson Education Inc. New Jersey.<br />
<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29496
Rhizosphere Interactions
2008-03-22T06:42:52Z
<p>Alorloff: /* Nitrogen Fixing Bacteria */</p>
<hr />
<div>==Rhizosphere==<br />
<br />
[[Image:rhizobact.jpg|thumb|250px|right|Rhizosphere [http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/rhizobact.jpg Source]]]<br />
<br />
The rhizosphere is a microecological zone in direct proximity of plant roots. It is functionally defined as the particulate matter and microorganisms that cling to roots after being gently shaken in water. The theoretical extent of the rhizosphere is dependent on the zone of influence of the plant roots and associated microorganisms. The rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane is the root epidermis and outer cortex where soil particles, bacteria and fungal hyphae adhere (Singer, 2006; Sylvia, 2005). The functional definition is the remaining microorganisms and soil particles after the roots have been shaken vigorously in water. There are more microbes in the rhizoplane than in the more loosely assoicated rhizosphere. This is determined by counting the number of colony forming units (CFUs) which are determined by spreading extracted soil microorganisms across an agar and counting the number of independent clusters of microorganisms. Microbes are most abundant where the integrety of the root is broken. For this reason, soil microorganisms are found on older rather than younger roots. Bacteria and fungi that colonize within the root are not considered a part of the rhizoplane, but instead called endophytes (Sylvia, 2005).<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Soil Texture====<br />
Movement of organic matter away from the root as well as bacteria colonizing new locations occurs more readily in sandy soils than clayey soils. Sand has larger pores between each grenule allowing microorganisms and exudates can travel. Therefore, the larger the granule size, the further the rhizosphere and microorganisms associated with it will extend into the surrounding soil. (Sylvia, 2005)<br />
<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous.<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
[[Image:rhizospherebacteria.jpg|thumb|250px|right|Rhizosphere Bacteria [https://www.soils.org/divisions/s03/images/rhizospherebacteria.jpg source]]]<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [http://en.wikipedia.org/wiki/Actinomycete acetinomycetes] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
[[Image:ectomycorrhizae.gif|thumb|200px|right|Ectomycorrhizae [http://www-mykopat.slu.se/Newwebsite/mycorrhiza/kantarellfiler/bilder/C.GIF Reference to Source of Image]]]<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
[[Image:arbuscular.jpg|thumb|200px|right|Image of Arbuscular Mycorrhizae[http://biology.kenyon.edu/fennessy/SrexMarx/arbgood.jpg Reference to Source of Image]]]<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
[[Image:nodes.jpg|thumb|300px|left|Image of N cycle [http://academic.reed.edu/biology/Nitrogen/images/part1/bigFL1.jpg Reference to Source of Image]]]<br />
Due to the high energetic cost of fixing dinitrogen, a significant part of nitrogen fixation occurs near the plant roots, where there is an influx of sugar to power the process. Some nitrogen fixation occurs in the rizosphere by free-living bacteria (the ability is found only in prokaryotes). When these otherwise free living bacteria form a close association with a plant they’re called “associative symbiotes”. An example of a free living nitrogen fixer is [[Azotobacter]]. <br />
<br />
There are several drawbacks to this lifestyle: 1. Nitrogen fixing bacteria are sensitive to fluxuations in oxygen. Many are aerobes who use oxygen as a terminal electron acceptor, but on the other hand, oxygen can poison the [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase enzyme]. Hence free-living bacteria need to take energetically costly steps such as having extremely fast respiration or producing large amounts slime to protect nitrogenase. Another disadvantage Associative symbiotes have do deal with is that they are in direct competition with the rest of the rizosphere for the available carbon. Experiments indicate that carbon is a limiting factor in rhizosphere nitrogen fixation. <br />
<br />
An alternate form of nitrogen-fixing lifestyle is to actually live in the plant root cells themselves. Bacteria who do this are called ”symbiotes” or “mutualistic symbiotes”, and an example of one such bacteria is Rhizobia. These bacteria form “nodules” on plants, which are huge masses of bacteria living inside plant cells which have been modified for the purpose. The process of forming a nodule requires recognition between bacteria and plant (usually very specific), and gene expression changes in both players. The plant provides carbon to the bacteria and the bacteria provide fixed nitrogen to the plant. The masses of bacteria produce leghemoglobin to protect nitrogenase from oxygen, and do not have to compete with other rhizosphere microbes for carbon (Sylvia, 2005).<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==Current Research==<br />
<br />
*In the article, [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TC3-4PYRKM2-1&_user=4421&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059598&_version=1&_urlVersion=0&_userid=4421&md5=d5dc6db07423535c2d31eedc48131fed ''Arbuscular mycorrhizal fungi enhance tolerance of vinca to high alkalinity in irrigation water,''] Cartmill and collegues found that arbuscular mycorrhizal fungi are capable of increasing the salt tolerance of plants. Applications for this finding include increasing the tolerance of crops to irrigation water of high alkalinity.<br />
<br />
==References==<br />
*Martin F., A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rodriguez, Rusty J, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
*Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
*Singer, Michael J and Donald N. Munns. 2006 ''Soils: an Introduction''. Pearson Education Inc. New Jersey.<br />
<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29494
Rhizosphere Interactions
2008-03-22T06:41:26Z
<p>Alorloff: /* Nitrogen Fixing Bacteria */</p>
<hr />
<div>==Rhizosphere==<br />
<br />
[[Image:rhizobact.jpg|thumb|250px|right|Rhizosphere [http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/rhizobact.jpg Source]]]<br />
<br />
The rhizosphere is a microecological zone in direct proximity of plant roots. It is functionally defined as the particulate matter and microorganisms that cling to roots after being gently shaken in water. The theoretical extent of the rhizosphere is dependent on the zone of influence of the plant roots and associated microorganisms. The rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane is the root epidermis and outer cortex where soil particles, bacteria and fungal hyphae adhere (Singer, 2006; Sylvia, 2005). The functional definition is the remaining microorganisms and soil particles after the roots have been shaken vigorously in water. There are more microbes in the rhizoplane than in the more loosely assoicated rhizosphere. This is determined by counting the number of colony forming units (CFUs) which are determined by spreading extracted soil microorganisms across an agar and counting the number of independent clusters of microorganisms. Microbes are most abundant where the integrety of the root is broken. For this reason, soil microorganisms are found on older rather than younger roots. Bacteria and fungi that colonize within the root are not considered a part of the rhizoplane, but instead called endophytes (Sylvia, 2005).<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Soil Texture====<br />
Movement of organic matter away from the root as well as bacteria colonizing new locations occurs more readily in sandy soils than clayey soils. Sand has larger pores between each grenule allowing microorganisms and exudates can travel. Therefore, the larger the granule size, the further the rhizosphere and microorganisms associated with it will extend into the surrounding soil. (Sylvia, 2005)<br />
<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous.<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
[[Image:rhizospherebacteria.jpg|thumb|250px|right|Rhizosphere Bacteria [https://www.soils.org/divisions/s03/images/rhizospherebacteria.jpg source]]]<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [http://en.wikipedia.org/wiki/Actinomycete acetinomycetes] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
[[Image:ectomycorrhizae.gif|thumb|200px|right|Ectomycorrhizae [http://www-mykopat.slu.se/Newwebsite/mycorrhiza/kantarellfiler/bilder/C.GIF Reference to Source of Image]]]<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
[[Image:arbuscular.jpg|thumb|200px|right|Image of Arbuscular Mycorrhizae[http://biology.kenyon.edu/fennessy/SrexMarx/arbgood.jpg Reference to Source of Image]]]<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
[[Image:nodes.jpg|thumb|300px|left|Image of N cycle [http://academic.reed.edu/biology/Nitrogen/images/part1/bigFL1.jpg Reference to Source of Image]]]<br />
Due to the high energetic cost of fixing dinitrogen, a significant part of nitrogen fixation occurs near the plant roots, where there is an influx of sugar to power the process. Some nitrogen fixation occurs in the rizosphere by free-living bacteria (the ability is found only in prokaryotes). When these otherwise free living bacteria form a close association with a plant they’re called “associative symbiotes”. An example of a free living nitrogen fixer is [[Azotobacter]]. <br />
<br />
There are several drawbacks to this lifestyle: 1. Nitrogen fixing bacteria are sensitive to fluxuations in oxygen. Many are aerobes who use oxygen as a terminal electron acceptor, but on the other hand, oxygen can poison the [nitrogenase enzyme http://en.wikipedia.org/wiki/Nitrogenase]. Hence free-living bacteria need to take energetically costly steps such as having extremely fast respiration or producing large amounts slime to protect nitrogenase. Another disadvantage Associative symbiotes have do deal with is that they are in direct competition with the rest of the rizosphere for the available carbon. Experiments indicate that carbon is a limiting factor in rhizosphere nitrogen fixation. <br />
<br />
An alternate form of nitrogen-fixing lifestyle is to actually live in the plant root cells themselves. Bacteria who do this are called ”symbiotes” or “mutualistic symbiotes”, and an example of one such bacteria is Rhizobia. These bacteria form “nodules” on plants, which are huge masses of bacteria living inside plant cells which have been modified for the purpose. The process of forming a nodule requires recognition between bacteria and plant (usually very specific), and gene expression changes in both players. The plant provides carbon to the bacteria and the bacteria provide fixed nitrogen to the plant. The masses of bacteria produce leghemoglobin to protect nitrogenase from oxygen, and do not have to compete with other rhizosphere microbes for carbon (Sylvia, 2005).<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==Current Research==<br />
<br />
*In the article, [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TC3-4PYRKM2-1&_user=4421&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059598&_version=1&_urlVersion=0&_userid=4421&md5=d5dc6db07423535c2d31eedc48131fed ''Arbuscular mycorrhizal fungi enhance tolerance of vinca to high alkalinity in irrigation water,''] Cartmill and collegues found that arbuscular mycorrhizal fungi are capable of increasing the salt tolerance of plants. Applications for this finding include increasing the tolerance of crops to irrigation water of high alkalinity.<br />
<br />
==References==<br />
*Martin F., A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rodriguez, Rusty J, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
*Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
*Singer, Michael J and Donald N. Munns. 2006 ''Soils: an Introduction''. Pearson Education Inc. New Jersey.<br />
<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29492
Rhizosphere Interactions
2008-03-22T06:37:11Z
<p>Alorloff: /* Nitrogen Fixing Bacteria */</p>
<hr />
<div>==Rhizosphere==<br />
<br />
[[Image:rhizobact.jpg|thumb|250px|right|Rhizosphere [http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/rhizobact.jpg Source]]]<br />
<br />
The rhizosphere is a microecological zone in direct proximity of plant roots. It is functionally defined as the particulate matter and microorganisms that cling to roots after being gently shaken in water. The theoretical extent of the rhizosphere is dependent on the zone of influence of the plant roots and associated microorganisms. The rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane is the root epidermis and outer cortex where soil particles, bacteria and fungal hyphae adhere (Singer, 2006; Sylvia, 2005). The functional definition is the remaining microorganisms and soil particles after the roots have been shaken vigorously in water. There are more microbes in the rhizoplane than in the more loosely assoicated rhizosphere. This is determined by counting the number of colony forming units (CFUs) which are determined by spreading extracted soil microorganisms across an agar and counting the number of independent clusters of microorganisms. Microbes are most abundant where the integrety of the root is broken. For this reason, soil microorganisms are found on older rather than younger roots. Bacteria and fungi that colonize within the root are not considered a part of the rhizoplane, but instead called endophytes (Sylvia, 2005).<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Soil Texture====<br />
Movement of organic matter away from the root as well as bacteria colonizing new locations occurs more readily in sandy soils than clayey soils. Sand has larger pores between each grenule allowing microorganisms and exudates can travel. Therefore, the larger the granule size, the further the rhizosphere and microorganisms associated with it will extend into the surrounding soil. (Sylvia, 2005)<br />
<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous.<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
[[Image:rhizospherebacteria.jpg|thumb|250px|right|Rhizosphere Bacteria [https://www.soils.org/divisions/s03/images/rhizospherebacteria.jpg source]]]<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [http://en.wikipedia.org/wiki/Actinomycete acetinomycetes] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
[[Image:ectomycorrhizae.gif|thumb|200px|right|Ectomycorrhizae [http://www-mykopat.slu.se/Newwebsite/mycorrhiza/kantarellfiler/bilder/C.GIF Reference to Source of Image]]]<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
[[Image:arbuscular.jpg|thumb|200px|right|Image of Arbuscular Mycorrhizae[http://biology.kenyon.edu/fennessy/SrexMarx/arbgood.jpg Reference to Source of Image]]]<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
[[Image:nodes.jpg|thumb|300px|left|Image of N cycle [http://academic.reed.edu/biology/Nitrogen/images/part1/bigFL1.jpg Reference to Source of Image]]]<br />
Due to the high energetic cost of fixing dinitrogen, a significant part of nitrogen fixation occurs near the plant roots, where there is an influx of sugar to power the process. Some nitrogen fixation occurs in the rizosphere by free-living bacteria (the ability is found only in prokaryotes). When these otherwise free living bacteria form a close association with a plant they’re called “associative symbiotes”. An example of a free living nitrogen fixer is [[Azotobacter]]. <br />
<br />
There are several drawbacks to this lifestyle: 1. Nitrogen fixing bacteria are sensitive to fluxuations in oxygen. Many are aerobes who use oxygen as a terminal electron acceptor, but on the other hand, oxygen can poison the nitrogenase enzyme. Hence free-living bacteria need to take energetically costly steps such as having extremely fast respiration or producing large amounts slime to protect nitrogenase. Another disadvantage Associative symbiotes have do deal with is that they are in direct competition with the rest of the rizosphere for the available carbon. Experiments indicate that carbon is a limiting factor in rhizosphere nitrogen fixation. <br />
<br />
An alternate form of nitrogen-fixing lifestyle is to actually live in the plant root cells themselves. Bacteria who do this are called ”symbiotes” or “mutualistic symbiotes”, and an example of one such bacteria is Rhizobia. These bacteria form “nodules” on plants, which are huge masses of bacteria living inside plant cells which have been modified for the purpose. The process of forming a nodule requires recognition between bacteria and plant (usually very specific), and gene expression changes in both players. The plant provides carbon to the bacteria and the bacteria provide fixed nitrogen to the plant. The masses of bacteria produce leghemoglobin to protect nitrogenase from oxygen, and do not have to compete with other rhizosphere microbes for carbon (Sylvia, 2005).<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==Current Research==<br />
<br />
*In the article, [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TC3-4PYRKM2-1&_user=4421&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059598&_version=1&_urlVersion=0&_userid=4421&md5=d5dc6db07423535c2d31eedc48131fed ''Arbuscular mycorrhizal fungi enhance tolerance of vinca to high alkalinity in irrigation water,''] Cartmill and collegues found that arbuscular mycorrhizal fungi are capable of increasing the salt tolerance of plants. Applications for this finding include increasing the tolerance of crops to irrigation water of high alkalinity.<br />
<br />
==References==<br />
*Martin F., A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rodriguez, Rusty J, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
*Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
*Singer, Michael J and Donald N. Munns. 2006 ''Soils: an Introduction''. Pearson Education Inc. New Jersey.<br />
<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29491
Rhizosphere Interactions
2008-03-22T06:36:46Z
<p>Alorloff: /* Nitrogen Fixing Bacteria */</p>
<hr />
<div>==Rhizosphere==<br />
<br />
[[Image:rhizobact.jpg|thumb|250px|right|Rhizosphere [http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/rhizobact.jpg Source]]]<br />
<br />
The rhizosphere is a microecological zone in direct proximity of plant roots. It is functionally defined as the particulate matter and microorganisms that cling to roots after being gently shaken in water. The theoretical extent of the rhizosphere is dependent on the zone of influence of the plant roots and associated microorganisms. The rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane is the root epidermis and outer cortex where soil particles, bacteria and fungal hyphae adhere (Singer, 2006; Sylvia, 2005). The functional definition is the remaining microorganisms and soil particles after the roots have been shaken vigorously in water. There are more microbes in the rhizoplane than in the more loosely assoicated rhizosphere. This is determined by counting the number of colony forming units (CFUs) which are determined by spreading extracted soil microorganisms across an agar and counting the number of independent clusters of microorganisms. Microbes are most abundant where the integrety of the root is broken. For this reason, soil microorganisms are found on older rather than younger roots. Bacteria and fungi that colonize within the root are not considered a part of the rhizoplane, but instead called endophytes (Sylvia, 2005).<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Soil Texture====<br />
Movement of organic matter away from the root as well as bacteria colonizing new locations occurs more readily in sandy soils than clayey soils. Sand has larger pores between each grenule allowing microorganisms and exudates can travel. Therefore, the larger the granule size, the further the rhizosphere and microorganisms associated with it will extend into the surrounding soil. (Sylvia, 2005)<br />
<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous.<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
[[Image:rhizospherebacteria.jpg|thumb|250px|right|Rhizosphere Bacteria [https://www.soils.org/divisions/s03/images/rhizospherebacteria.jpg source]]]<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [http://en.wikipedia.org/wiki/Actinomycete acetinomycetes] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
[[Image:ectomycorrhizae.gif|thumb|200px|right|Ectomycorrhizae [http://www-mykopat.slu.se/Newwebsite/mycorrhiza/kantarellfiler/bilder/C.GIF Reference to Source of Image]]]<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
[[Image:arbuscular.jpg|thumb|200px|right|Image of Arbuscular Mycorrhizae[http://biology.kenyon.edu/fennessy/SrexMarx/arbgood.jpg Reference to Source of Image]]]<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
[[Image:nodes.jpg|thumb|300px|left|Image of N cycle [http://academic.reed.edu/biology/Nitrogen/images/part1/bigFL1.jpg Reference to Source of Image]]]<br />
Due to the high energetic cost of fixing dinitrogen, a significant part of nitrogen fixation occurs near the plant roots, where there is an influx of sugar to power the process. Some nitrogen fixation occurs in the rizosphere by free-living bacteria (the ability is found only in prokaryotes). When these otherwise free living bacteria form a close association with a plant they’re called “associative symbiotes”. An example of a free living nitrogen fixer is "[[Azotobacter]]". <br />
<br />
There are several drawbacks to this lifestyle: 1. Nitrogen fixing bacteria are sensitive to fluxuations in oxygen. Many are aerobes who use oxygen as a terminal electron acceptor, but on the other hand, oxygen can poison the nitrogenase enzyme. Hence free-living bacteria need to take energetically costly steps such as having extremely fast respiration or producing large amounts slime to protect nitrogenase. Another disadvantage Associative symbiotes have do deal with is that they are in direct competition with the rest of the rizosphere for the available carbon. Experiments indicate that carbon is a limiting factor in rhizosphere nitrogen fixation. <br />
<br />
An alternate form of nitrogen-fixing lifestyle is to actually live in the plant root cells themselves. Bacteria who do this are called ”symbiotes” or “mutualistic symbiotes”, and an example of one such bacteria is Rhizobia. These bacteria form “nodules” on plants, which are huge masses of bacteria living inside plant cells which have been modified for the purpose. The process of forming a nodule requires recognition between bacteria and plant (usually very specific), and gene expression changes in both players. The plant provides carbon to the bacteria and the bacteria provide fixed nitrogen to the plant. The masses of bacteria produce leghemoglobin to protect nitrogenase from oxygen, and do not have to compete with other rhizosphere microbes for carbon (Sylvia, 2005).<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==Current Research==<br />
<br />
*In the article, [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TC3-4PYRKM2-1&_user=4421&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059598&_version=1&_urlVersion=0&_userid=4421&md5=d5dc6db07423535c2d31eedc48131fed ''Arbuscular mycorrhizal fungi enhance tolerance of vinca to high alkalinity in irrigation water,''] Cartmill and collegues found that arbuscular mycorrhizal fungi are capable of increasing the salt tolerance of plants. Applications for this finding include increasing the tolerance of crops to irrigation water of high alkalinity.<br />
<br />
==References==<br />
*Martin F., A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rodriguez, Rusty J, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
*Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
*Singer, Michael J and Donald N. Munns. 2006 ''Soils: an Introduction''. Pearson Education Inc. New Jersey.<br />
<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29490
Rhizosphere Interactions
2008-03-22T06:33:04Z
<p>Alorloff: /* Nitrogen Fixing Bacteria */</p>
<hr />
<div>==Rhizosphere==<br />
<br />
[[Image:rhizobact.jpg|thumb|250px|right|Rhizosphere [http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/rhizobact.jpg Source]]]<br />
<br />
The rhizosphere is a microecological zone in direct proximity of plant roots. It is functionally defined as the particulate matter and microorganisms that cling to roots after being gently shaken in water. The theoretical extent of the rhizosphere is dependent on the zone of influence of the plant roots and associated microorganisms. The rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane is the root epidermis and outer cortex where soil particles, bacteria and fungal hyphae adhere (Singer, 2006; Sylvia, 2005). The functional definition is the remaining microorganisms and soil particles after the roots have been shaken vigorously in water. There are more microbes in the rhizoplane than in the more loosely assoicated rhizosphere. This is determined by counting the number of colony forming units (CFUs) which are determined by spreading extracted soil microorganisms across an agar and counting the number of independent clusters of microorganisms. Microbes are most abundant where the integrety of the root is broken. For this reason, soil microorganisms are found on older rather than younger roots. Bacteria and fungi that colonize within the root are not considered a part of the rhizoplane, but instead called endophytes (Sylvia, 2005).<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Soil Texture====<br />
Movement of organic matter away from the root as well as bacteria colonizing new locations occurs more readily in sandy soils than clayey soils. Sand has larger pores between each grenule allowing microorganisms and exudates can travel. Therefore, the larger the granule size, the further the rhizosphere and microorganisms associated with it will extend into the surrounding soil. (Sylvia, 2005)<br />
<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous.<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
[[Image:rhizospherebacteria.jpg|thumb|250px|right|Rhizosphere Bacteria [https://www.soils.org/divisions/s03/images/rhizospherebacteria.jpg source]]]<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [http://en.wikipedia.org/wiki/Actinomycete acetinomycetes] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
[[Image:ectomycorrhizae.gif|thumb|200px|right|Ectomycorrhizae [http://www-mykopat.slu.se/Newwebsite/mycorrhiza/kantarellfiler/bilder/C.GIF Reference to Source of Image]]]<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
[[Image:arbuscular.jpg|thumb|200px|right|Image of Arbuscular Mycorrhizae[http://biology.kenyon.edu/fennessy/SrexMarx/arbgood.jpg Reference to Source of Image]]]<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
[[Image:nodes.jpg|thumb|300px|left|Image of N cycle [http://academic.reed.edu/biology/Nitrogen/images/part1/bigFL1.jpg Reference to Source of Image]]]<br />
Due to the high energetic cost of fixing dinitrogen, a significant part of nitrogen fixation occurs near the plant roots, where there is an influx of sugar to power the process. Some nitrogen fixation occurs in the rizosphere by free-living bacteria (the ability is found only in prokaryotes). When these otherwise free living bacteria form a close association with a plant they’re called “associative symbiotes”. An example of a free living nitrogen fixer is [Azotobacter| Azotobacter]. <br />
<br />
There are several drawbacks to this lifestyle: 1. Nitrogen fixing bacteria are sensitive to fluxuations in oxygen. Many are aerobes who use oxygen as a terminal electron acceptor, but on the other hand, oxygen can poison the nitrogenase enzyme. Hence free-living bacteria need to take energetically costly steps such as having extremely fast respiration or producing large amounts slime to protect nitrogenase. Another disadvantage Associative symbiotes have do deal with is that they are in direct competition with the rest of the rizosphere for the available carbon. Experiments indicate that carbon is a limiting factor in rhizosphere nitrogen fixation. <br />
<br />
An alternate form of nitrogen-fixing lifestyle is to actually live in the plant root cells themselves. Bacteria who do this are called ”symbiotes” or “mutualistic symbiotes”, and an example of one such bacteria is Rhizobia. These bacteria form “nodules” on plants, which are huge masses of bacteria living inside plant cells which have been modified for the purpose. The process of forming a nodule requires recognition between bacteria and plant (usually very specific), and gene expression changes in both players. The plant provides carbon to the bacteria and the bacteria provide fixed nitrogen to the plant. The masses of bacteria produce leghemoglobin to protect nitrogenase from oxygen, and do not have to compete with other rhizosphere microbes for carbon (Sylvia, 2005).<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==Current Research==<br />
<br />
*In the article, [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TC3-4PYRKM2-1&_user=4421&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059598&_version=1&_urlVersion=0&_userid=4421&md5=d5dc6db07423535c2d31eedc48131fed ''Arbuscular mycorrhizal fungi enhance tolerance of vinca to high alkalinity in irrigation water,''] Cartmill and collegues found that arbuscular mycorrhizal fungi are capable of increasing the salt tolerance of plants. Applications for this finding include increasing the tolerance of crops to irrigation water of high alkalinity.<br />
<br />
==References==<br />
*Martin F., A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rodriguez, Rusty J, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
*Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
*Singer, Michael J and Donald N. Munns. 2006 ''Soils: an Introduction''. Pearson Education Inc. New Jersey.<br />
<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29489
Rhizosphere Interactions
2008-03-22T06:28:48Z
<p>Alorloff: /* Nitrogen Fixing Bacteria */</p>
<hr />
<div>==Rhizosphere==<br />
<br />
[[Image:rhizobact.jpg|thumb|250px|right|Rhizosphere [http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/rhizobact.jpg Source]]]<br />
<br />
The rhizosphere is a microecological zone in direct proximity of plant roots. It is functionally defined as the particulate matter and microorganisms that cling to roots after being gently shaken in water. The theoretical extent of the rhizosphere is dependent on the zone of influence of the plant roots and associated microorganisms. The rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane is the root epidermis and outer cortex where soil particles, bacteria and fungal hyphae adhere (Singer, 2006; Sylvia, 2005). The functional definition is the remaining microorganisms and soil particles after the roots have been shaken vigorously in water. There are more microbes in the rhizoplane than in the more loosely assoicated rhizosphere. This is determined by counting the number of colony forming units (CFUs) which are determined by spreading extracted soil microorganisms across an agar and counting the number of independent clusters of microorganisms. Microbes are most abundant where the integrety of the root is broken. For this reason, soil microorganisms are found on older rather than younger roots. Bacteria and fungi that colonize within the root are not considered a part of the rhizoplane, but instead called endophytes (Sylvia, 2005).<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Soil Texture====<br />
Movement of organic matter away from the root as well as bacteria colonizing new locations occurs more readily in sandy soils than clayey soils. Sand has larger pores between each grenule allowing microorganisms and exudates can travel. Therefore, the larger the granule size, the further the rhizosphere and microorganisms associated with it will extend into the surrounding soil. (Sylvia, 2005)<br />
<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous.<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
[[Image:rhizospherebacteria.jpg|thumb|250px|right|Rhizosphere Bacteria [https://www.soils.org/divisions/s03/images/rhizospherebacteria.jpg source]]]<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [http://en.wikipedia.org/wiki/Actinomycete acetinomycetes] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
[[Image:ectomycorrhizae.gif|thumb|200px|right|Ectomycorrhizae [http://www-mykopat.slu.se/Newwebsite/mycorrhiza/kantarellfiler/bilder/C.GIF Reference to Source of Image]]]<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
[[Image:arbuscular.jpg|thumb|200px|right|Image of Arbuscular Mycorrhizae[http://biology.kenyon.edu/fennessy/SrexMarx/arbgood.jpg Reference to Source of Image]]]<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
[[Image:nodes.jpg|thumb|300px|left|Image of N cycle [http://academic.reed.edu/biology/Nitrogen/images/part1/bigFL1.jpg Reference to Source of Image]]]<br />
Due to the high energetic cost of fixing dinitrogen, a significant part of nitrogen fixation occurs near the plant roots, where there is an influx of sugar to power the process. Some nitrogen fixation occurs in the rizosphere by free-living bacteria (the ability is found only in prokaryotes). When these otherwise free living bacteria form a close association with a plant they’re called “associative symbiotes”. An example of a free living nitrogen fixer is Azotobacter. <br />
<br />
There are several drawbacks to this lifestyle: 1. Nitrogen fixing bacteria are sensitive to fluxuations in oxygen. Many are aerobes who use oxygen as a terminal electron acceptor, but on the other hand, oxygen can poison the nitrogenase enzyme. Hence free-living bacteria need to take energetically costly steps such as having extremely fast respiration or producing large amounts slime to protect nitrogenase. Another disadvantage Associative symbiotes have do deal with is that they are in direct competition with the rest of the rizosphere for the available carbon. Experiments indicate that carbon is a limiting factor in rhizosphere nitrogen fixation. <br />
<br />
An alternate form of nitrogen-fixing lifestyle is to actually live in the plant root cells themselves. Bacteria who do this are called ”symbiotes” or “mutualistic symbiotes”, and an example of one such bacteria is Rhizobia. These bacteria form “nodules” on plants, which are huge masses of bacteria living inside plant cells which have been modified for the purpose. The process of forming a nodule requires recognition between bacteria and plant (usually very specific), and gene expression changes in both players. The plant provides carbon to the bacteria and the bacteria provide fixed nitrogen to the plant. The masses of bacteria produce leghemoglobin to protect nitrogenase from oxygen, and do not have to compete with other rhizosphere microbes for carbon (Sylvia, 2005).<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==Current Research==<br />
<br />
*In the article, [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TC3-4PYRKM2-1&_user=4421&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000059598&_version=1&_urlVersion=0&_userid=4421&md5=d5dc6db07423535c2d31eedc48131fed ''Arbuscular mycorrhizal fungi enhance tolerance of vinca to high alkalinity in irrigation water,''] Cartmill and collegues found that arbuscular mycorrhizal fungi are capable of increasing the salt tolerance of plants. Applications for this finding include increasing the tolerance of crops to irrigation water of high alkalinity.<br />
<br />
==References==<br />
*Martin F., A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rodriguez, Rusty J, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
*Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
*Singer, Michael J and Donald N. Munns. 2006 ''Soils: an Introduction''. Pearson Education Inc. New Jersey.<br />
<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29326
Rhizosphere Interactions
2008-03-18T18:36:31Z
<p>Alorloff: /* Nitrogen Fixing Bacteria */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rhizoplane are closer to the actual roots than the microbes in the rhizosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rhizoplane than in the more loosely assoicated rhizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rhizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
Due to the high energetic cost of fixing nitrogen dinitrogen, a significant part of nitrogen fixation occurs near the plant roots, where there is an influx of sugar to power the process. Some nitrogen fixation occurs in the rizosphere by free-living bacteria (the ability is found only in prokaryotes). When these otherwise free living bacteria form a close association with a plant they’re called “associative symbiotes”. An example of a free living nitrogen fixer is Azotobacter. <br />
<br />
There are several drawbacks to this lifestyle: 1. Nitrogen fixing bacteria are sensitive to fluxuations in oxygen. Many are aerobes who use oxygen as a terminal electron acceptor, but on the other hand, oxygen can poison the nitrogenase enzyme. Hence free-living bacteria need to take energetically costly steps such as having extremely fast respiration or producing large amounts slime to protect nitrogenase. Another disadvantage Associative symbiotes have do deal with is that they are in direct competition with the rest of the rizosphere for the available carbon. Experiments indicate that carbon is a limiting factor in rhizosphere nitrogen fixation. <br />
<br />
An alternate form of nitrogen-fixing lifestyle is to actually live in the plant root cells themselves. Bacteria who do this are called ”symbiotes” or “mutualistic symbiotes”, and an example of one such bacteria is Rhizobia. These bacteria form “nodules” on plants, which are huge masses of bacteria living inside cells which have been modified for the purpose. The process of forming a nodule requires recognition between bacteria and plant (usually very specific). The plant provides carbon to the bacteria and the bacteria provide fixed nitrogen to the plant. The masses of bacteria produce leghemoglobin to protect nitrogenase from oxygen, and do not have to compete with other rhizosphere microbes for carbon (Sylvia, 2005).<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
*F. Martin, A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rusty J Rodriguez, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29325
Rhizosphere Interactions
2008-03-18T18:35:46Z
<p>Alorloff: /* Nitrogen Fixing Bacteria */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rhizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rhizoplane are closer to the actual roots than the microbes in the rhizosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rhizoplane than in the more loosely assoicated rhizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rhizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====pH====<br />
Several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
The availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rhizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
Due to the high energetic cost of fixing nitrogen dinitrogen, a significant part of nitrogen fixation occurs near the plant roots, where there is an influx of sugar to power the process. Some nitrogen fixation occurs in the rizosphere by free-living bacteria (the ability is found only in prokaryotes). When these otherwise free living bacteria form a close association with a plant they’re called “associative symbiotes”. An example of a free living nitrogen fixer is Azotobacter. <br />
<br />
There are several drawbacks to this lifestyle: 1. Nitrogen fixing bacteria are sensitive to fluxuations in oxygen. Many are aerobes who use oxygen as a terminal electron acceptor, but on the other hand, oxygen can poison the nitrogenase enzyme. Hence free-living bacteria need to take energetically costly steps such as having extremely fast respiration or producing large amounts slime to protect nitrogenase. Another disadvantage Associative symbiotes have do deal with is that they are in direct competition with the rest of the rizosphere for the available carbon. Experiments indicate that carbon is a limiting factor in rhizosphere nitrogen fixation. <br />
<br />
An alternate form of nitrogen-fixing lifestyle is to actually live in the plant root cells themselves. Bacteria who do this are called ”symbiotes” or “mutualistic symbiotes”, and an example of one such bacteria is Rhizobia. These bacteria form “nodules” on plants, which are huge masses of bacteria living inside cells which have been modified for the purpose. The process of forming a nodule requires recognition between bacteria and plant (usually very specific). The plant provides carbon to the bacteria and the bacteria provide fixed nitrogen to the plant. The masses of bacteria produce leghemoglobin to protect nitrogenase from oxygen, and do not have to compete with other rhizosphere microbes for carbon.<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
*F. Martin, A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rusty J Rodriguez, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Talk:Soil_Environment&diff=29293
Talk:Soil Environment
2008-03-17T06:40:21Z
<p>Alorloff: </p>
<hr />
<div>I got confused by the sentence "Soils that are coarse textured are less likely to have a well-defined structure and therefore fewer structured pore space than s soil high in clay content.S. carpocapsae (diameter=25um) move more in fine sandy loam soil than in clay soil.[5]" is S. Carpocapse a bacteia? what does the first s stand for? [[User:Alorloff|Alorloff]] 06:40, 17 March 2008 (UTC)<br />
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I'm wondering about the first sentence of the introduction? I'm not sure if is a typo? What about nutrients? Great pictures! Heather<br />
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Maybe you could also add factors that affect CEC capacity, and which ionic species are more tightly held, and therefore less available for microbes or transport through the soil. [[User:Jmmullane|Jmmullane]] 06:06, 15 March 2008 (UTC)<br />
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You stated: "The CEC is the total amount of exchangeable cations that a soil can hold at a specific pH [1]. The positively charged soil particles allow for charged soil microorganisms (due to charged organic molecules) to be attracted or repelled from soil." This confused me because you say the soil particles are positively charged, but you also say that cations are exchanged. It is my understanding that the soil particles are negatively charged, providing them with the capacity to interact with cationic nutrients (CEC). Perhaps you could clarify that for me.[[User:Jmmullane|Jmmullane]] 05:59, 15 March 2008 (UTC)<br />
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I think you are missing one item for current research. In the current research section it would also be helpful if you provided a brief description of the research as opposed to just citing it.[[User:Jmmullane|Jmmullane]] 05:48, 15 March 2008 (UTC)<br />
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Hey, now you can link to the rhizosphere page that our group has created! [user jbaumgartel]<br />
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It might be good to relate the information you have presented about soil texture back to the effect that it has on microbial life in the soil. [user jbaumgartel]<br />
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Great job you guys!! I saw a lot of detail and new information. The only thing I saw wrong was that I believe you need three new studies and I only saw two. [user bhsparks]<br />
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Soil water might be a subject worthy of a little more description. It seems like a rate limiting factor, one that governs microbial activity as well as mobility.<br />
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A link in your Plant Growth-Promoting Rhizobacteria (PGPR)section to the Rhizosphere page would be nice. [[User:Icclark|Icclark]] 06:37, 14 March 2008 (UTC)<br />
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To get a subscript, do <sub>this</sub> [[User:Njblackburn|Njblackburn]] 04:51, 14 March 2008 (UTC)<br />
Great thanks. Didn't know that. Figured out superscript too![[User:Kjmuzikar|Kjmuzikar]] 05:21, 14 March 2008 (UTC)<br />
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In your intro you say "Microbial activity basically means the generation of microbial." microbial what?[[User:Njblackburn|Njblackburn]] 04:45, 14 March 2008 (UTC)<br />
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Hi everybody- great job overall. I have listed a few suggestions for your site:<br />
In the CEC section, I’m pretty sure soils (mineral surfaces) are negatively charged and microbes are positively charged. –It might be a good idea to just briefly define under each section soil texture, soil pores, and soil structure.—for the soil water section, you may want to include that it is a necessary habitat for some microbes (which types?).—for the temperature section, you have described Q10, you may want to introduce the term here.—You may want to combine the “soil structure” and “aggregate” section somehow.—You may want to change the section heading “PGRP” to just rhizobacteria, since you also have DRMO’s included in this section. <br />
I think some pictures would be great too. Heather <br />
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Good broad covering of the subject. One suggestion I would have is possibly taking the information under "Organism Intertaions" and making a distinct chart. That way it's visually pleasing and sets the information apart. [[kamackey]]<br />
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Maybe this could use some pictures? Maybe the organisms u talked about, or the rhizobia. Just something to make it pretty. -David La ````[[User:Dtla|Dtla]] 02:45, 14 March 2008 (UTC)<br />
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I have heard that anion exchange capacity (not as significant as cec) can play a role in soil environments. If true you may want to add a short section regarding this.[[User:Njppatel|Njppatel]] 18:36, 13 March 2008 (UTC)<br />
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Also you may want to add a section about how aggregates get formed, other than that the information is great[[User:Njppatel|Njppatel]] 18:36, 13 March 2008 (UTC)<br />
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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 />
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I suggest replacing microflora with "interactions with other microorganisms".----Kate Scow<br />
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Bioavailability :<br />
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Definition of bioavailability is not quite right. You can go to book and lecture notes, or other sites, and develop better definition.---Kate<br />
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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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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 />
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To get subheadings, use various numbers of equal signs before and after the word (see template code).<br />
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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 />
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[[User:Irina.chakraborty|Irina C]] 18:48, 28 January 2008 (UTC)<br />
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Hi soil environment group. Please use section formats as in the template. You're the first group to start! great!!<br />
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[[User:Irina.chakraborty|Irina C]] 04:58, 28 January 2008 (UTC)</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Talk:Bioremediation&diff=29286
Talk:Bioremediation
2008-03-17T06:27:26Z
<p>Alorloff: </p>
<hr />
<div>Wow nice page! Two suggestions: 1. a typo "The removal of nitrogen is a two stage stage process than involves nitrification and denitrification" to "The removal of nitrogen is a two stage stage process THAT involves nitrification and denitrification" 2. A sentence about how P putida actually detects/reports presence of TNT would be nice. [[User:Alorloff|Alorloff]] 06:27, 17 March 2008 (UTC)<br />
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I like how you included pictures of the different PAH structures. I think it would strengthen the page to show pictures of the other contaminants, and discuss how they are broken down in a bit more detail. Oxic vs. anoxic? byproducts? Great job overall, Heather<br />
<br />
One more thing: the brief description of co-metabolism is a little unclear. <br />
You wrote: "The breakdown of PAHs can occur when microorganisms use PAH as their sole energy and carbon source and also through the co-metabolisms process. Co-metabolism refers to when an enzyme directed at another compound also degrades PHA. This has been shown to be an important phenomenon in breaking down larger aromatic chains, by does not directly lead to complete oxidation to carbon dioxide [5]." <br />
Perhaps you could say something like, "Cometabolism refers to the transformation of a substrate by a microorganism that derives its energy/carbon from a second substrate." Also, in the last sentence I think "by" should be "but." Keep up the good work! [[User:Jmmullane|Jmmullane]] 04:37, 15 March 2008 (UTC)<br />
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Thank you for the comments. I made some changes, hopefully it is more clear now...[[User:Icclark|Icclark]] 00:10, 17 March 2008 (UTC)<br />
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Maybe you guys could consider re-organizing the examples of microorganisms so that they are in the same order as the pollutants that they degrade or even incorporate the microorganisms into the corresponding pollutant section. That might make things flow a little easier.[[User:Jmmullane|Jmmullane]] 04:24, 15 March 2008 (UTC)<br />
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I agree, but not all pollutants have a corresponding microbe, and we like having all the microbes together, so we might stick with the format for now. Thanks [[User:Icclark|Icclark]] 00:34, 17 March 2008 (UTC)<br />
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"Polynuclear aromatic compounds (PAHs)" should be "Polycyclic aromatic hydrocarbons (PAHs)" and under that particular heading, mutagens is misspelled.[[User:Jmmullane|Jmmullane]] 04:19, 15 March 2008 (UTC)<br />
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Thanks Polynuclear changed to polycyclic. [[User:Icclark|Icclark]] 00:10, 17 March 2008 (UTC)<br />
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I love the page! The degradation diagrams that accompany the organic compounds are extremely informative and easy to follow. You did a great job with your citations as well.[[User:Jmmullane|Jmmullane]] 05:57, 14 March 2008 (UTC)<br />
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Verrrrry good, but maybe a bit dense: I agree with Pbwebb. The info is good, but maybe you could put a "lighter" summary in/ just after your intro so someone just mildly interested and knowledgable could get the important stuff without being bogged down in the more technical stuff (I know that would be a lot of work, and won't be at all offended if you ignore this)[[User:Njblackburn|Njblackburn]] 05:09, 14 March 2008 (UTC)<br />
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Italics for the microbes' names! put two apostrophes at the beginning and end of the italicized section like ''this'' [[User:Njblackburn|Njblackburn]] 05:05, 14 March 2008 (UTC)<br />
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informative yes most def. this is a super complex issue and hot topic in science. work of selling your subject. I felt like I got rushed into the details prematurely. how can your wiki page appeal to a wider audience? what will award your page with more "hits." thats just my 10 cents. cheers [[User:Pbwebb|Pbwebb]] 04:40, 14 March 2008 (UTC) <br />
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Wow, this looks fabulous! I love the images- Great job!<br />
Heather<br />
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Nice job!!I also liked how you presented the illustrations. I read a recent paper that evaluated bioremediation of aquifers contaminated with uranium with the aid of nitrate and nitrate dependent Fe(II)-oxidizing microorganisms. It is in the journal of geomicrobiology by Senko et al., 2005. Check it out..Cheers[[User:Egrgutierrez|Egrgutierrez]] 03:31, 14 March 2008 (UTC)---- <br />
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Also great use of pictures to illustrate aromatic compounds[[User:Njppatel|Njppatel]] 18:44, 13 March 2008 (UTC)<br />
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Great page, i especially liked how you gave a real life example of the exon valdez spill to illustrate the concept of bioremdiation[[User:Njppatel|Njppatel]] 18:43, 13 March 2008 (UTC)<br />
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The Microbe page that our group created is for [[Phanerochaete chrysosporium]] <br />
[[User:Sdemetriou|Sdemetriou]] 01:24, 11 March 2008 (UTC) <br />
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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 />
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[[User:Kmscow|Kate Scow]] 01:38, 10 March 2008 (UTC)<br />
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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 />
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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 />
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<br />
<br />
<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 />
* At the end of your comment, type four hyphens "----" to create a line to separate your comment from the next commentator. <br />
* Make a note on this page below the comment after you've addressed it. Add the ( &#126;&#126;&#126;&#126; ) after your note so we know who addressed the comment. Your note could look something like .. "Good idea, we fixed it.[[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)" or "I don't think we need to do this because.. [[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)"<br />
----<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)<br />
<br />
A lot of information in the page. Good. I would like to merge the metablic pathway to the example pollutant so that everyone can know how the pollutant is degraded.</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29099
Rhizosphere Interactions
2008-03-15T06:01:04Z
<p>Alorloff: /* References */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
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====Texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
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====pH====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
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the availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
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==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
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Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
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Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
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==Microbial Communities==<br />
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===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
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===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
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In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
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==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
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Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
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Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
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===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
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Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
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===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
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The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
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<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
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=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
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=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
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====Nitrogen Fixing Bacteria====<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
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A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
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''[[Agrobacterium tumefaciens]]''<br />
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''[[Alcaligenes]]'' spp.<br />
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''[[Bacillus subtilis]]''<br />
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''[[Azospirillum brasilense]]''<br />
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''[[Pseudomonas fluorescens]]''<br />
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''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
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''[[Pseudomonas]]'' spp.<br />
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''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
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''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
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(Sylvia, 2005)<br />
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==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
*F. Martin, A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
*Rusty J Rodriguez, Joan Henson, Elizabeth Van Volkenburgh, Marshal Hoy, Leesa Wright, Fleur Beckwith, Yong-Ok Kim, Regina S Redman "Stress tolerance in plants via habitat-adapted symbiosis" The ISME Journal (07 Feb 2008).<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=29078
Rhizosphere Interactions
2008-03-15T04:02:29Z
<p>Alorloff: /* References */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere:” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rhizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====Water Potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====Texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====pH====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
the availible habitat that microbes are limited in part by pH of the soil. Fungi are found in more acidic soils than alkaline, and bacteria have a very broad pH spectrum where they can survive. The influincing effects of pH in the rhizosphere is critical in supporting a biologically diverse microbial community.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allows the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
In times of flooding, when too much moisture accumulates around the base of the tree, a bacterial pathogen Armillaria may infect and cause root rot.<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
Up to 15% of the root surface area is covered with rhizosphere-specific microorganisms - providing many sites for biological interactions. A range of interactions are present in the rhizosphere: from beneficial symbiotic relationships to detrimental pathogenic interactions. (Sylvia, 2005) <br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
Microorganisms in the rhizosphere complete both chemical and physical modifications to the soil profile in and around the rhizosphere that affect plants. They can be beneficial to the plant (by pathogen suppression) or detrimental (by competition for nutrients). <br />
<br />
Chemical changes occur as a result of humification of organic matter. The resultant mineralization of various organic compounds (phosphorous, sulfur, and nitrogen, for example) provides plants with forms of nutrition that are readily available for uptake. The turnover of microbial populations also results in the release of nutrients. The fixation of atmospheric dinitrogen by both asymbiotic and symbiotic bacteria results in increases to the available nitrogen pool that can be accessed by plants in and near the rhizosphere. Symbiotic mycorrhizae cause an increase in the effective rooting area of plants, thereby providing added nutrient mining capabilities to the plant. Rhizosphere microbes can also release plant growth regulators. <br />
<br />
Physical changes occur primarily through the production of extracellular polymeric substances such as polysaccharides and glomalin, which improve soil aggregation and soil texture. The presence of mucigel in the rhizoplane is crucial to the water relations of plants, providing a bridge that prevents dessication by maintaining the water column during water stress events. (Sylvia, 2005)<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
In addition to soil properties and the types of microorganisms present in a soil, plants play an important role in the community diversity of rhizosphere microorganisms. Plant roots cause chemical and physical changes to the soil they inhabit and these changes will affect the microbial diversity in and around the rhizosphere. Root exudates will select for/against certain populations of microorganisms. Many plants exhibit genetic resistance/tolerance to rhizosphere microorganisms; the variety of plant will determine, in part, the community makeup of the microorganisms in the rhizospere. The ability of a plant to form symbiotic relationships with soil microbes will also determine rhizosphere microbial populations. The age and health of the plants present will also play a role in the microbial community dynamics of the rhizosphere. Plant roots increase the tilth of a soil and subsequently affect the physical properties of the soil. <br />
<br />
Plants can also compete with rhizosphere microorganisms for resources like water and nutrients. (Sylvia, 2005)<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Inoculants===<br />
Inoculation of fields with the soil from other fields has been practiced for centuries as a method of inoculation. Modern seed companies are dipping seeds in beneficial inoculants before sale. However, the specific conditions surrounding the seed at germination and the specific soil characteristics determining the ability of the soil to support a population of desirable rhizosphere microbes will be the ultimate determinants in the successful colonization of the desired inoculant. Carriers of inoculants are also being explored, such as peat and other potting media. The primary organisms being used for these products are mycorrhizal fungi, dinitrogen-fixing bacteria, and beneficial rhizobacteria. Some work has explored the possibility of using biological control organisms as inoculants on seeds or seedlings. (Sylvia, 2005)<br />
<br />
A partial list rhizosphere microorganisms that have been used as inoculatns:<br />
<br />
''[[Agrobacterium tumefaciens]]''<br />
<br />
''[[Alcaligenes]]'' spp.<br />
<br />
''[[Bacillus subtilis]]''<br />
<br />
''[[Azospirillum brasilense]]''<br />
<br />
''[[Pseudomonas fluorescens]]''<br />
<br />
''[http://en.wikipedia.org/wiki/Pseudomonas_putida Psuedomonas putida]''<br />
<br />
''[[Pseudomonas]]'' spp.<br />
<br />
''[[Pseudomonas syringae]]'' pv. ''tabaci''<br />
<br />
''[http://en.wikipedia.org/wiki/Trichoderma_harzianum Trichoderma harzianum]''<br />
<br />
(Sylvia, 2005)<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<br />
F. Martin, A. Aerts, D. Ahrén, A. Brun, E. G. J. Danchin, F. Duchaussoy, J. Gibon, A. Kohler, E. Lindquist, V. Pereda, A. Salamov, H. J. Shapiro, J. Wuyts, D. Blaudez, M. Buée, P. Brokstein, B. Canbäck, D. Cohen, P. E. Courty, P. M. Coutinho, C. Delaruelle, J. C. Detter, A. Deveau, S. DiFazio, S. Duplessis, L. Fraissinet-Tachet, E. Lucic, P. Frey-Klett, C. Fourrey, I. Feussner, G. Gay, J. Grimwood, P. J. Hoegger, P. Jain, S. Kilaru, J. Labbé, Y. C. Lin, V. Legué, F. Le Tacon, R. Marmeisse, D. Melayah, B. Montanini, M. Muratet, U. Nehls, H. Niculita-Hirzel, M. P. Oudot-Le Secq, M. Peter, H. Quesneville, B. Rajashekar, M. Reich, N. Rouhier, J. Schmutz, T. Yin, M. Chalot, B. Henrissat, U. Kües, S. Lucas, Y. Van de Peer, G. K. Podila, A. Polle, P. J. Pukkila, P. M. Richardson, P. Rouzé, I. R. Sanders, J. E. Stajich, A. Tunlid, G. Tuskan, I. V. Grigoriev "The genome of :Laccaria bicolor: provides insights into mycorrhizal symbiosis" Nature 452, 88 - 92 (06 Mar 2008)<br />
<br />
<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Scow, K. Soil Microbiology class notes. Winter 2008, University of California, Davis.<br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28483
Rhizosphere Interactions
2008-03-10T09:25:08Z
<p>Alorloff: /* Symbiotic or Mutualistic Relationships */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allow the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The microbial partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28482
Rhizosphere Interactions
2008-03-10T09:24:14Z
<p>Alorloff: /* Symbiotic or Mutualistic Relationships */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allow the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of ''Laccaria Bicolor'' (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The symbiotic partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28481
Rhizosphere Interactions
2008-03-10T09:22:50Z
<p>Alorloff: /* Symbiotic or mutualistic Relationships */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allow the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
===Symbiotic or Mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of Laccaria Bicolor <italic> (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The symbiotic partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28480
Rhizosphere Interactions
2008-03-10T09:22:35Z
<p>Alorloff: /* Symbiotic Relationships */</p>
<hr />
<div>==Rhizosphere==<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil.<br />
<br />
==Rhizoplane==<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
==Physical Environment==<br />
====water potential====<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
====texture====<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
====ph====<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
==Plant-Derived Compounds==<br />
Plant-derived compounds are responsible for providing the additional carbon that allow the rhizosphere to host a large variety of organisms. These compounds fall into five categories: exudates, secretions, mucilages, mucigel, and lysates.<br />
<br />
Exudates include surplus sugars, amino acids, and aeromatics that diffuse out of cells to the intercellular space and surrounding soil. Due to their diffusive nature, exudates are limited to compounds of low molecular weights. Secretions are byproducts of metabolic activity. Because they are actively released from the cell, secretions can be of both low and high molecular weight. When an epidermal root cell dies and is broken open, lysates from within the cell become available to the surrounding microbial community.<br />
<br />
Mucilages are cells sloughed off the root cap as the root grows. Abrasive forces of the root against soil particulate matter is responsible for the removal of cells. These cells consist of cellulose, pectin, starch, and lignin. Mucigel is a slime coating the surface of a root that increases the connectivity between plant roots and the surrounding soil. It is more common on the main body of the root and root hairs than the tip. During dry spells, mucigels are responsible for allowing plants to continue to uptake water and nutrients. (Sylvia, 2005)<br />
<br />
==Microbial Communities==<br />
<br />
===Bacteria===<br />
Bacteria are the most numerous organisms in the soil, averaging between 10^6 to 10^9 organisms per gram of rizosphere soil. Due to their small mass, they only account for a small amount of the biomass of soil. Nonsporulating rods, [http://en.wikipedia.org/wiki/Pseudomonads pseudomonads], and [[acetinomycetes]] are the most common bacteria in the soil. (Sylvia, 2005)<br />
<br />
===Fungi===<br />
Both pathogenic and symbiotic fungi associate with the rhizosphere. They average between 10^5 and 10^6 organisms per gram of rhizosphere soil. [http://en.wikipedia.org/wiki/Zygomycetes Zygomycetes] and [http://en.wikipedia.org/wiki/Hyphomycetes hyphomycetes] establish the most readily in the rhizosphere because they metabolize simple sugars. (Sylvia, 2005)<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
===Symbiotic or mutualistic Relationships===<br />
In a relationship, the plant usually provides a source of carbon and the bacteria or fungus fills some other more specialized function. In many cases the association is not absolutely necessary for the survival of both members, but provides significant benefit. <br />
<br />
The recently sequenced genome of Laccaria Bicolor <italic> (an ectomycorrhizal fungus) shows a excess of enzymes used in ammonia uptake, and a lack of enzymes that would be needed to degrade plant wall material. Thus, it is assumed the fungus is providing nitrogen (and perhaps other nutrients), and a guarantee not to attack to the tree in return for glucose. (Martin, 2008). As described below, fungi are also often an important source of phosphorous. <br />
<br />
The symbiotic partner can also help the plant to survive in an otherwise inhospitable environment. For example, specific endophytes have been shown to confer heat resistance to grasses that grow in a hydrothermal area, or salt tolerance to costal grasses. (Rodreguez, 2008)<br />
<br />
<br />
<br />
====Mycorrhizal Fungi====<br />
Over 80 percent of all land plants have a mutualistic relationship with one or more mycorrhizal fungi. Mycorrhizal fungi extend the effective root length by 100 fold or more. It would therefore seem appropiate that mycorrhiza means fungus-root in German. Not only do they increase the surface area over which nutrients and water can be taken up by the plant, but fungal hyphae can reach into smaller pores than roots can. The most valuable asset mycorrhizae provide is accessing immobile nutrients, such as phospherous. In return, the plant passes a significant amount of its carbon reserves to the fungi. (Sylvia, 2005)<br />
<br />
=====Ectomycorrhizae=====<br />
Ectomycorrhizae interact with the plant root by producing a net-like structure called a Hartig net that weaves between the root cortical cells. A sheath or mantle of fungal tissue covering part or all of the root is responsible for most of the increase in surface area caused by mycorrhiaze. Some fungi, such as ''[http://en.wikipedia.org/wiki/Boletus Boletus] betulicola'', have only a narrow range of plants they can associate with. Other fungi have a much larger range of host plants. One such fungus, ''[http://en.wikipedia.org/wiki/Pisolithus_tinctorius Pisolithus tinctorius]'', associates with 46 tree species and eight genera. (Sylvia, 2005)<br />
<br />
=====Arbuscular Mycorrhizae=====<br />
Arbuscular mycorrhiza is also referred to as endomycorrhiza because it has a branched arbuscule that grows within the root cortical cell. Direct connection between the plant and fungal cytoplasm allows the transfer of nutrients from the fungi to the plant and carbon from the plant to the fungi to be more efficient. Examples of mycorrhizal fungi include ''[http://en.wikipedia.org/wiki/Glomus_%28fungus%29 Glomus] tenue'' and ''[[Scutellospora]]''. (Sylvia, 2005)<br />
<br />
====Nitrogen Fixing Bacteria====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Talk:Rhizosphere_Interactions&diff=28477
Talk:Rhizosphere Interactions
2008-03-10T07:59:39Z
<p>Alorloff: </p>
<hr />
<div>Sorry, my bad. I didn't see your comment. I hope you didn't do too much preparation. <br />
[[User:Alorloff|Alorloff]] 07:48, 10 March 2008 (UTC)<br />
<br />
&#126;&#126;&#126;&#126;<br />
----<br />
<br />
<br />
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 />
=== 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 />
* At the end of your comment, type four hyphens "----" to create a line to separate your comment from the next commentator. <br />
* Make a note on this page below the comment after you've addressed it. Add the ( &#126;&#126;&#126;&#126; ) after your note so we know who addressed the comment. Your note could look something like .. "Good idea, we fixed it.[[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)" or "I don't think we need to do this because.. [[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)"<br />
----<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>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Talk:Rhizosphere_Interactions&diff=28471
Talk:Rhizosphere Interactions
2008-03-10T07:48:20Z
<p>Alorloff: </p>
<hr />
<div>Sorry, my bad. I didn't read your comment (I'm still learning to navigate these pages). I hope you didn't do too much preparation. <br />
[[User:Alorloff|Alorloff]] 07:48, 10 March 2008 (UTC)<br />
<br />
&#126;&#126;&#126;&#126;<br />
----<br />
<br />
<br />
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 />
=== 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 />
* At the end of your comment, type four hyphens "----" to create a line to separate your comment from the next commentator. <br />
* Make a note on this page below the comment after you've addressed it. Add the ( &#126;&#126;&#126;&#126; ) after your note so we know who addressed the comment. Your note could look something like .. "Good idea, we fixed it.[[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)" or "I don't think we need to do this because.. [[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)"<br />
----<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>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Talk:Rhizosphere_Interactions&diff=28470
Talk:Rhizosphere Interactions
2008-03-10T07:44:09Z
<p>Alorloff: </p>
<hr />
<div>Sorry, my bad. I didn't read your comment (I'm still learning to navigate these pages). I hope you didn't do too much preparation. <br />
<br />
&#126;&#126;&#126;&#126;<br />
----<br />
<br />
<br />
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 />
=== 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 />
* At the end of your comment, type four hyphens "----" to create a line to separate your comment from the next commentator. <br />
* Make a note on this page below the comment after you've addressed it. Add the ( &#126;&#126;&#126;&#126; ) after your note so we know who addressed the comment. Your note could look something like .. "Good idea, we fixed it.[[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)" or "I don't think we need to do this because.. [[User:Irina.chakraborty|Irina C]] 23:05, 6 March 2008 (UTC)"<br />
----<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>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28126
Rhizosphere Interactions
2008-03-09T20:10:53Z
<p>Alorloff: /* ph */</p>
<hr />
<div>==Introduction==<br />
The rizosphere refers to the region of soil near plant roots. Compared to the rest of soil, this area is relatively luxurious- nutrients are more plentiful and bacteria abound. Sylvia et al compare the rizosphere to an oasis. <!--Others in this group, please add more--><br />
<br />
==Soil Environment Associated with Plants==<br />
<br />
===Rhizoplane===<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
===Rhizosphere===<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil. <br />
<br />
====Physical Environment====<br />
======water potential======<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
======texture======<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
======ph======<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
====Plant Exudates====<br />
<br />
====Microbial Communities====<br />
<br />
=====Bacteria=====<br />
<br />
=====Archaea=====<br />
<br />
=====Fungi=====<br />
<br />
===Other===<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
===Symbiotic Relationships===<br />
<br />
====Mycorrhizal Fungi====<br />
<br />
====Other====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28125
Rhizosphere Interactions
2008-03-09T20:10:33Z
<p>Alorloff: /* texture */</p>
<hr />
<div>==Introduction==<br />
The rizosphere refers to the region of soil near plant roots. Compared to the rest of soil, this area is relatively luxurious- nutrients are more plentiful and bacteria abound. Sylvia et al compare the rizosphere to an oasis. <!--Others in this group, please add more--><br />
<br />
==Soil Environment Associated with Plants==<br />
<br />
===Rhizoplane===<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
===Rhizosphere===<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil. <br />
<br />
====Physical Environment====<br />
======water potential======<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
======texture======<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous<br />
<br />
=ph=<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
====Plant Exudates====<br />
<br />
====Microbial Communities====<br />
<br />
=====Bacteria=====<br />
<br />
=====Archaea=====<br />
<br />
=====Fungi=====<br />
<br />
===Other===<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
===Symbiotic Relationships===<br />
<br />
====Mycorrhizal Fungi====<br />
<br />
====Other====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28124
Rhizosphere Interactions
2008-03-09T20:10:09Z
<p>Alorloff: /* water potential */</p>
<hr />
<div>==Introduction==<br />
The rizosphere refers to the region of soil near plant roots. Compared to the rest of soil, this area is relatively luxurious- nutrients are more plentiful and bacteria abound. Sylvia et al compare the rizosphere to an oasis. <!--Others in this group, please add more--><br />
<br />
==Soil Environment Associated with Plants==<br />
<br />
===Rhizoplane===<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
===Rhizosphere===<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil. <br />
<br />
====Physical Environment====<br />
======water potential======<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
<br />
=texture=<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous <br />
=ph=<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
====Plant Exudates====<br />
<br />
====Microbial Communities====<br />
<br />
=====Bacteria=====<br />
<br />
=====Archaea=====<br />
<br />
=====Fungi=====<br />
<br />
===Other===<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
===Symbiotic Relationships===<br />
<br />
====Mycorrhizal Fungi====<br />
<br />
====Other====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28123
Rhizosphere Interactions
2008-03-09T20:09:35Z
<p>Alorloff: /* Physical Environment */</p>
<hr />
<div>==Introduction==<br />
The rizosphere refers to the region of soil near plant roots. Compared to the rest of soil, this area is relatively luxurious- nutrients are more plentiful and bacteria abound. Sylvia et al compare the rizosphere to an oasis. <!--Others in this group, please add more--><br />
<br />
==Soil Environment Associated with Plants==<br />
<br />
===Rhizoplane===<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
===Rhizosphere===<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil. <br />
<br />
====Physical Environment====<br />
=water potential=<br />
The plant roots which the rhizosphere is associated with can effect the physical environment of the rhizosphere. As as plants transpire water with more force during the day than during the night, they change the soil water potential immediately near their roots and so the rhizosphere undergoes fluctuations that the bulk soil avoids.<br />
=texture=<br />
Plant roots compact the soil on the short term as they grow, but once they die and decay, can actually leave soil more porous <br />
=ph=<br />
several factors can lower the pH in the rhizosphere. Respiration leads to carbon dioxide (and eventually to bicarbonate/carbonic acid) generation. In addition to respiration of the roots themselves, the rhizosphere is very rich in carbon results in other organisms from prokaryotes to fungi to small animals living and respiring in the rhizosphere more than in the bulk soil.<br />
<br />
====Plant Exudates====<br />
<br />
====Microbial Communities====<br />
<br />
=====Bacteria=====<br />
<br />
=====Archaea=====<br />
<br />
=====Fungi=====<br />
<br />
===Other===<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
===Symbiotic Relationships===<br />
<br />
====Mycorrhizal Fungi====<br />
<br />
====Other====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28115
Rhizosphere Interactions
2008-03-09T19:53:44Z
<p>Alorloff: /* Rhizoplane */</p>
<hr />
<div>==Introduction==<br />
The rizosphere refers to the region of soil near plant roots. Compared to the rest of soil, this area is relatively luxurious- nutrients are more plentiful and bacteria abound. Sylvia et al compare the rizosphere to an oasis. <!--Others in this group, please add more--><br />
<br />
==Soil Environment Associated with Plants==<br />
<br />
===Rhizoplane===<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. The distinction between bacteria which live in the rizoplane and those who live inside the root is made by naming the latter "endophytes"<br />
<br />
===Rhizosphere===<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil. <br />
<br />
====Physical Environment====<br />
<br />
====Plant Exudates====<br />
<br />
====Microbial Communities====<br />
<br />
=====Bacteria=====<br />
<br />
=====Archaea=====<br />
<br />
=====Fungi=====<br />
<br />
===Other===<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
===Symbiotic Relationships===<br />
<br />
====Mycorrhizal Fungi====<br />
<br />
====Other====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28099
Rhizosphere Interactions
2008-03-09T19:20:31Z
<p>Alorloff: </p>
<hr />
<div>==Introduction==<br />
The rizosphere refers to the region of soil near plant roots. Compared to the rest of soil, this area is relatively luxurious- nutrients are more plentiful and bacteria abound. Sylvia et al compare the rizosphere to an oasis. <!--Others in this group, please add more--><br />
<br />
==Soil Environment Associated with Plants==<br />
<br />
===Rhizoplane===<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated rizosphere. Those microbes who are directly in contact with the roots tend to be found where the integrety of the root is broken. Perhaps because of this, they also tend to be found on older rather than younger roots. <br />
<br />
===Rhizosphere===<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil. <br />
<br />
====Physical Environment====<br />
<br />
====Plant Exudates====<br />
<br />
====Microbial Communities====<br />
<br />
=====Bacteria=====<br />
<br />
=====Archaea=====<br />
<br />
=====Fungi=====<br />
<br />
===Other===<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
===Symbiotic Relationships===<br />
<br />
====Mycorrhizal Fungi====<br />
<br />
====Other====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28096
Rhizosphere Interactions
2008-03-09T19:19:02Z
<p>Alorloff: /* Rhizoplane */</p>
<hr />
<div>==Introduction==<br />
The rizosphere refers to the region of soil near plant roots. Compared to the rest of soil, this area is relatively luxurious- nutrients are more plentiful and bacteria abound. Sylvia et al compare the rizosphere to an oasis. <!--Others in this group, please add more--><br />
<br />
==Soil Environment Associated with Plants==<br />
<br />
===Rhizoplane===<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water. There are more microbes (as counted by CFU) in the rizoplane than in the more loosely assoicated [rizosphere]<br />
<br />
===Rhizosphere===<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil. <br />
<br />
====Physical Environment====<br />
<br />
====Plant Exudates====<br />
<br />
====Microbial Communities====<br />
<br />
=====Bacteria=====<br />
<br />
=====Archaea=====<br />
<br />
=====Fungi=====<br />
<br />
===Other===<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
===Symbiotic Relationships===<br />
<br />
====Mycorrhizal Fungi====<br />
<br />
====Other====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28043
Rhizosphere Interactions
2008-03-09T07:17:39Z
<p>Alorloff: /* Rhizosphere */</p>
<hr />
<div>==Introduction==<br />
The rizosphere refers to the region of soil near plant roots. Compared to the rest of soil, this area is relatively luxurious- nutrients are more plentiful and bacteria abound. Sylvia et al compare the rizosphere to an oasis. <!--Others in this group, please add more--><br />
<br />
==Soil Environment Associated with Plants==<br />
<br />
===Rhizoplane===<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water.<br />
<br />
===Rhizosphere===<br />
There are several subjective definitions of “rhizosphere” one is the zone of influence of plant roots- that may vary for the specific influence being tracked and the specific environment. A more general, functional definition is “the dirt that clings to roots after gentle shaking in water”. In general the rizosphere is a metabolically busier, faster moving, more competitive environment than the surrounding soil. <br />
<br />
====Physical Environment====<br />
<br />
====Plant Exudates====<br />
<br />
====Microbial Communities====<br />
<br />
=====Bacteria=====<br />
<br />
=====Archaea=====<br />
<br />
=====Fungi=====<br />
<br />
===Other===<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
===Symbiotic Relationships===<br />
<br />
====Mycorrhizal Fungi====<br />
<br />
====Other====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=28042
Rhizosphere Interactions
2008-03-09T07:17:02Z
<p>Alorloff: /* Rhizoplane */</p>
<hr />
<div>==Introduction==<br />
The rizosphere refers to the region of soil near plant roots. Compared to the rest of soil, this area is relatively luxurious- nutrients are more plentiful and bacteria abound. Sylvia et al compare the rizosphere to an oasis. <!--Others in this group, please add more--><br />
<br />
==Soil Environment Associated with Plants==<br />
<br />
===Rhizoplane===<br />
The rizoplane refers to the environment in immediate physical contact with the roots. Microbes that live in the rizoplane are closer to the actual roots than the microbes in the risosphere. The functional definition is everything remaining after the roots have been shaken vigorously in water.<br />
<br />
===Rhizosphere===<br />
<br />
====Physical Environment====<br />
<br />
====Plant Exudates====<br />
<br />
====Microbial Communities====<br />
<br />
=====Bacteria=====<br />
<br />
=====Archaea=====<br />
<br />
=====Fungi=====<br />
<br />
===Other===<br />
<br />
==Biotic Interactions in the Rhizosphere==<br />
<br />
===General Impacts on Plants of Rhizosphere Microorganisms===<br />
<br />
===General Impacts on Rhizosphere Microorganisms of Plants===<br />
<br />
===Symbiotic Relationships===<br />
<br />
====Mycorrhizal Fungi====<br />
<br />
====Other====<br />
<br />
===Innoculants===<br />
<br />
==References==<br />
*Sylvia, D., Fuhrmann,J., Hartel, P., Zuberer, D. 2005. ''Principles and Applications of Soil Microbiology''. Pearson Education Inc. New Jersey.<br />
<!--[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.--><br />
<br />
Edited by students of [mailto:kmscow@ucdavis.edu Kate Scow]</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=27290
Rhizosphere Interactions
2008-01-30T07:21:55Z
<p>Alorloff: </p>
<hr />
<div>Template:Biorealm Soil Microbiology<br />
Contents<br />
[hide]<br />
<br />
* List of topics<br />
* 2 Introducion<br />
* 3 Process - key points<br />
o 3.1 Subsection 1<br />
+ 3.1.1 Subsection 1a<br />
+ 3.1.2 Subsection 1b<br />
o 3.2 Subsection 2<br />
* 4 Key Microorganisms in ______<br />
* 5 Section 3<br />
* 6 Current Research<br />
* 7 References<br />
<br />
[edit] List of topics<br />
<br />
<br />
<br />
1. Nitrogen cycle including GHG<br />
2. Carbon cycle including GHG, decomp, soil OM<br />
3. Geomicrobiology - other elements<br />
4. Rhizosphere: environment and mycorrhizal fungi<br />
5. Soil environment and physical factors controlling microbial activity<br />
6. Flooded soils<br />
7. Bioremediation <br />
<br />
[edit] Introduction<br />
<br />
The rizosphere refers to the region of soil near plant roots. Compared to the rest of soil, this area is relatively luxurious- nutrients are more plentiful and bacteria abound. Sylvia et al compare the rizosphere to an oasis. (Others in this group, please add more!)<br />
<br />
<br />
Irina C<br />
<br />
Describe briefly the process you will address and the significance of soil microorganisms in the process (what functions do they perform?).<br />
[edit] Process - key points<br />
Populations of Soil Fauna<br />
Microflora Movement <br />
Plant-Microbe Interactions<br />
Describe the process, using as many sections/subsections as you require. Look at the list of other topics. Which involve processes similar to yours? Create links where relevant.<br />
<br />
[edit] Seed and root environment<br />
<br />
Info to be added about seed and root environment here<br />
<br />
[edit] Plant-derived compounds<br />
<br />
etc..<br />
<br />
[edit] innoculations<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)<br />
<br />
[edit] Subsection 2<br />
[edit] Key Microorganisms in ______<br />
<br />
Identify and describe some microorganisms involved. Do they already have their own microbewiki pages? Add links. Create at least one page for a microbe relevant to your topic. Template will appear soon.<br />
[edit] Section 3<br />
<br />
Topic of your choice.<br />
[edit] Current Research<br />
<br />
Enter summaries of recent research here--at least three required<br />
[edit] References<br />
<br />
[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.<br />
<br />
Edited by student of Kate Scow</div>
Alorloff
https://microbewiki.kenyon.edu/index.php?title=Rhizosphere_Interactions&diff=27289
Rhizosphere Interactions
2008-01-30T07:10:12Z
<p>Alorloff: </p>
<hr />
<div>Template:Biorealm Soil Microbiology<br />
Contents<br />
[hide]<br />
<br />
* List of topics<br />
* 2 Introducion<br />
* 3 Process - key points<br />
o 3.1 Subsection 1<br />
+ 3.1.1 Subsection 1a<br />
+ 3.1.2 Subsection 1b<br />
o 3.2 Subsection 2<br />
* 4 Key Microorganisms in ______<br />
* 5 Section 3<br />
* 6 Current Research<br />
* 7 References<br />
<br />
[edit] List of topics<br />
<br />
<br />
***AMBER WAS HERE***<br />
<br />
1. Nitrogen cycle including GHG<br />
2. Carbon cycle including GHG, decomp, soil OM<br />
3. Geomicrobiology - other elements<br />
4. Rhizosphere: environment and mycorrhizal fungi<br />
5. Soil environment and physical factors controlling microbial activity<br />
6. Flooded soils<br />
7. Bioremediation <br />
<br />
[edit] Introduction<br />
<br />
The point of this template is to give you a general idea of the layout of your page. You are not completely restricted to this format, so feel free to try out different things. We'll give you feedback as you work on your pages. Make sure to copy the "code" of this page to your own page before editing.<br />
<br />
Irina C<br />
<br />
Describe briefly the process you will address and the significance of soil microorganisms in the process (what functions do they perform?).<br />
[edit] Process - key points<br />
Populations of Soil Fauna<br />
Microflora Movement <br />
Plant-Microbe Interactions<br />
Describe the process, using as many sections/subsections as you require. Look at the list of other topics. Which involve processes similar to yours? Create links where relevant.<br />
[edit] Subsection 1<br />
[edit] Subsection 1a<br />
[edit] Subsection 1b<br />
[edit] Subsection 2<br />
[edit] Key Microorganisms in ______<br />
<br />
Identify and describe some microorganisms involved. Do they already have their own microbewiki pages? Add links. Create at least one page for a microbe relevant to your topic. Template will appear soon.<br />
[edit] Section 3<br />
<br />
Topic of your choice.<br />
[edit] Current Research<br />
<br />
Enter summaries of recent research here--at least three required<br />
[edit] References<br />
<br />
[Sample reference] Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500.<br />
<br />
Edited by student of Kate Scow</div>
Alorloff