https://microbewiki.kenyon.edu/api.php?action=feedcontributions&user=Alexzhu&feedformat=atommicrobewiki - User contributions [en]2024-03-28T21:21:24ZUser contributionsMediaWiki 1.39.6https://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105936Agricultural microbiology2014-12-10T05:54:49Z<p>Alexzhu: /* Minimization of ecological harms */</p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
<br />
[[File:myocompare.jpg|thumb|350px|right|[http://halfhillfarm.com/wp-content/uploads/2013/04/mycocompare.jpg Figure 1] Comparison of plant growth with and without mycorrhizal symbiosis. Used with permission; photograph by Half Hill Farm in Woodbury, Tennessee.]]<br />
<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include [https://microbewiki.kenyon.edu/index.php/Aspergillus Aspergillus], Mucor, Penicillium Trichoderma, Alternaria, and [http://en.wikipedia.org/wiki/Rhizopus Rhizopus] [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil [https://microbewiki.kenyon.edu/index.php/Plant_Growth_Promoting_Bacteria bacteria] colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that convert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like [https://microbewiki.kenyon.edu/index.php/Mycorrhizae mycorrhizal fungi] produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe<sup>3+</sup> scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores [http://en.wikipedia.org/wiki/Chelation chelate] and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
<br />
[[File:Soybeanrootnodules.jpg|thumb|350px|right|[http://upload.wikimedia.org/wikipedia/commons/6/60/Soybean-root-nodules.jpg Figure 2] Root nodules formed on the roots of soybean plants. Each nodule contains billions of nitrogen-fixing <i>Rhizobiacea</i> bacteria. Photograph taken by USDA, and is of public domain.]]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Fixation_and_Agriculture Nitrogen fixation], nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not an effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture continues to shrink over time. In order to produce supplies to meet the demands of mouths, farm animals, and [http://en.wikipedia.org/wiki/Biofuel biofuel] production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as [http://en.wikipedia.org/wiki/Algae algae]. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
=Further Reading=<br />
<br />
[http://academy.asm.org/index.php/browse-all-reports/800-how-microbes-can-help-feed-the-world I]-American Society for Microbiology on "How Microbes can Help Feed the World"<br />
<br />
[http://aem.asm.org/ II]-Journal of Applied and Environmental Microbiology<br />
<br />
[http://en.wikipedia.org/wiki/Soil_microbiology III]-Wikipedia article on soil microbiology<br />
<br />
=References=<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by Alex Zhu, a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jennifer Talbot at Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105935Agricultural microbiology2014-12-10T05:54:11Z<p>Alexzhu: /* Maximization of food production */</p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
<br />
[[File:myocompare.jpg|thumb|350px|right|[http://halfhillfarm.com/wp-content/uploads/2013/04/mycocompare.jpg Figure 1] Comparison of plant growth with and without mycorrhizal symbiosis. Used with permission; photograph by Half Hill Farm in Woodbury, Tennessee.]]<br />
<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include [https://microbewiki.kenyon.edu/index.php/Aspergillus Aspergillus], Mucor, Penicillium Trichoderma, Alternaria, and [http://en.wikipedia.org/wiki/Rhizopus Rhizopus] [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil [https://microbewiki.kenyon.edu/index.php/Plant_Growth_Promoting_Bacteria bacteria] colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that convert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like [https://microbewiki.kenyon.edu/index.php/Mycorrhizae mycorrhizal fungi] produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe<sup>3+</sup> scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores [http://en.wikipedia.org/wiki/Chelation chelate] and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
<br />
[[File:Soybeanrootnodules.jpg|thumb|350px|right|[http://upload.wikimedia.org/wikipedia/commons/6/60/Soybean-root-nodules.jpg Figure 2] Root nodules formed on the roots of soybean plants. Each nodule contains billions of nitrogen-fixing <i>Rhizobiacea</i> bacteria. Photograph taken by USDA, and is of public domain.]]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Fixation_and_Agriculture Nitrogen fixation], nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not an effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture continues to shrink over time. In order to produce supplies to meet the demands of mouths, farm animals, and [http://en.wikipedia.org/wiki/Biofuel biofuel] production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
=Further Reading=<br />
<br />
[http://academy.asm.org/index.php/browse-all-reports/800-how-microbes-can-help-feed-the-world I]-American Society for Microbiology on "How Microbes can Help Feed the World"<br />
<br />
[http://aem.asm.org/ II]-Journal of Applied and Environmental Microbiology<br />
<br />
[http://en.wikipedia.org/wiki/Soil_microbiology III]-Wikipedia article on soil microbiology<br />
<br />
=References=<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by Alex Zhu, a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jennifer Talbot at Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105934Agricultural microbiology2014-12-10T05:50:12Z<p>Alexzhu: /* Fertilizer efficiency */</p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
<br />
[[File:myocompare.jpg|thumb|350px|right|[http://halfhillfarm.com/wp-content/uploads/2013/04/mycocompare.jpg Figure 1] Comparison of plant growth with and without mycorrhizal symbiosis. Used with permission; photograph by Half Hill Farm in Woodbury, Tennessee.]]<br />
<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include [https://microbewiki.kenyon.edu/index.php/Aspergillus Aspergillus], Mucor, Penicillium Trichoderma, Alternaria, and [http://en.wikipedia.org/wiki/Rhizopus Rhizopus] [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil [https://microbewiki.kenyon.edu/index.php/Plant_Growth_Promoting_Bacteria bacteria] colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that convert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like [https://microbewiki.kenyon.edu/index.php/Mycorrhizae mycorrhizal fungi] produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe<sup>3+</sup> scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores [http://en.wikipedia.org/wiki/Chelation chelate] and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
<br />
[[File:Soybeanrootnodules.jpg|thumb|350px|right|[http://upload.wikimedia.org/wikipedia/commons/6/60/Soybean-root-nodules.jpg Figure 2] Root nodules formed on the roots of soybean plants. Each nodule contains billions of nitrogen-fixing <i>Rhizobiacea</i> bacteria. Photograph taken by USDA, and is of public domain.]]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Fixation_and_Agriculture Nitrogen fixation], nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not an effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
=Further Reading=<br />
<br />
[http://academy.asm.org/index.php/browse-all-reports/800-how-microbes-can-help-feed-the-world I]-American Society for Microbiology on "How Microbes can Help Feed the World"<br />
<br />
[http://aem.asm.org/ II]-Journal of Applied and Environmental Microbiology<br />
<br />
[http://en.wikipedia.org/wiki/Soil_microbiology III]-Wikipedia article on soil microbiology<br />
<br />
=References=<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by Alex Zhu, a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jennifer Talbot at Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105933Agricultural microbiology2014-12-10T05:47:56Z<p>Alexzhu: /* Pathogen deterrence */</p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
<br />
[[File:myocompare.jpg|thumb|350px|right|[http://halfhillfarm.com/wp-content/uploads/2013/04/mycocompare.jpg Figure 1] Comparison of plant growth with and without mycorrhizal symbiosis. Used with permission; photograph by Half Hill Farm in Woodbury, Tennessee.]]<br />
<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include [https://microbewiki.kenyon.edu/index.php/Aspergillus Aspergillus], Mucor, Penicillium Trichoderma, Alternaria, and [http://en.wikipedia.org/wiki/Rhizopus Rhizopus] [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil [https://microbewiki.kenyon.edu/index.php/Plant_Growth_Promoting_Bacteria bacteria] colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that convert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like [https://microbewiki.kenyon.edu/index.php/Mycorrhizae mycorrhizal fungi] produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe<sup>3+</sup> scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores [http://en.wikipedia.org/wiki/Chelation chelate] and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
<br />
[[File:Soybeanrootnodules.jpg|thumb|350px|right|[http://upload.wikimedia.org/wikipedia/commons/6/60/Soybean-root-nodules.jpg Figure 2] Root nodules formed on the roots of soybean plants. Each nodule contains billions of nitrogen-fixing <i>Rhizobiacea</i> bacteria. Photograph taken by USDA, and is of public domain.]]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Fixation_and_Agriculture Nitrogen fixation], nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
=Further Reading=<br />
<br />
[http://academy.asm.org/index.php/browse-all-reports/800-how-microbes-can-help-feed-the-world I]-American Society for Microbiology on "How Microbes can Help Feed the World"<br />
<br />
[http://aem.asm.org/ II]-Journal of Applied and Environmental Microbiology<br />
<br />
[http://en.wikipedia.org/wiki/Soil_microbiology III]-Wikipedia article on soil microbiology<br />
<br />
=References=<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by Alex Zhu, a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jennifer Talbot at Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105932Agricultural microbiology2014-12-10T05:47:14Z<p>Alexzhu: /* Nitrogen */</p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
<br />
[[File:myocompare.jpg|thumb|350px|right|[http://halfhillfarm.com/wp-content/uploads/2013/04/mycocompare.jpg Figure 1] Comparison of plant growth with and without mycorrhizal symbiosis. Used with permission; photograph by Half Hill Farm in Woodbury, Tennessee.]]<br />
<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include [https://microbewiki.kenyon.edu/index.php/Aspergillus Aspergillus], Mucor, Penicillium Trichoderma, Alternaria, and [http://en.wikipedia.org/wiki/Rhizopus Rhizopus] [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil [https://microbewiki.kenyon.edu/index.php/Plant_Growth_Promoting_Bacteria bacteria] colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that convert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like [https://microbewiki.kenyon.edu/index.php/Mycorrhizae mycorrhizal fungi] produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe<sup>3+</sup> scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
<br />
[[File:Soybeanrootnodules.jpg|thumb|350px|right|[http://upload.wikimedia.org/wikipedia/commons/6/60/Soybean-root-nodules.jpg Figure 2] Root nodules formed on the roots of soybean plants. Each nodule contains billions of nitrogen-fixing <i>Rhizobiacea</i> bacteria. Photograph taken by USDA, and is of public domain.]]<br />
<br />
[https://microbewiki.kenyon.edu/index.php/Nitrogen_Fixation_and_Agriculture Nitrogen fixation], nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
=Further Reading=<br />
<br />
[http://academy.asm.org/index.php/browse-all-reports/800-how-microbes-can-help-feed-the-world I]-American Society for Microbiology on "How Microbes can Help Feed the World"<br />
<br />
[http://aem.asm.org/ II]-Journal of Applied and Environmental Microbiology<br />
<br />
[http://en.wikipedia.org/wiki/Soil_microbiology III]-Wikipedia article on soil microbiology<br />
<br />
=References=<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by Alex Zhu, a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jennifer Talbot at Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105931Agricultural microbiology2014-12-10T05:45:29Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
<br />
[[File:myocompare.jpg|thumb|350px|right|[http://halfhillfarm.com/wp-content/uploads/2013/04/mycocompare.jpg Figure 1] Comparison of plant growth with and without mycorrhizal symbiosis. Used with permission; photograph by Half Hill Farm in Woodbury, Tennessee.]]<br />
<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include [https://microbewiki.kenyon.edu/index.php/Aspergillus Aspergillus], Mucor, Penicillium Trichoderma, Alternaria, and [http://en.wikipedia.org/wiki/Rhizopus Rhizopus] [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil [https://microbewiki.kenyon.edu/index.php/Plant_Growth_Promoting_Bacteria bacteria] colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that convert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like [https://microbewiki.kenyon.edu/index.php/Mycorrhizae mycorrhizal fungi] produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe<sup>3+</sup> scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
<br />
[[File:Soybeanrootnodules.jpg|thumb|350px|right|[http://upload.wikimedia.org/wikipedia/commons/6/60/Soybean-root-nodules.jpg Figure 2] Root nodules formed on the roots of soybean plants. Each nodule contains billions of nitrogen-fixing <i>Rhizobiacea</i> bacteria. Photograph taken by USDA, and is of public domain.]]<br />
<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
=Further Reading=<br />
<br />
[http://academy.asm.org/index.php/browse-all-reports/800-how-microbes-can-help-feed-the-world I]-American Society for Microbiology on "How Microbes can Help Feed the World"<br />
<br />
[http://aem.asm.org/ II]-Journal of Applied and Environmental Microbiology<br />
<br />
[http://en.wikipedia.org/wiki/Soil_microbiology III]-Wikipedia article on soil microbiology<br />
<br />
=References=<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by Alex Zhu, a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jennifer Talbot at Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105853Agricultural microbiology2014-12-02T23:43:16Z<p>Alexzhu: /* Mechanisms of plant growth promotion */</p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
<br />
[[File:myocompare.jpg|thumb|350px|right|[http://halfhillfarm.com/wp-content/uploads/2013/04/mycocompare.jpg Figure 1] Comparison of plant growth with and without mycorrhizal symbiosis. Used with permission; photograph by Half Hill Farm in Woodbury, Tennessee.]]<br />
<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include [https://microbewiki.kenyon.edu/index.php/Aspergillus Aspergillus], Mucor, Penicillium Trichoderma, Alternaria, and [http://en.wikipedia.org/wiki/Rhizopus Rhizopus] [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil [https://microbewiki.kenyon.edu/index.php/Plant_Growth_Promoting_Bacteria bacteria] colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like [https://microbewiki.kenyon.edu/index.php/Mycorrhizae mycorrhizal fungi] produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe<sup>3+</sup> scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
<br />
[[File:Soybeanrootnodules.jpg|thumb|350px|right|[http://upload.wikimedia.org/wikipedia/commons/6/60/Soybean-root-nodules.jpg Figure 2] Root nodules formed on the roots of soybean plants. Each nodule contains billions of nitrogen-fixing <i>Rhizobiacea</i> bacteria. Photograph taken by USDA, and is of public domain.]]<br />
<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
=Further Reading=<br />
<br />
[http://academy.asm.org/index.php/browse-all-reports/800-how-microbes-can-help-feed-the-world I]-American Society for Microbiology on "How Microbes can Help Feed the World"<br />
<br />
[http://aem.asm.org/ II]-Journal of Applied and Environmental Microbiology<br />
<br />
[http://en.wikipedia.org/wiki/Soil_microbiology III]-Wikipedia article on soil microbiology<br />
<br />
=References=<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by Alex Zhu, a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105852Agricultural microbiology2014-12-02T23:40:48Z<p>Alexzhu: /* Plant growth-promoting rhizobacteria (PGPR) */</p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
<br />
[[File:myocompare.jpg|thumb|350px|right|[http://halfhillfarm.com/wp-content/uploads/2013/04/mycocompare.jpg Figure 1] Comparison of plant growth with and without mycorrhizal symbiosis. Used with permission; photograph by Half Hill Farm in Woodbury, Tennessee.]]<br />
<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include [https://microbewiki.kenyon.edu/index.php/Aspergillus Aspergillus], Mucor, Penicillium Trichoderma, Alternaria, and [http://en.wikipedia.org/wiki/Rhizopus Rhizopus] [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil [https://microbewiki.kenyon.edu/index.php/Plant_Growth_Promoting_Bacteria bacteria] colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe<sup>3+</sup> scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
<br />
[[File:Soybeanrootnodules.jpg|thumb|350px|right|[http://upload.wikimedia.org/wikipedia/commons/6/60/Soybean-root-nodules.jpg Figure 2] Root nodules formed on the roots of soybean plants. Each nodule contains billions of nitrogen-fixing <i>Rhizobiacea</i> bacteria. Photograph taken by USDA, and is of public domain.]]<br />
<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
=Further Reading=<br />
<br />
[http://academy.asm.org/index.php/browse-all-reports/800-how-microbes-can-help-feed-the-world I]-American Society for Microbiology on "How Microbes can Help Feed the World"<br />
<br />
[http://aem.asm.org/ II]-Journal of Applied and Environmental Microbiology<br />
<br />
[http://en.wikipedia.org/wiki/Soil_microbiology III]-Wikipedia article on soil microbiology<br />
<br />
=References=<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
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<!--Do not remove this line--><br />
Entry created by Alex Zhu, a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105851Agricultural microbiology2014-12-02T23:39:05Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
<br />
[[File:myocompare.jpg|thumb|350px|right|[http://halfhillfarm.com/wp-content/uploads/2013/04/mycocompare.jpg Figure 1] Comparison of plant growth with and without mycorrhizal symbiosis. Used with permission; photograph by Half Hill Farm in Woodbury, Tennessee.]]<br />
<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include [https://microbewiki.kenyon.edu/index.php/Aspergillus Aspergillus], Mucor, Penicillium Trichoderma, Alternaria, and [http://en.wikipedia.org/wiki/Rhizopus Rhizopus] [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe<sup>3+</sup> scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
<br />
[[File:Soybeanrootnodules.jpg|thumb|350px|right|[http://upload.wikimedia.org/wikipedia/commons/6/60/Soybean-root-nodules.jpg Figure 2] Root nodules formed on the roots of soybean plants. Each nodule contains billions of nitrogen-fixing <i>Rhizobiacea</i> bacteria. Photograph taken by USDA, and is of public domain.]]<br />
<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
=Further Reading=<br />
<br />
[http://academy.asm.org/index.php/browse-all-reports/800-how-microbes-can-help-feed-the-world I]-American Society for Microbiology on "How Microbes can Help Feed the World"<br />
<br />
[http://aem.asm.org/ II]-Journal of Applied and Environmental Microbiology<br />
<br />
[http://en.wikipedia.org/wiki/Soil_microbiology III]-Wikipedia article on soil microbiology<br />
<br />
=References=<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by Alex Zhu, a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105850Agricultural microbiology2014-12-02T23:35:36Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
<br />
[[File:myocompare.jpg|thumb|350px|right|[http://halfhillfarm.com/wp-content/uploads/2013/04/mycocompare.jpg Figure 1] Comparison of plant growth with and without mycorrhizal symbiosis. Used with permission; photograph by Half Hill Farm in Woodbury, Tennessee.]]<br />
<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe<sup>3+</sup> scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
<br />
[[File:Soybeanrootnodules.jpg|thumb|350px|right|[http://upload.wikimedia.org/wikipedia/commons/6/60/Soybean-root-nodules.jpg Figure 2] Root nodules formed on the roots of soybean plants. Each nodule contains billions of nitrogen-fixing <i>Rhizobiacea</i> bacteria. Photograph taken by USDA, and is of public domain.]]<br />
<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
=Further Reading=<br />
<br />
[http://academy.asm.org/index.php/browse-all-reports/800-how-microbes-can-help-feed-the-world I]-American Society for Microbiology on "How Microbes can Help Feed the World"<br />
<br />
[http://aem.asm.org/ II]-Journal of Applied and Environmental Microbiology<br />
<br />
[http://en.wikipedia.org/wiki/Soil_microbiology III]-Wikipedia article on soil microbiology<br />
<br />
=References=<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by Alex Zhu, a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105849Agricultural microbiology2014-12-02T23:34:24Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
<br />
[[File:myocompare.jpg|thumb|350px|right|[http://halfhillfarm.com/wp-content/uploads/2013/04/mycocompare.jpg Figure 1] Comparison of plant growth with and without mycorrhizal symbiosis. Used with permission; photograph by Half Hill Farm in Woodbury, Tennessee.]]<br />
<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe<sup>3+</sup> scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
<br />
[[File:Soybeanrootnodules.jpg|thumb|350px|right|[http://upload.wikimedia.org/wikipedia/commons/6/60/Soybean-root-nodules.jpg Figure 2] Root nodules formed on the roots of soybean plants. Each nodule contains billions of nitrogen-fixing <i>Rhizobiacea</i> bacteria. Photograph taken by USDA, and is of public domain.]]<br />
<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
[http://academy.asm.org/index.php/browse-all-reports/800-how-microbes-can-help-feed-the-world I]-American Society for Microbiology on "How Microbes can Help Feed the World"<br />
<br />
[http://aem.asm.org/ II]-Journal of Applied and Environmental Microbiology<br />
<br />
[http://en.wikipedia.org/wiki/Soil_microbiology III]-Wikipedia article on soil microbiology<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by Alex Zhu, a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105848Agricultural microbiology2014-12-02T23:17:13Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
<br />
[[File:myocompare.jpg|thumb|350px|right|[http://halfhillfarm.com/wp-content/uploads/2013/04/mycocompare.jpg Figure 1] Comparison of plant growth with and without mycorrhizal symbiosis. Used with permission; photograph by Half Hill Farm in Woodbury, Tennessee.]]<br />
<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe<sup>3+</sup> scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
<br />
[[File:Soybeanrootnodules.jpg|thumb|350px|right|[http://upload.wikimedia.org/wikipedia/commons/6/60/Soybean-root-nodules.jpg Figure 2] Root nodules formed on the roots of soybean plants. Each nodule contains billions of nitrogen-fixing <i>Rhizobiacea</i> bacteria. Photograph taken by USDA, and is of public domain.]]<br />
<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
[http://academy.asm.org/index.php/browse-all-reports/800-how-microbes-can-help-feed-the-world I]-American Society for Microbiology on "How Microbes can Help Feed the World"<br />
<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by Alex Zhu, a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=File:Soybeanrootnodules.jpg&diff=105847File:Soybeanrootnodules.jpg2014-12-02T23:07:24Z<p>Alexzhu: </p>
<hr />
<div></div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105846Agricultural microbiology2014-12-02T23:07:09Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
<br />
[[File:myocompare.jpg|thumb|350px|right|[http://halfhillfarm.com/wp-content/uploads/2013/04/mycocompare.jpg Figure 1] Comparison of plant growth with and without mycorrhizal symbiosis. Used with permission; photograph by Half Hill Farm in Woodbury, Tennessee.]]<br />
<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe<sup>3+</sup> scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
<br />
[[File:Soybeanrootnodules.jpg|thumb|350px|right|[http://upload.wikimedia.org/wikipedia/commons/6/60/Soybean-root-nodules.jpg Figure 2] Root nodules formed on the roots of soybean plants. Each nodule contains billions of <i>Rhizobiacea</i> bacteria. Photograph taken by USDA, and is of public domain.]]<br />
<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
<br />
<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by (Alex Zhu), a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105845Agricultural microbiology2014-12-02T23:01:21Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
<br />
[[File:myocompare.jpg|thumb|350px|right|[http://halfhillfarm.com/wp-content/uploads/2013/04/mycocompare.jpg Figure 1] Comparison of plant growth with and without mycorrhizal symbiosis. Used with permission; photograph by Half Hill Farm in Woodbury, Tennessee.]]<br />
<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe<sup>3+</sup> scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
<br />
<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by (Alex Zhu), a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105844Agricultural microbiology2014-12-02T23:00:36Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
<br />
[[File:myocompare.jpg|thumb|350px|right|[http://halfhillfarm.com/wp-content/uploads/2013/04/mycocompare.jpg Figure 1] Comparison of plant growth with and without mycorrhizal symbiosis. Used with permission; photograph by Half Hill Farm in Woodbury, Tennessee]]<br />
<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe<sup>3+</sup> scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
<br />
<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by (Alex Zhu), a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=File:Myocompare.jpg&diff=105843File:Myocompare.jpg2014-12-02T22:59:41Z<p>Alexzhu: </p>
<hr />
<div></div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105842Agricultural microbiology2014-12-02T06:50:22Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe<sup>3+</sup> scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
<br />
<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by (Alex Zhu), a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105841Agricultural microbiology2014-12-02T06:49:24Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. '''Fe<sup>3+</sup>''' scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
<br />
<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by (Alex Zhu), a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105840Agricultural microbiology2014-12-02T06:46:07Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
<br />
<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by (Alex Zhu), a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105839Agricultural microbiology2014-12-02T06:45:20Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting Rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
<br />
<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<br />
<!--Do not remove this line--><br />
Entry created by (Alex Zhu), a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105838Agricultural microbiology2014-12-02T06:45:00Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting Rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
<br />
<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.<br />
<br />
<!--Do not remove this line--><br />
Entry created by (Alex Zhu), a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105837Agricultural microbiology2014-12-02T06:36:35Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting Rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
<br />
<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: <i>Academic</i>, 2010. Print.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. <i>Web of Science</i>, 2010. Web.<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. <i>Canadian Journal of Microbiology</i>, 2004. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. <i>Environment International</i>, 18 Dec. 2006. Web.<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] - promix site<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] - usda site<br />
<br />
<!--Do not remove this line--><br />
Entry created by (Alex Zhu), a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105836Agricultural microbiology2014-12-02T06:14:42Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting Rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
<br />
<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." <i>Elsevier Microbiological Research</i> 163 (2008): 173-81. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." <i>Elsevier Ltd</i> (1989): 39-44. Web.<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] - smith read book<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." <i>Springer</i> 85 (2009): 1-12. Web. <br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] - zhao 2010<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] - dobbelaere 2001<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] - bashan 2004<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] Kale, Radha D., Mallesh B. C, Kubra Bano, and Bagyaraj D. J. "Influence of Vermicompost Application on the Available Macronutrients and Selected Microbial Populations in a Paddy Field." <i>Soil Biology Biochemistry</i> 24.12 (1992): 1317-320. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." <i>Elsevier Journal of Biotechnology</i> 66 (1998): 91-99. Web.<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." <i>Applied Microbiological Biotechnology</i> 84 (2009): 11-18. Web.<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] - chen 2006<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] - promix site<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] - usda site<br />
<br />
<!--Do not remove this line--><br />
Entry created by (Alex Zhu), a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105835Agricultural microbiology2014-12-02T05:53:59Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting Rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
<br />
<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] - ahmad 2008<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] - kloepper 1989<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] - smith read book<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - adesemoye 2009<br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] - zhao 2010<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] - dobbelaere 2001<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] - bashan 2004<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] - kale 1992<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] - tengerdy 1998<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] - berg 2009<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] - chen 2006<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] - promix site<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] - usda site<br />
<br />
<!--Do not remove this line--><br />
Entry created by (Alex Zhu), a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) at [http://www.bu.edu/biology/ Boston University] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Jenny Talbot at the Boston University]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105834Agricultural microbiology2014-12-02T05:50:58Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting Rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
<br />
<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] - ahmad 2008<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] - kloepper 1989<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] - smith read book<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - adesemoye 2009<br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] - zhao 2010<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] - dobbelaere 2001<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] - bashan 2004<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] - kale 1992<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] - tengerdy 1998<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] - berg 2009<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] - chen 2006<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] - promix site<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] - usda site<br />
<br />
<!--Do not remove this line--><br />
Entry created by (Alex Zhu), a student of [http://www.bu.edu/biology/people/faculty/talbot/ Jenny Talbot] in BI311 (Microbiology) in [http://www.bu.edu/biology/ The Department of Biology of Boston University's College of Arts & Sciences] Fall 2014.<br />
<br />
<!--Do not edit or remove this line-->[[Category:Pages edited by students of Nora Sullivan at the Claremont Colleges]]</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105833Agricultural microbiology2014-12-02T05:42:12Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting Rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant [http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]].<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels [http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]]. Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included [http://www.pthorticulture.com/en/[12]].<br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
<br />
<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] - ahmad 2008<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] - kloepper 1989<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] - smith read book<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - adesemoye 2009<br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] - zhao 2010<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] - dobbelaere 2001<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] - bashan 2004<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] - kale 1992<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0168165698001382[9]] - tengerdy 1998<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2092-7#page-1[10]] - berg 2009<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[11]] - chen 2006<br />
<br />
<br>[http://www.pthorticulture.com/en/[12]] - promix site<br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[13]] - usda site</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105832Agricultural microbiology2014-12-02T05:27:59Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting Rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]], while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake [http://www.publish.csiro.au/?paper=PP01074[6]] [http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]].<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [http://www.sciencedirect.com/science/article/pii/003807179290111A[8]]. Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant. (Tengerdy 1998)<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis. (Kale 1992) The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels. (Berg 2009) Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more. (Adesemoye 2009) <br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants [http://www.sciencedirect.com/science/article/pii/S0160412007000037[13]].<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included. <br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[15]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
<br />
<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] - ahmad 2008<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]] - kloepper 1989<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]] - smith read book<br />
<br />
<br>[http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]] - adesemoye 2009<br />
<br />
<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070418/ [5]] - zhao 2010<br />
<br />
<br>[http://www.publish.csiro.au/?paper=PP01074[6]] - dobbelaere 2001<br />
<br />
<br>[http://www.nrcresearchpress.com/doi/abs/10.1139/w04-035[7]] - bashan 2004<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/003807179290111A[8]] - kale 1992<br />
<br />
<br><br />
<br />
<br><br />
<br />
<br><br />
<br />
<br><br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/S0160412007000037[13]] - chen 2006<br />
<br />
<br><br />
<br />
<br>[http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[15]] - usda site</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105831Agricultural microbiology2014-12-02T05:12:22Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]. AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus [http://link.springer.com/article/10.1007/s00253-009-2196-0#page-1[4]].<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting Rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] (Zhao, Yunde 2010 Auxin biosynthesis), while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake. (Dobbelaere 2001, Bashan 2004)<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants. (Kale 1992) Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant. (Tengerdy 1998)<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis. (Kale 1992) The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels. (Berg 2009) Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. (Ahmad 2008)<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more. (Adesemoye 2009) <br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants. (Chen 2006; Adesemoye 2009)<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems. (Adesemoye)<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included. <br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[#####]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.<br />
<br />
==Further Reading==<br />
<br />
<br />
<br />
<br />
==References==<br />
[http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]<br />
<br />
<br>[http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]<br />
<br />
<br>[http://books.google.com/books?hl=en&lr=&id=qLciOJaG0C4C&oi=fnd&pg=PP2&ots=zpsXk_TxtI&sig=IZ7TBVrTrmH3Wp6hXydK_Cp9Pcs#v=onepage&q&f=false[3]]<br />
<br />
<br><br />
<br />
<br><br />
<br />
<br><br />
<br />
<br><br />
<br />
<br><br />
<br />
<br></div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105830Agricultural microbiology2014-12-02T04:58:41Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus. (Adesemoye 2009)<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting Rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] (Zhao, Yunde 2010 Auxin biosynthesis), while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake. (Dobbelaere 2001, Bashan 2004)<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants. (Kale 1992) Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant. (Tengerdy 1998)<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis. (Kale 1992) The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels. (Berg 2009) Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. (Ahmad 2008)<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more. (Adesemoye 2009) <br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants. (Chen 2006; Adesemoye 2009)<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems. (Adesemoye)<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included. <br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year [http://www.ers.usda.gov/topics/farm-practices-management/chemical-inputs/fertilizer-use-markets.aspx[#####]]. A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105829Agricultural microbiology2014-12-02T04:57:13Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere] [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]]. Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize [http://www.sciencedirect.com/science/article/pii/0167779989900577[2]]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus. (Adesemoye 2009)<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting Rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] (Zhao, Yunde 2010 Auxin biosynthesis), while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake. (Dobbelaere 2001, Bashan 2004)<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants. (Kale 1992) Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant. (Tengerdy 1998)<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis. (Kale 1992) The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels. (Berg 2009) Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. (Ahmad 2008)<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more. (Adesemoye 2009) <br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants. (Chen 2006; Adesemoye 2009)<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems. (Adesemoye)<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included. <br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year. (USDA) A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105828Agricultural microbiology2014-12-02T04:55:49Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere]. [http://www.sciencedirect.com/science/article/pii/S0944501306000437[1]] Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize. (Kloepper 1989) AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus. (Adesemoye 2009)<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting Rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] (Zhao, Yunde 2010 Auxin biosynthesis), while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake. (Dobbelaere 2001, Bashan 2004)<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants. (Kale 1992) Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant. (Tengerdy 1998)<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis. (Kale 1992) The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels. (Berg 2009) Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. (Ahmad 2008)<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more. (Adesemoye 2009) <br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants. (Chen 2006; Adesemoye 2009)<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems. (Adesemoye)<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included. <br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year. (USDA) A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105827Agricultural microbiology2014-12-02T04:41:57Z<p>Alexzhu: </p>
<hr />
<div>{{Uncurated}}<br />
Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere]. (Ahmad 2008) Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize. (Kloepper 1989) AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus. (Adesemoye 2009)<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting Rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] (Zhao, Yunde 2010 Auxin biosynthesis), while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake. (Dobbelaere 2001, Bashan 2004)<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants. (Kale 1992) Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant. (Tengerdy 1998)<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis. (Kale 1992) The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels. (Berg 2009) Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. (Ahmad 2008)<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more. (Adesemoye 2009) <br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants. (Chen 2006; Adesemoye 2009)<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems. (Adesemoye)<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included. <br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year. (USDA) A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105826Agricultural microbiology2014-12-02T04:38:34Z<p>Alexzhu: </p>
<hr />
<div>Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the [http://en.wikipedia.org/wiki/Rhizosphere rhizosphere]. (Ahmad 2008) Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==[https://en.wikipedia.org/wiki/Arbuscular_mycorrhiza Arbuscular mycorrhizal fungi] (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of [http://en.wikipedia.org/wiki/Hypha hyphal] networks surrounding the plant roots they colonize. (Kloepper 1989) AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus. (Adesemoye 2009)<br />
<br />
==[https://en.wikipedia.org/wiki/Rhizobacteria#Plant_growth-promoting_rhizobacteria Plant growth-promoting Rhizobacteria] (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other [http://en.wikipedia.org/wiki/Auxin auxins] (Zhao, Yunde 2010 Auxin biosynthesis), while others supply the plant with nutrients from the soil. [http://en.wikipedia.org/wiki/Plant_hormone Phytohormone] expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake. (Dobbelaere 2001, Bashan 2004)<br />
<br />
==[http://en.wikipedia.org/wiki/Rhizobia Nitrogen-fixing rhizobia]==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants. (Kale 1992) Symbiotic rhizobia form anaerobic nodules on the roots of [http://en.wikipedia.org/wiki/Legume legumes] and express genes for enzymes like [http://en.wikipedia.org/wiki/Nitrogenase nitrogenase] to [https://en.wikipedia.org/wiki/Rhizobacteria#Nitrogen_fixation fix nitrogen] into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant. (Tengerdy 1998)<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis. (Kale 1992) The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels. (Berg 2009) Crop rotation, especially involving legumes and their [http://en.wikipedia.org/wiki/Rhizobia <i>Rhizobia</i>] symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of [http://en.wikipedia.org/wiki/Plant_pathology plant pathogens]. Some PGPRs produce [https://en.wikipedia.org/wiki/Siderophore siderophores], compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. (Ahmad 2008)<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more. (Adesemoye 2009) <br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants. (Chen 2006; Adesemoye 2009)<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems. (Adesemoye)<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included. <br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year. (USDA) A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105825Agricultural microbiology2014-12-02T03:02:37Z<p>Alexzhu: </p>
<hr />
<div>Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many [http://en.wikipedia.org/wiki/Symbiosis symbiotic] relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the rhizosphere. (Ahmad 2008) Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==Arbuscular mycorrhizal fungi (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of hyphal networks surrounding the plant roots they colonize. (Kloepper 1989) AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus. (Adesemoye 2009)<br />
<br />
==Plant growth-promoting Rhizobacteria (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other auxins (Zhao, Yunde 2010 Auxin biosynthesis), while others supply the plant with nutrients from the soil. Phytohormone expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake. (Dobbelaere 2001, Bashan 2004)<br />
<br />
==Nitrogen-fixing rhizobia==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants. (Kale 1992) Symbiotic rhizobia form anaerobic nodules on the roots of legumes and express genes for enzymes like nitrogenase to fix nitrogen into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant. (Tengerdy 1998)<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis. (Kale 1992) The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels. (Berg 2009) Crop rotation, especially involving legumes and their Rhizobia symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of plant pathogens. Some PGPRs produce siderophores, compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. (Ahmad 2008)<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more. (Adesemoye 2009) <br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants. (Chen 2006; Adesemoye 2009)<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems. (Adesemoye)<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included. <br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year. (USDA) A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105824Agricultural microbiology2014-12-02T00:39:19Z<p>Alexzhu: </p>
<hr />
<div>Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many symbiotic relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the rhizosphere. (Ahmad 2008) Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==Arbuscular mycorrhizal fungi (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of hyphal networks surrounding the plant roots they colonize. (Kloepper 1989) AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus. (Adesemoye 2009)<br />
<br />
==Plant growth-promoting Rhizobacteria (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other auxins (Zhao, Yunde 2010 Auxin biosynthesis), while others supply the plant with nutrients from the soil. Phytohormone expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake. (Dobbelaere 2001, Bashan 2004)<br />
<br />
==Nitrogen-fixing rhizobia==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants. (Kale 1992) Symbiotic rhizobia form anaerobic nodules on the roots of legumes and express genes for enzymes like nitrogenase to fix nitrogen into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant. (Tengerdy 1998)<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis. (Kale 1992) The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels. (Berg 2009) Crop rotation, especially involving legumes and their Rhizobia symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of plant pathogens. Some PGPRs produce siderophores, compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. (Ahmad 2008)<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more. (Adesemoye 2009) <br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants. (Chen 2006; Adesemoye 2009)<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems. (Adesemoye)<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included. <br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year. (USDA) A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105823Agricultural microbiology2014-12-02T00:39:04Z<p>Alexzhu: </p>
<hr />
<div>Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many symbiotic relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the rhizosphere. (Ahmad 2008) Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
<br />
==Arbuscular mycorrhizal fungi (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of hyphal networks surrounding the plant roots they colonize. (Kloepper 1989) AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus. (Adesemoye 2009)<br />
<br />
==Plant growth-promoting Rhizobacteria (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other auxins (Zhao, Yunde 2010 Auxin biosynthesis), while others supply the plant with nutrients from the soil. Phytohormone expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake. (Dobbelaere 2001, Bashan 2004)<br />
<br />
==Nitrogen-fixing rhizobia==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants. (Kale 1992) Symbiotic rhizobia form anaerobic nodules on the roots of legumes and express genes for enzymes like nitrogenase to fix nitrogen into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant. (Tengerdy 1998)<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis. (Kale 1992) The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels. (Berg 2009) Crop rotation, especially involving legumes and their Rhizobia symbionts, is practiced precisely for this reason. <br />
<br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of plant pathogens. Some PGPRs produce siderophores, compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. (Ahmad 2008)<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more. (Adesemoye 2009) <br />
<br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants. (Chen 2006; Adesemoye 2009)<br />
<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems. (Adesemoye)<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included. <br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year. (USDA) A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105822Agricultural microbiology2014-12-02T00:38:31Z<p>Alexzhu: </p>
<hr />
<div>Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many symbiotic relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the rhizosphere. (Ahmad 2008) Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
==Arbuscular mycorrhizal fungi (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of hyphal networks surrounding the plant roots they colonize. (Kloepper 1989) AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus. (Adesemoye 2009)<br />
==Plant growth-promoting Rhizobacteria (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other auxins (Zhao, Yunde 2010 Auxin biosynthesis), while others supply the plant with nutrients from the soil. Phytohormone expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake. (Dobbelaere 2001, Bashan 2004)<br />
==Nitrogen-fixing rhizobia==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants. (Kale 1992) Symbiotic rhizobia form anaerobic nodules on the roots of legumes and express genes for enzymes like nitrogenase to fix nitrogen into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant. (Tengerdy 1998)<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis. (Kale 1992) The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels. (Berg 2009) Crop rotation, especially involving legumes and their Rhizobia symbionts, is practiced precisely for this reason. <br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of plant pathogens. Some PGPRs produce siderophores, compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. (Ahmad 2008)<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more. (Adesemoye 2009) <br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants. (Chen 2006; Adesemoye 2009)<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems. (Adesemoye)<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included. <br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year. (USDA) A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105821Agricultural microbiology2014-12-02T00:37:22Z<p>Alexzhu: </p>
<hr />
<div>Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many symbiotic relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the rhizosphere. (Ahmad 2008) Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
==Arbuscular mycorrhizal fungi (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of hyphal networks surrounding the plant roots they colonize. (Kloepper 1989) AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus. (Adesemoye 2009)<br />
==Plant growth-promoting Rhizobacteria (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other auxins (Zhao, Yunde 2010 Auxin biosynthesis), while others supply the plant with nutrients from the soil. Phytohormone expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake. (Dobbelaere 2001, Bashan 2004)<br />
==Nitrogen-fixing rhizobia==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants. (Kale 1992) Symbiotic rhizobia form anaerobic nodules on the roots of legumes and express genes for enzymes like nitrogenase to fix nitrogen into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant. (Tengerdy 1998)<br />
<br />
=Mechanisms of plant growth promotion=<br />
On the microscopic landscape of a root surface, different symbionts use unique methods to infect. Once anchored, some bacteria express genes that covert soil and atmospheric molecules into compounds valuable to the plant, such as nitrogen and phosphorous containing compounds. Others like mycorrhizal fungi produce vast networks of hyphae that essentially function as additional root surface area to mine soil for nutrients; they also provide some pathogen protection to the host roots. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) At the plant-fungi interface, fungi provide plants with compounds—ammonium, nitrate, amino acids, inorganic phosphate, and organic compounds like urea—in exchange for plant carbohydrates acquired through photosynthesis. (Kale 1992) The sloughed off cells from plant roots are important sources of carbon for organisms dwelling in the rhizosphere. These symbiotic relationships not only increase the bioavailability of crucial elements to plants, but also improve soil fertility by increasing labile carbon and nitrogen levels. (Berg 2009) Crop rotation, especially involving legumes and their Rhizobia symbionts, is practiced precisely for this reason. <br />
==Pathogen deterrence==<br />
Plant-associated microorganisms also exhibit traits that increase host plant fitness indirectly through the suppression of plant pathogens. Some PGPRs produce siderophores, compounds that bind iron in the soil. Fe3+ scarceness is due to its low solubility. At the same time, iron happens to be essential for several cellular processes; PGPR siderophores chelate and uptake iron from the rhizosphere, leaving little to none left for pathogens. Many of these PGPRs also synthesize enough HCN to produce an antifungal effect, among other fungicides. (Ahmad 2008)<br />
<br />
=Cycling of bioavailable elements=<br />
Absorption of nitrogen, phosphorous, and other nutrients from the soil by plant roots is limited by transporters located on root cells. This partially explains the importance of symbiotic soil microbes in their supportive roles of promoting crop health, growth, and yield.<br />
==Nitrogen==<br />
Nitrogen fixation, nitrification, denitrification, and nitrogen mineralization are the four dominant microbial processes that drive nitrogen through producer ecosystems. Nitrogen fixers such as Rhizobacteria and Azospirillum convert atmospheric nitrogen into ammonia. It is then transported to the plant to take part in cellular growth through processes like DNA replication, protein synthesis, and more. (Adesemoye 2009) <br />
==Phosphorous==<br />
Likewise, phosphorous is also a vital element necessary for plant prosperity. It is mostly found in insoluble rock reserves, with some phosphates present as organic phosphorus compounds in soil organic matter. Another reason why plants experience difficulty obtaining phosphorous is because a majority of soil phosphorous precipitates with metals such as iron, aluminum, and calcium, preventing its uptake by plant roots. AMF and PGPR inoculants aid plants by solubilizing mineral phosphates, converting them to forms able to be assimilated by plants. (Chen 2006; Adesemoye 2009)<br />
==Fertilizer efficiency==<br />
In an attempt to promote as much growth as possible, farmers often apply large quantities of fertilizer to crops. This brute-force method is not a very effective option. Depending on qualities of the soil, the crops involved, and microbial symbionts, only 10% to 40% is taken up by crops. Thus, roughly 60% to 90% of applied fertilizer is lost to watersheds, groundwater, and other aquatic systems. (Adesemoye)<br />
<br />
=Maximization of food production=<br />
As the human population continues its climb, land available for agriculture has been shrinking over time. In order to produce supplies to meet the demands of mouths, farm animals, and biofuel production, the efficiency of food production per acre must be optimized. Microbial inoculants are one of the ways in which food production efficiency can be improved. Plant growth-promoting soil organisms increase net crop uptake of soil nutrients, resulting in larger crops and higher yields of harvested food. Besides farmland inoculants, practical applications of agricultural microbiology also include potting soil with mycorrhizal spores included. <br />
<br />
=Minimization of ecological harms=<br />
With regards to agricultural food production, there is a balance between two opposing human desires. On one hand, it is highly desirable to produce as much food as possible—on the other, we must also keep in mind our obligation to as little harm as we can manage to our home. Since 1975, the United States alone applies over twenty million tons of agricultural fertilizers to crop fields each year. (USDA) A majority of the fertilizers remain unabsorbed and travel into other parts of adjacent ecosystems, where they are utilized by organisms such as algae. This ultimately results in a series of events that off-sets the preexisting balance of the ecosystem. Applications of microbiology in agriculture aim to minimize the use of fertilizer, but at the same time, provide another mode for environmental disruption. We must be mindful of the fragility of nature, and cautiously monitor the conditions of microorganisms produced in laboratories and inoculated into farmland.</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105820Agricultural microbiology2014-12-02T00:34:19Z<p>Alexzhu: </p>
<hr />
<div>Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many symbiotic relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
=Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the rhizosphere. (Ahmad 2008) Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
==Arbuscular mycorrhizal fungi (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of hyphal networks surrounding the plant roots they colonize. (Kloepper 1989) AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus. (Adesemoye 2009)<br />
==Plant growth-promoting Rhizobacteria (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other auxins (Zhao, Yunde 2010 Auxin biosynthesis), while others supply the plant with nutrients from the soil. Phytohormone expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake. (Dobbelaere 2001, Bashan 2004)<br />
==Nitrogen-fixing rhizobia==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants. (Kale 1992) Symbiotic rhizobia form anaerobic nodules on the roots of legumes and express genes for enzymes like nitrogenase to fix nitrogen into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant. (Tengerdy 1998)<br />
<br />
=2. Description and significance=<br />
Describe the appearance, habitat, etc. of the organism, and why you think it is important.<br />
*Include as many headings as are relevant to your microbe. Consider using the headings below, as they will allow readers to quickly locate specific information of major interest*<br />
=3. Genome structure=<br />
Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence?<br />
=4. Cell structure=<br />
Interesting features of cell structure. Can be combined with “metabolic processes”<br />
=5. Metabolic processes=<br />
Describe important sources of energy, electrons, and carbon (i.e. trophy) for the organism/organisms you are focusing on, as well as important molecules it/they synthesize(s).<br />
=6. Ecology=<br />
Habitat; symbiosis; contributions to the environment.<br />
=7. Pathology=<br />
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br />
=7. Key microorganisms=<br />
Include this section if your Wiki page focuses on a microbial process, rather than a specific taxon/group of organisms<br />
=8. Current Research=<br />
Include information about how this microbe (or related microbes) are currently being studied and for what purpose<br />
=9. References=<br />
It is required that you add at least five primary research articles (in same format as the sample reference below) that corresponds to the info that you added to this page.<br />
[Sample reference] Faller, A., and Schleifer, K. "Modified Oxidase and Benzidine Tests for Separation of Staphylococci from Micrococci". Journal of Clinical Microbiology. 1981. Volume 13. p. 1031-1035.</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105819Agricultural microbiology2014-12-02T00:34:06Z<p>Alexzhu: </p>
<hr />
<div>Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many symbiotic relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
=1. Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the rhizosphere. (Ahmad 2008) Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
==Arbuscular mycorrhizal fungi (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of hyphal networks surrounding the plant roots they colonize. (Kloepper 1989) AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus. (Adesemoye 2009)<br />
==Plant growth-promoting Rhizobacteria (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other auxins (Zhao, Yunde 2010 Auxin biosynthesis), while others supply the plant with nutrients from the soil. Phytohormone expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake. (Dobbelaere 2001, Bashan 2004)<br />
==Nitrogen-fixing rhizobia==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants. (Kale 1992) Symbiotic rhizobia form anaerobic nodules on the roots of legumes and express genes for enzymes like nitrogenase to fix nitrogen into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant. (Tengerdy 1998)<br />
<br />
=2. Description and significance=<br />
Describe the appearance, habitat, etc. of the organism, and why you think it is important.<br />
*Include as many headings as are relevant to your microbe. Consider using the headings below, as they will allow readers to quickly locate specific information of major interest*<br />
=3. Genome structure=<br />
Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence?<br />
=4. Cell structure=<br />
Interesting features of cell structure. Can be combined with “metabolic processes”<br />
=5. Metabolic processes=<br />
Describe important sources of energy, electrons, and carbon (i.e. trophy) for the organism/organisms you are focusing on, as well as important molecules it/they synthesize(s).<br />
=6. Ecology=<br />
Habitat; symbiosis; contributions to the environment.<br />
=7. Pathology=<br />
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br />
=7. Key microorganisms=<br />
Include this section if your Wiki page focuses on a microbial process, rather than a specific taxon/group of organisms<br />
=8. Current Research=<br />
Include information about how this microbe (or related microbes) are currently being studied and for what purpose<br />
=9. References=<br />
It is required that you add at least five primary research articles (in same format as the sample reference below) that corresponds to the info that you added to this page.<br />
[Sample reference] Faller, A., and Schleifer, K. "Modified Oxidase and Benzidine Tests for Separation of Staphylococci from Micrococci". Journal of Clinical Microbiology. 1981. Volume 13. p. 1031-1035.</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105818Agricultural microbiology2014-12-02T00:33:24Z<p>Alexzhu: </p>
<hr />
<div>Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many symbiotic relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
=1. Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the rhizosphere. (Ahmad 2008) Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
==a. Arbuscular mycorrhizal fungi (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of hyphal networks surrounding the plant roots they colonize. (Kloepper 1989) AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus. (Adesemoye 2009)<br />
==b. Plant growth-promoting Rhizobacteria (PGPR)==<br />
This broad group of soil bacteria colonizes developing plant roots. Plant growth is promoted in a variety of fashions; some bacteria synthesize plant growth hormones like indoleacetic acid and other auxins (Zhao, Yunde 2010 Auxin biosynthesis), while others supply the plant with nutrients from the soil. Phytohormone expression by PGPR have also been proposed to promote the growth of roots through improved water and mineral uptake. (Dobbelaere 2001, Bashan 2004)<br />
==c. Nitrogen-fixing rhizobia==<br />
Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants. (Kale 1992) Symbiotic rhizobia form anaerobic nodules on the roots of legumes and express genes for enzymes like nitrogenase to fix nitrogen into bioavailable compounds for their host plants. Nitrogen is an element ubiquitously found in amino acids, proteins, and many other cellular components; its bioavailability is crucial to the growth of a plant. (Tengerdy 1998)<br />
<br />
=2. Description and significance=<br />
Describe the appearance, habitat, etc. of the organism, and why you think it is important.<br />
*Include as many headings as are relevant to your microbe. Consider using the headings below, as they will allow readers to quickly locate specific information of major interest*<br />
=3. Genome structure=<br />
Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence?<br />
=4. Cell structure=<br />
Interesting features of cell structure. Can be combined with “metabolic processes”<br />
=5. Metabolic processes=<br />
Describe important sources of energy, electrons, and carbon (i.e. trophy) for the organism/organisms you are focusing on, as well as important molecules it/they synthesize(s).<br />
=6. Ecology=<br />
Habitat; symbiosis; contributions to the environment.<br />
=7. Pathology=<br />
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br />
=7. Key microorganisms=<br />
Include this section if your Wiki page focuses on a microbial process, rather than a specific taxon/group of organisms<br />
=8. Current Research=<br />
Include information about how this microbe (or related microbes) are currently being studied and for what purpose<br />
=9. References=<br />
It is required that you add at least five primary research articles (in same format as the sample reference below) that corresponds to the info that you added to this page.<br />
[Sample reference] Faller, A., and Schleifer, K. "Modified Oxidase and Benzidine Tests for Separation of Staphylococci from Micrococci". Journal of Clinical Microbiology. 1981. Volume 13. p. 1031-1035.</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105817Agricultural microbiology2014-12-02T00:31:47Z<p>Alexzhu: /* 1. Classification */</p>
<hr />
<div>Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many symbiotic relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
=1. Plant-microbe symbiosis=<br />
Strains of free-living bacteria, actinomycetes, fungi, and protozoa have coevolved with a variety of plants to produce symbiotic relationships that often benefit one or more of the organisms involved. A majority of these plant growth promoting organisms colonize the surface of plant roots, known as the rhizosphere. (Ahmad 2008) Among these, there are three major groups of microbial inoculants used on agricultural crops:<br />
==a. Arbuscular mycorrhizal fungi (AMF)==<br />
AMF species produce structures like arbuscules and vesicles (sites of nutrient transfer and storage, respectively). They also build scaffoldings of hyphal networks surrounding the plant roots they colonize. (Kloepper 1989) AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms. (Smith & Read, 2010. Mycorrhizal Symbiosis (book)) AMF symbiosis promotes host plant uptake of nitrogen and phosphorous. They are most commonly found in well-aerated and cultivated top soils. Common genera include Aspergillus, Mucor, Penicillium Trichoderma, Alternaria, and Rhizopus. (Adesemoye 2009)<br />
<br />
=2. Description and significance=<br />
Describe the appearance, habitat, etc. of the organism, and why you think it is important.<br />
*Include as many headings as are relevant to your microbe. Consider using the headings below, as they will allow readers to quickly locate specific information of major interest*<br />
=3. Genome structure=<br />
Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence?<br />
=4. Cell structure=<br />
Interesting features of cell structure. Can be combined with “metabolic processes”<br />
=5. Metabolic processes=<br />
Describe important sources of energy, electrons, and carbon (i.e. trophy) for the organism/organisms you are focusing on, as well as important molecules it/they synthesize(s).<br />
=6. Ecology=<br />
Habitat; symbiosis; contributions to the environment.<br />
=7. Pathology=<br />
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br />
=7. Key microorganisms=<br />
Include this section if your Wiki page focuses on a microbial process, rather than a specific taxon/group of organisms<br />
=8. Current Research=<br />
Include information about how this microbe (or related microbes) are currently being studied and for what purpose<br />
=9. References=<br />
It is required that you add at least five primary research articles (in same format as the sample reference below) that corresponds to the info that you added to this page.<br />
[Sample reference] Faller, A., and Schleifer, K. "Modified Oxidase and Benzidine Tests for Separation of Staphylococci from Micrococci". Journal of Clinical Microbiology. 1981. Volume 13. p. 1031-1035.</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105816Agricultural microbiology2014-12-02T00:29:46Z<p>Alexzhu: </p>
<hr />
<div>Agricultural microbiology is a field of study concerned with plant-associated microbes. It aims to address problems in agricultural practices usually caused by a lack of biodiversity in microbial communities. An understanding of microbial strains relevant to agricultural applications is useful in the enhancement of factors such as soil nutrients, plant-pathogen resistance, crop robustness, fertilization uptake efficiency, and more. The many symbiotic relationships between plants and microbes can ultimately be exploited for greater food production necessary to feed the expanding human populace, in addition to safer farming techniques for the sake of minimizing ecological disruption.<br />
=1. Classification=<br />
==a. Higher order taxa==<br />
Domain; Phylum; Class; Order; Family; Genus<br />
Include this section if your Wiki page focuses on a specific taxon/group of organisms<br />
=2. Description and significance=<br />
Describe the appearance, habitat, etc. of the organism, and why you think it is important.<br />
*Include as many headings as are relevant to your microbe. Consider using the headings below, as they will allow readers to quickly locate specific information of major interest*<br />
=3. Genome structure=<br />
Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence?<br />
=4. Cell structure=<br />
Interesting features of cell structure. Can be combined with “metabolic processes”<br />
=5. Metabolic processes=<br />
Describe important sources of energy, electrons, and carbon (i.e. trophy) for the organism/organisms you are focusing on, as well as important molecules it/they synthesize(s).<br />
=6. Ecology=<br />
Habitat; symbiosis; contributions to the environment.<br />
=7. Pathology=<br />
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br />
=7. Key microorganisms=<br />
Include this section if your Wiki page focuses on a microbial process, rather than a specific taxon/group of organisms<br />
=8. Current Research=<br />
Include information about how this microbe (or related microbes) are currently being studied and for what purpose<br />
=9. References=<br />
It is required that you add at least five primary research articles (in same format as the sample reference below) that corresponds to the info that you added to this page.<br />
[Sample reference] Faller, A., and Schleifer, K. "Modified Oxidase and Benzidine Tests for Separation of Staphylococci from Micrococci". Journal of Clinical Microbiology. 1981. Volume 13. p. 1031-1035.</div>Alexzhuhttps://microbewiki.kenyon.edu/index.php?title=Agricultural_microbiology&diff=105815Agricultural microbiology2014-12-02T00:27:55Z<p>Alexzhu: Created page with "=1. Classification= ==a. Higher order taxa== Domain; Phylum; Class; Order; Family; Genus Include this section if your Wiki page focuses on a specific taxon/group of organisms ..."</p>
<hr />
<div>=1. Classification=<br />
==a. Higher order taxa==<br />
Domain; Phylum; Class; Order; Family; Genus<br />
Include this section if your Wiki page focuses on a specific taxon/group of organisms<br />
=2. Description and significance=<br />
Describe the appearance, habitat, etc. of the organism, and why you think it is important.<br />
*Include as many headings as are relevant to your microbe. Consider using the headings below, as they will allow readers to quickly locate specific information of major interest*<br />
=3. Genome structure=<br />
Describe the size and content of the genome. How many chromosomes? Circular or linear? Other interesting features? What is known about its sequence?<br />
=4. Cell structure=<br />
Interesting features of cell structure. Can be combined with “metabolic processes”<br />
=5. Metabolic processes=<br />
Describe important sources of energy, electrons, and carbon (i.e. trophy) for the organism/organisms you are focusing on, as well as important molecules it/they synthesize(s).<br />
=6. Ecology=<br />
Habitat; symbiosis; contributions to the environment.<br />
=7. Pathology=<br />
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.<br />
=7. Key microorganisms=<br />
Include this section if your Wiki page focuses on a microbial process, rather than a specific taxon/group of organisms<br />
=8. Current Research=<br />
Include information about how this microbe (or related microbes) are currently being studied and for what purpose<br />
=9. References=<br />
It is required that you add at least five primary research articles (in same format as the sample reference below) that corresponds to the info that you added to this page.<br />
[Sample reference] Faller, A., and Schleifer, K. "Modified Oxidase and Benzidine Tests for Separation of Staphylococci from Micrococci". Journal of Clinical Microbiology. 1981. Volume 13. p. 1031-1035.</div>Alexzhu