Agricultural microbiology

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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.

Plant-microbe symbiosis

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 [1]. Among these, there are three major groups of microbial inoculants used on agricultural crops:

Arbuscular mycorrhizal fungi (AMF)

Figure 1 Comparison of plant growth with and without mycorrhizal symbiosis. Used with permission; photograph by Half Hill Farm in Woodbury, Tennessee.

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 [2]. AMF species are highly abundant and play a vital role in their ecosystems by promoting plant growth through numerous mechanisms [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 [4].

Plant growth-promoting rhizobacteria (PGPR)

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 [5], 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 [6] [7].

Nitrogen-fixing rhizobia

Triple-bonded diatomic nitrogen, constituting about 78% of our atmosphere, is highly stable and unable to be used by plants [8]. 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 [9].

Mechanisms of plant growth promotion

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 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 [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 [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 [10]. Crop rotation, especially involving legumes and their Rhizobia symbionts, is practiced precisely for this reason.

Pathogen deterrence

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. [1]

Cycling of bioavailable elements

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.


Figure 2 Root nodules formed on the roots of soybean plants. Each nodule contains billions of nitrogen-fixing Rhizobiacea bacteria. Photograph taken by USDA, and is of public domain.

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 [4].


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 [11].

Fertilizer efficiency

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 [4].

Maximization of food production

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 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 [12].

Minimization of ecological harms

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 [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.

Further Reading

I-American Society for Microbiology on "How Microbes can Help Feed the World"

II-Journal of Applied and Environmental Microbiology

III-Wikipedia article on soil microbiology


[1] Ahmad, Farah, Iqbal Ahmad, and M. S. Khan. "Screening of Free-living Rhizospheric Bacteria for Their Multiple Plant Growth Promoting Activities." Elsevier Microbiological Research 163 (2008): 173-81. Web.

[2] Kloepper, Joseph W., Ran Lifshitz, and Robert M. Zablotowicz. "Free-living Bacterial Inocula for Enhancing Crop Productivity." Elsevier Ltd (1989): 39-44. Web.

[3] Smith, Sally E., and David J. Read. Mycorrhizal Symbiosis. 3rd ed. N.p.: Academic, 2010. Print.

[4] - Adesemoye, Anthony O., and Joseph W. Kloepper. "Plant–microbes Interactions in Enhanced Fertilizer-use Efficiency." Springer 85 (2009): 1-12. Web.

[5] Zhao, Yunde. "Auxin Biosynthesis and Its Role in Plant Development." National Center for Biotechnology Information. Web of Science, 2010. Web.

[6] Dobbelaere, Sofie et al. "Responses of Agronomically Important Crops to Inoculation with Azospirillum." Csiro Publishing - Functional Plant Biology. Csiro, 03 Sept. 2001. Web.

[7] Bashan, Yoav, Gina Holguin, and Luz E. De-Bashan. "Azospirillum-plant Relationships: Physiological, Molecular, Agricultural, and Environmental Advances (1997-2003) -." NRC Research Press. Canadian Journal of Microbiology, 2004. Web.

[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." Soil Biology Biochemistry 24.12 (1992): 1317-320. Web.

[9] Tengerdy, Robert P., and George Szakacs. "Perspectives in Agrobiotechnology (Review Article)." Elsevier Journal of Biotechnology 66 (1998): 91-99. Web.

[10] Berg, Gabriele. "Plant–microbe Interactions Promoting Plant Growth and Health: Perspectives for Controlled Use of Microorganisms in Agriculture." Applied Microbiological Biotechnology 84 (2009): 11-18. Web.

[11] Zhuang, Xuliang, Jian Chen, Hojae Shim, and Zhihui Bai. "New Advances in Plant Growth-promoting Rhizobacteria for Bioremediation." Science Direct. Environment International, 18 Dec. 2006. Web.

[12] "PRO-MIX." Premier Tech Horticulture and Agriculture. N.p., n.d. Web. 1 Dec. 2014.

[13] Fertilizer Use & Markets. United States Department of Agriculture. N.p. Last updated July 12, 2013.

Entry created by Alex Zhu, a student of Jenny Talbot in BI311 (Microbiology) at Boston University Fall 2014.