Role of Soil Microbes

Microorganisms, macro effects.

What do Microorganisms do?

A diverse microbiome is the foundation of productive soil. Healthy soil includes bacteria, archaea, fungi, algae, nematodes, protozoa, and small animals such as springtails, mites, and earthworms. These microorganisms decompose organic matter, release available nutrients, synthesize new materials which are beneficial to plant growth, and can suppress other pathogenic microorganisms. Some soil organisms such as earthworms produce humus in their digestive tract or excrete glue-like materials which help bind soil minerals and organic matter.

Soil microorganisms cannot synthesize organic matter, so they rely on residues and remnants of plants and animals to survive. Decaying plant roots, harvest residues, and root exudates are all natural inputs of carbon to the soil. Mulches, biochar, and manures also feed the microbial community. As soil microorganisms decompose these carbon sources, they build humus, a stable form of soil carbon. Humus is rich in nitrogen, mainly in the form of amino acids.

Figure from Pagano, M. C., Correa, E. J. A., Duarte, N. F., Yelikbayev, B., O’Donovan, A., and Gupta, V. K. (2017). Advances in eco-efficient agriculture: the plant-soil mycobiome. Agriculture.

Numerous studies have demonstrated the wide range of potential benefits that these microorganisms can provide to plants. Beneficial microbes including fungi can create pathogen-suppressive soil and prevent pathogens from infecting plants. For example, the bacterium Pseudomonas fluorescens has been shown to inhibit germination and growth of Fusarium mold in the rhizosphere. Nitrogen-fixing bacteria are a well-known example of beneficial bacteria. They can make atmospheric N available to plants, lowering the need for N fertilizers. But some of the most important of the soil microorganisms are the plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF).

 

Figure from Adesemoye, A. O., Torbert, H. A., and Kloepper, J. W. (2009). Plant growth-promoting rhizobacteria allow reduced application rates of chemical fertilizers. Plant Microbe Interactions.

Plant Growth-Promoting Rhizobacteria

PGPR are a group of bacteria that form beneficial relationships with the roots of plants, enhancing their ability to uptake water and nutrients. PGPR produce phytohormones which stimulate plant growth, promoting root development and increasing plant biomass. They produce organic acids and other compounds that make nutrients like phosphate and potassium more soluble in water. These organic acids play many roles in soil and plant health. Other PGPR produce siderophores, which bind to iron and make it more bioavailable to the plant. PGPR can also induce pathogen defense mechanisms, or even produce compounds that make plants more drought- or salt-tolerant.

Arbuscular Mycorrhizal Fungi

Similarly to PGPR, AMF have been shown to provide a wide range of benefits to plants, such as enhanced photosynthetic capacity, improved nutrient uptake, and increased antioxidant defense during periods of stress. AMF forms a network of fine mycelia through the soil and connect the roots of plants, increasing water and nutrient uptake by the plant. AMF can access microsites in the soil, improving mineral nutrition. They can also redistribute water during periods of drought, and can prevent toxic ions from entering plant roots in salty soil.

Further Reading

Adesemoye, A. O., Torbert, H. A., and Kloepper, J. W. (2009). Plant growth-promoting rhizobacteria allow reduced application rates of chemical fertilizers. Plant Microbe Interactions.

Bashan, Y. (1999) Interactions of Azospirillum spp. in soils: A review. Biology and Fertility of Soils.

Choudhary, D. K. and Varma, A. (2016). Microbial-mediated Induced Systemic Resistance in Plants. Springer Nature.

Couillerot, O., Combaret-Prigent, C., Caballero-Mellado, J., and Moenne-Loccoz, Y. (2009). Pseudomonas fluorescens and closely-related fluorescent pseudomonads as biocontrol agents of soil-borne phyotopathogens. Applied Microbiology.

Jackson, W. R. (1993). Humic, Fulvic and Microbial Balance: Organic Soil Conditioning. Umi Research Press.

Kohnke, H. and Franzmeier, D. P. (1995). Soil Science Simplified. Waveland Press.

Kuypers, M. M. M., Marchant, H. K., and Kartal, B. (2018). The microbial nitrogen-cycling network. Nature Reviews Microbiology.

Pagano, M. C., Correa, E. J. A., Duarte, N. F., Yelikbayev, B., O’Donovan, A., and Gupta, V. K. (2017). Advances in eco-efficient agriculture: The plant-soil mycobiome. Agriculture.

Rana, A., Saharan, B., Nain, L., Prasanna, R., and Shivay, Y. (2012). Enhancing micronutrient uptake and yield of wheat through bacterial PGPR consortia. Soil Science and Plant Nutrition.

Sacca, M. L., Caracciolo, A. B., Di Lenola, M., and Grenni, P. (2017). Ecosystem services provided by soil microorganisms. In M. Lukac, P. Grenni, and M. Gamboni (Eds.), Soil Biological Communities and Ecosystem Resilience. Springer.

Sneh, B., Dupler, M., Elad, Y., and Baker, R. (1984). Chlamydospore germination of Fusarium oxysporum f. sp. cucumerinum as affected by fluorescent and lytic bacteria from a Fusarium-suppressive soil. Ecology and Epidemiology. https://www.apsnet.org/publications/phytopathology/backissues/Documents/1984Abstracts/Phyto74_1115.htm

Zhang, H., Sun, Y., Xie, X., Kim, M., Dowd, S., and Paré, P. W. (2009). A soil bacterium regulates plant acquisition of iron via deficiency-inducible mechanisms. The Plant Journal.