Tapping the ‘plant microbiome’ to improve farming and plant health

Understanding microbial activity in rhizosphere – the critical zone where plant roots, microbes and minerals interface – is critical to promoting plant health. Pacific Northwest National Laboratory, CC BY-NC

People are increasingly aware of the link between the trillions of microbes that live within our bodies and human health. Studies have found that a healthy population of bacteria, or a microbiome, in a person can prevent food allergies and even treat depression.

Just as in the human body, these types of tiny bugs can play an beneficial role in plant health. Growth-promoting bacteria or fungi can be added to plants or soil in a variety of ways – in seed coats, suspended in water and sprayed on plants or soil, or mixed into mulches that are added to the soil or placed around plant stems.

Study of this microscopic world has been going on for decades but is now attracting more interest from researchers looking for environmentally benign methods to improve agriculture.

Nitrogen fixing

All plants in natural soil have associations with microbes, including bacteria and fungi. The symbiotic relationship between plants and microbes has been evolving for at least four million years: fossil evidence shows structures formed between early land plants and what appear to be fungi.

Plants have evolved to rely on microbes for growth, particularly in challenging environments. For example, microbes that are important to plant growth include bacteria and fungi that fix nitrogen from the air, making nitrogen available to plants for growth. These microbes often live inside special structures know as root nodules, which live on the surface of roots.

The impact of soil microbes on agricultural plant growth was first formally described in 1904 by Lorenz Hiltner, though agricultural treatments aimed at modifying microbial activity in soil have been used since Roman times. For example, the Romans would grow plants that form associations with nitrogen-fixing bacteria (clover, alfalfa) in crop rotations to improve soil fertility. They didn’t know why the clover and alfalfa plants helped improve the growth of other crops grown in the soil, but we now know that these plants can enhance levels of nitrogen in soil, via the activity of nitrogen-fixing bacteria.

Pacific Northwest National Laboratory, CC BY

There are also thousands of species of fungi that form structures known as mycorrhizae with different plant hosts. These structures are thought to have enabled plants to colonize land and are beneficial in that they allow the plant to exchange sugars for nutrients and water scavenged from the surrounding soil by fungi. Mycorrhizae extend into the plant root, allowing fungal tissue to wrap around or penetrate into plant cells to form the structures where nutrient exchanges occur. Microbes that form specialized structures with the help of plants, and live in a mutually beneficial partnership with plants, are known as symbiotes.

Lodgepole pine balancing act

At the same time, there is a whole host of non-symbiotic, or free-living bacteria and fungi that are beneficial to plants. They can live in the soil surrounding plant roots (a region called the rhizosphere), on plant surfaces or even live within the tissues of the plant itself. Beneficial microbes that live within plant tissues, whether they are symbiotes or not, are in a unique position to affect plant metabolism and health.

For example, free-living microbes, known collectively as endophytes, can suppress plant pathogens or other harmful organisms. Endophytes can also assist plant growth directly by regulating plant hormones, activating plant immune responses and providing the plant with additional nutrients. Since the 1990s, scientists have isolated endophytes from plant tissue and can describe communities of endophytes in terms of gene sequences to better understand their functions.

Understanding microbial communities in crops can reduce the amount of pesticides used or make plants drought-resistent. Kyle Spradley / Curators of the University of Missouri, CC BY-NC
Although endophytes have great potential to improve plant growth and health, finding non-symbiotic microbes that consistently produce significant positive growth responses under highly variable field conditions remains a challenge. Simply adding a microbe that can improve plant growth may not always be enough because the other bacteria and fungi surrounding and interacting with the plant will also have effects, as does the plant’s environment.

For example, a bacterium known to improve the growth of lodgepole pine can be derailed by the presence of a single other competing bacterium. This effect was seen both for a plant-beneficial bacterium that was an endophyte, and one that simply lived on the plant root surface, according to a study.

Microbial cocktail

What this means is that if you have isolate a microbe that has plant-beneficial effects under controlled conditions, you can’t be certain it will work under real-world conditions unless it is tested thoroughly.

It also means that it may be very important to take into consideration the composition of microbial communities the plant is exposed to – whether it’s the soil, root surfaces, the aboveground plant surfaces – when determining the conditions needed for optimal activity of plant-beneficial microbes.

The quest for finding microbes that can be used in plant agriculture for improving plant growth or health has a long history. As we learn more about the complicated interactions of plants with their microbiomes and the environment, we grow closer to understanding how these ancient practices can be refined and used in the future.

To learn more, some suggested reading:

Bent, E. 2006. Induced systemic resistance mediated by plant growth-promoting rhizobacteria (PGPR) and fungi (PGPF). In Multigenic and Induced Systemic Resistance in Plants, edited by S. Tuzun and E. Bent. Pages 225-258.

Curl, E.A. and Truelove, B. 1986. The Rhizosphere. Springer-Verlag, New York NY USA. 288 pages.

Gaiero, J.R. et al. 2013. Inside the root microbiome: bacterial root endophytes and plant growth promotion. American Journal of Botany 100(9):1738-1750.

Glick, B.R. 2012. Plant growth-promoting bacteria: mechanisms and applications. Scientifica Volume 2012, Article ID 963401, http://dx.doi.org/10.6064/2012/963401

Lugtenberg, B. and Kamilova, F. 2009. Plant growth promoting rhizobacteria. Annual Review of Microbiology 2009;63:541-56. doi:10.1146/annurev.micro.62.081307.162918.

Pal, K. K. and B. McSpadden Gardener, 2006. Biological Control of Plant Pathogens. The Plant Health Instructor DOI: 10.1094/PHI-A-2006-1117-02.

Smith, J.L. and Collins, H.P. 2007. Management of organisms and their processes in soils. Chapter 17 in Soil Microbiology, Ecology and Biochemistry, doi:10.1016/B978-0-08-047514-1.50021-4

Smith, S.E. and Read, D.J. 2008. Mycorrhizal symbiosis, 3rd edition. Academic Press/Elsevier, San Francisco CA USA. 787 pages.