By Larry Cooper, with Rita Abi-Ghanem, PhD

Good farmers farm crops, great farmers farm the soil. Important to having great soil is building an active and diverse microbiome that will structure the soil and move and process nutrients in ways most beneficial to plants. The more microbes there are in a soil, the more fertile that soil becomes. In this series, we discuss the many important roles that soil microorganisms play in producing fertile soil and healthy crops.

In Part 3 of this series, we look at Biocontrol of Plant Pathogens.

Healthy crop soil is teeming with billions of microbes per square inch. Too small for the human eye to see, the accumulated body mass of microbes in a crop field can exceed 1 ton per acre. Plants depend on these tiny creatures for many important health and growth functions, and crop yields are greatly influenced by whether or not the microbes are present in sufficient numbers and with sufficient diversity to do their jobs.

In previous articles in this series, we discussed how microbes break down plant and animal matter into humus, releasing minerals in soluble forms that are easier for plants to absorb. Microbes bring nutrients into the soil from the atmosphere (nitrogen fixation) and from locked up mineral reserves that are already in the soil. They also degrade soil pollutants and help to hold soil aggregates together while increasing porosity, creating channels through which roots can grow and water can flow—increasing infiltration and reducing runoff.

Plants and certain microbial groups can have a symbiotic relationship: plants provide microbes with energy in the form of carbohydrates (a typical plant can give up 25%–45% of its total carbohydrate reserves to feed its microbes), and in return microbes bring in nitrogen, phosphorus, micronutrients, and water while performing other essential functions that contribute to the plant’s growth and vigor.

One of those essential functions that we’ll discuss in greater detail is biocontrol—preventing the growth or activity of plant pathogens.


Microorganisms have three main pathways for biocontrol of plant pathogens: antagonism (producing metabolites, such as antibiotics, that directly inhibit the pathogens), competition (out-competing the pathogens for life-sustaining resources, particularly carbon), and induced resistance (by which the microorganisms trigger plants to better defend themselves).

Most microbes produce one or more antibiotics that suppress plant pathogens and the diseases they cause. Several microorganisms are known to produce multiple antibiotics that suppress more than one pathogen, which enhances biological control.

When nonpathogenic microbes are abundant, they protect a plant through rapid colonization and consumption of nutrients so that the nutrients are not as available to pathogens, in effect starving the pathogens out. This is particularly effective when the nonpathogenic microbes colonize sites where water and carbon-containing nutrients are most readily available—such as exit points of secondary roots. It is thought that soil-borne pathogens that infect through mycelial (the branching threads of a fungus) contact are particularly susceptible to competition for nutrient resources.1

Other microbes, such as strains of Pseudomonas sp. and Trichoderma sp., are known to continually trigger plants’ own defenses throughout the plants’ lifecycles.

It’s not unusual for a microbe to deploy multiple mechanisms of biocontrol: as an example, consider vesicular arbuscular mycorrhizal (VAM) fungi (see illustration at the top of this post). Studies of VAM fungi have shown that they can prevent root-knot nematode infections by reducing access sites and stimulating host defenses. They can also increase a plant’s stress tolerance, enhance plant nutrition, change the physical structure of roots through lignification, and even change the chemical composition of plant tissues such as antifungal chitinase.1

The Benefits of Equilibrium and Diversity

It’s important to understand that the great majority of microbes (perhaps as high as 98%) are beneficial or neutral to plants, and the natural state is for plants and microbes to achieve a biological equilibrium. When something happens to disturb this equilibrium, pathogenic microbes have a chance to exert their influence and damage plants, siphoning off energy from the host in a way that affects growth and vigor. While the immediate inclination of a grower might be to attempt to kill off these pathogens, it’s quite impossible to kill off harmful microbes without killing off the beneficial microbes as well. The best long-term solution is to return the biosphere to equilibrium so that the pathogens are overwhelmed and suppressed by beneficial microbes. This leads to both direct biocontrol of the pathogens—through competition, antagonism, predation, and parasitism—and to indirect control through induced plant resistance and plant growth promotion.

By achieving a healthy microbial diversity in the soil, the soil food web is preserved and the chances are maximized that beneficial microbes will be present in sufficient numbers that they will out-compete and out-perform the pathogens and contribute to vigorous plant growth that will be more tolerant of diseases.

Carbon: The Energy Currency of Soil

The single most limiting factor for healthy microbial growth, after adequate moisture, is the availability of organic carbon sources. A recent USDA-NRCS video2 quotes Dr. Kris Nichols of the Rodale Institute as saying that “Carbon is the energy currency of soil.” Most soil microorganisms require carbon to build their bodies and to oxidize for energy. When planning nutrition for your crops, be sure to plan the carbon-based nutrition required by the beneficial microbes in your crops’ rhizospheres. Meeting the nutritional needs of soil microbes is important for soil fertility and optimal crop yield.

Through this series of blog posts, “Microorganisms: The Living Engine of Soil,” we’ve stressed that having a healthy and diverse “microbiome” of microorganisms in crop soil is essential to successful farming:

Healthy microorganism diversity = healthy soil =
healthy plants = greater yields.

The greatest yields come from a cultivated understanding of the symbiotic relationship between plants and their microorganisms and a careful tending of that essential microbiome.

Our product line is built on our 45+ years’ experience with using carbon-based nutrition to build healthy soils and improve plant growth to increase yields. Ask your Fertilgold® Organics sales representative about how we can help build your soil and increase yields.


  1. Pal K and Gardener B. Biological Control of Plant Pathogens. The American Phytopathological Society Website, available at
  2. USDA-NRCS Video Series: Unlock the Secrets in the Soil, Chapter 5, Keep a Live Root in the Soil, or “A Radicle Idea.” June 10, 2016. Available at

About the Author

Larry Cooper

Director, Sustainability & Knowledge Management, Huma, Inc. Lifelong learner, master gardener, rescuer of greyhounds, grandpa. Once served detention for placing ecology flag on top of his high school.

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