Katy Dynarski, PhD - - Microbes

How Microbes Make Soils—and Crops—Healthier

Like the human body, soils are home to a teeming microbiome providing services that scientists are just beginning to understand. A single teaspoon of soil contains more microbes than there are humans on Earth, representing tens of thousands of distinct microbial species. Though invisible to the naked eye, these microbes make up a diverse belowground ecosystem responsible for many of soil’s important functions. As research into the soil microbiome continues, scientists are discovering countless ways that this invisible ecosystem supports the development of healthy soils and crops.

The soil microbiome consists of various too-small-to-see organisms that include arthropods, nematodes, bacteria, fungi, and archaea, each contributing unique capabilities to the soil ecosystem. These diverse organisms interact with each other in complex networks that can break apart plant matter and then chemically digest it, mine soil minerals, and create brand-new chemical compounds. In doing so, the soil microbiome actively contributes to soil and crop health by building up the physical structure of soils, driving soil nutrient recycling, and producing compounds that help crops persist against environmental stressors.

A single teaspoon of soil contains more microbes than there are humans on Earth.

Microbes Build Soil Physical Structure

Soil’s ability to store water and oxygen comes from its structure, which typically consists of soil particles stuck together in stable formations called aggregates.

Microbes play a key role in the development of these formations by releasing glue-like sugar substances that can stick soil mineral particles together and create new aggregates. Some of the benefits of aggregate formation include improved water infiltration rates and water-holding capacity, as well as reduced soil compaction and runoff.

Proper soil structure also depends on having sufficient soil organic matter. Like aggregates, soil microbes also play a major role in the formation of soil organic matter. Many of the microbes in soils are what’s known as decomposers—they eat old plant material, like dead roots and fallen leaves, to build up their biomass, storing the carbon they consume in their bodies. When these microbes die, their carbon-rich bodies add to the soil organic matter, with recent research demonstrating that microbial bodies are actually the main ingredient in stabilized soil organic matter.

Recent research demonstrates that microbial bodies are the main ingredient in stabilized soil organic matter.

Microbes Recycle Soil Nutrients

Microbes are also active participants in soil nutrient cycling and play a key role in the storage, and eventual release, of plant-essential nutrients. When decomposer microbes consume plant material in their quest for carbon, they release some of the nutrients locked in those tissues back into the soil, making them available for future plant consumption. These recycling transformations can help maintain a steady supply of plant-available nutrients in the soil.

This microbial recycling can also help growers use applied fertilizers more efficiently. Scientists at the Berkeley Lab are currently investigating how soil microbes can resolubilize leftover phosphorus from fertilizer. When phosphate fertilizer is applied to crops, some of it cannot be absorbed through their roots and remains locked away in the soil. Certain microbes can release enzymes that transform this unavailable phosphorus into a form that crops can absorb. The Berkeley Lab researchers are looking into the creation of microbial soil amendments to accelerate this recycling, helping growers get the most from their fertilizer applications.

Microbes Strengthen Crop Health

The soil microbiome can also act as an immune system for soils, helping ward off pests and pathogens that can cause plant diseases.

In a study of a sugar beet field that had grown resistant to a root fungus pathogen, researchers discovered that disease suppression came not from the crops, but from the soil microbes. Microbial biodiversity was the key to this service; the scientists found that not one, but 17 different types of microbes that contributed this disease suppression.

“Individual organisms have been associated with disease-suppressive soil before, but we demonstrated that many organisms in combination are associated with this phenomenon,” commented Gary Andersen, one of the researchers at the Berkeley Lab involved with the study.

Soil microbes can also contribute to plant resiliency against other environmental stressors such as drought. In a recent meta-analysis, researchers at Northern Arizona University discovered that when crops were inoculated with certain bacteria, yields increased up to 45 percent. The benefits of these growth-promoting bacteria becoming more pronounced when crops were grown under drought conditions. The scientists suggested that the bacteria were able to provide this benefit by producing special biofilms that increased crop drought resistance, and they are now looking into developing microbial amendments that can confer this drought resistance to more crops.

The soil microbiome can act as an immune system for soils, helping ward off pests and pathogens.

Building Up Your Soil’s Microbiome

Understanding the wide range of soil microbes, their individual functions, and their relationships to each other is a massive scientific undertaking.

“What we're trying to understand now is whether there is a specific microbial community made up of certain organisms at certain quantities that is associated with a healthy soil,” explains Deirdre Griffin, a doctoral candidate at the University of California, Davis, studying the connection between soil microbiology and soil health.

As of now, there is no known “ideal” soil microbiome, and biotechnologies like microbial amendments for soil are still in their infancy and should be treated with caution. As the body of scientific knowledge about the soil microbiome grows, such technologies are likely to advance. Current research seeks to combine information about microbial functions that contribute to soil health with genetic information to learn more about who some of the major players are.

Griffin adds that though we don’t know exactly which microbes help support soil health (yet), we do know that supporting a large and diverse microbial ecosystem is important.

“Giving microbes enough food, water, and nutrients will help them stay active and do many of the functions we look for,” she advises. “The best rule of thumb is to think about feeding the soil with whatever organic matter inputs you're able to incorporate into your system, be it compost amendments, cover cropping, crop residue incorporation, or all of the above.”

This translates to great news for growers who already utilizing soil conservation practices like reducing tillage, adding compost to fields, or incorporating cover crops. These practices can help minimize disturbance to the soil ecosystem and provide microbes with plenty of food, adding “support for a healthy soil microbiome” to the list of benefits of managing for soil health.

As with all soil conservation practices, your local university cooperative extension, regional NRCS soil health specialist, and the Soil Health Institute can all be valuable resources for learning more about practices to support healthy soil biology in your specific region. And there’s never been a better time to try out new soil conservation practices; scientists are discovering more and more perks of cultivating a diverse, active soil microbiome on the farm.