Using Cover Crops to Direct the Soil Microbiome

Soil Microbes—Why Do We Care?

Healthy soil is teeming with biological diversity, including microbes (bacteria, fungi, archaea, protozoa, and viruses), plant roots, earthworms, nematodes, and insects. The "soil microbiome" encompasses the vast microbial life within soil, though microbiomes exist everywhere — from oceans and clouds to your wallet and belly button! Soil microbiomes are especially interesting, as they are some of the most species-diverse environments on Earth. A single gram of soil can contain 10 billion bacterial cells and likely between 2,000–50,000 bacterial species!

Soil-dwelling bacteria and fungi have profound impacts on agricultural productivity and are the backbone of healthy agroecosystems. While a few microbes cause plant disease, many improve plant health by helping with nutrient acquisition, plant host defense, and producing hormones that promote plant growth. Microbes performing these services can be found in almost any handful of soil, but their efficiency can vary dramatically. Intentional microbial management can direct soil microbiome functioning towards its full potential, helping to support specific agricultural goals, much like we do with plants. So, how can we achieve this?

Cover Crops to Boost Beneficial Microbes

Several approaches can be taken to soil microbiome management, including the application of beneficial microbial products and inputs like manure and compost or the removal of harmful pathogens (e.g., soil steaming, anaerobic disinfestation, etc.). In the past 15 years, the study of soil microbiology has changed dramatically with increasingly advanced research tools (Note 1). This has sparked renewed interest from scientists to manage soil microbiomes another way, by fostering beneficial populations that already exist in your soil through targeted farm management practices.

An increasingly popular strategy to achieve sustainable soil health involves the use of cover crops, which are typically fast-growing annual plants that are used between growing seasons of major cash crops. Some effects of cover crops on soil health are well understood, like erosion control, improved soil structure, increased organic matter, and weed suppression. However, there is less clarity on how cover crops influence the soil microbiome, which is a key component of soil health. Let's break down what we do know.

Note 1. A Brief History of How We Study Soil Microbes and Why We Are in the Middle of a Research Revolution:

To effectively manage soil microbiomes, it's essential to first understand their complex ecology. Traditionally, studying soil microbes was challenging because it relied on growing them in laboratory settings—a technique known as "culturing." However, we now know that only about 1% of the microbial diversity in soil can be grown in a laboratory, leaving most unaccounted for. Within the last 15 years, breakthroughs in DNA sequencing technology have made it possible to study microbiomes in much more detail, allowing scientists to better understand how they are structured, how they function, and how different agricultural practices shape them. This has completely changed our understanding of the soil microbial world and opened new doors for improving agricultural sustainability through microbiome management.

Cover Crops Provide Microbial Food Sources

Cover crops play a key role in shaping soil microbiomes through the carbon they add to soil, which occurs in two main ways. First, cover cropping leads to the buildup of plant residues, contributing to the accumulation of soil organic matter, nutrient cycling, and microbial abundance and activity. Second, cover crops secrete root exudates —  organic compounds such as sugars, amino acids, phenolic acids, and flavonoids — that act as a chemical "buffet" of food sources for microbes. Different plant species (and even different genotypes of the same plant species) can have completely different exudate profiles, and they can change throughout the lifespan of the plant. This creates the chemical diversity that allows different groups of microbes to thrive. Just as some animals use foods that humans cannot consume (e.g., cows eat grass), different types of microbes differ in their food preferences and will be drawn to different plant species. In some cases, exudation may be used to specifically promote microbes that are beneficial to the plant.

Cover Crops Create Microbial Habitats

If you could zoom in about 100X into a soil, you would see that the microbial landscape is full of peaks and valleys, "rivers," and biological deserts. Cover crops alter the physical landscape of the soil, impacting soil structure, moisture retention, aeration, compaction, and temperature regulation. These physical changes within the soil environment can build microbial habitats, significantly impacting their diversity, abundance, and activity (Table 1).

Like humans, populations of soil microbes are not evenly spaced; think of dense cities separated by sparse rural areas. Different microbes will adapt to local micro-climates in the soil, and there are "hotspots" of microbial activity where nutrients are abundant, such as around plant root tips (where roots secrete exudates), also known as the "rhizosphere effect." In contrast, in soil compartments where access to nutrients is scarce, many microbes will migrate away or enter a state called "dormancy," where they slow or entirely stop their metabolism, effectively "hibernating" until conditions for growth improve. A critical area of research now focuses on distinguishing between active and dormant microbes, as only about 1–5% (on average) of soil microbes are metabolically active at any time and perform key functions like nutrient cycling or disease suppression. Scientists are actively working to understand which microbes are consistently active in soil, which become active under different conditions, and whether those that are active are also the most important for agricultural productivity and ecosystem health.

Cover crops can also modify soil microbiomes by altering the chemical landscape in soil, such as pH and nutrient availability. Brassicas, for instance, release sulfur-containing compounds, which can lower the pH in soil.  Different pH conditions can promote or suppress specific groups of microbes, including beneficial species and pathogens (Figure 2). Soil microbes are extremely sensitive to changes in pH, making cover crops and residues a potential tool for shaping microbial communities.

Do Cover Crops Create Predictable Changes in the Soil Microbiome?

A current goal of research is to find consistent patterns across farms. This is easier to do for microbes that are known to have strong effects on crop yields. Among these, Arbuscular mycorrhizal fungi (AMF, sometimes referred to as vesicular-arbuscular mycorrhizae, or VAM) have been extensively researched because of their clear benefits to plants. These AMF are microbial "superstars" when it comes to providing nutrients and protecting plants against pathogens and environmental extremes like heat or drought. They also contribute to overall soil health by producing glomalin-related soil proteins, a sort of "biological glue" that binds soil particles together, improving soil structure and carbon storage.

AMF are especially known for their ability to improve phosphorus uptake, particularly in low phosphorous conditions; studies have claimed that AMF could reduce the need for chemical fertilizer by up to 50%. AMF does not associate with every cover crop species, suggesting the potential to select cover crops strategically to promote AMF populations (Table 2). AMF colonization in cash crops is often higher following the use of cover crops that associate with mycorrhizal fungi, like rye or oats, compared to non-mycorrhizal cover crops like canola or radish, or fields that have been left fallow. In cases where non-mycorrhizal cover crops are used, mixing them with a mycorrhizal-associated species may mitigate reductions in AMF (for instance, mixing radishes with oats).

Legumes have also been studied extensively for their ability to selectively promote populations of nitrogen-fixing bacteria called rhizobia, which can have symbiotic relationships with legumes by forming root nodules, where they fix nitrogen (enhancing N availability to the plant) and receive a safe environment and nutrients in return. Research has shown that some rhizobia form symbiotic relationships specific to certain groups of legumes. For example, rhizobia that associate with vetch are specific to plants like vetch, peas, and faba beans and do not form nodules or fix nitrogen for soybeans which require Bradyrhizobium japonicum or Bradyrhizobium elkanii. Free-living nitrogen-fixing bacteria can also contribute to improving nitrogen uptake in plants associating with plant roots (without forming nodules). Some genera in this group include Azotobacter and Gluconacetobacter, which have been targeted for commercial inoculant development, with some developers reporting that they can contribute 10-30 lbs. of nitrogen per acre (e.g., Pivot Bio). These microbes present a potential tool for supplementing soil nitrogen and reducing reliance on synthetic fertilizers and will likely become even more effective as scientists uncover the strength of their associations with different plant species.

More generally, many studies indicate that using cover crops increases microbial abundance, diversity (especially with cover crop mixtures), and metabolic activity, which are all broadly associated with increased soil health. There is also some evidence that rotating cover crop species over consecutive growing seasons could aid in pathogen suppression since different crops leave a unique profile of carbon sources that can shift the composition of soil microbes. Brassicas, in particular, have been shown to produce compounds that can directly suppress fungal pathogens. Such findings indicate highly promising prospects for microbiome management and have driven researchers to continue pulling apart these complex relationships.

The Future for Cover Crop-Mediated Microbial Management

Since we know how important microbes are for agriculture, there is a will for more concrete solutions for microbial management. Current research suggests that cover cropping has the potential to boost key aspects of the soil microbiome typically associated with healthy soils, such as microbial biomass and diversity, and the presence of well-studied beneficials such as AMF and nitrogen fixers, which may allow farmers to reduce reliance on chemical inputs while maintaining crop yields. Ultimately, this could reduce the environmental footprint of agriculture and lead to more resilient growing systems. Nevertheless, the reality is that we are still working toward a model of microbial management where we can use cover cropping "prescriptions" to enhance target microbial functions. A message to farmers is to keep your eyes on the horizon. Ongoing research in the coming decades is likely to refine cover cropping strategies and develop farmer-accessible tools to better direct soil microbiome functioning for more resilient, sustainable agriculture.

This article reflects the collaborative efforts of the authors, with Sarah Richards as the primary author responsible for writing the article. Kara Reardon contributed a key table and revisions, and Terry Bell, Estelle Couradeau, Heidi Reed, and Sjoerd Duiker provided valuable feedback.

Citation for this article:

Richards Sarah, Reardon Kara, Bell Terrence, Couradeau Estelle, Reed Heidi, & Duiker Sjoerd. (2025). Using cover crops to direct the soil microbiome. Penn State Extension. doi: 10.26207/5ks1-wr57

Additional Resources

• Several articles written by Penn State research scientists have been published on eOrganic and the Penn State Extension website, and are excellent sources of information for farmers who want to learn more about soil microbes (Soil Microbes in Organic Cropping Systems 101, Understanding and Managing Soil Microbes) and the various approaches that can be taken to manage them beyond cover cropping (Management of Soil Microbes on Organic Farms).
• Colorado State University. (n.d.). Cover crops and the soil microbiome. Human Nature. Retrieved from 
• Ohio State University Extension. (n.d.). Soil Bacteria: What They Are and How They Help Soil.
• North Carolina State University Extension. (n.d.). Soil Biological Health.
• University of Wisconsin-Madison Extension. (n.d.). Mycorrhizae.
• Sokol, N. W., Kuebbing, S. E., Karlsen-Ayala, E., & Bradford, M. A. (2020). Evidence for the direct effects of cover crops on soil microbial communities. Soil Biology and Biochemistry, 145, 107771. 
• Rodale Institute. (n.d.). How to Inoculate Arbuscular Mycorrhizal Fungi on the Farm – Part 1.
• South Dakota State University Extension. (n.d.). Fall Cover Crops Boost Soil Arbuscular Mycorrhizal Fungi, Which Can Lead to Reduced Inputs.
• *O'Callaghan, M., Ballard, R. A., & Wright, D. (2022). Soil microbial inoculants for sustainable agriculture: Limitations and opportunities. Soil Use and Management, 38(3), 1340–1369. doi.org/10.1111/sum.12811
  • This article contains a table with examples of soil inoculant products and their claimed functions.
• Purdue University Extension. (n.d.). Soil Health Assessment: A Guide for Farmers and Landowners. 
• Penn State Extension. (n.d.). Interpretation of Soil Health Tests.