Harnessing the Power of Microbes for Healthier Agriculture

July 15, 2026 by James F. White, Jr.

The Loss of Microbial Diversity in Modern Agriculture

In natural situations, plants use microbes to enhance their own health and hardiness, and to get the nutrients that they require for growth. These microbes include mycorrhizal fungi, soil microbes, and fungal, bacterial, and algal endophytes (endophytes are microbes that live in plants without causing disease). In modern agriculture, we have lost many of the native microbial endophytes that live inside plants, and we have destroyed or damaged many of the microbial communities that reside in soils. The loss of soil and plant microbiology leaves plants weakened and more susceptible to stresses and diseases—and leaves them dependent on chemical inputs for cultivation. In essence, we have destroyed the agency of plants for their own cultivation and made them dependent on humans for almost everything they require for growth and protection from disease and insects. As a practical outcome, worldwide, we are overusing synthetic chemistry to cultivate crops with negative outcomes for the environment, people, and animals. And the continued overuse of chemistry further damages microbial communities in soils and plants.

Reversing the Damage to Plants and Soils

To reverse the damage that we have done to soil and plant microbial communities, we must begin to cultivate crops using microbiology—and reduce the excessive use of synthetic chemistry. Regenerative and organic agriculture are practical approaches to heal soil microbial and plant endophyte communities. The use of diverse cover crops is an important way to rebuild soil microbial communities because each cover crop adds microbiology to soils and builds organic matter in soils that serves as a food source and reservoir for soil microbes. Other ways to rebuild microbial communities include the use of plant ferments, composts, extracts, and microbial or algal bio-stimulants. In addition, the use of animal dung adds nutrients, organic materials, and microbes to soils.

Why Are Microbes Important to Plants?

Microbes enable plants to obtain nutrients from soils, enhance nutrient use efficiency, enable plants to grow and develop properly, increase plant resistance to oxidative stresses (heat, salt, heavy metals, etc.), and protect plants from fungal pathogens and insect pests.

A. Plants obtain nutrients through the “farming” of soil microbes (Figure 1).

Crop plants that are provided with sufficient microbes, on and within seeds, and in microbially diverse soils, acquire more nutrients and become more “nutrient dense” than plants growing under “microbially starved” conditions. This is because plants cultivate or “farm” microbes and use them to make nutrients available in soils and to transport those nutrients to plants.

One process that plants use to obtain nutrients from soil microbes is called the “rhizophagy cycle” (rhizo=root; phagy=eating). In the rhizophagy cycle, soil microbes alternate between a free-living phase in soils where microbes acquire nutrients and an endophytic symbiotic phase within root cells where nutrients are extracted oxidatively from microbes. The rhizophagy cycle is initiated upon seed germination when the emergent root tip begins to secrete microbe attractants in the form of exudates that contain sugars, vitamins, organic acids, and other nutrients.

Some of the microbes (often bacteria) accumulating at root tips are internalized into root epidermal cells. As root epidermal cells develop, they produce reactive oxygen (superoxide) that oxidizes cell walls from microbes leaving them as “wall-less protoplasts”. Some of the nutrients obtained by plants using rhizophagy are derived from nutrients obtained from the oxidation of microbe cell walls by the root cells. Thus, the nutrients that are within microbes themselves feed the development of plants. Of course, additional nutrients may be obtained through mycorrhizal symbiosis and through the solubilization of nutrients in soils and their direct absorption into roots. Plants obtain nutrients for growth through all the biological processes that are available to them.

Figure 1. Diagram of the rhizophagy cycle. In the rhizophagy cycle, soil microbes alternate between a free-living phase in soils where microbes acquire nutrients and an endophytic symbiotic phase within root cells where nutrients are extracted oxidatively from microbes. Photos courtesy of James White

B. Proper plant development requires that microbes are present within plant cells (Figure 2).

It is only now becoming appreciated how dependent plants are on endophytic microbes for development. Endophytes have been shown to affect the development of roots in terms of increasing root growth, root branching, root hair growth, and root gravitropism. Without endophytes in roots, root growth and development are largely suppressed. One notable effect of endophytic microbes is root hair elongation. In experiments where we remove microbes from plants, plant root hairs do not elongate. This is because the bacteria within root hairs accumulate at the root hair tips and produce hormones (e.g., ethylene, nitric oxide, etc.). Thus, the endophytic microbes in plants participate directly in root cell growth and development. Root hairs that contain numerous endophyte protoplasts become longer than those with only a few microbes. The dependency of plants on microbes for root development is an indication of how important microbes are to plants.

Figure 2: Bermuda grass seedling root containing Pseudomonas endophyte. All brown spots in roots are intracellular bacteria. Photos courtesy of James White

C. Microbes increase plant resistance to oxidative stress.

Plants that are actively engaged in rhizophagy cycle activity express more antioxidants than those growing in soils without, or with reduced, microbes. These antioxidants include enzymes like peroxidases and superoxide dismutase, and non-enzyme antioxidants, including phenolics, flavonoids and terpenoids, etc. Many of these antioxidants are also healthful components of foods—essentially, this is another component of increasing the nutrient density of crops. The increased levels of antioxidants in plants makes plants more resistant to oxidative stresses. Oxidative stress may stem from many environmental stresses, including heat, drought, heavy metals, salt, etc. Thus, growing plants using microbiology makes plants hardier and more tolerant to abiotic stresses. Because of these stress-protective effects, endophytes represent a hedge, or “insurance”, against climate extremes that may stress out crops growing in soils with poor microbe diversity.

D. Microbes protect plants from fungal pathogens and insect pests (Figure 3).

Plants that are rich in microbial endophytes through growth in microbial-rich soils also show more resistance to diseases and insect pests. This enhanced pest-resistance effect is likely due to three reasons: 1) plants are more tolerant to the oxidative stresses imposed by the fungal or insect pests; 2) plants with endophytes contain more antioxidant substances (e.g., terpenoids and phenolics) that affect growth and disease expression of the pathogen or deters feeding by insects; and 3) some bacterial endophytes or other soil microbes colonize pathogenic fungal hyphae and reduce virulence of the pathogen, resulting in a slower growing microbe that does not incite disease.

Figure 3: In this experiment, basil seeds with and without protective microbes were grown with and without Fusarium pathogens. The seeds with microbes survived while the ones without microbial protection died. Basil seedlings with microbes intact. Photos courtesy of James White

Conclusions

The integration of microbiology into agricultural practices offers a promising path to creating more sustainable and resilient farming systems. By reestablishing microbial diversity in both soils and plants, we can enhance crop health, nutrient density, and resistance to environmental stresses, while reducing the harmful effects of over-reliance on synthetic chemicals. The overriding agronomic reasons for growing crops in microbially rich soils is that plants are healthier, hardier, and more resistant to biotic and abiotic stresses. It is a further benefit to consumers of the crops (animals and humans) that plants grown using microbes are dense in nutrients, including minerals, antioxidant amino acids, and phenolics, among other nutrients.

Embracing methods like regenerative agriculture, organic farming, and the strategic use of microbial stimulants not only benefits plant growth but also contributes to the long-term health of ecosystems. As we face increasing environmental challenges, a shift towards microbiome-centered agriculture is essential for cultivating crops that are not only more productive but also more sustainable for future generations.

Relevant Literature

White JF, Kingsley KL, Verma SK, Kowalski KP. Rhizophagy Cycle: An Oxidative Process in Plants for Nutrient Extraction from Symbiotic Microbes. Microorganisms. 2018; 6(3):95. https://doi.org/10.3390/microorganisms6030095
Chang X, Kingsley KL, White JF. Chemical Interactions at the Interface of Plant Root Hair Cells and Intracellular Bacteria. Microorganisms. 2021; 9(5):1041. https://doi.org/10.3390/microorganisms9051041
Chang X, Young B, Vaccaro N, Strickland R, Goldstein W, et al. 2023. Endophyte symbiosis: Evolutionary development and impacts of plant agriculture. Grass Research 3:18 doi: 10.48130/GR-2023-0018

James F. White, Jr.

Professor of Plant Pathology, Rutgers University

Dr. White specializes in symbiosis research, particularly endophytic microbes. He is the author of more than 180 articles, and author and editor of reference books on the biology, taxonomy, and phylogeny of fungal endophytes. He and students in his lab are exploring diversity of endophytic microbes and the various impacts that they have on host plants.