Rhizophagy

October 23, 2026 by Dr. James F. White, Jr.

Plants Farming Their Own Microbes!

We typically think of plants as organisms that need our chemical fertilizers, but they actually don't depend on them. Plants develop their own methods for getting nutrients, and they involve microbes. Most people do not realize that plants are basically eating microbes by ingesting, degrading, digesting, and stripping nutrients from them. They maintain them as endosymbionts in the plant cells for a period of time. This is a fundamental change in how we think of plants. Plants are cultivators of microbes. They are not just growing in the soil, waiting for us to apply nutrients to them. The consumption of microbes to get nutrients is called microbivory, but the eating of microbes and the process is referred to as Rhizophagy—rhizo (root) and phagy (eating).

Over the past few years it has become clear that plants use their roots to cultivate soil microbes as well as extracting nutrients from them. This nutrient extraction process was outlined in 2018 in an article published online in the journal Microorganisms¹. The process is called the 'rhizophagy cycle' (pronounced 'rye-zo-FAY-gee'). In the rhizophagy cycle, microbes cycle between the soil and a phase inside root cells. Microbes provide nutrients to plants in two ways: 1) microbes acquire nutrients (nitrogen, phosphorus, zinc, etc.) in the soil—and these nutrients are extracted directly from microbes inside root cells through exposure to plant-produced superoxide in root cells—causing leakage from nutrients from microbes; 2) microbes go into the soil and solubilize soil nutrients (potassium, sulfur, boron, etc.) and these nutrients are absorbed by plant roots from the soil solution. It has been estimated that rhizophagy cycle microbes may provide 30% or more of mineral nutrients needed by plants.

Figure 1. The root of Phragmites australis - “common reed grass” - with a cloud of bacteria around the root tip where bacteria enter root cells. Photos by Professor James F. White Jr. Rutgers University-New Brunswick

Plants 'Farm' Soil Microbes in the Rhizophagy Cycle

The rhizophagy cycle works like this: Initially microbes grow on the root in a zone outside the root tip meristem where roots secrete exudates (carbohydrates and other nutrients) to cultivate them (Figure 1). Microbes are absorbed into root tip meristem cells located within the periplasmic spaces (the space between the cell wall and plasma membrane) (Figure 2). In the periplasmic spaces of root cells, microbes are doused with superoxide by the root cell, and this strips the cell walls from the microbes, causing them to become naked protoplasts. The naked protoplasts of microbes are then circulated around the root cell in a process called cyclosis. It is thought that this constant circulation of microbes within root cells is a way to increase the flow of nutrients into root cells from the microbes. Superoxide produced by root cells degrades some of the microbes and induces nutrient leakage from the microbe cells by damaging the microbe cell membranes. Bacteria in root epidermal cells trigger root hair elongation, and as hairs elongate, microbes are ejected from root hair tips (Figure 3), reforming cell walls as they emerge back into the soil where they may obtain additional nutrients. This sustainable cycle occurs in all root tips of plants. Plants like grass crops (wheat, rice, and corn) with fibrous roots and many root tips obtain more nutrients from the rhizophagy cycle than plants with fewer root tips.

Figure 2. Corn seedling (A) and bacteria (arrows) within root cells in B and C.

What Does This Mean for Agriculture?

The rhizophagy cycle shows that plants develop an intimate connection with microbes, to the extent that microbes enter into the plant root cells themselves. In addition to plants obtaining nutrients, the rhizophagy cycle microbially suppresses plant pathogens in soils and increases the oxidative stress tolerance in plants. Basically, the rhizophagy cycle results in healthy plants, and without it plants may be poorly developed and more susceptible to disease and stress. While the rhizophagy cycle usually functions automatically in plants, it emphasizes the need to manage soils to maintain soil health, including the many microbes that live in healthy soils. Further, the rhizophagy cycle is also a process where nitrogen fixation from the air could happen in root hairs. Future work on the process could result in cereals and other plants that produce their own nitrogen as in legumes, reducing the need for nitrogen fertilizer applications.

The rhizophagy cycle delivers multiple benefits that enhance plant health and resilience naturally. This process improves nutrient acquisition by providing plants with readily available organic nitrogen and boosting uptake of essential minerals like NPK, calcium, and magnesium, while simultaneously stimulating root hair development and hormone production for stronger plant growth. Additionally, the cycle triggers systemic resistance that protects plants against diseases and pests, increases antioxidant levels for drought and stress tolerance, and creates a microbial environment that naturally suppresses weed growth.

Is There Something We Should Do Differently Now?

We should encourage functioning of the rhizophagy cycle by increasing microbial activity in the soil with organic amendments. It is possible to suppress the rhizophagy cycle by use of sterilized or chemically treated seeds that remove or inhibit the symbiotic microbes on seeds. This is what happens in cotton where seeds are treated with acids that kill symbiotic microbes leaving seedlings that grow poorly and are vulnerable to diseases.

Figure 3. Tall fescue root hair showing brown stained bacteria within hair and blue-stained bacteria after ejection from hair tip.

To activate and energize the rhizophagy cycle on your farm, maximize photosynthesis by applying essential minerals like magnesium, iron, phosphorus, boron, and nitrogen, which increases root exudates that feed beneficial microbes. Extend the growing season beyond the typical 3-4 months for a cash crop by planting cover crops and kickstart the cycle early by coating seeds with microbial inoculants paired with nutritional treatments. Finally, minimize fungicide and herbicide use to preserve beneficial microbes (buffering with humic or fulvic acids when chemicals are necessary), and ensure adequate calcium through lime, gypsum, or liquid applications to support critical root tip growth and cell division.

Why Are Regenerative Farmers Interested in the Rhizophagy Cycle?

The dogmatic prevailing view of plant nutrition has been that plants only absorb into their roots inorganic nutrients (like nitrates or phosphates) that are soluble in soil water. However, organic farmers have long believed that increasing organic material in soils results in better plant growth, and that plants somehow get nutrients from the soil organics. The rhizophagy cycle shows how plants get nutrients from organic materials added to soils in providing a linkage between soil organic material, soil microbes, and plants. In the rhizophagy cycle, microbes go from plants into the soil, acquire nutrients of various kinds, and carry nutrients back to plants, enter plant root cells where plants oxidatively extract nutrients from microbes, then plants deposit microbes back into the soil from tips of root hairs to continue the cycle.

Diagram of the rhizophagy cycle: microbes enter root cell periplasmic spaces carrying nutrients from soil, nutrients are extracted from microbes by reactive oxygen produced by NOX on root cell plasma membranes, and microbes exit root hairs exhausted of nutrients to recharge with nutrients in the rhizosphere

Not only is the rhizophagy cycle more evidence that healthy soils with diverse microbes and organic materials are better for plants, but also microbes that vector on seeds are important. Many of the seed microbes function in the rhizophagy cycle, so we want to conserve the microbes on seeds. In addition, we may be able to learn how to manage the rhizophagy cycle so that we can increase plant growth significantly, while reducing use of inorganic fertilizers. Some of the rhizophagy microbes increase growth of their particular host plants, but inhibit growth of other plant species. In view of this, we may be able to develop these microbes into 'bioherbicides' to favor growth of some plants, but inhibit weedy plants. In the future it may be possible to cultivate plants using only microbes to increase plant growth, while suppressing diseases and weeds.

References

White, J.F.; Kingsley, K.L.; Verma, S.K.; Kowalski, K.P. Rhizophagy Cycle: An Oxidative Process in Plants for Nutrient Extraction from Symbiotic Microbes. Microorganisms 2018, 6, 95. https://doi.org/10.3390/microorganisms6030095
White, J.F.; Kingsley, K.L.; Verma, R.; Obi, N.; Dvinskikh, S. et al. Review: Endophytic Microbes and Their Potential Applications in Crop Management. Pest Management Science 09/2019; 75(10): 2543-2548., DOI:10.1002/ps.5527.

Dr. James F. White, Jr.

Professor of Plant Pathology, Rutgers University

James F. White, Jr., is Professor of Plant Pathology at Rutgers University. Dr. White obtained his M.S. in Mycology and Plant Pathology from Auburn University, Alabama, and his Ph.D. in Mycology from the University of Texas, Austin in 1987. 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.