How Plants Extract Nutrients

James Frances White
Wednesday, 13th March 2019

James Francis White explains how plants extract nutrients from soil microbes with the rhizophagy cycle.

Over the past few years it has become clear that plants are able to extract nutrients directly from soil microorganisms in their roots. This nutrient extraction process was outlined recently in an article published online in the journal Microorganisms. 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 acquire nutrients in the soil; nutrients are extracted from microbes through exposure to plant-produced reactive oxygen inside root cells. Nutrients like nitrogen and minerals are provided to plants directly from microbes through the rhizophagy cycle.

The Rhizophagy Cycle

In the rhizophagy cycle, plants ‘farm’ bacteria and fungi to get nutrients from them. Initially microbes grow on the root in a zone outside the root tip meristem where roots secrete carbohydrates and other nutrients to cultivate them. Microbes enter root tip meristem cells, locating within the periplasmic spaces (the space between the cell wall and plasma membrane). In the periplasmic spaces of root cells, microbes lose cell walls, becoming naked protoplasts. As root cells mature, microbes are doused with reactive oxygen (superoxide) produced on the root cell plasma membranes. Reactive oxygen degrades some of the microbes, also inducing electrolyte leakage, effectively extracting nutrients from microbes. Surviving bacteria in root epidermal cells trigger root hair elongation, and as hairs elongate, microbes exit at the hair tips, reforming cell walls as microbes emerge into the soil where they may obtain additional nutrients. This sustainable cycle occurs in all root tips of plants. Plants with more root tips obtain more nutrients from the rhizophagy cycle.


A root of Bermuda grass with bacteria growing around the root and entering the root cells at the root tip meristem. Reactive oxygen (brown coloration) is evident in the root cells at the root tip.

What Does This Mean For Gardeners? 

The rhizophagy cycle shows that plants develop an intimate connection with microbes, to the extent that microbes enter into the plant root cells themselves. Through the rhizophagy cycle plants obtain nutrients, but also the rhizophagy cycle microbes suppress plant pathogens in soils and increase 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. The rhizophagy cycle functions automatically in plants most of the time. 

Gardeners could 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. Potting mixes with antimicrobials should probably be avoided because that might inhibit the rhizophagy cycle. 

The prevailing view of plant nutrition (dogma) has been that plants only absorb into their roots inorganic nutrients (like nitrates or phosphates) that are soluble in soil water. However, organic gardeners have long believed that increasing organic material in soils results in better plant growth and that plants 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, symbiotic 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.

Yeast (Rhodotorula sp.) exiting the tips of root hairs of a clover seedling. The smaller spherical structures in root hairs are the yeast protoplasts.

The Future?

The rhizophagy cycle is definitely 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 without use of inorganic fertilizers or with minimal use of inorganic fertilizers. Some of the rhizophagy microbes increase growth of their particular host plant but inhibit growth of other plant species. Here, 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, and suppress diseases and weeds.

James Francis White Jr., is a professor at the Department of Plant Biology at Rutgers University, New Brunswick, New Jersey.


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.

Useful links

Nitrogen fixing plants and microbes

Soil restoration - using plants to fix nitrogen