Endophytes, rhizophagy and One Health


The first week of this past August, I heard a presentation by Dr. James F. White, Jr. at the Acres’ Soil Health Summit in Sacramento, California. This was a very provocative presentation. Unfortunately, to my knowledge, this presentation wasn’t audio or video recorded.  Dr. White is a professor of plant pathology at Rutgers University and his research largely revolves around rhizophagy and plant endophytes. Rhizophagy is a process where plants attract and take in soil microbes (bacteria and yeast) through the meristems of their root tips. These internalized microbes (endophytes) are either broken down with superoxides for their nutrients or move through and into different parts of the plants including leaves and seeds. This blog post that follows below is largely my understanding of Dr. White’s research as well as some additional ruminations that White’s research provoked. This understanding and these thoughts are based, in part, on the live presentation I attended plus other recently recorded presentations by White that go over some similar and additional content. Two of the video clips embedded below are from a couple of those other recently recorded podcasts and presentations.


With plant nutrition, the prevailing chemical paradigm is that a plant’s roots obtain solubilized macro and micro nutrients in soil or other growth mediums. In industrial or hydroponic systems, these nutrients can be fed to the roots of plants directly. While in organic systems, nutrients can be added to the soil to feed the roots of plants.  

Though as I detailed in a prior blog, Restoring the plant’s soil microbiome, plants have multiple ways to obtain macro and micro nutrients. Plants can also obtain nutrients via mycorrhizal networks, rhizophagy and foliar spray applications. Mycorrhizal networks and rhizophagy are both ways plants actively seek nutrients in the soil and subsoil to feed themselves. This greatly reduces the need for external inputs.

But mycorrhizal fungi networks and rhizophagy require healthy soils. In such soils, there’s a diverse array of plants and root types exuding a wide array of carbon metabolites out of their roots to attract fungi and bacteria. Roots exude fats to form mycorrhizal associations (Keymer & Gutjahr 2018). Roots also exude other carbon compounds (sugars, amino acids, acids, etc) to attract bacteria and single cell fungi (yeast) that they “consume” and extract nutrients from as part of the rhizophagy cycle (White et al. 2018). By greatly reducing or inhibiting root exudations, many traditional and modern agricultural practices greatly reduce or limit mycorrhizal associations and rhizophagy. Bare fallows, tillage, synthetic nitrogen, seed coats, pesticides, and mono-cropping all reduce or destroy a plant’s ability to obtain nutrients via these other pathways.

When land is kept free of vegetation by cultivation, as is the case with bare fallows, obviously there are no plants to exude any carbon metabolites. Consequently, no mycorrhizal associations or rhizophagy will occur. This is why keeping living roots in the ground for as long as possible is one of the six basic soil health principles.

When plants are given synthetic nitrogen, they also stop exuding carbon metabolites. So this also prevents mycorrhizal associations and rhizophagy from occurring. Mycorrhizal fungi are able to acquire free amino acids in the soils and make these amino acids plant available (Makarov 2019). Amino acids are a source of organic nitrogen that can be utilized by plants. The cell walls of bacterial necromass are a source of these free amino acids. So are the cell walls of the endophytes “consumed” by plant roots that are broken down by superoxide during the rhizophagy cycle. In the embedded video below, Dr. White describes a completely different process he discovered recently showing how endophytes, which migrate up from the soil into the leaves of plants, also produce nitric oxide. That nitric oxide interacts with the superoxides produced by the plant to form nitrates that are absorbed by the plant cells as follows:   NO + 2O(-)  –> ONOO(-) –> NO3(-). The nitric oxide functions as an antioxidant to protect the bacteria from being oxidized by the superoxide (Micci et al. 2022).

Likewise tillage shreds mycorrhizal networks and also oxidizes soil carbon. Soils with less soil carbon have worse soil structure. Soils with poor soil structure allow less water infiltration and contain less oxygen. Rhizophagy requires oxygen to form the superoxide used to breakdown the cell walls of endophytes consumed as well as the superoxide that interacts with the nitric oxide from endophytes to form nitrates as just described above. So, less oxygen means the plants have less capability to obtain macro and micro nutrients in the soil and from endophytes in their leaves. What’s the ideal amount of oxygen? According to a correspondence with Dr. White, that hasn’t yet been determined. But the compaction and loss of soil structure resulting in less soil oxygen caused by repeated tillage is obviously less than ideal.  As is the loss of larger soil organisms that tunnel through soil like worms, dung beetles and small burrowing mammals (e.g. pika and prairie dogs).  These too provide routes for air and water into the soil. They also provide additional nutrients from transported (by dung beetles) or excreted manures and urine (Chen et al. 2022). Tillage pretty much destroys this network of underground tunnels that aerate soils as well as the burrowing bees, worms and other small critters formerly populating these soil ecosystems. 

As an aside, when looking at aerated non-turned composting systems like the Johnson-Su bioreactor, perforated PVC pipes are initially installed vertically to allow for airflow down into the compost (see picture below). These pipes are removed after these vertical passages have been established. Not turning the compost maintains fungi, and the tunnels created by the perforated PVC pipes allow for a wider array of bacteria and fungi formation in more uniform ratios of bacteria to fungi. So, it would be interesting to see if burrowing mammals perform a similar function that increases the amount and diversity of soil microbial life in soils at deeper and deeper levels.

Mycorrhizal fungi and worm/dung beetle/small mammal tunnel networks are also largely destroyed by the wide array of agricultural pesticides used including fungicides, rodenticides, insecticides and herbicides. Glyphosate, for example, destroys arbuscular mycorrhizal fungi [AMF] networks making soils more bacteria dominant (Helander et al 2019). Fungicides kill both AMF and saprophytic fungi. And rodenticides obviously, as its name implies, kills rodents. Many of pesticides can also be applied as seed treatments. Neonicotinoid insecticides are applied to a wide array of crop seeds including soybeans, cotton, wheat, canola, etc. Neonicotinoids have had devastating adverse collateral impacts upon bee populations (Mogren & Lundgren, 2016).

As soils degrade, losing organic matter and microbial diversity, plant aren’t as capable to feed themselves via mycorrhizal and rhizophagy pathways. Thus plants become more and more dependent on external inputs for nutrition in both traditional organic and modern industrial farming systems. These inputs include natural occurring inputs like manure, mined inputs like phosphorus, and manufactured inputs like synthetic nitrogen.

As recent news has demonstrated in Sri Lanka, reducing synthetic fertilizer inputs can’t be done overnight, especially when massive amounts of naturally occurring inputs aren’t immediately available. Yields drop off quickly. So any transition to regenerative organic/agro-ecological ways of farming require a transition period to ween plants off of their fertilizer and synthetic fertilizer dependency as healthier soils are restored. And contrary to a lot of prevailing misconceptions, once healthy biologically active soils are restored, regenerative agro-ecological farmers can achieve comparable yields to conventional farmers with much greater profit margins due to much lower input costs.


While plants can grow a lot of above ground biomass being fed most or all of their nutrients, especially in conventional industrial systems, plants grown this way tend to have less micro-nutrients. This is due to many of the traditional and convention practices listed above. Again, for example, synthetic nitrogen reduces plant exudation so rhizophagy doesn’t occur. So plants don’t take in microbes through their root tips and extract the nutrients from those microbes. Herbicides like glyphosate also chelate minerals too tightly so that these minerals aren’t plant available (Mertens et al 2018).

Recent research has shown that plants grown in regenerative systems have higher amounts of minerals, vitamins and phytonutrients. Meats from livestock fed forage grown in regenerative systems also have much better nutrient profiles (Montgomery et al 2022). 

Plus when plants are deficient in certain micro-nutrients other problems arise. For example, plants deficient in micro-nutrients don’t as effectively form the phytonutrients they use as defenses to ward off insects. Thus micro-nutrient deficient plants are more susceptible to pests and need more pesticides. Conversely, plants fed excess macro-nutrients, particularly nitrogen, are also more susceptible to insects since many pests are attracted to excess nitrates that accumulate in plant stems and leaves.

Other specific nutrient deficiencies, like manganese deficiency, can reduce the rate of photosynthesis. As I explained in a prior blog, manganese and water conducted up from the soil through a plant’s phloem are needed for hydrolysis, which is an initial step in starting the Calvin Cycle that converts atmospheric CO2 is into glucose (C6H12O6). As the below video details, manganese is required for hydrolysis, the splitting of water into an oxygen (O2), hydrogen and free electrons. The free electrons created via this reaction then go through a series of electron transport transfers until NADPH is formed and used in the Calvin Cycle. Therefore, if plants are deficient in manganese, the Calvin Cycle doesn’t have as many free electrons available to produce as much glucose. This, in turn, means less carbon for root exudates (carbon metabolites). Thus fewer microbes are attracted to meristems of root tips to be absorbed as endophytes and used in rhizophagy cycle or in plant leaves for nitrogen fixation. So, again, this reduces the plant’s ability to obtain its own nutrients.

During White’s lecture that I attended in early August at the Acres Soil health Summit, he noted how endophytes become part of seeds so that when seeds fall to the ground and germinate, the seeds help to re-establish the plant’s microbiome in the soil.  So later, I also thought to myself, if a human or animal in nature ate plants with seeds and that went through their respective digestible tracts and pooped out these seeds in their respective manure, wouldn’t that do the same thing  while adding fertilizer?

Another question popped into my head a few days later. That question was whether or not endophytes that entered meristems from the soil, weren’t zapped by superoxide and circulated through plants into leaves (and other edible parts of plants) became part of our intestinal and gut microbiomes after we consumed those plants with these endophytes?

I meant to send Dr. White some questions, but didn’t get around to it until I heard him on a podcast several weeks later where one of the interviewers specifically asked White the question I had about whether or not consumed endophytes become part of human microbiomes? The video clip below is White’s response to that interviewer’s question during that podcast. As you’ll hear from White’s response, he answers that yes, the endophytes in plants are many of the same microbes that end up in our gut microbiomes.

Another paper on “one health” (Banerjee & vander Heijden 2022) I read shortly after hearing White’s presentation, provoked even more thoughts. As the first sentence from this paper’s abstract notes:  “The concept of one health highlights that human health is not isolated but connected to the health of animals, plants and environments.” Below is an illustration from that paper. This illustration shows how various soil microbes are also in plant’s leaves, human guts, and the guts of other animals. The paper noted consumption of dirt directly, consumption of dirt still on plants, and inhalation of dust as possible pathways for soil microbes to get into these other places. Though the paper made no mention of rhizophagy or endophytes. So any consumption of microbes via plants suggested by this paper would more likely be of epiphytes, bacteria on the surface of plants.  

Rhizophagy is a more direct pathway that soil microbes take up from the soil into the plants we eat, and into the animal products we consume. Though, as demonstrated above, many farming practices reduce rhizophagy so less endophytes end up in cultivated plants than wild ones. Many modern food production and sanitation practices in modern societies further reduce the amount of any epiphytes on and endophytes in plants and animal products we eat or drink then poop, pee or lactate.

In more natural settings, microbial movement would be cyclical up from soil into (endophytes) and onto (epiphytes) plants into our guts and the milk, eggs, organs of the animals consumed, and then excreted back out by us (without going through a waste treatment center) or other animals to be reincorporated into soils. There too microbes become incorporated into the guts of decomposers (e.g. flies and dung beetles). Then those decomposers get consumed by larger insects, then birds, amphibians, etc. throughout the food web up the various food chains. So the food web is also a microbial web of interconnected microbiomes. Therefore, is it really any wonder why the human microbiome in modern society is a lot less diverse than those human microbiomes of indigenous peoples more directly connected to the land where these people hunt or forage a lot of their food? 

As Dr. White noted in a correspondence, “… the great collapse in the human microbiome in modern society has a lot to do with our practices in consuming sterilized and canned or frozen foods with antimicrobials (known as preservatives) included in them…” When you look at processes like pasteurization that too would kill of all beneficial microbes with any pathogens. So our over rigorous application of Germ Theory has been both a blessing and a curse. Other more traditional preservation practices like fermentation though increase microbial diversity. So endophyte/epiphyte rich plants could basically function like compost teas used in soils. The same is true of raw and fermented dairy products where microbes not killed by pasteurization could be kept alive and replicated to supplement the bacteria in our digestive tracts.


Whether in human guts or the guts of other creatures, mankind needs a more balanced approach to Germ Theory, one that’s also cognizant of Terrain Theory. These theories need to be considered complimentary rather than opposing theories. A similar less destructive balance is also required in the fields, orchards and forests where the animal and plant foods we consume are grown or raised. We can’t continue to dump pesticides and antibiotics into soils and our bodies that kill off all the beneficial microbes to save us from a few pathogens, weeds and pests. We need to better isolate pathogens while preserving beneficial symbionts. Therefore, we also need to adopt agricultural and medical practices that utilize beneficial microbes to optimize inherent immune systems to protect ourselves and the foods we eat from pathogens. 

As described above, adopting soil health practices that restore soil health increase the ways plants can nourish and protect themselves. This makes those plants more resilient and less reliant on external inputs. It does this by reestablishing mycorrhizal and rhizophagy pathways destroy by various traditional and modern agricultural practices. When these pathways are restored, particularly the rhizophagy pathway, the “one health” connection is restored. This is the microbial ecosystem connection between soils, plants, humans and other animals. When this connection is restored, this also increases the diversity of the human microbiome as well as the capability to support our innate and adaptive immune systems.

Thus, as always, soil health, plant health, human health and other animal health are all interconnected with planetary health. Everything is connected.


Keymer, A. & Gutjahr, C.  2018. Cross-kingdom lipid transfer in arbuscular mycorrhiza symbiosis and beyond

White, J.F. et al 2018 Rhizophagy Cycle- An Oxidative Process in Plants for Nutrient Extraction from Symbiotic Microbes

Makarov, M. 2019. The Role of Mycorrhiza in Transformation of Nitrogen Compounds in Soil and Nitrogen Nutrition of Plants: A Review

Micci, A et al. 2022 Histochemical Evidence for Nitrogen-Transfer Endosymbiosis in Non-Photosynthetic Cells of Leaves and Inflorescence Bracts of Angiosperms

Chen, Y.Y. et al 2022 Effect of the presence of plateau pikas on the ecosystem services of alpine meadows

Helander, M et al 2018 Glyphosate decreases mycorrhizal colonization and affects plant-soil feedback

Mogren, C.L. & Lundgren, J.G. 2016 Neonicotinoid-contaminated pollinator strips adjacent to cropland reduce honey bee nutritional status

Mertens, M et al 2018. Glyphosate, a chelating agent—relevant for ecological risk assessment

Mongomery, D. R. et al 2022 Soil health and nutrient density: preliminary comparison of regenerative and conventional farming

Banerjee, S & vander Heijden, M.G.A. 2022 Soil microbiomes and one health

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