Restoring the plant’s soil microbiome

Preface: The below content is a cursory overview of numerous plant and soil microbiological processes. This overview is intended as an introduction to these processes. So rather than a detailed dissertation on each item, with lots of references, a lot of processes have been reduced to very concise outlines for the purpose of brevity. Most of what’s noted is also transcribed from memory and thus not necessarily ascribed to a specific source.

Vegetables, fruits and meats consumed today are significantly lower in macro and micro nutrient content than the same foods consumed fifty to sixty years ago (Thomas 2007).. There are several reasons for this, including the selective breeding of sweeter but less nutritious plants. Though, a bigger reason for this drop off in nutrients is the degradation of soil health. Many immediately assume that degradation is due to the depletion of the nutrients in the soil. But as farmer, author and educator Gabe Brown explained in this short video clip below, today there isn’t a shortage of macro or micro nutrients in the soil, but instead what’s lacking is an healthy soil ecosystem. An unhealthy ecosystem doesn’t have the proper composition of soil microbes to make the existing macro and micro nutrients in the soil available to plants in a form that the plants can utilize.

Soils are not depleted of macro & micro-nutrients. Soils are missing the necessary biology needed to make macro & micro-nutrients available to plants

Before describing what and how conventional /industrial and traditional/organic agricultural management practices undermine soil health by making nutrients less plant available, a better understanding of how the soil-plant ecosystem works is essential. Once this ecosystem is better understood and then optimized, a truly regenerative farm or ranch can drastically reduce, if not eliminate, the need for both synthetic and organic inputs for fertility as well as for pest control while simultaneously increasing the rate of photosynthesis and carbon sequestration.

To begin to understand the soil-plant ecosystem, it helps to start with an analogy to human physiology…that is to an inverted human mouth and gut microbiome. So, as former NRCS soil conservationist Ray Archuleta has noted in several of his presentations, the leaves and stems of a plant are its “mouth” that feed sugars and other exudates to microbes in the soil around the soils roots, the rhizosphere. This rhizosphere is the plant’s “gut” that contains huge numbers of bacteria, fungi, protozoa, archaea, viruses, and other microscopic creatures. The connection between plants and their “gut” is a two way street compromising of the xylem and the phloem. The xylem is a pathway in a plant’s vascular tissue that conducts water and minerals up from the rhizosphere through the roots. The phloem works generally, but not exclusively, in the opposite direction. Carbon dioxide (CO2) taken in through stomata on the undersides of the leaves of plants is converted via the Calvin Cycle into glucose. This sugar and other metabolites are conducted through the phloem, another area of vascular tissue, down out through the roots into the soil in exchange for nutrients provided by soil microbes. Though, based on the pressure of sugar in the phloem, flow may also be upward to other parts of the plant.

In reality these two parallel pathways are more like a loop, that is they form a cycle, since the minerals and water taken up through the roots from the soil are essential for enzyme creation, protein formation and photosynthesis. With photosynthesis, for example, manganese along with water conducted up from the soil are needed for hydrolysis, which is an initial step in starting the Calvin Cycle that converts CO2 is into glucose (C6H12O6). As the below video details, manganese is required for this splitting of water (hydrolysis) into a oxygen (O2), hydrogen and free electrons. The free electrons then go through a series of electron transport transfers until NADPH is formed and used in the Calvin Cycle. Thus, if plants are deficient in manganese, photosynthesis is less efficient. Manganese also activates other enzymes that are important for the production of plant defense compounds including phenolics, cyanogenic glycosides and lignin (Burnell 1988). So if plants are deficient in manganese, they’re also more susceptible to insects plus contain less phytonutrients (and are thus also less nutritious). Other macro and micro-nutrients (minerals) affect plants in similar and other ways particularly with plant defenses. So deficiencies in these other nutrients also make plants more susceptible to insect infestations. Weak plants attract pests. Not unlike people, with weakened immune systems, are more susceptible to viral infections (e.g. Covid-19).

Different plants have different types of roots that go to different depths and exude different metabolites. Root types are broadly classified as dicots (tap roots) and monocots (fibrous roots). In a diverse poly-culture, like a prairie, roots of different types going to different depths and exuding different metabolites source different macro and micro-nutrients that are then conducted back up to the plants. Roots of perennial plants can go very deep into the soil.. Plants can also symbiotically exchange different nutrients with one another via arbuscular mycorrhizal fungi [AMF] networks. These AMF networks interconnect almost all the different root systems of the different plants, thus the more variety of plants and different types and depths of roots….the better. More plant diversity also increases the amount of carbon sequestration (Xu et al. 2020).

Almost all plants, aside from a few, form either ectomycorrhiza or endomycorrhiza associations with their roots that interconnect plants as noted above. These fungi associations also significantly extend the reach of root systems so plants can obtain water and nutrients from much farther away in the soil and sub-soil. Around ninety percent of plants form endomycorrhiza associations that are arbuscular mycorrhizal fungi [AMF] associations. With this type of association, the hyphae of the fungi literally attach themselves to the cellular membrane of a plant roots. The cell walls of AMF are made of chitin (C8H13O5N)n, a polysaccharide made of carbon and nitrogen. Consequently when AMF dies and becomes necromass, it becomes a source of both soil organic carbon [SOC] and soil organic nitrogen [SON] used in the formation of soil organic matter [SOM]. The necromass of soil bacteria also forms SOM containing SON and SOC (Liang et al 2019).

Additionally, the cell walls of bacterial necromass contain protein, which is a source of organic nitrogen. These cell walls break down and become free amino acids that AMF can absorb via diffusion and transport back to the plant to utilized along with other nutrients like phosphorus and water (Makarov 2019). AMF networks also use carbonic acid (H2CO3) to break down or weather rocks and other aggregates in sub-soils (Hoffland 2004, Martino 2010).  Thus AMF networks are essential for sourcing other micro nutrients to as far down as roots and their associated AMF can go into the soil and sub-soil. Additionally fungi, not just AM- fungi, secrete oxalic acid (C2H2O4), one of the strongest organic acids on the planet. Fungi use this acid to drill through granite to extract elemental nutrients. Oxalic acid is very highly involved in sequestering significant amounts of atmospheric CO2 as inorganic carbon oxalates and carbonates deposited in soils across the planet.

a plant roots with arbuscular mycorrhizal fungi associations

Consequently plants without AMF networks can’t gather or share as many macro and micro-nutrients. Moreover plants without AMF networks have less macro and micro nutrients available to conduct up from the soil through the roots via the xylem into the plant to create enzymes, and secondary metabolites needed for plant defense mechanisms as well as for processes like photosynthesis. Less photosynthesis equals less carbon exudates via the microbial carbon pump and thus less soil organic matter with less deep soil carbon sequestration. So it really shouldn’t be any wonder that Dr. David Johnson (in his ongoing research at Cal State Chico and NMSU with biologically enhanced agricultural management also know as B.E.A.M.) has been finding that soils that have higher fungi to bacteria ratios have greater rates of plant growth that sequester a lot more carbon than bacterial dominated soils. In this video clip below, Johnson states this relationship between fungi to bacteria ratios also coincides with a eleven fold increase in the amount of plant available manganese in the soil. With the same amount of sunlight and water, according to Dr. Johnson, there’s a five fold increase in photosynthetic capacity of the plants. Furthermore, Dr. Johnson conveyed to me via email, microbes secrete phytohormones that also increase plant growth. Again, refer above to an explanation and video of manganese’s essential role in photosynthesis for hydrolysis to start the flow of electrons to initiate the Calvin Cycle to convert CO2 to glucose. The AMF makes more manganese available.

Nutrients that effective AMF networks gather and share, that aren’t bound or oxidized, are also taken up by the plant roots through two additional processes: Rhizophagy and ion exchanges. In the rhizophagy cycle, plants “consume” bacteria. Consumed bacteria within the plant’s roots are known as endophytes. Superoxides are excreted within the roots to break down the cell walls of the endophytes and extract their nutrients. Next the remains of these endophytes are “spit” out through root hairs back into the rhizosphere where these fragments then reassemble as new bacteria and use AMF networks as pathways to gather more minerals. After this occurs, the bacteria come back to the root tips to feed on exuded sugars and metabolites, where they again get sucked back into the plant, and the cycle repeats itself all over again. The below video is a long webinar featuring this rhizophagy process as presented by Dr. James White, the researcher who has been researching this process for a long time (White et al 2018, White et al. 2019). So to better understand rhizophagy, please make some time to watch this entire video.

Plant nutrient uptake through AMF and the rhizophagy cycle may be unfamiliar concepts to many agronomists and soil scientists. What’s more familiar is passive and active ion uptake of different mineral cations or anions through diffusion or other mechanisms by roots in the soil (or in hydroponic systems with roots in other mediums). Cations lose electrons and thus are positively charged (oxidized) whereas anions gain electrons and thus are negatively charged (reduced). Certain charged states of different minerals (mainly cations) are more easily absorbed than other charged states, since this is contingent upon the cation exchange capacity [CEC] of the soil. Different types of soils have different cation exchange capacities. Below are two parts of a three part video that explains these various mineral absorption pathway theories. Please watch these first two parts to better understand these theories.

Ion exchange is the basis for a lot of modern agro-chemistry. So different fertilizers and other amendments in different molecules with different mineral cations are added to soils in order to increase nutrient uptake of different minerals by the plants especially nitrogen, potassium and phosphorus [NPK]. Different ionization states of minerals are more capable of being utilized by plants. One factor determining the amount of uptake of mineral from soils is the pH of the soil. Certain minerals are more or less available at different pH levels. But despite the prevailing dogma, pH isn’t the only variable affecting nutrient uptake. Another variable is involved. That variable is the redox potential represented by the symbol Eh. Where pH is the exchange of protons between elements in the soil either acidifying or alkalizing soil, Eh is the exchange of electrons between elements in the soil. The loss of an electron is oxidation. The gain of an electron is reduction. Both Eh and pH may be altered by the root exudates exuded by roots as a function of photosynthesis. Different levels of Eh and pH are conducive to different microbial communities. (Olivier 2012). This gets quite involved and a full more detailed explanation is beyond the scope of this blog post. For more information, please read the paper cited and watch the video just below.

Now one of the problems with a lot of conventional or industrial agronomy is that it reduces plant nutrition to just ions and inorganic nutrients as measured by the cation exchange capacity [CEC] and pH of a soil. Thus the most common soil testing only tests for macro and micro nutrients in certain inorganic forms. When these forms are deemed as being deficient, more and more inputs are added to the agro-system. Some people refer to this as the more-on way of farming. Lime can raise soil pH, and macro nutrients like nitrogen can be added to soils to generate a lot of plant growth. Though this plant growth is lower in nutrient content because it adversely impacts the other ways plants obtain nutrients as described above and further detailed below. Some forms of nitrogen also require more irrigation for nutrient uptake. So it’s really no wonder that during the “green revolution”, when industrial methods of farming became more widespread, the amount of irrigated land more than doubled (Steinfeld et al 2006) as also noted in this clip below.

A clip on irrigation and the Green Revolution from a 2012 talk by Sandra Postel, Director,The Global Water Policy Project. Founded in 1994 by Postel, a leading authority on international freshwater issues.

Another issue is that plant uptake of these inorganic amendments is limited. So a lot of the added nutrients end up leaching into ground water or running off into water ways where nitrates and phosphates cause hypoxia and algae blooms ultimately leading to dead zones in the ocean like the one in the Gulf of Mexico.

Then too, synthetic nitrogen requires a lot of energy to make, releases a lot of carbon dioxide and methane during production, and then a lot of nitrous oxide after synthetic nitrogen is applied to fields and some of it volatilizes. So it’s a very large source of greenhouse gases. One recent study from Cornell University (Zhou et al 2019) noted than the amount of methane released during production of synthetic nitrogen fertilizer was one hundred times greater than what was self-reported by the industry. The Haber Bosch process requires a lot of energy to split dinitrogen (N2) into nitrogen to bind with the hydrogen derived from methane (CH4) to form ammonia (NH4). A lot of methane escapes during extraction (fracturing) and during the Haber Bosch process along with CO2.

Mined phosphorous and potash have a lot of issues as well. But I digress, the broader adverse environmental impacts of NPK fertilizers are a topic for another blog post. What’s more germane here is that inputs for fertility and pest control along with other conventional AND traditional agricultural practices disrupt the plant/soil nutrient cycle by undermining soil “gut” health. NPK’s, pesticides, monocropping, tillage, seed treatments, and bare fallows all are detrimental to healthy soil guts and especially to arbuscular mycorrhizal networks. When the soil gut is weakened, and AMF associations not formed, plants can no longer get nutrients via the pathways described above and become more reliant upon external inputs in both conventional/industrial systems and traditional/organic ones.

Pesticides (fungicides, insecticides, herbicides, etc) change the composition of the soil gut’s microflora, that is the microbial mix, typically for the worse making the soils more bacterial. Glyphosate, for example, is a herbicide that adversely impacts arbuscular mycorrhizal fungi [AMF] associations (Helander et al 2018). Thus there’s no AMF to mine nutrients from the soil or exchange nutrients between plants, Glyphosate also acts as a chelator (Mertens et al 2018) that binds a number of minerals including manganese. Therefore, the micro nutrients already in the soil are bound in the soil and also can’t be exchanged with the plants via microbes or AMF. More specifically, less manganese means reduced photosynthesis, since as described above manganese is required for hydrolysis. Less photosynthesis, in turn, means less carbon exudates and fewer microbes since the microbes feed off of these exudates. With fewer microbes and no AMF, there’s also less future necromass to become soil organic matter [SOM]. Thus less soil organic carbon [SOC], and less soil organic nitrogen [SON]. But that’s not all. With reduced nutrient uptake, plants are less nutritious. Whatever livestock eats the plants are also less nutritious.

Additionally, as explained above, less mineral uptake also means less production of plant defense compounds including phenolics, cyanogenic glycosides and lignin. This results in weaker plants more prone to infestation, and the need for even more chemicals including insecticides and fungicides to controls pests. So chemical inputs used to solve one problem create other pest problems requiring more chemical inputs as a solution. This is a never ending vicious circle that benefits the corporate profits and business models of agro-chemical companies rather than the bottom lines and bank accounts of farmers.

Organic pesticides also adversely impact the soil microbiome by altering the microbial mix. So it’s not as if organic or traditional practices are beyond reproach when it comes to weakening the soil’s gut, and thus the ability of plants to get nutrition without the need for so many external inputs. David Montgomery in his book, Dirt: The Erosion of Civilizations, details how modern agrochemicals were a replacement for other inputs like bird and bat guano. As noted in my prior blog post Soy !01, soybean meal was another input used for nitrogen fertilizer. Today, especially on large commercial certified organic farms, copious amounts of organic inputs are added to soil for fertility. These inputs include the just mentioned guano, a rich source of nitrogen, transported from places like Peru and the Philippines as well as certified composted manures, bone meal, and chicken feathers often sourced from confined animal operations.

The rational for adding all these organic inputs is not dissimilar from adding synthetic and mined inputs. It’s the belief that soil is like a bank account, and that when you remove plants from the system, it’s like withdrawing from that bank account, so more “money” in the form of nutrients needs to be added back into the bank account so that this account doesn’t get overdrawn. Or, in other words, removing plants removes nutrients and soils become depleted or degraded. This is a long held belief, and commonly held belief. It also is wrong. The soil doesn’t become depleted. Instead, the soil loses its capacity to function. So, the soil and plant system can no longer work to sufficiently mine and cycle nutrients all by itself.

Why does soil lose its capacity to function properly and be self sustaining in traditional and organic systems? One big reason is tillage. Tillage destroys AMF networks. Any associations between different root systems are shredded by the plow or rototiller. Tillage also destroys the soil structure reducing spaces for air and water. This leads to soil compaction. After a while, hard pans also form. This reduces the reach of root systems for water and nutrients. So plant roots without AMF associations have a much smaller reach to source nutrients in the soil. Plus tillage oxidizes soil and this limits nutrient uptake by either reducing or oxidizing minerals into ionization states of minerals that are less plant available.

Another reason soil loses its capacity to function to provide nutrients in both traditional and conventional systems are bare or chemical fallows. Without any plants, there aren’t any roots in the ground. So there are no exudates or metabolites being exuded into the soil. There also aren’t any roots for AMF to associate with. Thus there’s a lot less microbial life including microbes that will become necromass or new SOM. Plus there’s no carbon being sequestered by the microbial carbon pump. Whatever microbial life that exists will consume whatever SOM there is and respire carbon. That respired carbon is not being captured and recycled for plant photosynthesis. Thus that carbon is being oxidized and becoming atmospheric CO2. Now the rational for bare or chemical fallows is that other plants would compete for and deplete nutrients plus use water. But this rational is misguided. When carbon is respired, and there’s less microbial life, soils aren’t as well structured (Neal et al, 2020) , contain less carbon, and thus they allow for less water to infiltrate and be retained. Plus there’s no nutrient cycling via the processes described above including not mining new nutrients from the subsoil via AMF. Thus bare fallows often do the exact opposite of what they’re suppose to do.

This is why cover crops are so essential. Living roots must be kept in the ground as long as possible to exude carbon and metabolites and allow AMF associations to form. Diverse cover crops are even better. Why? With different roots systems at different depths exuding more exudates in exchange for different minerals, soil microbial biomass, including fungal biomass, is increased (Eisenhower et al 2017). Again, more microbial biomass results in more necromass, and necromass is the primary source for SOM containing both SOC and SON (Liang et al 2020). Thus more soil carbon and better soil structure also allows for more infiltration of water and oxygen providing a better habitat for other soil inhabitants like worms and dung beetles.

Conversely this is why monocrops are bad for soil health, especially when grown without cover crops and with bare fallows as well as with simple crop rotations (e.g. corn-soy-corn). There’s no diversity of roots or depths of roots. Many of these monocrops are also grown from treated seeds dressed with antifungals and antibacterials that weaken the soil gut plus also don’t form AMF associations. Thus in these cropping systems, crops can’t mine or exchange nutrients via AMF and also don’t obtain many nutrients via rhizophagy. The crops become entirely reliant upon inputs particularly NPK’s.

Now when cover crops are used. they can be terminated several ways without having to resort to herbicide (mainly glyphosate) burn downs. These other ways include winter kills and roller crimpers. But probably the best way, where possible that also provides another revenue stream for the farmer, is reintegrating ruminant livestock. With good grazing management, ruminants are mowers, solar powered composters, and manure distributors. Cellulose that goes through the rumen of cattle, sheep and goats gets broken down quickly. This is especially true in more arid and semi-arid environments. This manure can be quickly utilized by dung beetles and incorporated into the soil. This fast breakdown by dung beetles of manure actually reduces the methane and nitrous oxide emissions of the manure (Iwasa et al 2015). The key thing with dung beetles, to reestablish dung beetle populations, is to discontinue the use of dewormers like Ivermectin. Since dung beetles are keystone species, that is they determine the shape of other insect communities, reestablishing their populations also reduces the need for any chemical control of parasites that may infect livestock (Pecenka & Lundgren 2019).

Though manure doesn’t only cycle and recycle nutrients, it also provides more microbes to the soil ecosystem as does urine and saliva. So the livestock’s microbiomes are interconnected with the soil’s gut, the rhizosphere. More microbes from livestock manure, urine and saliva increase the amount of microbes in the soil (Esei et al 2013). More microbes means more future necromass. So livestock further increase the rate of SOM formation. Plus the microbes in a ruminant’s saliva also increase plant growth (Gullap et al 2011), which increases photosynthesis and thus further bolsters the soil-plant ecosystem by increasing the amount of exudates pumped into the soil by the microbial carbon pump (also known as the liquid carbon pathway). With good grazing management when cattle graze off the tops of grasses, the cattle keep grasses in a vegetative phase rather than allow grasses to proceed into a reproductive phase. What this does is redirect more carbon exudates down into the soil (Wilson et al 2018) . Gabe Brown further explains what ruminant grazing does to increase carbon sequestration in this video just below.

To summarize, soils are generally NOT deficient in nutrients as Gabe notes in the very first video above. Instead, due to both industrial AND organic practices,  the soil’s “gut” has been compromised by synthetic and organic inputs as wells farming practices like tillage and bare fallows. So what’s missing is a healthy soil gut with the right microbiology including AMF networks to obtain a bounty of minerals.  Inputs adversely affecting soil gut health include BOTH synthetic AND organic inputs that have been used for weeds, insects, and fertility. What regenerative Ag does differently than both traditional/organic and industrial/conventional Ag systems is reduce the need for so many inputs after the health of the soil’s gut has been restored. Though this restoration and regeneration may take some time given how long the plant/soil’s gut health has been abused.

As detailed above, many of these micro-nutrients also enhance the rate of photosynthesis. More photosynthesis, in turn, means more root exudates feeding more bacteria and fungi that dies and becomes necromass which, in turn, becomes soil organic matter [SOM] sequestering more deeply stored carbon.. So, in other words, healthy soil guts mean healthier more mineral dense and nutritious plants with increased rates of photosynthesis resulting in more exudates and thus higher rates of soil carbon sequestration that are well beyond what many old peer review papers have determined is possible. How much carbon can then be sequestered? We won’t know unless we optimized the soil-plant ecosystem, which can’t be done until we restore the health of the rhizosphere, the plant’s soil gut or microbiome.


Thomas, D. 2007. The Mineral Depletion of Foods Available to US as A Nation 1940–2002 – A Review of the 6th Edition of McCance and Widdowson.

Burnell, J.N. 1988. The biochemistry of manganese in plants. Pages 125-137 in Manganese in soils and plants. Graham et al.

Xu, S et al 2020. Species richness promotes ecosystem carbon storage: evidence from biodiversity-ecosystem functioning experiments

Liang, C. et al. 2019. Quantitative assessment of microbial necromass contribution to soil organic matter.

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

Hoffland, E. et al. 2004. The role of fungi in weathering

Martino, E. and Perotto, S. 2010. Mineral Transformations by Mycorrhizal Fungi

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

White, J.F. et al 2019 Review- Endophytic microbes and their potential applications in crop management

Olivier, H 2012 Redox potential Eh and pH as drivers of soil-plant-microorganism systems- A transdisciplinary overview pointing to integrative opportunities for agronomy

Steinfeld, H et al 2006 Livestock’s Long Shadow. p. 13.

Zhou, X et al 2019 Estimation of methane emissions from the U.S. ammonia fertilizer industry using a mobile sensing approach

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

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

Neal, A.L. et al 2020 Soil as an extended composite phenotype of the microbial metagenome

Eisenhauer, N et al. 2017. root biomass and exudates link plant diversity with soil bacterial and fungal biomass

Liang, C et al 2020 Microbial necromass on the rise: The growing focus on its role in soil organic matter development

Iwasa, M et al 2015 Effects of the Activity of Coprophagous Insects on Greenhouse Gas Emissions from Cattle Dung Pats and Changes in Amounts of Nitrogen, Carbon, and Energy

Pecenka, J.R. and Lundgren, J. G. 2019. Effects of herd management and the use of ivermectin on dung arthropod communities in 7 grasslands.

Edsei, L et al 2013. The effect of solid cattle manure on soil microbial activity and on plate count microorganisms in organic and conventional farming systems

Gullap, M. K. et al 2011. The effect of bovine saliva on growth attributes and forage quality of two contrasting cool season perennial grasses grown in three soils of different fertility

Wilson, C. H et al 2018 Grazing enhances below ground carbon allocation, microbial biomass, and soil carbon in a subtropical grassland

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