Farming as if symbiosis matters

It never hurts to rethink why we do things, or to reconsider what we think we are doing in the world. Our changing understanding of all disciplines demands it, if our actions and inquiries are to reflect our understanding of the Universe and all it contains. Dark matter and dark energy were not part of the understanding that my generation was schooled in, but no current thinking in physics or cosmology can be pertinent without considering these elements and forces today. In the same way, biology has been transformed from the study of “who eats who” in an evolutionary battle of the species, to something more akin to “who resides within whom,” and to what effect. One of my early personal revelations was that a cow was not a cow without its gut bacteria (“microbiome” was not a term in circulation at the time), because it could not digest grass without the fermentations provided by “outside/inside” helpers. Symbiosis made a cow a cow. In my young life, this was a fact that shaped a developing worldview, and led to the understanding that a farm is an ecosystem, as surely as a forest or a meadow. At the time, some ecologists and early organic farmers were the only ones thinking of farms in this light.

The Symbiotic World

Lynn Margulis revived a century-old hypotheses in 1967 when she published a paper proposing that modern eukaryotic cells were not the product of gradual linear evolution, but rather a process of “endosymbiotic” fusion between unrelated prokaryotic cells, including Proteobacteria that became mitochondria, and Cyanobacteria that became chloroplasts. Her paper was rejected more than a dozen times before she found a publisher, and it was met with a lot of eyerolling and cold water. Some of the tenets of her theory have not been verified (that flagella and cilia derived from the corkscrew motility of spirochetes, for example), but she was without doubt correct regarding mitochondria and plastids, as we now know that they contain their own DNA arranged in circular chromosomes, as is typical of all bacteria. DNA replication within these organelles is completely independent of the cell’s own DNA found in the nucleus. The power of the endosymbiotic theory of evolution is that it proves that adaptation does not necessarily follow linear traces of genetic inheritance forming independent branches in a tree of life, but rather, that the branches can graft together across genetic divides. And so, we see that on the cellular scale, we have a basic similarity to cows; a human cell is not a cell without its proteobacterial inhabitants, the mitochondria. The same is true for plants; they are not fully plants without their cyanobacterial plastids that capture light energy.

Endosymbiotic evolution is, in a fractal sense, a corollary to the symbiotic evolution that we are now accustomed to seeing all around us every day, at least if you garden or farm or have a naturalist’s eye on a walk in the woods. The lichens and the legumes are our textbook examples of (endo-?) symbiotic evolution. All the grazing animals are “themselves” because of their gut microbiomes, as are we and all the earth’s consumers. Our digestion, health, and mental well-being are completely dependent on the multitudes that inhabit us, with whom we share no genetic relation. The Human Genome Project tells us nothing about the microgenomes upon which we depend to be human. Plants are equally infused with “others” in the form of bacterial and fungal “endophytes” that weave their films and hyphae among the plant’s cells from root tips to flowers to seeds in a network that supports plant health and adaptation to the environment. Plant endophytes can secrete hormones and antibiotics that promote growth, resist pathogens, aid nutrient uptake and utilization, and synthesize chemical constituents that are often attributed to the plant itself. Seeds are infused with these endophytes, which generally promote germination, and help pioneer species (such as wild lettuce) establish symbiotic communities in their root zones that confer drought resistance and promote soil tilth through flocculation, the attraction of clay soil particles into aggregates. In an important sense, seed endophytes broaden the genetic resources that support seedling establishment and subsequent growth. Plants are not entire beings without their bacterial and fungal cohorts, much like cows without theirs.

Crimson clover, symbiotic partner to nitrogen-fixing bacteria, and to organic farmers.

Zooming out a bit more, we recognize that flowering plants without pollinators may not complete their life cycles. Seed bearing plants without birds and herbivores, may not have their seeds dispersed. Plants without predacious beetles and parasitoid wasps may be consumed by root maggots, aphids, and caterpillars. At this scale, we are in familiar and observable ecological territory, the zone where we can watch the action and appreciate the dynamics. This is biology in which we may have been schooled; familiar territory for farmers and gardeners and naturalists, but which we may forget is deeply symbiotic and represents the same degree of integration and nesting that we recognize in a cow or clover with their entrained bacteria and bodily microbiomes.

A pugnacious leaf-cutter bee.

The symbiotic territory that remains a mystery for most of us is below our feet. Soil is inscrutable as a whole. We can pull it apart in pieces of various sizes, or make a paste of it for chemical analysis. We can peel it back in thin layers, or trench it into cross sections. But we can’t see or smell or listen into it as a whole, as we might the ocean or a river. We can’t readily observe it functioning in three dimensions over time. Experimentalists can devise various means to observe certain parameters of soil metabolism, or to watch a cross section of activities behind a sheet of glass, but for most of us who work with soil to grow crops… we are in the dark about what we are doing with (or to) soil and its symbiotic communities. Most of us who work with soil are doing as we were educated, or learned from others, or just what seems to make sense from our perspective. Our perspective is part of the challenge, because most of us assume that soil should be soft in our hands, or even soft enough to plunge our hands into; we assume that plants need a soft medium to extend their roots without resistance, to fully attain the richness we have tilled into it. It is as if we have not noticed all the trees and grass and “weeds” growing tall and fulfilling their life cycles without any assistance or soil “preparation” at all.

Plants growing in unmanaged, undegraded landscapes are living in community with natural soil ecology and the myriad symbiotic relationships that underlie that ecology. The sustainability of such systems seems evident and unremarkable. The leaves and bodies complete their lives, fall, and return to earth. In another season they grow and unfurl in equal splendor to what passed before. In farming systems, where the “fat of the land” is harvested and sent from the land, it is less evident that the growth of crops (using irrigation, tillage, and fertility/pest/weed control inputs) is sustainable. If the cost of these inputs (intended to balance the export of food) or their availability become limiting, it isn’t clear that the viability of the farming operation will persist. We can measure this balance grossly as profitability, or as soil nutrient status, as organic matter content, as rates of soil erosion, or status of biodiversity above and within the soil. Soil quality itself is an indicator that captures many of these parameters. Aggregate size and stability say plenty. An increase in bulk density tells us that the soil contains less “space,” less porosity, fewer passageways for life’s activities, and channels for roots seeking deep water and fertility. This tells us that we have not performed as sustainably as a meadow would do on its own, powered by its own ecology that is balanced through symbiotic relationships.

“Farming like a meadow,” an aspiration for organic growers, is easier said than done. Meadows do not grow corn, tomatoes, or broccoli. Meadows do not directly feed people, because we are not grazers. We can eat what grazes there, but that will not alone sustain our varied diets. In my essay, ‘A Minimal Till’ (2023), I discuss the challenges of commercial scale crop farming without tillage and the limitations of some No Till strategies that employ tarping (“occultation”) and deep mulching with straw or compost. Without wishing to repeat entirely what was written before, I will just say that tarps (which I have used) have limitations of scale, and have unique downsides of their own: they are plastic, they may leach hormone-mimicking plasticizers, they isolate the soil and its community from air and light for months at a time, they drown large numbers of invertebrates in water pools, and some day they will be landfill material. Straw or hay mulch is full of weed seeds, and if it is an off-farm input, it carries hazards of herbicide contamination because hay and grain crops are frequently treated with clopyralid to control thistles and nightshade. This herbicide persists in crops treated with it, and even in the manure that follows digestion of these crops (an insidious problem). Mulching with compost deeply enough to smother weed competition overdoses the land with nitrogen and phosphorus. A recent Cornell study (results published in Growing For Market, September 2024) found that a 2” compost layer (not enough to smother weeds in my experience) provided 800# of nitrogen/acre per application, and 340# of phosphorus. That is more than 4 times as much N as even an extraordinary yield of a demanding crop can utilize. Over 4 years of these applications, more than 4000# of N/acre had been applied. After 4 years the phosphorous availability was measured to be 165#/acre (40# is considered a high level), with the excess over that amount being converted to unavailable forms of phosphate. This is an insane amount of wasted nutrient that could be much better used in smaller doses. The excess N and available P likely leached into the water table. This is not a sustainable use of compost.

An occultation tarp pulled back, showing perennial morning glory stems.

Same area after one pass of skim tillage. This removes tops of perennial weeds and tufted grasses to create a uniform planting surface.

Occulted soil surface on the right, after one skim till, on the left.

In ‘A Minimal Till’ I describe my experiments using a “skim tillage” technique that removes the crowns of closely mowed cover crops or weeds with less than 2” of tillage depth, creating a mulching layer of topsoil mixed with shredded plant material. This is inspired by the arid climate method of soil moisture conservation called “dust mulching,” which breaks the capillarity that brings water to the surface. I use a riding mower and a BCS tiller to do this, but recognize that a flail mower followed by a 1-2” deep power harrow would be the best equipment for this purpose. By doing this in the afternoon I avoid killing earthworms and beetles that avoid daylight and arid conditions by burrowing in during the dry part of the day. These two invertebrate groups are among the most critical for maintaining soil structure and reducing soil bulk density, as I will discuss further below. The intention of skim tillage is to remove plant competition, freeing the root zone and the light zone for the benefit of crop species, and to create a mulching layer of loose soil and organic matter that shelters the bulk soil and surface-dwelling invertebrates from sun and wind and pelting rain. Transplanting and direct sowing occurs in shallow furrows that push the mulching layers aside to reveal the undisturbed soil beneath. Surface cultivation for weed control works only the loose mulching layer around the crop plants and pathways, maintaining its surface shielding function during the growing season. Organic matter in this surface layer is consumed by worms and other decomposers when they arise at night for their hunting and feeding activities (most surface feeders are nocturnal). ‘A Minimal Till’ provides more detail about how we manage this system.

Area mulched by winter-killed cover crop, followed by mowing. Furrows, made with a wheel hoe, will receive amendments, be stirred with a stirrup blade, then transplanted so that roots grow into undisturbed soil.

Organic growers tend to see themselves as a part of the farm ecosystem, not apart from it. For better or worse, indeed we are. Our activities have more apparent impact than other members of the ecosystem, at least until an outbreak of disease or grasshoppers or root maggots cuts us down to size, and we realize our true lack of control. But we do act with intention, adding water and nutrients and crop rotations that push toward greater productivity, and thereby tilt food web activities to levels that would not be attained without us. We can observe this productivity boost in real time, and take pride in our ability “to farm,” unless we begin to notice imbalances with our likeness attached; algae in the pond, crusting soil that impedes water uptake, dense soil at season’s end, crops that don’t size up, watery vegetables lacking taste, aphid infestation… the list can be long for both our problems and our mistakes. We can approach these problems with balanced fertilization, watchful irrigation, cover cropping, judicious application of compost, planting flowers and hedges that feed and shelter beneficial insects, improving air circulation, monitoring pest levels, introducing beneficial microbes and predator insects, better choices in crop varieties and rotations; we have deep tool boxes. But we don’t have deep knowledge of what we cannot observe, and the biggest piece of that knowledge iceberg is underground.

When soil mulch is scraped aside on dry pathways, we can see that nightcrawlers are active there every night.

The Symbiotic Soil

Soil quality is dependent on the soil type (portions of sand, silt, and clay), soil composition (parent material, organic matter, nutrient content), moisture content, and biological activity, among other factors (slope, aspect, latitude, altitude, etc.). For arable soils, good soil quality is not just a matter of chemistry, texture, and moisture, it is largely dependent on structure. Structure is defined by the size and shape of soil aggregates, and the amount and size of pore spaces between the aggregates. Aggregates are composed of soil particles (sand, silt, and clay) that are bound together by organic “glues,” generally organic matter from decomposed plants, animals, and microbes, as well as exudates from roots, animals, fungi, microflora/fauna, and bacteria. Glomalin is the most important aggregate binder found in soil. This is a glycoprotein exudate of mycorrhizal fungi that reside in plant roots and the surrounding rhizosphere, where they convey phosphorus from mineral soil directly to plant roots in a plant-available form, in exchange for carbohydrates from the plant’s photosynthesis. This is among the most important and ancient symbiotic relationships in the soil community (and the history of terrestrial evolution). Glomalin itself comprises the largest portion of stored carbon in soils (up to 27%), even more than humic acid. Soil aggregates can be classified into several distinct forms that create different sizes and shapes of pores between them. The pore shapes have strong effects on the movement of water and air through the soil, as well as the penetration of plant roots and movement of soil organisms through the soil. Granular and blocky structure provide high permeability, platey and massive aggregates have low permeability. But the most important contributor to permeability and reduced bulk density is the biological activity of the soil food web—the living, moving, soil mixing behaviors of invertebrates, fungi, and plant roots.

Living soil; worms and other burrowers create porosity and soil structure by their movements and exudates.

The soil food web underlies whatever we do as growers. The details of lives in the underground have long been obscure. The rhizosphere, with its bacterial and fungal associations, has received a lot of attention and appreciation in the last 25 years, unveiling the majesty of plant/microbe interactions. When I started farming, no one discussed that plant roots exude their precious carbohydrates into the root zone (if this was even known), essentially feeding and promoting fungi that deliver phosphorus to the root in available form, and feeding bacteria that release nitrogen from humus for root uptake. Less has been said about the food web that underlies soil quality and structure, that creates space within the soil that allows water and air to circulate freely and roots to penetrate deeply. The Xerces Society for Invertebrate Conservation has published Farming with Soil Life, A Handbook for Supporting Soil Invertebrates and Soil Health on Farms (2021) to help growers appreciate and visualize the creatures that make up the soil food web. The bulk of the book describes 73 groups of organisms from the micro to the macro scale that comprise the soil food web from bottom to top; their size, diets, life cycles, behaviors, and ecological roles. This publication is the source for much of the information I will convey here, and I suggest it as a reference for anyone who works with soil.

As is the general rule in ecology, smaller beings are consumed by larger beings all along the food web. But it is interesting to note that within every scale of organisms (and within many related groups), there are predators, herbivores, scavengers, and decomposers; all the niches are filled at every level. The smallest microfauna, the protozoans, live in water films around soil particles where they eat bacteria, brown algae, and slime molds, releasing plant-useable nutrients. The slightly larger water-film mesofauna, rotifers, include predators of protozoans, grazers of bacteria, algae and fungi, and scavengers of all the broken bits. Tardigrades sharing the water-film realm are predators and omnivores of rotifers and all the smaller beings, as well as nematodes, that in turn eat everything smaller than themselves, as well as other nematodes and small insects. Nematodes can also be food for predatory fungi, that snare their prey in specialized hoops or nets of sticky hyphae. Nematodes are the most numerous animals on earth, and it has been proposed that if all the plants and features of the landscape were rendered transparent, the outlines of everything would be shown in nematodes (D.A. Cob, 1914). Potworms, which are true annelid worms (from 1-30mm), are unpigmented consumers of fungi, bacteria, organic matter, feces, minerals, and soil, just like their larger earthworm cousins. They mix soil with their diets leaving cast trails of fertility for plants in the top half inch of earth.

The mesofauna arthropods (small insects and crustaceans) are critical links in the soil food web, consuming nematodes, fungi, and one another, while becoming food for larger arthropods like beetles and ants. Almost half of this group are mites, which play specialized roles as dispersers of bacteria and fungi as they travel between the surface and deep subsoil layers. They play multiple ecological roles as predators of other mites, springtails, insect eggs and larvae, and nematodes, as well as decomposers, detrivores, and grazers of bacteria, algae, and fungi. Springtails themselves are predators of other springtails, rotifers, and nematodes, as well as grazers of bacteria and fungi. They have been found to prefer pathogenic fungal species in greenhouse environments. Two springtail groups are surface litter dwellers, and 2 groups are soil dwellers, demonstrating the diversity of ecological niches any one group can fill through adaptive radiation. The Proturans decompose the dead while burrowing 10” deep; the Diplurans establish protected boundaries around their predacious hunting grounds, eating everything smaller than themselves; the Bristletails scavenge dead insects and graze algae, fungi, and detritus; and the Thrips act like predators in one case, grazers in another, and disease vectoring pests for farmers in the worst case. All the while, these arthropods are food for arthropods larger than themselves, and they make significant contributions to soil organic matter as they die.

Worm middens of walnut leaves. Beneath every pile is a burrow. This is where leaves go.

On the scale of Macrofauna, the most important species for soil structure and quality are the almighty earthworms. As a group they represent the largest portion of faunal biomass, and their soil processing produces casts that are 50% higher in major nutrients than the surrounding soil, releasing minerals that are otherwise unavailable to plants. Along with beetles and ants, earthworms are major structural engineers within the soil, creating pore space and channels for water infiltration, gas exchange, and root penetration into the subsoil. Anecic worms (“emerging” worms), are comprised of two groups with distinct feeding and burrowing behavior. The familiar large nightcrawlers (Lumbricus) are pigmented and have vertical, unbranched burrows that reach to bedrock or eight feet (whichever comes first), and emerge to the surface at night to deposit their casts (poop), to gather fresh debris, and mate. They drag leaves and detritus to their holes and deep into the earth for feeding. I have found green kale leaves four inches deep while taking soil samples in winter. The entrance to their burrow is commonly stuffed and piled high with stems and leaf petioles from collected food stores, and once you learn to recognize these worm middens, they are every leafy place you walk. Each nightcrawler has its own permanent burrow, so each midden corresponds to an individual worm (so you can count them!). The second anecic type (Aporrectodea), also emerges from its permanent burrow to deposit casts on the surface, but it feeds mostly on partially decomposed organic matter found by burrowing complex, branching channels though the topsoil. Despite their shallower reach, Aporrectodea burrows can be more than three times as long as Lumbricus burrows. As structural engineers, their impact on porosity in the topsoil is extensive.

Nightcrawler (Lumbricus), with ground beetles, sheltering under a tarp during the day.

Endogeic worms are smaller and less pigmented than nightcrawlers, spending almost all their lives in the soil in essentially horizontal, tiered burrows. There are two ecological groups, one that skirts the surface looking for organic matter (emerging during rain to migrate to new ground) and dwelling in the top eight inches of soil, filling its burrows with casts as it feeds. Deep burrowing endogeic worms are unpigmented, and spend all their lives consuming soil (with bacteria and microfauna) and organic matter in the subsoil, filling their burrows with casts as they forage. Endogeic worms are critical bioturbators, mixing soil and organic matter, enriching the root zone with plant-available major and micro nutrients.

An endogeic worm, with an impression of its burrow. These worms can disappear into soil pores much smaller than their own diameters, which this one did moments after this photo.

Epigeic worms live at the surface in the litter layer and around plants, only burrowing to escape predators. These are very pigmented and active (as in “red wigglers”), and include those found in compost piles and manure pats in pastures. They are major fragmenters and decomposers, but leave their casts no deeper than half an inch from the surface. Asian jumping worms are an undesirable invasive species (Amynthas agrestis) of epigeic worms, currently spreading in the US. Their casts are devoid of nutrients (with the texture of coffee grounds), and because they outcompete other worm species, they can have serious negative impacts on soil fertility that can lead to native plant declines. This is one worm that is not a good symbiotic partner to growers.

Other non-arthropod macrofauna include the important decomposers and fragmenters, Woodlice (pillbugs and sowbugs), that have strong mouthparts and their own gut bacteria to break down the least nutritive kinds of detritus. Millipedes are primary decomposers and fragmenters of leaves with strong chewing ability (they don’t bite) that live in litter, but burrow deeply into soil where they lay and protect egg nests. They live up to eleven years, and degrade more than 10% of annual leaf fall each year. Centipedes, on the other hand, can deliver a serious bite to humans, using venomous stingers on their front legs that they employ as predators of earthworms and insects. Spiders, pseudoscorpions, and scorpions are also venomous predators that are important biocontrols of insect populations at the surface and deep in the soil. Harvestmen (daddy-longlegs) are not venomous (despite the legend), but are key predators, decomposers, and scavengers.

Insect macrofauna are hugely diverse and numerous. They include decomposers like Silverfish, Cockroaches, and Termites (major ecosystem engineers), Earwigs that eat aphids, plants, and detritus, mixing soil in the process, and Mole Crickets that are active burrowers. Burrower Bugs and Cicadas dig deeply among perennial roots to feed on sap. Flies (Diptera) are ubiquitous decomposers of plants and flesh, and food for other insects, birds, fish, amphibians, and mammals. Three quarters of all flies are soil dwelling as larvae, where they are key earth movers and food for many. Blowflies, Flesh flies, and House flies are predators, parasites, and decomposers. Long Legged flies and Robber flies are aggressive soil predators as larvae (consuming beetle larvae and grasshopper eggs), and swift flying predators as adults, eating everything from bees, to moths and butterflies. Bee flies are familiar to gardeners as pollinators, but eat soil insects as larvae. The familiar Flower flies (Syrphids) mimic the body patterns of stinging bees and are very important pollinators, but their larvae are often plant-dwelling predators of aphids, or soil dwelling detritus feeders.

Syrphid fly adults are important pollinators that mimic bee appearance. Their larvae are major aphid predators.

Soldier fly larvae are detritus fragmenters.

Long legged flies are pollinators and avid predators of mosquitos and other flies, aphids, thrips, spider mites, white flies, leafhoppers, small caterpillars, and more.

Beetles are major players in soil and farm ecosystems. Firefly beetle larvae eat snails and slugs, Soldier and Rove beetle larvae and adults are significant soil predators and biocontrols for root maggots and their eggs. Ground beetles are among the most important life-long on-farm predators, consuming snails and slugs (and their eggs), caterpillars, root worms, and root maggots, along with weed seeds, fungi, and carrion. They guard over eggs that they lay in soil, and their larvae are predacious soil dwellers and burrowers. Adults live for four years, but only produce one generation of offspring per year. They are a tillage sensitive species, and benefit from perennial tufted-grass “beetle banks” (reserves) that parallel crop fields. Dung beetles are fully symbiotic with grazers in range or pasture ecosystems, burying more than a ton of dung 24” deep per acre each year, and consuming more than their weight in dung every day. Hister beetles are predators of insects, especially fly maggots. They are symbiotic with both Dung beetles and Carrion beetles by reducing fly competition for each one’s food resources. They commonly carry hitchhiking mites that are also maggot predators. Carrion beetles and Burying beetles are the major carrion decomposers on the landscape, and are able to smell carrion from long distances. They are strong fliers and arrive at the scene of animal death quickly. They consume maggots to prevent competition, and frequently carry hitchhiking predatory mites that also eat maggots. Beetles are second only to earthworms in their impact on soil structure through their burrowing and active lives in the soil.

Carrion beetle with hitchhiking symbiotic predatory mites. These mites eat fly maggots and eggs that would compete with the beetles for animal flesh.

Ants, bees, and wasps have tremendous impacts on farm ecosystems, and significant impact on soil structure. Ants act as predators, aphid shepherds, seed dispersers, and soil movers, all of which have an impact on soil and farm ecology. Ants in the temperate zone can move up to 30 tons of soil per acre each year, creating porosity and mixing soil horizons. The Ground Nesting bees are critical pollinators of crops and native plants, and vigorous soil diggers, making burrows for nests that can be from centimeters to three feet deep, provisioned with pollen at the bottom to feed a single egg per burrow. I came across one of these burrows filled with bright yellow pollen last summer while using a garden fork to soften a bed for carrots. It was about four inches deep. My skim tillage didn’t disturb it, but my garden fork did. Bumble bee queens dig shallow burrows for overwintering during the fall. They emerge early in spring to feed on dandelions and other first-flowers, and commonly find a rodent hole to make their nest for summer, containing 25-400 workers and the queen. Untilled ground is essential for Bumbles to have nesting opportunities. Ground-Nesting Predatory wasps are both pollinators and important biocontrol predators on farms. Vespid and Sphecid wasps are solitary nesters that feed insects to their ground-dwelling larvae, which become soil insect predators themselves. Adults are highly animated nectar feeders that go mad for certain umbel species, like sea holly (Eryngium). The Parasitoid wasps (1-20mm) are without doubt the most significant biocontrol symbionts for farmers and gardeners, controlling populations of aphids, caterpillars, leaf miners, weevils, stored seed/grain pests, and soil dwelling insects. Some of these are wingless, and might be mistaken for large ants (like the Velvet Ants, which are really parasitoid wasps with wicked stings). They use modified stingers as ovipositors to inject their eggs into insects, where they hatch into larvae and consume their hosts before emerging as adult wasps. Endogenous viral elements and venom are injected along with the eggs to shut down the immune system of the host, protecting eggs from attack. The Polydnaviruses responsible for this effect have been endosymbiotic partners with wasps for over 100 million years, and are replicated along with wasp DNA. There is no true distinction between the wasp and its viral elements; the parasitoid wasp is not a parasitoid wasp without its virus.

A queen bumble bee, and a fuzzy red solitary bee (that I haven’t been able to identify).

The Limits of Resilience

There is resilience in biodiversity, and the deep biodiversity of the soil food web explains how and why we can farm the soil in complete ignorance of its elegant functionality. The undisturbed soil ecosystem is suffused with delicate networks of mycelium and passageways transporting air and water, sugars and communication chemicals, grazers and their predators, elemental nutrients, electric charge and bacteria, arthropods, and plant roots; from the surface to the bedrock. When tillage disrupts these networks, populations shift and the functional ecology reverts to a simplified version of its previous elegance. Fungi fragmentation disrupts root associations and nutrient transport, to be replaced by bacterial predominance in decomposition and rapid nutrient release to plants and denitrifying bacteria. The sudden oxygenation of the topsoil stimulates bacteria that consumes organic matter that previously cemented aggregates into peds, the units of soil texture, allowing them to dissolve into particles, thereby degrading soil structure. Ground-Nesting bees, wasps and beetles may have their nests destroyed, losing a generation or a year’s reproductive opportunity. Worm burrows are destroyed, and possibly the adult worms themselves, leaving behind their freed nutrients in a scramble of granulated soil that growers can sink their hands into. Plant roots disperse into the retexturized soil in all directions, taking in the nutrients flooding the rootzone in a relative flash. The crops grow quickly, supplied by the sudden surfeit of nitrogen from scrambled life and stimulated bacteria. The grower can look on proudly, his farming ability validated, his soft dark soil steaming with life cleaning up on death and disarray.

This works for some time, and for some soils longer than others. The passageways and mycelial networks are reestablished by the resurging populations of resilient species, old associations are reunited, young worms replace dead worms, and bees, wasps, and beetles redig their burrows or are replaced by in-migration. But over time tillage reduces worm population by 50-100%, with similar effects on beetles and others that live and nest in the tillage zone. The deeper and more frequent the tillage, the more profound the long-term effects are for the macrofauna and fungal networks that contribute to soil quality and structure. In my clay soil with a blocky aggregate structure, three years of tillage changed the post-tillage texture from granular to dust, despite compost applications. The season-end bulk density was high, the water permeability was low. The soil lacked structure. When wet, it was mush. When dry, it was a brick. This soil is unlike the soil I learned to farm with, far less forgiving in its response to tillage. I learned something new on this farm.

Recovery of Symbiosis

What I read and what I have seen suggests that it requires three or more years (perhaps a decade) for soil to regain its original activity, porosity, and structure after a period of regular tillage is ended. In the interim, it can test a grower’s belief “in the system,” because the granular texture tillage provided falls like a failed cake when you cease (at least, in our soil), leaving a massive texture to work with as we continued farming. Adding organic nutrients and compost at the surface helps somewhat with successful growing, but taprooting cover crops are the best route to the recovery of porosity, and cereals/grasses the best reaggregaters of soil particles. We weed with wheel hoes that slice plants off just below the crown, and hand weed by slicing just below the crown with a serrated sickle (aka “magic tool”), leaving roots and microbiomes in the soil, and leaving plant bodies in the walkways between beds. We add topdressings of nutritive mulch to the bed surface as food for nightcrawlers and detritus-feeding beetles. Not all mulches are equally favored by surface feeders. Some beetle and weevil grubs that feed on roots in the soil emerge as adults that favor leaves of the same species that they were raised on. Obviously, insects have taste preferences. Broadleaf species disappear from the surface faster than grass clippings or clumps. Grasses have very tough tissues, which is fine as a protective surface layer, but my emphasis is on the nutritive quality of the mulching material. For this purpose, nothing is better than leguminous hay or chopped clippings.

Red clover is a tap-rooted legume, excellent for increasing soil porosity and releasing soil phosphorus for the benefit of crops that follow.

Legumes, of course, are a rich source of nitrogen, something the soil community appreciates as much as our crops. As important though, legumes are very good at scavenging and releasing phosphate from insoluble sources in the soil. A study of phosphate cycling between cover crops and cash crops has shown that fava beans and clovers (especially red clover) are superior at timely delivery of their absorbed phosphorus to cash crops that follow them in rotation, as compared to cereal grains or grasses. The fibrous root systems of cereal/grass cover crops are very good at recovering available phosphate, but their tough fibers don’t release that phosphate for two years. Whereas, fava and red clover were found to not just absorb available phosphate, but to extract it from insoluble sources, and to release it in their first season of return to the soil, benefiting crops that immediately follow the cover crop. Other broadleaf species have similar rates of phosphate recycling, particularly phacelia and dandelion. Indeed, “weeds” in general are superior to cereal cover crops in their timely release of phosphate and other nutrients to following crops.

With this in mind, we’ve begun to grow red clover and phacelia together as “mulch crops” that are harvested with a bagging lawn mower and spread on production beds in midsummer after the final cultivation, before the canopy closes. The covering is not thick, not intended to smother weeds or bury the surface, but enough to feed earthworms, beetles, millipedes, sowbugs, mites, and fungi, and to provide them shelter. The clover/phacelia at mid-bloom becomes too massive to mow and bag as it stands, so I “comb it down” with a disc set straight which crimps or cuts some of it, and lays it all down with stems running parallel in one direction. After a few days, some of the biomass has dried into hay, and the living stems have turned their tips upward. In this condition I can mow (in the direction they have been laid down) and bag a mixture of dry and green material that is easy to handle and spread between maturing crops. The cover crop can be mowed again in a week or two as leaves regrow and the stems attempt to stand back up. After this, the red clover will regrow more stems from the crown that can provide another cutting going into fall. Fava beans can also be treated this way, but is more difficult to bag because of larger stem pieces. In each case, portions of the plant stems remain attached to the crown, lying parallel atop the soil as a protective cover.

Seed crops are often top-heavy as the crop matures, like this lettuce, and are prone to lodging (falling over) in wind or wet weather. Firm soil and deep roots resist lodging.

The root systems of weeds and crops tell the story of recovering soil structure. When tillage had done its worst, roots proliferated in the top four inches of soil where water and nutrients tended to accumulate, but flattened out at the tillage pan six inches deep. Top heavy crops would topple over in the wind as the soft soil and short roots failed to resist lodging. Three years after ending tillage, the root systems entirely changed their architecture. Now we find taproots extending more than a foot deep before their breaking point, with fewer feeder roots near the surface. The roots now follow burrows and channels created by soil life, rather than forming a bottle-brush of growth in all directions through a tilled soil profile. If we pull pigweed and sow thistle in August, we can feel the moisture from the subsoil on their root tips. We find lateral roots growing away from the drip irrigation zone toward the unwatered walkways where they proliferate into fine white feeder roots just below the surface soil mulch, likely following and finding nutrients. Apparently, they are following lateral worm burrows, regardless of the relative aridity of the path soil. When crops are pulled up by the roots in autumn, they are firmly rooted into soil with structure that pulls apart with aggregate granularity, rather than blocky clods. Top heavy seed-bearing plants seldom lodge now, despite our strong afternoon winds. In winter, nightcrawler middens dot the walkways and beds and clover leys, where yesterday I counted twenty in less than a square yard. Every dead zinnia stem I pulled dangled with endogeic worms about the rotting roots, while millipedes scurried into the dark peds, and tiny white diplurans waved their antennae as springtails sprang about.

Amaranth and sacred basil root systems from undisturbed soil show deep taproots that follow vertical pores and lateral feeder roots that likely follow horizontal worm burrows.

Skim tillage conserves the structure that the symbiotic soil community imparts on the underground world. If growers can adapt our cropping techniques to work within this structure rather than imposing our own through deep tillage, we might find a more sustainable balance, perhaps a truly symbiotic balance, between our work, and the work of worms.

—FHM 1/9/25