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“This is called shadow microscopy,” says Robb, the co-owner of Compostella Farm in southern Mississippi, bringing the microorganisms into focus. It’s a way of viewing living specimens under an oblique light, so they appear backlit and magnified, like a shadow box theater. Just prior to this, he diluted the sample in water and shook it, like a “hurricane or earthquake, any biblical catastrophe motion for that soil.” This broke apart the soil’s structure so he could see everything holding it together, like the dark brown curl of fungi.

Soil microorganisms busy decomposing, magnified by shadow microscopy.
(Photo credit: Timothy Robb)

“This is what a really good, healthy fungi strand looks like,” he says. Its uniform, segmented structure, thickness, and color are often good signs, though he adds that it’s not a hard and fast rule, just clues that this might be an architect of healthy soil.

As a vegetable farmer, Robb is mostly in the business of life. But his interest in building healthy soil led him down into this shadowy world of decay, where microbes shuffle carbon and nutrients in an endless cycle that sustains all life on Earth. This world appears chaotic at first glance, but Robb insists that it is elegant. An orderly marketplace, really. He’s been working to understand and strengthen this underground economy to replenish his soil.

Researchers have increasingly recognized how essential fungi are to sequestering carbon in the soil and some have come to appreciate the outsized role they play in supporting crop health, mitigating climate change, and even sheltering crops from disease. As fungi’s vast benefits come to light, more farmers are tapping into this vital network, learning how to work with beneficial fungi to encourage its growth in the soil, swapping tilling for microscopes.

This growing interest in fungal networks on farms quietly challenges the underpinnings of U.S. agriculture. The prevailing model involves taking care of the crop’s nutritional needs with chemicals, bumping up the nitrogen, phosphorus, and potassium in an effort to maximize the yield of the crop. Farm ecosystems are controlled with herbicides that kill weeds and fungicides that kill the fungi in the soil. Common practices, like tilling the soil, disturb the fungal networks and then deepen the dependence on chemical inputs.

“We’re reliant on these cheap inputs that are no longer cheap,” says soil ecologist Adam Cobb, whose research focuses on mycorrhizal fungi. He notes that farmers are then subject to the whims of a global market, which tends to skyrocket in price during geopolitical conflicts.

These chemical-based practices degrade the soil over time, stripping it of its ability to cycle carbon and nutrients without its supportive network of decomposers. But working to both protect and encourage fungi on farms is a way to reverse course. Robb sees his work of coaxing beneficial fungi back into the soil, which he largely learned from an online program called the Soil Food Web School, as both a challenge to mainstream agriculture and as a way forward to restore agricultural soils.

“It’s a criticism of how agriculture is currently conducted,” says Robb. “And it’s a methodology of introducing the microorganisms that are absent from the soil—the chain of organisms that release different minerals from rocks, clay, or silt particles in the soil.”

The Nutrient-for-Carbon Exchange

Mycorrhizal fungi, which encompass thousands of species, can form large, underground networks, connected by branching filaments called hyphae, threading through the soil in every direction. One type of this fungi, known as arbuscular mycorrhizal, attaches directly to the cell membranes of a plant’s root, facilitating a smooth delivery. Other microbes in the soil, like protozoa and nematodes, participate in this cycling, too, digesting fungi and bacteria to release their nutrients in a more available form to plants.

“The microbes engineered habitats around the plant roots that would be high in organic matter and make it more efficient for them to be able to obtain water and nutrients that they could then–in this carbon economy–essentially sell it to the plant,” says Kris Nichols, a leading researcher on soil microbiology. “It’s really an economic relationship.”

This relationship becomes especially interesting when business is booming—when the plants are delivering a lot of carbon into the soil that is used to build larger and larger fungal networks while distributing carbon across the soil profile. The carbon accumulates in the soil in many forms, from fungal cell walls to soil aggregates, or pellets of very alive soil that Nichols describes as “little microbial towns,” like economic hubs.

When these microbial communities develop, mycorrhizal fungi use their hard-earned carbon to build a protective coating around them, sheltering them from disturbances while more stably storing carbon. To the naked eye, these pellets look like crumbs in the soil.

The accumulation of carbon in the soil effectively slows the carbon cycle, causing carbon to linger in the ground for a longer period of time rather than quickly releasing into the atmosphere, where it takes the form of carbon dioxide, a greenhouse gas driving climate change. That’s the goal of what’s been popularly described as “climate-friendly farming,” or regenerative agriculture: keeping as much carbon in the soil for as long as possible, in part by keeping these underground networks undisturbed.

And increasingly, fungi have gained scientific recognition for their essential role in slowing this life-ending and -giving cycle. A recent study found that the world’s mycorrhizal fungi store the equivalent of a third of fossil-fuel emissions.

How Farmers Can Tap Into Fungal Networks

There’s no shortage of bacteria on the slide. It’s common for agricultural soils to be dominated by bacteria, which Robb is hoping to shift on his farm, building a more balanced ratio of fungi to bacteria in his soil. It’s not that bacteria should be scorned; they too are important decomposers that collaborate with fungi. But it’s hard to beat fungi at its game, rightfully a kingdom of its own. Fungi, more complex organisms, are more efficient at storing carbon across vast networks in the soil and more effective at delivering nutrients for certain plants.

The ratio of fungi to bacteria depends on the plants, explains Robb. He mostly grows salad greens across 3 acres of farmland. For his bok choy, mustards, and kale, he’s aiming for a 1-to-3 ratio of fungi to bacteria, but his lettuce requires a bit more fungi, closer to 1-to-1. He steeps the compost like a tea, extracting the microorganisms in water, and then runs it through his irrigation system.

“You’re introducing millions of fungi and bacteria species to the soil. And that’s as far as the management really needs to go, because once the plant gets established, then it’s controlling [the relationship with the microbes],” says Robb. He’s essentially just giving a plant options, a pool of microbes at its service.

In addition to applying compost tea, Robb supports fungal life by creating mulch from wood chips, which the fungi help decompose.

Robb shows me a pile of wood chips softening in the sun. It’s just 3 months old, but already threaded with fine white hairs of saprophytic fungi, resembling a cobweb. “When you can see it visually like this, what you’re actually seeing are like thousands of strands wrapped around each other,” says Robb, given that hypha are just several microns in size.

Before planting, he’ll also coat his seeds in a mycorrhizal treatment, a powder of spores. This inoculates this critical, network-building fungi in the soil. So as soon as the plant germinates, the fungi will be available to swap nutrients for carbon. Periodically, he’ll feed the fungi, adding liquid kelp, fish hydrolysate, and humic and fulvic acids to encourage its growth.

Every month or so, Robb peers at a soil sample under the microscope, assessing his progress. It has been about a year since he bought his first microscope and began surveying the local microbes. Most of his soil still isn’t where he’d like it to be, still dominated by bacteria, but it’s steadily improving. He essentially started from scratch on sandy soil that couldn’t hold onto much water or nutrients.

The most visible marker of improvement, at least to the naked eye, might be the crops themselves. A couple years ago, he observed “a precipitous decline in the quality” of his vegetables. They were yellowing and stunted. His lettuce was drooping. Disease was a regular occurrence. This prompted him to look into how to build soil that could hold onto more nutrients, which led him to fungi.

So far, his focus on improving decomposition has improved the health of his crops—now, rows of mostly bright green, leafing, upright crops emerge from dark brown, lush soil.

A Symbiotic Relationship That Predates Humans

“We had a very mineral land base, but we didn’t have soil,” said microbiologist Kris Nichols. As plants began washing up on shore, it’s thought that mycorrhizal fungi helped them siphon nutrients and water, providing what they needed to move to land, in a symbiotic relationship for the ages.

“We know that this relationship existed,” said Nichols. “We have the genetic markers and we have the fossilized plant roots to be able to see, structurally, that it has been this same type of relationship for hundreds of millions of years.”

It has taken a while for the role of fungi in supporting plants and soil health to gain mainstream scientific recognition, however. Elaine Ingham, a pioneer in the field of soil microbiology, recalls facing pushback in the early 1980s when she proposed researching the role of soil microorganisms for her dissertation at Colorado State University. She met with her professors to propose her field of inquiry, only to be sternly dismissed.

“They’d look me in the eye and say, ‘You don’t know what you’re talking about. Bacteria and fungi in the soil—they’re just there. They don’t do anything,’” she recalls. “All of them agreed that I was endangering my ability to get a job at the other end of my research project.”

But Ingham was undeterred. “I wanted to understand what bacteria and fungi in the soil were there for,” she says. “In all the literature I looked at, you couldn’t find anything about what these organisms in the soil actually do.” With the blessing of her advisor, she was allowed to pursue a dissertation project, along with her husband Russell Ingham, studying how soil fungi, bacteria, and nematodes interact with plants.

It was the start of her life’s work to help peel back the layers of the mysterious world of microbes within the soil. To date, the vast majority of the millions of fungi species on Earth remain unknown by scientists, but it’s now abundantly clear that many fungi play a critical role in soil health. Ingram, who grew up on a farm, now works with farmers to reintroduce soil fungi through the Soil Food Web School.

Robb came to learn how to work with fungi on his farm when he stumbled upon the school by chance in a footnote of a book. He attended the program without a background in science, but it didn’t take him long to feel comfortable behind a microscope. It was an “aha moment” when he realized his soil was depleted of fungi and other microbes—with this, he had the clarity of a diagnosis.

The Vast, Untapped Potential of Fungi

The roots of a cowpea plant, with fungi stained in blue, under a microscope.(Photo credit: Adam Cobb)

“We never leave our soil bare. It is always covered with straw, leaf mold, or wood chips,” says Leah Penniman, the co-founder of Soul Fire Farm in upstate New York. “We like to think of these wood chips as encouraging the fungi from the native forest around to come into our fields and partner with our orchards and with our crops.”

In 2006, when she started Soul Fire Farm, the soil was very degraded and the organic matter—which includes soil carbon—was only at 3 percent. But they’ve since increased it to 10 percent to 12 percent in some areas. “That has been through a partnership with fungi,” Penniman says. Slowly but surely, fungi have emerged from the forest, building carbon in the soil.

Robb also thinks of the forest on the outskirts of his fields. The trees have a relationship with mycorrhizal fungi and microbes that take care of all their needs, without any human intervention. “Those are nitrogen-rich plants, and nobody’s applying fertilizer,” he says.

He currently adds organic nitrogen to his farm, but hopes to add less and less, allowing the fungi and microbes to increasingly take over in tending to his crops.