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Fungi Are Helping Farmers Unlock the Secrets of Soil Carbon

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Timothy Robb peers into a microscope to reveal the underground realm of the living and dying within a fistful of soil. On the glass slide, he sees clumps of golden-brown minerals and organic matter particles, like pebbled splotches of ink. Nearly everything else in the landscape is a microbe, a motley crew of roving shapes, preparing to eat or be eaten. Hairy orbs of protozoa glide around in search of snacks in the flecks of bacteria scattered all around. A nematode, a microscopic worm, thrashes through the scene in a hurry. A tubular strand of fungi stands still, perhaps absorbing the dust of dead plants.

“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.

“It’s a criticism of how agriculture is currently conducted, and it’s a methodology of introducing the microorganisms that are absent from the soil.”

“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

Fungi are effectively merchants of carbon. In the soil, they give plants the water and nutrients they need, while the plants provide fungi with carbohydrates (i.e., carbon) from photosynthesis. Fungi can act like a second set of roots, extending the plant’s ability to draw in water and nutrients.

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.

Fungi threading through the soil of Compostella Farm in Mississippi. (Photo credit: Grey Moran)

Fungi threading through the soil of Compostella Farm in Mississippi. (Photo credit: Grey Moran)

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.

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