Rick Haney, gangly and garrulous, paces in front of a congregation of government conservationists, working the room for laughs before he gets to the hard data. The U.S. Department of Agriculture soil scientist points to an aerial photograph of research plots outside his facility in Temple, Texas. “Our drones took this shot,” he says, then shakes his head. “Kidding. We don’t have any drones.”

Forty sets of shoulders jerk in amusement. Paranoia about the federal government is acute in Texas, and Haney’s audience—field educators from the USDA’s Natural Resources Conservation Service (NRCS), part of a corps of around six thousand that works directly with farmers nationwide—hail from around the state. They’re used to suspicious scowls from farmers, who are as skeptical of the feds as they are of the outsiders who dwell on the downsides of agriculture. For the most part, the people in this room are both: feds and outsiders.

But what if those downsides—unsustainable farming practices—are also bad for a farmer’s bottom line? It’s the question Haney loves to raise during training sessions like this one, which the NRCS (today’s iteration of the Dust Bowl–era Soil Conservation Service) convenes around the country as part of a soil health campaign launched in 2012. Haney is a star at these events because he brings the imprimatur of science to something many innovative farmers have already discovered: despite what the million-dollar marketing campaigns of agrichemical companies say, farmers can use less fertilizer without reducing yields, saving both money and landscapes.

“Our entire agriculture industry is based on chemical inputs, but soil is not a chemistry set,” Haney explains. “It’s a biological system. We’ve treated it like a chemistry set because the chemistry is easier to measure than the soil biology.”

In nature, of course, plants grow like mad without added synthetic fertilizer, thanks to a multimillion-year-old partnership with soil microorganisms. Plants pull carbon dioxide from the atmosphere through photosynthesis and create a carbon syrup. About 60 percent of this fuels the plant’s growth, with the remaining exuded through the roots to soil microorganisms, which trade mineral nutrients they’ve liberated from rocks, sand, silt, and clay—in other words, fertilizer—for their share of the carbon bounty. Haney insists that ag scientists are remiss if they don’t pay more attention to this natural partnership.

“I’ve had scientific colleagues tell me they raised 300 bushels of corn [per acre] with an application of fertilizer, and I ask how the control plots, the ones without the fertilizer, did,” Haney says. “They tell me 220 bushels of corn. How is that not the story? How is raising 220 bushels of corn without fertilizer not the story?” If the natural processes at work in even the tired soil of a test plot can produce 220 bushels of corn, he argues, the yields of farmers consciously building soil health can be much higher.

Less than 50 percent of the synthetic fertilizer that farmers apply to most crops is actually used by plants, with much of the rest running off into drainage ditches and streams and, later, concentrating with disastrous effects in lakes and oceans. Witness the oxygen-free dead zone in the Gulf of Mexico or tap water tainted by neurotoxin-producing algae in Ohio: both phenomena are tied to fertilizer runoff. Farmers often apply fertilizer based on advice from manufacturers and university extension agents who are faithful to the agrochemical mindset, using formulas that tie X amount of desired yield to Y pounds of fertilizer applied per acre. Or they apply fertilizer based on a standard test that gauges the amount of inorganic nitrogen, potassium, and phosphorus—the basic ingredients of chemical fertilizers, often referred to as NPK—in a soil sample. Or they apply what they put on the year before, or what their neighbor applied, and then maybe a little bit more, hoping for a jackpot combination of rain, sunshine, and a good market.

“Farmers are risk averse,” Haney says. “They’ve borrowed a half million dollars for a crop that could die tomorrow. The last thing they want to worry about is whether they put on enough fertilizer. They always put on too much, just to be safe.”

The standard soil test, developed some sixty years ago, focuses only on the chemical properties of soil. Haney began developing his test in the early 1990s to focus instead on the soil’s biology. Based on the vigor of the microscopic community in a farmer’s soil, his recommendations usually call for far less than what the farmer hears elsewhere. The yields of those who heed his advice often remain the same, or rise.

A single teaspoon of healthy soil holds billions of soil microorganisms, including bacteria, fungi, and other tiny life forms. These organisms crowd around the roots of plants, jostling and competing for carbon exudates that plants dole out according to their needs. Sometimes the plant trades a squirt for a mineral nutrient like zinc or potassium. Sometimes the plant offers treats in exchange for help defending against a pest or disease. The plants aren’t just responding to the various microscopic bidders, either: they can change the formula of their exudates and send chemical messages—kind of like lighting a flare—to attract specific players with specific services. For instance, scientists have discovered that when corn rootworm larvae attack some older varieties of corn (not the modern varieties bred for high yield), the plant sends out a chemical signal to beckon a nematode that feasts on this pest. “They’re sending out an SOS to this very specific organism,” says Ray Weil, an ecologist at the University of Maryland and an author of the classic textbook The Nature and Property of Soils. “‘Dinner is here—come and help yourself!’”

When we admire good soil’s dark chocolate-cake sponginess and sweet smell, we’re admiring the handiwork of trillions of soil microorganisms over time. They eat carbon and expire carbon dioxide, just as we do, but they also “fix” a percentage of that carbon in the soil. Barring disturbance, it stays there for a very long time. Some is used to make a carbon-based glue with which the microorganisms engineer soil into tiny clusters to protect themselves and control the flow of air and water in their habitat. Thus, good soil is more like a coral reef than a rock, with about 50 percent of its volume comprising these open pockets.

Photosynthesis is the only process that safely and inexpensively removes carbon dioxide from the atmosphere, allowing carbon that is a problem in the skies to become a boon for the land. Based on this principle, one hundred governments and nonprofits launched the 4/1000 Initiative at the recent Paris climate talks, calling for an increase of carbon in the world’s soils by 0.4 percent per year. This relatively small boost will not only radically improve soil fertility but also, the coalition claims, halt the annual rise of atmospheric carbon dioxide.As a high school student in Oklahoma, Rick Haney worked for wheat and cattle farmers and dreamed about getting into farming himself. But then, as now, land was expensive, so he shelved that particular fantasy. When he graduated, his classmates voted him most likely to be either dead or in a rock band in ten years. Instead, he drifted in and out of science classes at Southwestern Oklahoma State University.Over the years, Haney continued to work alongside his farmer friends, sometimes pulling fifteen-hour days. “I watched these guys take out big loans and struggle every year,” Haney says. “Every time their plants or animals died, it was money down a black hole. My uncle encouraged me to get an advanced degree to help guys like that.”

Studying at Texas A&M for a masters and then a PhD—which he wouldn’t receive until he was forty-two years old—Haney began questioning the wisdom of the standard soil test, in use since the mid-1900s, when synthetic fertilizers were embraced by farmers who saw them as a quick path to productivity. The standard test determines how much nitrogen, potassium, and phosphorus a soil sample contains. But that made no sense to Haney. “It’s not about single molecules,” he says. “Soil health is all about complex systems.”

The test Haney ultimately developed begins with drying a soil sample to suspend the microorganisms’ activity. When the sample is rewetted, the microorganisms roar back into business, exhaling a burst of carbon dioxide. Haney measures that burst, which demonstrates the health of the farmer’s resident microbiotic community—its vigor is the most important indicator of soil fertility. Then he uses more water and weak acids, akin to those in plant exudates, to extract the nitrogen in the sample. The standard soil test measures only inorganic nitrogen, the kind that’s found in chemical fertilizers and that plants can use immediately. It ignores organic nitrogen, which that hard-working community of microorganisms can transform into a plant-available form. The Haney Test is more time consuming and costly than the standard test, but it reveals to farmers how much total nitrogen is already in the soil and helps them slash expensive chemical fertilizers.

Three years ago, Haney presented his work at an NRCS meeting. After he took his seat, one of those field educators barreled across the room and flung out his arms, shouting, “Where have you been all my life?” Thanks to that felicitous meeting, Haney’s lab in Temple now tests some five thousand soil samples per year: ten big commercial labs and a few international labs use it as well. Despite some friction with the ag schools, use of the Haney Test—which is now promoted nationwide by thousands of USDA conservation field educators—is surging. It hasn’t replaced the standard test, but it’s often employed alongside the standard test by farmers who want to help their land become both more productive and more resilient.

The nation’s ag schools, which rely on agribusiness for much of their funding, have found Haney’s test underwhelming. And even if they do accept its basic premise, says Will Brinton—founder of the Woods End soil lab in Mount Vernon, Maine, and the developer of an alternative test, called Solvita, that measures soil microbial respiration—soil analysis that focuses on biology presents a retooling challenge for labs invested in chemistry-intensive technology. “They have a lot to lose if the farmers in their region adopt another approach,” Brinton says. “Like any industry, they’re set up in a certain way and don’t want to change.”

Among the commodity farmers who have taken Haney’s recommendations to heart, and to the bank, is Dave Brandt, of Carroll, Ohio. Since 2004, when he began using the Haney Test, Brandt has been able to cut fertilizer use on 1,400 acres and eliminate it entirely on 480, with an annual savings of $32,000 and no decrease in yields. In fact, his yields are consistently higher than his county’s average: last year, he raised 10 to 20 bushels more corn per acre, 14 bushels more soybeans, and 30 bushels more wheat.

At meetings with farmers around the country, the NRCS soil-health team illustrates the vibrant life of soil microorganisms and their partnerships with plants. They want farmers to understand why—in light of new scientific understandings of soil ecology—many farming practices they learned in ag school, and which are encouraged by the big ag companies, actually damage those microorganisms’ hidden habitat.

Consider the image of a farmer pulling a heavy machine across a field, turning jumbled green into freshly turned brown—it may be iconic, but it is an exceptionally unnatural process. Nothing in nature churns up soil to such a depth and over such vast areas. Tilling disrupts communities of microorganisms and shatters the soil’s coral-reef structure. The soil is briefly fluffed up, but as soon as water falls on the land soil particles settle tightly against each other, leaving little room for air and water. Tilling also dries the soil and allows the carbon fixed there to combine with oxygen and join the load of carbon dioxide already warming our skies.

“Look at that soil!” says David Lamm, the NRCS’s national soil-health team leader, flashing a slide to the Temple audience of a recently tilled landscape—acres and acres without vegetation. “It’s naked, hungry, thirsty, and running a fever.”

Lamm and his team preach no-till agriculture, in which farmers cut a tiny slit in the soil instead of creating a furrow, often planting their seeds in the residue of crops harvested in an earlier season. They promote cover crops, which both fight weeds and protect the soil from erosion and extreme weather when farmers are not growing a market crop, and they highlight best practices from progressive farmers around the country who “terminate” these cover crops with mowers or grazing cattle instead of herbicide. Cover crops get more roots in the ground and thus more exudates to feed microorganisms. That means more carbon in the ground: a recent report by the Natural Resources Defense Council found that planting cover crops (one of the tools promoted by the 4/1000 Initiative) on half the corn and soybean acres in the top ten agricultural states could sequester more than 19 million metric tons of carbon annually, the equivalent of taking more than 4 million cars off the road. Those teeming microorganisms will, in turn, deliver to market crops a steady stream of nitrogen, potassium, phosphorus, and other sustenance.

Ray Weil, the University of Maryland ecologist, believes that farmers will someday fertilize their fields using nothing but cover-crop combinations, carefully selected for specific market crops and growing conditions. Haney’s already on it. He recently built a new piece of equipment he calls the Frankenbreather, which measures the activity of a soil sample’s microorganisms on an hourly basis. He wets the samples with weak acids from different plants commonly used as cover crops and compares how the vigor of the microorganisms changes depending on which acid he uses. Once he’s got the test up and running, he hopes to give each farmer a recipe for the cover-crop combination that will best feed his or her particular constellation of soil microorganisms. Thus fortified, the underground workforce may provide to plants so many nutrients that the farmer won’t need any chemical fertilizers at all.

Ohio farmer Dave Brandt adopted both no-till agriculture and cover cropping on his family farm in the 1970s. Over the years, he has demonstrated that certain cover crops change the mineral balance in his soil: for instance, sunflowers concentrate zinc. At the soil-health training in Texas, I met a younger farmer who is following in Brandt’s footsteps.

Twenty years ago, Jonathan Cobb, now thirty-eight, left the 2,500-acre farm that his sharecropping grandfather started in Rogers, Texas, in 1905, happily swapping a life in agriculture for a marketing career in Fort Worth. He had sweet recollections of his mother bringing dinner to the fields and the family ending its workday against the setting sun. But his life was now in the city.

Then, in 2007, Cobb helped out with a harvest. He noticed how his parents were struggling, and he and his wife, Kaylyn, an accountant, decided to return to the farm. But Cobb hated what farming had become. He hated the monotony of tilling, fertilizing, and spraying row crops. His family was using more chemicals, along with expensive GMO seeds, and getting the same yields it had in the 1980s. He hated how the landscape itself had changed. The farm ponds, which had been filled with plants and insects and fish when Cobb was growing up, were now lifeless. After four years, Cobb told his parents that he and Kaylyn were leaving. It was the hardest conversation he had ever had.

Shortly thereafter, Cobb was searching Monster.com for jobs when his father asked him to attend an NRCS meeting where the Haney Test would be discussed. Cobb had been to dozens of meetings that looked just like this one: his father used to grow test plots for Monsanto, and sessions with company reps were part of the deal. He was sure this meeting would be just as useless and irritating as all the others, except with government conservationists. And government conservationists, he thought, were idiots.

But as the soil-health team ran through its spiel, Cobb started to see his land and farming in an entirely different way. It was dismaying at first. “I had made up my mind to leave [the farm], and I didn’t want to hear any of this,” Cobb told me as I sat with Kaylyn and his sister Jennifer on their parents’ screened porch, festooned with tiny white lights. “I couldn’t get it out of my mind, though. At the end of the day it made so much sense. I talked to Kaylyn later, and we thought we might be able to stay and make this work and keep the farm going.”

Jonathan, Kaylyn, and Jennifer began a crash course in soil health, studying everything the NRCS sent their way, consulting with Dave Brandt and other pioneers. They began changing their practices: no tilling, less fertilizer, lots of cover crops, the reintroduction of livestock. The land responded in amazing ways, with greater productivity and natural diversity. The neighbors responded in annoyingly predictable ways. Farmers take a lot of pride in keeping their land tidy, with neat brown rows of bare soil between crops and not a weed in sight. Cobb’s family owned only 250 acres of the 1,200 they now farmed, and the rented acres were highly coveted. After one landowner heard complaints that his fields were looking trashy, he decided to find new tenants for those acres.

That was fine with the Cobbs, as they had decided to work less land with more concentrated management. They now farm 450 acres and are moving away from row crops like cotton and wheat to grow food for their own cattle, sheep, and pork, which they sell to consumers eager for pasture-raised meat. The farm looks beautiful, if different. And there is growing interest in what they are doing: the landlord who previously evicted them has asked them to return and relaunch a soil-health regimen on his land.

Rick Haney doesn’t crow over this transformation his work helped drive. He’s so full of admiration and empathy for farmers that he doesn’t want to take credit for their initiative. “There are farmers all over the place who have figured out how to grow crops by working with nature,” he insists. “And nature has always had the science right.”