The Woman Who Knew What Dirt Was
"After four hundred million years of farming…"
It was during the Devonian Era, roughly 400 million years ago, that plants evolved the ability to produce the hard, lignin-rich tissues that form the trunks of trees. And so in the Devonian Era, plants invented trees. Trees then invented coal. They got buried underground and led to, you know, coal deposits for the first time. And that coal, that carbon removal, pulled huge amounts of carbon out of the atmosphere and lowered global temperatures. So that’s how we think of this (biochar)—it’s a million-year-old sort of geological technology for regulating the CO2 in the atmosphere.
—Alan Ransil, CEO, Devonian Systems
We live in a civilization that has mastered the impressive trick of feeding eight billion people while systematically destroying the very thing that makes that possible. We have separated the farmer from the soil, the soil from its biology, and the biology from the planet’s future, and then called this progress. We have tenure committees, Nobel Prizes and quarterly earnings reports to prove it.
The US, like most industrialized countries, has spent the past 90 years cultivating an addiction to fertilizer at the expense of soil, but now that the War in the Epstein Strait has cut off nearly half of the world’s urea and a third of ammonia, a large fraction of the world’s fertilizer is stuck at the Strait. Urea prices have increased by >50% for the spring planting season in the Northern Hemisphere. The price shock and shortage of fertilizer could reduce maize and other major grain planting and, later, harvests in the US. If you are wondering why the prices at the butcher’s counter have doubled, maize is the main feedstock for US beef, poultry, and dairy.
We can’t say we weren’t warned. Elaine Ruth Ingham, née Stowe, was born in St. Paul on June 26, 1952. Her father was chairman of the veterinary science department at the University of Minnesota. She was introduced to microscopes at age six, spending her childhood peering into a world invisible to everyone around her. She took an M.S. in microbiology from Texas A&M, and a Ph.D. from Colorado State.
Mr. Haber and Mr. Bosch
What Ingham was mapping, with growing obsession and increasingly sophisticated instrumentation, was what she called the soil food web. The soil food web is the complex community of bacteria, fungi, protozoa, nematodes, and microarthropods that cycle nutrients, protect plants, and build soil structure. This community — the invisible ecosystem beneath our feet — had been quietly running the planet’s food and waste management department for approximately four hundred million years before Mr. Haber got with Mr. Bosch to make artificial nitrogen for weapons and accidentally discovered fertilizer. The invention of the Haber-Bosch process allowed us to make ammonia (NH3) from air faster and cheaper than microbes do, with consequences that are still revealing themselves in the dead zones of the Gulf of America.
Haber-Bosch did for soil microbes what D.O.G.E. did for government jobs and what A.I. may do for most desk jobs. It was the Great Unemployer. It was also ethnic cleansing on an unimaginable scale as diverse soil microbes, many never typed or cataloged, vanished forever. The Green Revolution promised abundance but left sterile soils and a chemically addicted food supply.
The soil food web consists of fungi and bacteria, which are preyed upon by protozoa, nematodes, microarthropods, and other larger organisms, with literally countless species of each. The population and ratio of these organisms is not arbitrary. Soil with a significant weed problem contains a high ratio of bacteria. Grassland areas harbor a higher number of fungi under the surface. The soil in a healthy orchard contains ten times more fungi than bacteria, and the fungal ratio in conifer forests is higher still. The plants, it turns out, are not passive recipients of soil chemistry. They are conductors of an orchestra they have been tuning for eons. In 1913, Haber and Bosch walked into the concert hall and unplugged the instruments.
Microscope Nerds
Ingham spent decades at Oregon State University conducting the painstaking work of actually counting things — organisms per gram of soil, species composition, functional relationships between layers of the food web. With a restored soil food web in place, plants can control nutrient cycling in their root zones, accessing minerals stored in organic matter and parent material, and maintaining a constant flow of nutrients they can control. The implications of this, if taken seriously, would render the entire synthetic fertilizer industry roughly as necessary as a screen door on a submarine.
In 1996, Ingham founded Soil Foodweb Inc., which works with soil testing laboratories to assess soil biology. She also became the author of the USDA’s Soil Biology Primer — a fact worth savoring. The USDA, that reliable weathervane of agribusiness interest, published a document authored by a woman who believed the answer to America’s soil crisis was not a new product from Monsanto or Cargill but the resurgence of a living system. The government printed it. Then largely ignored it. Business as usual on the Potomac.
But Ingham kept working. She developed compost teas and methods for inoculating degraded soils with biology from healthy ones. Her approach has been used to successfully restore the ecological functions of soils on six continents. Antarctica presumably had enough going on. Give that a little more time.
I’m delighted to say I actually taught her something she didn’t know. When I invited her to instruct a segment of our carbon farming course in 2009 at The Farm Ecovillage Training Center, we toured my gardens. She asked why I had planted comfrey at intervals in every raised bed.
“Feeding the microbes,” I said.
I explained how comfrey’s deep taproot extended well below the fine topsoil and the hard clay subsoil, penetrating cracks in the limestone ten or more feet down. Comfrey’s roots are thick, black on the outside and white/slimy inside, allowing them to go deep, bring up nutrients—minerals—and distribute them to the plant’s fibrous laterals spread widely near the surface. They feed the soil food web by dynamically accumulating potassium, phosphorus, and nitrogen.
Some people consider comfrey an invasive plant, and if mismanaged, it can be. The roots make it hard to eradicate once established. But as my late friend Adam Turtle remarked, “If it were dollar bills coming out of the ground, would you call it invasive?”
Showdown in the Laboratory
In the early 1990s, a European genetic engineering company was preparing to field test and then commercialize a genetically engineered soil bacterium called Klebsiella planticola. In the lab, it had never outgrown its petri plates and so had been declared safe for the environment. The hybrid had been engineered to convert plant waste into ethanol — a charming ambition that could have given us renewable fuel and new libations. But there is no free Happy Hour.
In the Oregon State tests, the plants in the trays all wilted and died. They’d O.D.’d on the alcohol. Ingham and a graduate student discovered that the engineered bacterium produces far more alcohol per gram of soil than is required to kill any terrestrial plant. They also learned that the parent bacterium is found in the root systems of all plants where it has been researched—corn, wheat, barley, trees and shrubs. If the engineered bacterium offspring outcompeted its native parents, it could lay waste to all terrestrial plants. A field trial of a self-replicating bacterium—unable to be recaptured once in the wild—could result in the death of green plants at a planet-scale. It would be a reverse Devonian Era, and then some.
After Ingham’s exposé, the gene-altered Klebsiella planticola was never commercialized. No open field trials were allowed.
Witchburning the Microbiologists
In the interest of what used to be called journalistic integrity and is now, somewhat defensively, called “responsible reporting,” it must be acknowledged that the picture is more complicated. Critics mounted sustained challenges to her claims before the New Zealand Royal Commission on Genetic Engineering, and the scientific debate over the precise magnitude of the risk was never fully resolved in a peer-reviewed forum. Nonetheless, it adversely affected Ingham’s employment and academic career.
The irony is exquisite. A scientist whose career was devoted to demonstrating that life in soil is far more complex, interconnected, and consequential than our regulatory frameworks assume, found her most dramatic warning undermined by those same complexities. Granted, she overstated some claims. She understated nothing about the inadequacies of her testing. It is clear that current testing procedures required by US regulatory agencies are completely inadequate in assessing the potential risks involved with genetically engineered organisms. The regulator’s blind spot that she identified remains essentially unchanged. We still test novel organisms the way we test chemicals, as though living things were inert — as though, once released, they would politely stay where we put them.
Healthy soil sequesters carbon, reduces the impacts of droughts, improves water quality, and makes food more nutritious. This is not a fringe theory. It is what soil does when it is alive. It is what soil stopped doing when we killed it with salt-based fertilizers and soil-sterilizing pesticides and the compaction of heavy machinery, and called the resulting yields a Green Revolution. We addicted eight billion people to chemicals, and we ran a third of those chemicals from the mines and factories to farms and garden stores around the world through a narrow Strait between Oman and Iran.
The vision Ingham offered — and it is a genuinely beautiful one — is of a planet in which the soil food web is restored not by government mandate or by some new technological disruption, but by people with microscopes and compost piles and an understanding of what they’re actually growing. Most soils can be regenerated within the first growing season using her methods. Much of the biology is not gone. It is waiting. It is patient in the way that bacteria are patient, which is to say, extraordinarily, indifferently, cosmically patient. We are the impatient ones.
Don’t Worry, Make Soil
The UN now warns that intensive farming, fertilizer overuse, and erosion have degraded soils, cutting yields and threatening food security. Elaine Ingham spent her last years teaching, writing, and corresponding with farmers on six continents who were watching their soils come back to life under the microscope. In October 2025, the Soil Foodweb School announced her retirement — and then, just four months later, she was gone.
She leaves behind a framework for understanding the living world that is, in its essentials, older than agriculture — but which we needed her to rediscover. The dirt we have been abusing is not inert matter—clusters of physical elements—but a civilization of its own, older than ours by several hundred million years, and rather more competent at managing a planet.
The soil is ready when we are. It always has been. If you garden, you can dispense with chemical fertilizer entirely. Compost your food scraps. Add biochar to speed the process and advance the climate into the Gretacene. If you can’t find biochar in the garden store, make it— it’s easy. Get that good black compost into the root zone. Weed. Water. Harvest. Repeat.
I will be giving a two-hour master class via Zoom on Saturday, May 9. Please join us. If the class is oversubscribed (as often happens), don’t worry! I will be posting a synopsis on my YouTube channel later.
Credit: animation by author using Dzine after Coyne, M.S. (1996), A Cartoon History of Soil Microbiology. 25: 30-36. https://doi.org/10.2134/jnrlse.1996.0030. Music by Bob Marley.
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We have a complete solution. We can restore whales to the ocean and bison to the plains. We can recover all the tremendous old-growth forests. We possess the knowledge and tools to rebuild savannah and wetland ecosystems. Coral reefs rebuilt with biorock build beaches faster than the seas are rising. It is not too late. All of these great works of nature are recoverable. We can have a human population sized to harmonize rather than destabilize. We can have an atmosphere that heats and cools just the right amount, is easy on our lungs and sweet to our nostrils with the scent of ten thousand flowers. All of that beckons. All of that is within reach.
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