The Dirt That Refused To Die

For 15 years, Sébastien Fontaine has been trying to kill dirt. The biochemist, who runs a lab at the French National Institute for Agriculture, Food, and Environment, wanted to know how much carbon is released by soil — just dirt alone, completely devoid of life. His team sealed dirt into jars and blasted them with sterilizing gamma radiation. Then they waited for the carbon dioxide released by the soil — a sign of ongoing microbial respiration — to drop.

They waited, and waited, and waited some more: weeks, then months. Under a microscope, the irradiated soil showed no signs of life, but it continued to emit carbon dioxide. The soil wouldn’t stop breathing.

Fontaine’s lab repeated the experiments and produced the same results. Finally, convinced that they weren’t dealing with an artifact of the experimental setup, they set out to find the source of breath in dead soil.

Now, Fontaine and his colleagues have reported that their soil samples continued to consume oxygen and spew carbon dioxide for six years. In a 2025 paper in Science Advances , they proposed that a metabolic process that powers much of life is also possible outside living cells. Their experiments point to how it could work in dirt, absent the living proteins that would typically organize it. If they’re right, some biochemical reactions, such as those that release the energy of carbon-rich sugar molecules, may not be unique to living things. Such reactions — known as metabolism when performed by cells — could even predate life on Earth, Fontaine said.

The experiments show “what happens to biomolecules when they’re left to their own devices,” said Joseph Moran , an organic chemist at the University of Ottawa who was not involved with the research. They’re finding that the chemistry of life is not exclusive to life, he added. “It’s the chemistry of geology.”

The Living Dead

When he made this accidental discovery, Fontaine was trying to establish a baseline for carbon in lifeless soil. Using a sterile syringe, the researchers periodically sampled the air in a hermetically sealed jar containing soil and measured its carbon content using a mass spectrometer. After radiation wiped out the soil microbes, the carbon emission rate declined quickly but didn’t disappear. It remained stable for over 100 days.

When he shared the results with other researchers, they advised him to treat it as an experimental artifact — a source of error not worth ferreting out — and move on. But he couldn’t. He needed to understand whether a metabolic process only known to occur in biological cells — a precisely orchestrated sequence of chemical reactions, requiring several molecules and enzymes — was unfolding in sterile soil. To see what was happening, his team added a dash of enzymes extracted from yeast cultures. Immediately, the soil’s carbon emissions spiked. This, they speculated, was because the enzymes had ramped up a reaction that was already happening.

Convincing the scientific community, however, was an uphill battle. When Fontaine submitted the manuscript to journals for publication, some reviewers “were highly positive, and others were really suspicious, especially concerning the sterility of the soil,” he recalled. In 2013 the results were published in the journal Biogeosciences . Still, Fontaine could not rest. Bruised by the harsh reviews, he decided to definitively prove that his irradiated soil samples remained free of life. Over the following decade, his lab would, in fits and starts, chip away at their obsession.

They considered the possibility that the soil wasn’t really dead, and tried to kill it harder with more radiation, pressure, and heat. Still, the soil continued to emit carbon for months.

Through an electron microscope, Benoit Kéraval, then a graduate student in Fontaine’s lab, found cells in the irradiated soil. But staining showed no RNA or DNA molecules, indicating that the cells were definitely dead. When they experimentally added microbes to simulate contamination, the cells rapidly recolonized the soil microcosm and released much more carbon dioxide. So what they were observing in the sterilized sample likely wasn’t a result of inadequate antiseptic measures.

By 2018, when Clémentin Bouquet joined the lab, the team was confident in its findings and ready to dig into the underlying mechanisms.

Dirty Electrons

For six years, Bouquet and Kéraval studied two sets of sealed, irradiated soil samples — one of normal soil, and one that was supplemented with glucose. For 142 days, they took regular air samples and saw the daily rate of carbon dioxide emissions decline but not disappear, just as they had before. Then the samples sat in an incubator for over 1,000 days, as the researchers focused on their other experiments into how microbes process and store carbon in soil.

When they measured the samples again, at days 1,606 and 2,442, the emissions had slowed further, but the soil was still breathing. The glucose-augmented samples sho…