The Dirt That Breathes: Life Without Life

For 15 years, Sébastien Fontaine has been trying to kill dirt. Fontaine is a biochemist who runs a laboratory at the French National Institute for Agriculture, Food, and Environment. His goal was simple: to determine how much carbon is released by soil that contains absolutely no life. To do this, his team sealed dirt samples into glass jars and exposed them to intense gamma radiation. This process was designed to sterilize the soil, killing any living microbes inside.

After the radiation treatment, the scientists waited. They monitored the jars for carbon dioxide, a gas that living organisms release when they breathe. If the soil was truly dead, the release of this gas should have stopped quickly. Instead, it did not. The soil continued to emit carbon dioxide for weeks, then months, and then years. Under a microscope, the irradiated soil showed no signs of any living organisms. Yet, the soil would not stop "breathing."

Fontaine’s lab repeated the experiments many times to ensure the results were not errors. Finally, convinced that their setup was correct, they began to investigate the source of this breath in dead soil. In a 2025 paper published in the journal Science Advances, Fontaine and his colleagues reported that their soil samples continued to consume oxygen and release carbon dioxide for six years. They proposed that a metabolic process, which usually powers living cells, can also occur outside of living bodies. Their experiments suggest that the chemistry of life is not exclusive to life itself.

Joseph Moran, an organic chemist at the University of Ottawa who was not involved in the research, noted that these experiments show what happens to biological molecules when they are left alone. "It’s the chemistry of geology," he said. This suggests that some biochemical reactions, such as those that release energy from sugar, may not be unique to living things. Fontaine believes these reactions could even predate life on Earth.

Fontaine made this accidental discovery while trying to establish a baseline for carbon in lifeless soil. His team used a sterile syringe to sample the air in sealed jars containing soil. They measured the carbon content using a mass spectrometer. After radiation killed the microbes, the rate of carbon emission dropped quickly. However, it did not disappear. The emissions remained stable for over 100 days.

When Fontaine shared these results with other researchers, they advised him to ignore them. They suggested the results were an experimental error, or an "artifact," not worth investigating. But Fontaine refused to give up. He needed to understand whether a metabolic process was occurring in sterile soil. Metabolism is a precise sequence of chemical reactions that usually requires enzymes, which are biological catalysts.

To test this, his team added enzymes extracted from yeast to the soil. Immediately, the carbon emissions spiked. Fontaine speculated that the enzymes had speeded up a reaction that was already happening on its own. This was a crucial clue. It suggested that the soil contained the necessary components for the reaction, even without living cells.

Convincing the scientific community was difficult. When Fontaine submitted his findings to journals, reviewers were divided. Some were positive, while others were highly suspicious about the sterility of the soil. The results were finally published in the journal Biogeosciences in 2013. Despite the publication, Fontaine remained unsatisfied. He wanted to definitively prove that his soil samples were free of life.

Over the next decade, his lab worked to eliminate any possibility of contamination. They tried harder methods to kill the soil, including more radiation, higher pressure, and greater heat. The soil continued to emit carbon for months. At one point, a graduate student named Benoit Kéraval found cells in the irradiated soil under an electron microscope. However, staining tests showed no RNA or DNA in these cells, indicating they were definitely dead. When the team added live microbes to the soil, the cells rapidly recolonized the area and released much more carbon dioxide. This confirmed that the low-level emissions in the sterilized samples were not due to leftover living organisms.

By 2018, when Clémentin Bouquet joined the lab, the team was confident in their findings. They were ready to dig deeper into the underlying mechanisms of this phenomenon.

For six years, Bouquet and Kéraval studied two sets of sealed, irradiated soil samples. One set was normal soil, and the other was supplemented with glucose, a type of sugar. They took regular air samples for 142 days. The daily rate of carbon dioxide emissions declined but never disappeared. Then, the samples sat in an incubator for over 1,000 days. During this time, the researchers focused on other experiments.

When they measured the samples again at 1,606 and 2,442 days, the emissions had slowed further. However, the soil was still breathing. The samples with added glucose showed higher emission rates. This strengthened Fontaine’s suspicion that non-biological materials in the soil could induce reactions similar to the metabolic breakdown of sugar.

In living cells, sugar is broken down into smaller carbon molecules. This process feeds the Krebs cycle, a series of reactions that strip high-energy electrons from carbon-rich molecules. These electrons then pass through reactions that consume oxygen. Many scientists found it difficult to believe this process could happen outside a cell. Cells contain enzymes that keep everything organized and increase the chances that molecules will interact.

Fontaine devised a fuel cell to detect electrons moving through the soil as an electric current. His team added soil that had been irradiated almost five years earlier and closed the circuit. A current passed through the soil that was several times higher than in a control setup with saltwater. Fontaine stated that this demonstrated that sterile soil supports a flow of electrons. This flow is indicative of processes that resemble the oxygen-dependent metabolism of the Krebs cycle.

In a 2025 preprint, Fontaine and his colleagues reported observing four of the eight intermediate molecules known to be part of the Krebs cycle in six-month-old sterile soil samples. Many of these molecules formed after the irradiation. The authors suggested that clumps of earth can indeed catalyze these reactions without the presence of life.

Joshua Schimel, a soil ecologist at the University of California, Santa Barbara, was not surprised by Fontaine’s findings. He explained that glucose naturally forms some Krebs-cycle intermediates when it is oxidized. Many soils are rich in iron oxides and aluminum oxides, which can catalyze this conversion.

The idea that metals can catalyze biochemical reactions is central to a theory about the origins of life. Metals such as iron and zinc are at the core of many ancient enzymes found in all life forms. Some researchers, including Moran, believe these metals might have catalyzed these reactions before life emerged. Studies suggest that the chemical reactions that break down glucose derivatives might have existed before the enzymes and genes that enable them in living cells.

Moran argued that we should organize our thoughts about life differently. "We should put metabolism at the base of what life is doing, and then genes are a way of controlling that at a higher level," he said.

Markus Ralser, a biochemist at Charité University Hospital in Berlin, agreed that cell-free metabolic reactions could be more common than previously thought. "This fits a bit into my thinking about how metabolism started in evolution," he said. He argued that if these processes were very hard to achieve, the planet would not be full of life now. However, this idea is complicated by the low-oxygen conditions in which life arose.

Another explanation for the results is that enzymes released from irradiated cells might still be active. Even when degraded, enzyme backbones might be capable of catalyzing reactions. Sudha Rajamani, an astrobiologist in India, noted this possibility. Ralser also agreed, stating his gut feeling is that there are still many enzymes in Fontaine’s soil samples.

To prove that metals and minerals carry out these reactions spontaneously, researchers would need to eliminate all enzymes. This is very difficult because it would require heating the soil to temperatures that would damage its structure. However, Bouquet noted that enzyme activity diminishes exponentially after leaving cells. Fontaine added that no enzyme is known to last six years. While enzymes from living or recently dead cells contribute to carbon emissions in real-world soils, Fontaine believes it is very unlikely that they caused the long-term respiration observed in his experiments.

For Bouquet, this years-long obsession has highlighted a profound truth. "Even in a context as close and familiar to us as terrestrial soil, we are not always able to distinguish or recognize processes that indicate the presence or absence of living organisms," he said. Now a researcher at the Collège de France, he is looking for prebiotic origins of other biochemical cascades. "I find it particularly interesting to imagine the survival of processes that may predate life itself, right there under our feet."