At the end of the Permian period, about 252 million years ago, animals started dying at ferocious rates. In just 20,000 years 90 percent of all species on the planet had gone extinct. What triggered this die-off? Researchers have been trying to figure that out for decades.

Because the scale of the extinctions was so large, paleobiologists and geochemists started looking for an equally massive disaster as the root cause. Some proposed that an asteroid struck Earth, similar to what ended the reign of the dinosaurs. More recently, they have focused on volcanoes in what is now modern-day Siberia that were highly active at the time. They spewed out large amounts of carbon dioxide and methane, an event documented in the chemical signatures of rocks from Xiakou, China. Scientists think that the surge in these gases warmed the planet and made its oceans more acidic, which, together, ultimately snuffed out most life.

In those same rocks, though, Dan Rothman, a geochemist at the Massachusetts Institute of Technology, saw a discrepancy with the volcano story. The chemical signatures indicated that the concentrations of carbon dioxide and methane kept rising over time. If the gases were the result of volcanic eruptions, one would expect that their levels would rise and then fall back down again. To Rothman and his colleagues, the pattern looked more like a biological factor—not unlike the exponential growth of microbes.

In a study published in April in the Proceedings of the National Academy of Sciences USA, the group names a methane-producing single-celled organism, Methanosarcina, as one of the main culprits behind the Permian extinctions.

The new hypothesis does not disregard the influence of the volcanoes. Instead the M.I.T. researchers think that the vast quantities of nickel deposited by the eruptions allowed Methanosarcina to flourish. The microbe, which had acquired the ability to produce methane right around the time of the extinctions, is dependent on nickel to metabolize organic material into the gas. As ocean currents carried the nickel around the globe, the sudden influx allowed Methanosarcina numbers to skyrocket.

That release of large amounts of methane caused temperatures and ocean acidification to increase, and oxygen levels plummeted as O2 was used in the natural conversion of methane to carbon dioxide. Species began to die off. Then Methanosarcina dined on the decomposition and released more methane, triggering a positive feedback loop.

The findings suggest that microbial evolution has important consequences for the evolution of the environment as a whole, Rothman says: “Microbes run this world. We just live in it.”

Some scientists are skeptical that a single microbe played such a big role in the Permian extinctions. Pennsylvania State University geochemist Lee Kump says that Rothman and his colleagues have not proved for certain that this is what happened because they studied only one group of rocks from southern China. “If this phenomenon led to these extinctions, then you would expect to see this in rocks around the world,” he says. “It's something the researchers still need to look for.”