Ancient whodunit may be solved: The microbes did it!

Methane-producing microbes may be responsible for the largest mass extinction in Earth’s history

David L. Chandler, MIT News

Click here for a compilation of media coverage

Evidence left at the crime scene is abundant and global: Fossil remains show that sometime around 252 million years ago, about 90 percent of all species on Earth were suddenly wiped out — by far the largest of this planet’s five known mass extinctions. But pinpointing the culprit has been difficult, and controversial.


MIT professor of geophysics Daniel Rothman stands next to part of the Xiakou formation in China. His right hand rests on the layer that marks the time of the end-Permian mass extinction event. Samples from this formation provided evidence for large amounts of nickel that were spewed from volcanic activity at this time, 252 million years ago. Photo courtesy of Daniel Rothman.

Now, a team of MIT researchers may have found enough evidence to convict the guilty parties — but you’ll need a microscope to see the killers.

The perpetrators, this new work suggests, were not asteroids, volcanoes, or raging coal fires, all of which have been implicated previously. Rather, they were a form of microbes — specifically, methane-producing archaea called Methanosarcina — that suddenly bloomed explosively in the oceans, spewing prodigious amounts of methane into the atmosphere and dramatically changing the climate and the chemistry of the oceans.

Volcanoes are not entirely off the hook, according to this new scenario; they have simply been demoted to accessories to the crime. The reason for the sudden, explosive growth of the microbes, new evidence shows, may have been their novel ability to use a rich source of organic carbon, aided by a sudden influx of a nutrient required for their growth: the element nickel, emitted by massive volcanism at just that time.

The new solution to this mystery is published this week in the Proceedings of the National Academy of Science by MIT professor of geophysics Daniel Rothman, postdoc Gregory Fournier, and five other researchers at MIT and in China.

The researchers’ case builds upon three independent sets of evidence. First, geochemical evidence shows an exponential (or even faster) increase of carbon dioxide in the oceans at the time of the so-called end-Permian extinction. Second, genetic evidence shows a change in Methanosarcina at that time, allowing it to become a major producer of methane from an accumulation of carbon dioxide in the water. Finally, sediments show a sudden increase in the amount of nickel deposited at exactly this time.

The carbon deposits show that something caused a significant uptick in the amount of carbon-containing gases — carbon dioxide or methane — produced at the time of the mass extinction. Some researchers have suggested that these gases might have been spewed out by the volcanic eruptions that produced the Siberian traps, a vast formation of volcanic rock produced by the most extensive eruptions in Earth’s geological record. But calculations by the MIT team showed that these eruptions were not nearly sufficient to account for the carbon seen in the sediments. Even more significantly, the observed changes in the amount of carbon over time don’t fit the volcanic model.

“A rapid initial injection of carbon dioxide from a volcano would be followed by a gradual decrease,” Fournier says. “Instead, we see the opposite: a rapid, continuing increase.”

“That suggests a microbial expansion,” he adds: The growth of microbial populations is among the few phenomena capable of increasing carbon production exponentially, or even faster.

But if living organisms belched out all that methane, what organisms were they, and why did they choose to do so at that time?

That’s where genomic analysis can help: It turns out that Methanosarcina had acquired a particularly fast means of making methane, through gene transfer from another microbe — and the team’s detailed mapping of the organism’s history now shows that this transfer happened at about the time of the end-Permian extinction. (Previous studies had only placed this event sometime in the last 400 million years.) Given the right conditions, this genetic acquisition set the stage for the microbe to undergo a dramatic growth spurt, rapidly consuming a vast reserve of organic carbon in the ocean sediments.

But there is one final piece to the puzzle: Those organisms wouldn’t have been able to proliferate so prodigiously if they didn’t have enough of the right mineral nutrients to support them. For this particular microbe, the limiting nutrient is nickel — which, new analysis of sediments in China showed, increased dramatically following the Siberian eruptions (which were already known to have produced some of the world’s largest deposits of nickel). That provided the fuel for Methanosarcina’s explosive growth.

The burst of methane would have increased carbon dioxide levels in the oceans, resulting in ocean acidification — similar to the acidification predicted from human-induced climate change. Independent evidence suggests that marine organisms with heavily calcified shells were preferentially wiped out during the end-Permian extinction, which is consistent with acidification.

“A lot of this rests on the carbon isotope analysis,” Rothman says, which is exceptionally strong and clear in this part of the geological record. “If it wasn’t such an unusual signal, it would be harder to eliminate other possibilities.”

John Hayes, a researcher at Woods Hole Oceanographic Institution who was not involved in the research, says this work is “a remarkable combination of physics, biochemistry, and geochemistry. It grows out of years of outstanding and patient work that has provided a highly refined time scale for the events that accompanied Earth’s most severe cluster of extinctions.”

Hayes adds that the team’s identification of one organism that may have been responsible for many of the changes is “the first time that the explosive onset of a single process has been recognized in this way, and it adds very important detail to our understanding of the extinction.”

While no single line of evidence can prove exactly what happened in this ancient die-off, says Rothman, who is also director of MIT’s Lorenz Center, “the cumulative impact of all these things is much more powerful than any one individually.” While it doesn’t conclusively prove that the microbes did it, it does rule out some alternative theories, and makes a strong and consistent case, he says.

The research was supported by NASA, the National Science Foundation, the Natural Science Foundation of China, and the National Basic Research Program of China.

Reprinted with permission of MIT News (

Media Coverage of Permian-Triassic Extinction Study

A paper published this week in the Proceedings of the National Academy of Science by MIT professor of geophysics Daniel Rothman and other members of the Foundations of Complex Life team suggests the P/T extinction resulted from methane-producing archaea called Methanosarcina suddenly blooming in the oceans. The MIT News office wrote a piece on the study, which we’ve reprinted on our news feed, but the paper has also been getting a great deal of media interest worldwide. Here’s a listing with some of the coverage:

2014 Northeastern Geobiology Symposium

gibbsThe Northeastern Geobiology Symposium is an annual daylong conference organized between the Northeastern Universities to encourage interaction, strengthen existing ties and build new collaborations in the Geobiology community. In particular, this conference is an excellent opportunity for graduate students to meet collaborators as well as for undergraduate students to meet prospective graduate advisors. The topics of interest will broadly revolve around the themes of environmental geomicrobiology and the co-evolution of life and environment through geological time.

The symposium will kick off with an invited speaker on Friday, March 28th at 6:30 pm, and continue on Saturday the 29th of March, 2014 with a light breakfast at 9:20 am followed by talks at 10 am, lunch at noon, more talks and poster sessions throughout the afternoon. Click here to download a detailed schedule. The location will be the Department of Geology and Geophysics, Yale University. The event will begin at 9:30 am with breakfast, talks will begin at 10 am and will continue until 5:30 pm with breaks for lunch and coffee. We will take a short break and then meet again at 6:30 for a poster session and a wine and cheese.

For more information, head to the symposium website.

Why Life Got Big


An exciting new paper from Foundations of Complex Life team members, recently published in Current Biology, offers a novel explanation for why organisms first evolved large size in the Ediacaran Period, 579–565 million years ago. Inspired by a 2009 FCL team retreat and field trip to Mistaken Point, Newfoundland, coauthors David Jacobs, Roger Summons, David Johnston, and Marc Laflamme used models of canopy flow to explain how sticking up into the water column provided rangeomorphs, some of these earliest multicellular organisms preserved at Mistaken Point, a competitive advantage over microbial mats.

Graphical_Abstract final?

Canopy flow—a process familiar from crops waving in the wind, like the wheat fields depicted by Van Gogh at the top of this post—induces large eddies or vortexes in the flow where faster-flowing current above meets current slowed down by the canopy below. Here’s a video of David Jacobs and his graduate student, David Gold, summarizing the paper in their own words:

The paper can be read here (subscription required), while UCLA has a press release here. The story was also covered by Science Daily.

New Website Launched

Welcome to the brand new web presence for Foundations of Complex Life, the NASA Astrobiology Institute MIT Team. After many years of service, we’ve left behind the Drupal site developed during our previous funding round, under the moniker Advances of Complex Life. We hope you find the new site useful and informative. While the transfer of resources to the new site is underway, you can can access the old site here if you are looking for something you can’t find on these pages.


We built this site using WordPress and the Sixteen Nine theme by Studiopress, with a great many adjustments and tweaks to suit our needs. For example, we changed the typography to reflect best practices for readability (you’re reading this in Cardo, a webfont provided by Google).