Ancient whodunit may be solved: Methane-producing microbes did it!

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.
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 Sciences 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 resulting outburst of methane produced effects similar to those predicted by current models of global climate change: a sudden, extreme rise in temperatures, combined with acidification of the oceans. In the case of the end-Permian extinction, virtually all shell-forming marine organisms were wiped out — consistent with the observation that such shells cannot form in acidic waters.
“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.”
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.

First Snapshot of Organisms Eating Each Other: Feast Clue to Smell of Ancient Earth

Apr. 29, 2013 — Tiny 1,900 million-year-old fossils from rocks around Lake Superior, Canada, give the first ever snapshot of organisms eating each other and suggest what the ancient Earth would have smelled like.
The fossils, preserved in Gunflint chert, capture ancient microbes in the act of feasting on a cyanobacterium-like fossil called Gunflintia — with the perforated sheaths of Gunflintia being the discarded leftovers of this early meal.

A team, led by Dr David Wacey of the University of Western Australia and Bergen University, Norway, and Professor Martin Brasier of Oxford University, reports in this week’s Proceedings of the National Academy of Sciences the fossil evidence for how this type of feeding on organic matter — called ‘heterotrophy’ — was taking place. They also show that the ancient microbes appeared to prefer to snack on Gunflintia as a ‘tasty morsel’ in preference to another bacterium (Huroniospora).

‘What we call ‘heterotrophy’ is the same thing we do after dinner as the bacteria in our gut break down organic matter,’ said Professor Martin Brasier of Oxford University’s Department of Earth Sciences, an author of the paper. ‘Whilst there is chemical evidence suggesting that this mode of feeding dates back 3,500 million years, in this study for the first time we identify how it was happening and ‘who was eating who’. In fact we’ve all experienced modern bacteria feeding in this way as that’s where that ‘rotten egg’ whiff of hydrogen sulfide comes from in a blocked drain. So, rather surprisingly, we can say that life on earth 1,900 million years ago would have smelled a lot like rotten eggs.’

The team analysed the microscopic fossils, ranging from about 3-15 microns in diameter, using a battery of new techniques and found that one species — a tubular form thought to be the outer sheath of Gunflintia — was more perforated after death than other kinds, consistent with them having been eaten by bacteria.

In some places many of the tiny fossils had been partially or entirely replaced with iron sulfide (‘fool’s gold’) a waste product of heterotrophic sulfate-reducing bacteria that is also a highly visible marker. The team also found that these Gunflintia fossils carried clusters of even smaller (c.1 micron) spherical and rod-shaped bacteria that were seemingly in the process of consuming their hosts.

Dr Wacey said that: ‘recent geochemical analyses have shown that the sulfur-based activities of bacteria can likely be traced back to 3,500 million years or so — a finding reported by our group in Nature Geoscience in 2011. Whilst the Gunflint fossils are only about half as old, they confirm that such bacteria were indeed flourishing by 1,900 million years ago. And that they were also highly particular about what they chose to eat.’

Paleo-Ocean Chemistry: New Data Challenge Old Views About Evolution of Early Life

Dec. 23, 2012 — A research team led by biogeochemists at the University of California, Riverside has tested a popular hypothesis in paleo-ocean chemistry, and proved it false.
The fossil record indicates that eukaryotes — single-celled and multicellular organisms with more complex cellular structures compared to prokaryotes, such as bacteria — show limited morphological and functional diversity before 800-600 million years ago. Many researchers attribute the delayed diversification and proliferation of eukaryotes, which culminated in the appearance of complex animals about 600 million years ago, to very low levels of the trace metal zinc in seawater.
As it is for humans, zinc is essential for a wide range of basic cellular processes. Zinc-binding proteins, primarily located in the cell nucleus, are involved in the regulation of gene transcription.
Eukaryotes have increasingly incorporated zinc-binding structures during the last third of their evolutionary history and still employ both early- and late-evolving zinc-binding protein structures. Zinc is, therefore, of particular importance to eukaryotic organisms. And so it is not a stretch to blame the 1-2-billion-year delay in the diversification of eukaryotes on low bioavailability of this trace metal.
But after analyzing marine black shale samples from North America, Africa, Australia, Asia and Europe, ranging in age from 2.7 billion years to 580 million years old, the researchers found that the shales reflect high seawater zinc availability and that zinc concentrations during the Proterozoic (2.5 billion to 542 million years ago) were similar to modern concentrations. Zinc, the researchers posit, was never biolimiting.
Study results appear online Dec. 23 in Nature Geoscience.
“We argue that the concentration of zinc in ancient marine black shales is directly related to the concentrations of zinc in seawater and show that zinc is abundant in these rocks throughout Earth’s history,” said Clint Scott, the first author of the research paper and a former UC Riverside graduate student. “We found no evidence for zinc biolimitation in seawater.”
Scott, now a research geologist with the U.S. Geological Survey, explained that the connection between zinc limitation and the evolution of eukaryotes was based largely on the hypothesis that Proterozoic oceans were broadly sulfidic. Under broadly sulfidic conditions, zinc should have been scarce because it would have rapidly precipitated in the oceans, he explained.
“However, a 2011 research paper in Nature also published by our group at UCR demonstrated that Proterozoic oceans were more likely broadly ferruginous — that is, low in oxygen and iron-rich — and that sulfidic conditions were more restricted than previously thought,” said Scott, who performed the research in the lab of Timothy Lyons, a professor of biogeochemistry and the principal investigator of the research project.
The research team argues that ferruginous deep oceans, combined with large hydrothermal fluxes of zinc via volcanic activity on the seafloor, maintained high levels of dissolved zinc throughout the oceans and provided a relatively stable marine reservoir of the trace metal over the past 2.7 billion years.
“The key challenge in understanding the early evolution of life is recognizing the environmental conditions under which that life first appeared and diversified,” Lyons said. “We have taken a very direct approach that specifically tracks the availability of essential micronutrients, and, to our surprise, zinc supplies in ancient seawater were much higher and less variable than previously imagined.
“We can imagine for the first time,” he quipped, “that zinc supplements were not on the shopping lists of our early eukaryotic ancestors, and so we better find another reason to explain the mysterious delay in their rise in the ocean.”
Scott, who graduated with a doctoral degree in geological sciences from UCR in 2009, and Lyons were joined in the study by Noah J. Planavsky, a former UCR graduate student in Lyons’ lab; Chris L. Dupont at the J. Craig Venter Institute, La Jolla, Calif.; Brian Kendall and Ariel D. Anbar at Arizona State University; Benjamin C. Gill at Virginia Polytechnic Institute and State University and also a former member of the Lyons lab; Leslie J. Robbins and Kurt O. Konhauser at the University of Alberta, Canada; Kathryn F. Husband and Simon W. Poulton at the University of Leeds, United Kingdom; Gail L. Arnold at the Max Planck Institute for Marine Microbiology, Germany; Boswell A. Wing at McGill University, Canada; and Andrey Bekker at the University of Manitoba, Canada.
The idea for the study was a direct consequence of the 2011 Nature paper by Planavsky, Scott, Lyons and others that challenged the hypothesis of broadly sulfidic oceans.
The international collaboration received funding for the study from numerous sources. In the U.S., funding came from the National Science Foundation, the NASA Astrobiology Institute and the Agouron Institute.

What are Fossils

Fossils (from Latin fossus, literally “having been dug up”) are the preserved remains or traces of animals, plants, and other organisms from the remote past. The totality of fossils, both discovered and undiscovered, and their placement in fossiliferous (fossil-containing) rock formations and sedimentary layers (strata) is known as the fossil record. The study of fossils across geological time, how they were formed, and the evolutionary relationships between taxa (phylogeny) are some of the most important functions of the science of paleontology. Such a preserved specimen is called a “fossil” if it is older than some minimum age, most often the arbitrary date of 10,000 years ago.  Hence, fossils range in age from the youngest at the start of the Holocene Epoch to the oldest from the Archaean Eon several billion years old. The observations that certain fossils were associated with certain rock strata led early geologists to recognize a geological timescale in the 19th century. The development of radiometric dating techniques in the early 20th century allowed geologists to determine the numerical or “absolute” age of the various strata and thereby the included fossils.

Like extant organisms, fossils vary in size from microscopic, such as single bacterial cells only one micrometer in diameter, to gigantic, such as dinosaurs and trees many meters long and weighing many tons. A fossil normally preserves only a portion of the deceased organism, usually that portion that was partially mineralized during life, such as the bones and teeth of vertebrates, or the chitinous exoskeletons of invertebrates. Preservation of soft tissues is rare in the fossil record. Fossils may also consist of the marks left behind by the organism while it was alive, such as the footprint or feces (coprolites) of a reptile. These types of fossil are called trace fossils (or ichnofossils), as opposed to body fossils. Finally, past life leaves some markers that cannot be seen but can be detected in the form of biochemical signals; these are known as chemofossils or biomarkers.