Researchers discover the first instance of living organisms producing elemental carbon

Carbon is the building block of all known life on our planet. The carbon cycle regulates the release and absorption of carbon from a number of natural sources — including the ocean, soil, geochemical processes, and human emissions — to maintain a delicate balance of this crucial element in our world.

An increase in carbon dioxide and methane in the atmosphere is partly responsible for the adverse effects of climate change experienced in Virginia and throughout the world.

New research at Virginia Tech, the University of Bremen, and the Max Planck Institute for Marine Microbiology has revealed that two kinds of microorganisms - methanogens and anaerobic methanotrophs – are able to produce a form of elemental carbon known as amorphous carbon.

For researchers who study methanogens and anaerobic methanotrophs, the discovery defies all previous expectations of what microorganisms can do, and sheds scientific light on some very interesting questions.

Why and how are these microorganisms making amorphous carbon? Is amorphous carbon being produced in large enough quantities to affect the carbon cycle on Earth?

“We never thought that amorphous carbon could be produced by living organisms because of the normally extreme chemical reactions that are needed to form it,” said Robert White, an emeritus professor of biochemistry in the College of Agriculture and Life Sciences. “This is the first report of amorphous carbon being produced by any organism on Earth, and we are very interested in the possible implications it may have for the carbon cycle.”

Their findings were published in the American Association for the Advancement of Science's open access multidisciplinary journal, Science Advances.

Amorphous carbon is a form of elemental carbon that lacks the hard, crystalline structure of graphite or diamond. The substance is usually formed under extreme temperatures and pressures, or during the burning of organic matter.

One place where amorphous carbon can be found is in your fireplace in the winter. When you burn firewood, the intensity of the heat creates a reaction that disintegrates the wood and leaves behind an ashy, black soot. That residual substance contains amorphous carbon.

Methanogens, or methane-producing microorganisms, have long piqued the interest of scientists because of their role in producing and releasing methane, a potent greenhouse gas, into the environment.

The microorganisms thrive in areas with high amounts of decayed organic matter and low-oxygen, such as wetlands, landfills, and cow stomachs. As these microorganisms eat the breakdown products of organic matter, they produce methane. 

The methane produced by these methanogens accounts for 90 percent of biologically produced methane, with 31 percent of this coming from cows alone.

Over the years, methanogen researchers have noticed little black specks forming inside their bacterial cultures during experiments. They had hypothesized that the specks were iron sulfide, another black material that is commonly formed in methanogenic growth media.

In other experiments with anaerobic methanotrophs, researchers found even more black material. Anaerobic methanotrophs are microorganisms that also thrive in the low-oxygen areas, but instead prefer the ocean floor. As they consume the methane that is seeping from the ocean floor, they convert it into carbon dioxide.

"I've always wondered, as have a number of other methanogen experts, what this black material is,” said Kylie Allen, the lead author on the study and an assistant professor of biochemistry in the College of Agriculture and Life Sciences and affiliate faculty of the Fralin Life Sciences Institute. “We used to think it was iron sulfide deposits in methanogenic cultures, but anaerobic methanotrophs produce far more of this black stuff.”

Overwhelmed with curiosity, a few methanogen researchers from across the world banded together and began to take a deeper, more analytical dive into these mysterious specks.

Gunter Wegener, a senior scientist at the MARUM Center for Marine Environmental Sciences and the Max Planck Institute for Marine Microbiology, cultured the anaerobic methanotrophs and sent them to Virginia Tech for further analysis. He leads one of the few labs in the world that can culture the ocean-dwelling microorganisms.

After receiving the anaerobic methanotrophs from Wegener, Allen and White began to isolate and analyze the amorphous carbon from methanogens and anaerobic methanotrophs.

Robert J. Bodnar, the G. C. Garvin Professor of geochemistry in the Virginia Tech Department of Geosciences in the College of Science, and Matthew Sublett Jr., a previous graduate student in the same department, used Raman spectroscopy to confirm the presence of a carbon-containing substance in these cultures that had characteristics similar to amorphous carbon.

Xu Feng, a scientist manager for the Surface Analysis Laboratory in Virginia Tech's Department of Chemistry, used x-ray photoelectron spectroscopy and elemental analysis to prove that the black substance was indeed primarily composed of pure carbon.

This mystery is solved, but now new ones show up in its wake.

“In these organisms, we are seeing this build up of amorphous carbon and they seem to be either making it on purpose, or it is a byproduct of their metabolism,” said Allen, who is also an affiliate of the Fralin Life Sciences Institute. “But we don’t know which one it is yet. This is something that we really want to figure out in the future.”

Allen maintains that researchers are a long way from determining its impacts on the carbon cycle, but it is possible that amorphous carbon has a role in keeping carbon in check.

Amorphous carbon is a relatively “unreactive” form of carbon. Limited evidence has shown that amorphous carbon can be naturally broken down in soils, but this process occurs extremely slowly and not to a large extent.

The carbon produced by anaerobic methanotrophs on the ocean floor could be trapped deep into the upper part of the Earth’s mantle, as tectonic plates shift overtop one another.  This "Deep Carbon" can subsequently be reintroduced to the atmosphere as CO2 by volcanic degassing, a process that would also occur over very long geological time frames.

Researchers know that this form of carbon is produced by methanogens and anaerobic methanotrophs, but they do not yet know how much. Wegener speculates that the formation of the amorphous carbon could point to a new carbon sink, or a portion of the carbon cycle that is able to absorb carbon dioxide from the atmosphere.

“It is also completely unclear how much elemental carbon is formed by microorganisms in nature and where it resides," said Wegener. "Moreover, because carbon is deposited in sediments and remains there over long periods of time, our results could point to a previously unknown natural carbon sink."