A New Way to Keep Tabs on Methane-Eating Microbes

Anaerobic methanotrophs are a group of microbes that consume methane and live a low-energy lifestyle in oxygen-free environments. A new study shows that measuring the ratio of rare isotopes of methane from marine sediments is a useful tool for tracking their activities, which previously have been hard to distinguish from those of microbes that make methane.

The amount of methane – a potent greenhouse gas – that escapes into the atmosphere would be far higher if it weren’t for the activities of a poorly understood group of microbes called anaerobic methanotrophs. These unusual organisms live in no- or low-oxygen locations, like marine and freshwater sediments, and gain energy by taking in copious amounts of methane and turning the gas into inorganic carbon compounds. Scientists think that anaerobic methanotrophs go a long way toward counteracting methane production from other microbes and chemical processes, but have struggled to accurately measure their influence.

Now, researchers have figured out a new way to track the activities of anaerobic methanotrophs. DCO researchers Jeanine Ash (Rice University, formerly of University of California, Los Angeles, USA), Tina Treude, Issaku Kohl, Edward Young (University of California, Los Angeles (UCLA), USA), and Barbara Sherwood Lollar (University of Toronto, Canada), with European collaborators Matthias Egger, Barry Cragg, R. John Parkes, and Caroline Slomp, detected methane consumption in Baltic Sea sediments by measuring clumped isotopologues. These rare molecules of methane have two isotopes – atoms with a different number of neutrons in the nucleus. Measurements of clumped isotopologues can give hints to a methane sample’s source and what might be eating it. This novel approach, described in a new paper in Geochemical Perspectives Letters [1] may help scientists to put a number on how much methane anaerobic methanotrophs consume. 

Schneiders and Ash
Luzie Schnieders (MARUM,Germany) and Ash (on the right) sample sediment for methane on the deck of the Greatship Manisha during IODP Expedition 347 to the Baltic Sea, fall 2013. Credit: Sophie Green

“Anaerobic methanotrophy had not been addressed before using clumped isotopologue signatures,” said Ash. Traditionally, scientists have used isotopic signatures of methane to determine what created a methane source – whether it came from methanogens (microbial), low-temperature chemical reactions (abiotic), or the high-temperature breakdown of old organic matter (thermogenic). But processes that consume methane have received less interest.  “This is natural if you think consumption simply removes methane from a system, but I think anaerobic methanotrophy is a little more complicated than that, and clumped isotopes is a promising new tool for investigating this aspect of methane cycling.”

Clumped isotopologues of methane carry either two hydrogen atoms with an extra neutron, called deuterium (CH2D2) or one carbon atom with an extra neutron and one deuterium (13CH3D). The extra neutrons give these molecules a miniscule difference in weight and size compared to an average methane molecule (CH4). 

One of the few instruments in existence that can differentiate between clumped isotopologues and “regular” methane is Panorama [2], developed by Young and colleagues at UCLA with support from DCO and other sources. This high-resolution mass spectrometer is sensitive enough to detect the tiny weight differences between isotopologues

As a graduate student in Young’s lab, Ash had a spot on International Ocean Drilling Program Expedition 347, a research cruise that traversed the coast of Sweden and Denmark, where researchers collected sediment samples from the Baltic Sea. “I boarded the boat in Kiel as a carbonate paleoceanographer,” said Ash. “Half of the scientists sailing were microbiologists and we had lots of time offshore to talk about what the other half were doing. By the time I got off that cruise I was really interested in the deep biosphere.” 

When Ash measured the clumped isotopologues from her samples, she noticed something odd. The methane appeared to shift to thermodynamic equilibrium with depth, or in other words, the ratio of the isotopologues matched what scientists would expect based on the temperature of the environment. This was strange because methanogens are very actively making methane in Baltic Sea sediments, and previous studies have shown that those activities affect the ratios of isotopologues. Something must be breaking and remaking methane bonds in the sediment.

To explain the results, Ash proposes that the action of anaerobic methanotrophs, which consume methane, is canceling out the signal from the methanogens, giving the appearance of equilibrium. 

“Anaerobic methanotrophy is my favorite metabolism because it’s so weird,” said Ash. Consuming methane without oxygen yields very little energy, so the archaea that perform anaerobic methanotrophy must work with bacteria that reduce sulfate to make this lifestyle energetically feasible. “Imagine if you, a human, couldn’t carry out your lifestyle of breathing oxygen without the direct help of an organism from another branch on the tree of life. That’s what anaerobic methanotrophs do.” The metabolism also uses some of the same enzymes required to make methane, and is essentially methanogenesis running in reverse.

Anaerobic methanotrophy also is very inefficient. Ash’s work suggests that the organisms take in more methane than they can process, and “spit out” the extra. During the molecule’s trip through the cell it interacts with enzymes that swap out hydrogen atoms, which affects the isotopes in the released methane. This processing effectively erases the isotopic signature created by methanogens. 

Scientists potentially could use that isotopic erasure as a marker of anaerobic methanotrophy. Clumped isotopologues may be especially useful for studies of anaerobic methanotrophy in subseafloor environments, which are the largest reservoirs of methane on the planet.   

Ash acknowledges that these findings, based on measurements from a single environment, are just the beginning and must be replicated elsewhere. She has returned to sea since her Baltic expedition, to collect sediment samples from off the coast of Antarctica in the Ross Sea, and also received samples from another expedition in the Gulf of Corinth, a deep inlet between the hand-shaped part of the Greece and the rest of the country. If she sees the same trends there, it will support the usefulness of clumped isotopologues – and instruments like Panorama – for detecting anaerobic methanotrophy. “Funding an instrument like the Panorama is a major task, and without it, work like this doesn’t happen,” said Ash. 

“I’m inspired by the exploration of the other ‘ocean worlds’ in our solar system like Europa and Enceladus, but there’s still so much that we don’t know about our own ocean world,” said Ash, “I hope this work pushes our understanding of this strange metabolism and its role in the global carbon cycle just a little bit further.”

In this video, Ash explains how she samples deep-sea sediments while working on board the JOIDES Resolution research vessel, during a recent trip to the Ross Sea. Credit: IODP 

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