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Without oxygen, microbes make a living off methane in Black Sea


A team of Russian and German scientists has discovered an unusual community of microbes living on methane vents in the Black Sea at depths where the water is almost devoid of oxygen.

The microbes form massive organic mats that cover the surface of rock pipes reaching up to four meters. These pipes are not preformed structures; rather, they are formed—and shaped—by the microbes' consumption of methane. The microbial mats consist of sulfur-reducing bacteria and species of Archaea, a domain of life distinct from plants, animals and bacteria.

Bubbles of free methane gas emanate from the tips of microbial reefs.

Understanding the energy cycles of these organisms could help efforts to develop methane as an alternative energy source and reveal information about the importance of methane to the early atmosphere of Earth.

"The microbial reef is like a coral reef," says Rudolf Amann of the Max Planck Institute for Marine Microbiology in Bremen, Germany, who was a member of the research team.

"The growth of the reef is guided by living organisms," says Amann. "The chimney-like structures are formed by the microbial mat."

These rock chimneys sit atop hundreds of interconnected methane vents that spew methane gas from the sea floor below. The chimneys disperse methane bubbles into the water, but they also distribute gas to the microbial mat. The "cavernous" nature of the build-ups promotes a flow of methane to the entire mat surface, the researchers report in Science.

Methane vents have been thought to occur west of the Crimea peninsula in the Black Sea. To explore the area, the Russo-German team launched an expedition aboard the Russian research vessel Professor Logachev. This was the launching pad for a manned submersible called JAGO.

The Black Sea reefs have three layers: surface mat, pink interior, and inner core of porous carbonate rock.

The microbial reefs were found at depths of around 230 meters. The German researchers were "completely surprised" to see the "spectacularly large formations," says Amann. Most of the Black Sea supports little or no life below 150 meters because of the oxygen-depleted waters. These "dead zones" are created by a limited flow of freshwater to the entire ecosystem.

For the first time, the researchers were able to extract the unusual microbes from their natural environment in order to study them in the laboratory. Small samples were removed from the mats using a mechanical arm on the submersible JAGO.

To keep these exotic organisms alive during their trip to the laboratory, the researchers designed special containers that resembled the microbe's 'home' environment—cold water with no oxygen but lots of methane.

Back in the laboratory, the researchers confirmed their suspicion that the microbes were eating methane. They traced the uptake of methane by first incubating thin sections of the samples in radioactive methane and then using imaging tools to analyze them.

The researchers also determined that a mixed community of organisms resides in the mats. Using fluorescent probes, the team identified sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus group and Archaea of the ANME-1 cluster.

These types of microorganisms are known to work in concert. Two years ago, methane-consuming Archaea and bacteria were found off the coast of Oregon. A team of researchers led by Antje Boetius, also of the Max Planck Institute for Marine Microbiology, discovered thick mats of microbes feeding off "methane-ice"—frozen methane seeping up from the sea floor.

The Oregon mats have much smaller communities of microbes than those in the Black Sea. They also lack carbonate pipe structures. Yet, the Oregon study provides the first direct evidence of methane-based symbiosis of Archaea and bacteria—a partnership that Amann says could exist between microbes living in the Black Sea.

The research vessels. The ship Professor Logachev at port (left). A researcher aboard the submersible JAGO (right).

Amann and colleagues are now studying the genetics behind how the Black Sea microbes interact with each other in their environment. They plan to sequence the genomes of these microbes to better understand their potentially symbiotic relationship.

Isolating individual organisms from the microbial community has proven difficult. As an alternative strategy, Amann is extracting large pieces of DNA from the mat samples and cloning them in bacteria so they can then be sequenced.

The impressive size of the Black Sea mats remains a puzzle. Microbial mats of this size are "rarely found" in environments without oxygen, the researchers note in the study. Without much energy, it has been thought that the environment cannot support large communities of organisms. One possible explanation for their existence is the absence of grazing by other animals, which cannot survive the harsh environment.

The exact age of these microbial mats is unknown, but the communities may be thousands of years old. The microbial reefs are, perhaps, snapshots of early Earth, when methane-loving microbes prospered under harsh conditions. The researchers suggest that large parts of the ancient ocean might have contained similar reefs.

"This community of microbes may somehow mimic the early history of earth," adds Amann.

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Michaelis, W. et al. Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane. Science 297, 1013-1015 (August 9, 2002).
Boetius, A. et al. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407, 623-626 (October 5, 2000).

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