Embargoed for release: Thursday, September 19, 2002, at 14:00 US Eastern Time

Scientists identify methane-consuming microbes from ocean depths

Methane oxidizing archaeal and bacterial aggregate from 
methane seep sediments visualized using confocal microscopy.

MOSS LANDING, California—Monterey Bay Aquarium Research Institute (MBARI) microbiologists report in the 20 July 2001 issue of the journal Science on new techniques that combine the identification of microorganisms with their biogeochemical activity. In the study, the researchers used the new approach to identify marine microbes that consume methane, an important greenhouse gas.

“The method is providing a new window into the microbial world. Now it’s possible to determine both the identity and function of naturally occurring microbes, at the level of single cells. We don’t even have to grow them in the laboratory to do it,” said Ed DeLong, leader of the research group.

“Until recently no one knew which microbes were involved in the oxidation of methane in anoxic marine sediments,” adds Victoria Orphan, first author of the Science paper. “By combining molecular and stable isotope techniques, we found a way to link specific microbes to this important ocean process.”

In collaboration with Christopher House of Pennsylvania State University and researchers from Woods Hole Oceanographic Institution and the University of California, Los Angeles, the MBARI group used a remotely operated vehicle to collect marine sediments from deep sea methane seeps in the Eel River Basin off California. Molecular probes were used to identify archaea and sulfate-reducing bacteria in the sediments. These microorganisms, 0.5 to 2 micrometers in diameter, can live without oxygen and have not been grown in culture. First the scientists applied RNA probes, then they used secondary ion mass spectrometry to determine stable carbon isotope ratios of the individual microbe cells and cell aggregates. This method distinguished microbes that use methane as a carbon source from those using carbon derived from photosynthesis or other organic carbon sources.

The researchers showed that the archaea and bacteria cells could be identified individually within the cell aggregates. The two kinds of microbes form a partnership to extract energy from methane in the absence of oxygen. The methane-oxidizing archaea at the core of the aggregate transfer carbon compounds to their sulfate-reducing bacterial partners in the outer layers of the aggregate. Since nearly 80 percent of the methane in marine sediments is removed by these methane-consuming microbes, the discovery provides new insight into a critical process. Orphan and her colleagues are excited by the implications of this research, as these techniques can be used to simultaneously identify environmentally important microorganisms and characterize their metabolic activities in nature.

Related paper: Nature 398: 802-805, 29 April 1999
Related news item: Nature 407: 577-579, 05 October 2000

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Push core close-up through methane seep. Chemosynthetic clams appear at top. Photo: (c) 1999 MBARI

Push core from Eel River Basin methane seep showing chemosynthetic clams, bacterial mats, and authigenic carbonate slabs. Photo: (c) 2000 MBARI

Figure shows the spatial arrangement of an individual methane oxidizing cell aggregate and the potential metabolic interactions between the archaea (cells in red) and bacteria (cells in green). Carbon isotopic data obtained with FISH-SIMS suggest the core of archaea are consuming methane directly and transferring carbon-13 depleted metabolites and hydrogen to the surrounding sulfate-reducing bacterial partners. Image: Victoria Orphan (c) 2001 MBARI

Methane-oxidizing cell aggregates were first identified in methane seep sediments using Fluorescent In Situ Hybridization assays (FISH) on glass slides with specific fluorescently-labeled ribosomal RNA probes (Inset). Those target cells staining with the probes were then relocated and analyzed in a ‘Secondary’ Ion Mass Spectrometer (SIMS). This combined technique allowed us to determine the ratio of carbon-12 to carbon-13 for individual cell aggregates, thus identifying those cells that had incorporated methane into their cell carbon. The graph shows a profile of carbon-13 through an individual aggregate (see blue arrows), consisting of a core of methane-consuming archaea enveloped by sulfate-reducing bacteria. Images: Victoria Orphan (c) 2001 MBARI

For additional information or images relating to this article, please contact: Kim Fulton-Bennett
831-775-1835, kfb@mbari.org