Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics
Methane cycling gets more diverse
The production and consumption of methane by microorganisms play a major role in the global carbon cycle. Although these processes can occur in a range of environments, from animal guts to the deep ocean, these metabolisms are confined to the Archaea. Evans et al. used metagenomics to assemble two nearly complete archaeal genomes from deep groundwater methanogens (see the Perspective by Lloyd). The two reconstructed genomes are members of the recently described Bathyarchaeota and not the phylum to which all previously known methane-metabolizing archaea belonged.
Abstract
Methanogenic and methanotrophic archaea play important roles in the global flux of methane. Culture-independent approaches are providing deeper insight into the diversity and evolution of methane-metabolizing microorganisms, but, until now, no compelling evidence has existed for methane metabolism in archaea outside the phylum Euryarchaeota. We performed metagenomic sequencing of a deep aquifer, recovering two near-complete genomes belonging to the archaeal phylum Bathyarchaeota (formerly known as the Miscellaneous Crenarchaeotal Group). These genomes contain divergent homologs of the genes necessary for methane metabolism, including those that encode the methyl–coenzyme M reductase (MCR) complex. Additional non-euryarchaeotal MCR-encoding genes identified in a range of environments suggest that unrecognized archaeal lineages may also contribute to global methane cycling. These findings indicate that methane metabolism arose before the last common ancestor of the Euryarchaeota and Bathyarchaeota.
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Volume 350 | Issue 6259
23 October 2015
23 October 2015
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Copyright © 2015, American Association for the Advancement of Science.
Submission history
Received: 11 June 2015
Accepted: 14 September 2015
Published in print: 23 October 2015
Acknowledgments
We thank E. Gagen and P. Hugenholtz for valuable comments and suggestions; K. Baublys, SGS-Leeder, and Australian Laboratory Services staff for sample collection; and M. Butler and S. Low for library preparation and sequencing. This study was supported by the Australian Research Council (ARC) Linkage Project (grant LP100200730) and the U.S. Department of Energy’s Office of Biological Environmental Research (award no. DE-SC0010574). D.H.P. is supported by the Natural Sciences and Engineering Research Council of Canada. S.J.R. is supported by an Australian Postgraduate Award Industry scholarship. G.W.T. is supported by an ARC Queen Elizabeth II Fellowship (grant DP1093175). The authors declare no conflicts of interest. Our Whole Genome Shotgun projects have been deposited in the DNA DataBank of Japan, the European Molecular Biology Laboratory repository, and NIH’s GenBank under the accession numbers LIHJ00000000 (BA1) and LIHK00000000 (BA2). The versions described in this paper are LIHJ01000000 (BA1) and LIHK01000000 (BA2). Non-euryarchaeotal Surat Basin mcrA sequences have been deposited under the accession numbers KT387805 to KT387832, and unprocessed reads have been deposited under the accession number SRX1122679.
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