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Open Access Highly Accessed Research article

A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments

Othilde Elise Håvelsrud123, Thomas HA Haverkamp34, Tom Kristensen23, Kjetill S Jakobsen34 and Anne Gunn Rike1*

Author affiliations

1 Norwegian Geotechnical Institute, Sognsveien 72, P.O. Box 3930 Ullevål Stadion, N-0806 Oslo, Norway

2 Department of Molecular Biosciences, University of Oslo, Blindernveien 31, P.O. Box 1041 Blindern, N-0316 Oslo, Norway

3 Microbial Evolution Research Group, MERG, Department of Biology, University of Oslo, Blindernveien 31, P.O. Box 1066 Blindern, N-0316 Oslo, Norway

4 Centre for Evolutionary and Ecological Synthesis (CEES), Department of Biology, University of Oslo, Blindernveien 31, P.O. Box 1066 Blindern, N-0316 Oslo, Norway

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Citation and License

BMC Microbiology 2011, 11:221  doi:10.1186/1471-2180-11-221

Published: 4 October 2011

Abstract

Background

Methane oxidizing prokaryotes in marine sediments are believed to function as a methane filter reducing the oceanic contribution to the global methane emission. In the anoxic parts of the sediments, oxidation of methane is accomplished by anaerobic methanotrophic archaea (ANME) living in syntrophy with sulphate reducing bacteria. This anaerobic oxidation of methane is assumed to be a coupling of reversed methanogenesis and dissimilatory sulphate reduction. Where oxygen is available aerobic methanotrophs take part in methane oxidation. In this study, we used metagenomics to characterize the taxonomic and metabolic potential for methane oxidation at the Tonya seep in the Coal Oil Point area, California. Two metagenomes from different sediment depth horizons (0-4 cm and 10-15 cm below sea floor) were sequenced by 454 technology. The metagenomes were analysed to characterize the distribution of aerobic and anaerobic methanotrophic taxa at the two sediment depths. To gain insight into the metabolic potential the metagenomes were searched for marker genes associated with methane oxidation.

Results

Blast searches followed by taxonomic binning in MEGAN revealed aerobic methanotrophs of the genus Methylococcus to be overrepresented in the 0-4 cm metagenome compared to the 10-15 cm metagenome. In the 10-15 cm metagenome, ANME of the ANME-1 clade, were identified as the most abundant methanotrophic taxon with 8.6% of the reads. Searches for particulate methane monooxygenase (pmoA) and methyl-coenzyme M reductase (mcrA), marker genes for aerobic and anaerobic oxidation of methane respectively, identified pmoA in the 0-4 cm metagenome as Methylococcaceae related. The mcrA reads from the 10-15 cm horizon were all classified as originating from the ANME-1 clade.

Conclusions

Most of the taxa detected were present in both metagenomes and differences in community structure and corresponding metabolic potential between the two samples were mainly due to abundance differences.

The results suggests that the Tonya Seep sediment is a robust methane filter, where taxa presently dominating this process could be replaced by less abundant methanotrophic taxa in case of changed environmental conditions.