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A microbial consortium couples anaerobic methane oxidation to denitrification

Abstract

Modern agriculture has accelerated biological methane and nitrogen cycling on a global scale1,2. Freshwater sediments often receive increased downward fluxes of nitrate from agricultural runoff and upward fluxes of methane generated by anaerobic decomposition3. In theory, prokaryotes should be capable of using nitrate to oxidize methane anaerobically, but such organisms have neither been observed in nature nor isolated in the laboratory4,5,6,7,8. Microbial oxidation of methane is thus believed to proceed only with oxygen or sulphate9,10. Here we show that the direct, anaerobic oxidation of methane coupled to denitrification of nitrate is possible. A microbial consortium, enriched from anoxic sediments, oxidized methane to carbon dioxide coupled to denitrification in the complete absence of oxygen. This consortium consisted of two microorganisms, a bacterium representing a phylum without any cultured species and an archaeon distantly related to marine methanotrophic Archaea. The detection of relatives of these prokaryotes in different freshwater ecosystems worldwide11,12,13,14 indicates that the reaction presented here may make a substantial contribution to biological methane and nitrogen cycles.

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Figure 1: AOM is coupled to the denitrification of nitrite by the enrichment culture after 16 months of enrichment.
Figure 2: Phylogeny and fluorescence in situ detection of the archaeal and bacterial members of the consortium mediating AOM coupled to denitrification.

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Acknowledgements

We thank B. Kartal, J. van de Vossenberg and M. Schmid for discussions, and J. G. Kuenen and M. Wagner for critical reading of the manuscript. We thank J. Eigensteyn and W. Geerts for technical support. M.S. and K.F.E. are supported by a VIDI grant from the Dutch Science Foundation (NWO). Help from G. Boedeltje in choosing the sampling location is also gratefully acknowledged. Author Contributions M.S., A.A.R., A.J.P.S. and K.T.P-S. performed the sampling; A.A.R. the enrichment, A.A.R., A.P. and K.F.E. the batch experiments and labelling; W.I.C.R., S.S. and J.S.S.D. the biomarker analysis; A.A.R. and K.T.P-S. the FISH analysis; A.A.R. the molecular analysis; and A.A.R. and H.J.M.O.C. the phylogeny and probe design. The research was conceived by M.S. and M.S.M.J., and pilot experiments were performed by K.T.P-S. A.A.R., A.P., K.F.E., S.S., J.S.S.D., H.J.M.O.C., M.S.M.J. and M.S. contributed to interpreting the data and writing the paper.

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Correspondence to Marc Strous.

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The 16S rRNA gene sequences have been deposited in GenBank under accession numbers DQ369741 (archaeal sequence) and DQ369742 (bacterial sequence). Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

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Raghoebarsing, A., Pol, A., van de Pas-Schoonen, K. et al. A microbial consortium couples anaerobic methane oxidation to denitrification. Nature 440, 918–921 (2006). https://doi.org/10.1038/nature04617

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