Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

An Erratum to this article was published on 18 September 2013

Abstract

Anaerobic oxidation of methane (AOM) is critical for controlling the flux of methane from anoxic environments. AOM coupled to iron1, manganese1 and sulphate2 reduction have been demonstrated in consortia containing anaerobic methanotrophic (ANME) archaea. More recently it has been shown that the bacterium Candidatus ‘Methylomirabilis oxyfera’ can couple AOM to nitrite reduction through an intra-aerobic methane oxidation pathway3. Bioreactors capable of AOM coupled to denitrification have resulted in the enrichment of ‘M. oxyfera’ and a novel ANME lineage, ANME-2d4,5. However, as ‘M. oxyfera’ can independently couple AOM to denitrification, the role of ANME-2d in the process is unresolved. Here, a bioreactor fed with nitrate, ammonium and methane was dominated by a single ANME-2d population performing nitrate-driven AOM. Metagenomic, single-cell genomic and metatranscriptomic analyses combined with bioreactor performance and 13C- and 15N-labelling experiments show that ANME-2d is capable of independent AOM through reverse methanogenesis using nitrate as the terminal electron acceptor. Comparative analyses reveal that the genes for nitrate reduction were transferred laterally from a bacterial donor, suggesting selection for this novel process within ANME-2d. Nitrite produced by ANME-2d is reduced to dinitrogen gas through a syntrophic relationship with an anaerobic ammonium-oxidizing bacterium, effectively outcompeting ‘M. oxyfera’ in the system. We propose the name CandidatusMethanoperedens nitroreducens’ for the ANME-2d population and the family Candidatus ‘Methanoperedenaceae’ for the ANME-2d lineage. We predict that ‘M. nitroreducens’ and other members of the ‘Methanoperedenaceae’ have an important role in linking the global carbon and nitrogen cycles in anoxic environments.

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Figure 1: Bioreactor performance data and microbial community composition.
Figure 2: Key carbon and nitrogen transformations in ‘Methanoperedens nitroreducens’.
Figure 3: Methane oxidation coupled to nitrate reduction in the AOM bioreactor.
Figure 4: Observed interactions between key populations in methane-fed bioreactors with differing nitrogen sources.

Accession codes

Primary accessions

Sequence Read Archive

Data deposits

Sequencing data are deposited at the NCBI Short Read Archive under accession numbers SRR925398, SRR925402 and SRR901892. Annotated assembled sequences were incorporated into the IMG system with the Taxon Object ID 2515154041.

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Acknowledgements

We thank the ACE sequencing team; M. Butler, F. May and S. Low for their help with the 454 pyrosequencing, Illumina and Ion Torrent sequencing and the DOE Joint Genome Institute for single-cell sequencing. We also thank P. Lu for assistance with bioreactor operation, R. Zeng and P. Lant for their contribution to the development of initial bioreactors, B. Keller, J. Li, Y. Rui and Y. Wang for chemical and isotopic analyses, and D. Willner for assistance with genomic analysis. We are grateful to J. Euzéby for etymological advice. This work is supported by the Australian Research Council (ARC) through projects DP0666762 and DP0987204 and strategic funds from the Australian Centre for Ecogenomics. G.W.T. is supported by an ARC Queen Elizabeth II Fellowship (DP1093175). P.H. is supported by an ARC Discovery Outstanding Researcher Award (DP120103498). Y.S. is supported by the China Scholarship Council.

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S.H. and Y.S. enriched the microorganisms in the parent bioreactor and performed batch and isotope labelling tests. S.H., Y.S., J.K. and Z.Y. performed the process data analysis. M.F.H. performed the sampling, preservation and nucleic acid extractions. M.F.H. prepared samples for single-cell genomics, metagenomic and metatranscriptomic sequencing. M.F.H. and G.W.T. performed the microbial community analysis. M.I. developed the bioinformatic tools. M.F.H., M.I., P.H. and G.W.T. performed the bioinformatics analyses. M.F.H., S.H., Z.Y., P.H., G.W.T. wrote the manuscript in consultation with all other authors.

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Correspondence to Zhiguo Yuan or Gene W. Tyson.

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Haroon, M., Hu, S., Shi, Y. et al. Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 500, 567–570 (2013). https://doi.org/10.1038/nature12375

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