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Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep

Nature volume 568, pages 108–111 (2019)Cite this article

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Abstract

Ethane is the second most abundant component of natural gas in addition to methane, and—similar to methane—is chemically unreactive. The biological consumption of ethane under anoxic conditions was suggested by geochemical profiles at marine hydrocarbon seeps1,2,3, and through ethane-dependent sulfate reduction in slurries4,5,6,7. Nevertheless, the microorganisms and reactions that catalyse this process have to date remained unknown8. Here we describe ethane-oxidizing archaea that were obtained by specific enrichment over ten years, and analyse these archaea using phylogeny-based fluorescence analyses, proteogenomics and metabolite studies. The co-culture, which oxidized ethane completely while reducing sulfate to sulfide, was dominated by an archaeon that we name ‘Candidatus Argoarchaeum ethanivorans’; other members were sulfate-reducing Deltaproteobacteria. The genome of Ca. Argoarchaeum contains all of the genes that are necessary for a functional methyl-coenzyme M reductase, and all subunits were detected in protein extracts. Accordingly, ethyl-coenzyme M (ethyl-CoM) was identified as an intermediate by liquid chromatography–tandem mass spectrometry. This indicated that Ca. Argoarchaeum initiates ethane oxidation by ethyl-CoM formation, analogous to the recently described butane activation by ‘Candidatus Syntrophoarchaeum’9. Proteogenomics further suggests that oxidation of intermediary acetyl-CoA to CO2 occurs through the oxidative Wood–Ljungdahl pathway. The identification of an archaeon that uses ethane (C2H6) fills a gap in our knowledge of microorganisms that specifically oxidize members of the homologous alkane series (CnH2n+2) without oxygen. Detection of phylogenetic and functional gene markers related to those of Ca. Argoarchaeum at deep-sea gas seeps10,11,12 suggests that archaea that are able to oxidize ethane through ethyl-CoM are widespread members of the local communities fostered by venting gaseous alkanes around these seeps.

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Fig. 1: Ethane oxidation with sulfate and major 16S rRNA gene phylotypes.
Fig. 2: Microscopic characterization of the Ethane12 culture.
Fig. 3: Phylogeny of McrA and identification of ethyl-coM.
Fig. 4: Basic reactions in archaeal oxidation of gaseous alkanes compared to methanogenesis.

Data availability

Metagenome sequence data are archived in the NCBI database under BioProject number PRJNA495932, including the draft genomes of Ca. Argoarchaeum ethanivorans (SAMN10235260), Eth-SRB1 (SAMN10235261) and Eth-SRB2 (SAMN10235262). The 16S rRNA gene amplicon reads have been submitted to the NCBI Sequence Read Archive (SRA) database under the accession number SRR8089822. The proteomics dataset has been deposited with the ProteomeXchange Consortium identifier PXD011597. Source Data for the quantitative growth experiments (Fig. 1a), FT–ICR–MS (Fig. 3b, c) and LC–MS/MS measurements (Fig. 3d–f) are provided. All other data are available in the paper or the Supplementary Information.

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Acknowledgements

We acknowledge R. Appel for assistance in cultivation and chemical analyses, K. Nerlich for CARD–FISH, J. M. Kaesler for FT–ICR–MS analyses, B. Scheer for proteomics analyses and K. T. Konstantinidis for support with metagenomics analyses. Research was funded by the Helmholtz Association and by the Max Planck Society. Further financial support was provided by the Helmholtz Association (grant ERC-RA-0020 to F.M.), the Strategic Priority Research Program of the Chinese Academy of Sciences (grants XDB15020302 and XDB15020402 to Y.-G.Z.) and the Chinese Scholarship Council (scholarship to S.-C.C.). We thank the shipboard science parties and submersible operation teams of the RV Seward Johnson II. Funding for the Gulf of Mexico cruise was provided by the US National Science Foundation (OCE-0085549) and the ACS Petroleum Research Fund (PRF-36834-AC2). The US Department of Energy and the US National Undersea Research Program provided funding for submersible operations. We acknowledge the Centre for Chemical Microscopy (ProVIS) at the Helmholtz Centre for Environmental Research for the use of their analytical facilities. ProVIS is supported by European Regional Development Funds (EFRE – Europe funds Saxony).

Reviewer information

Nature thanks Mike Jetten, Derek Lovley, Rudolf K. Thauer and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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Author notes

  1. Ulrike Jaekel

    Present address: Department for Research Infrastructures, The Research Council of Norway, Oslo, Norway

Authors and Affiliations

  1. Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany

    Song-Can Chen, Niculina Musat, Matthias Schmidt, Nedal Said, Federica Calabrese, Hryhoriy Stryhanyuk, Hans-Hermann Richnow & Florin Musat

  2. State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China

    Song-Can Chen & Yong-Guan Zhu

  3. Department of Analytical Chemistry, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany

    Oliver J. Lechtenfeld & Heidrun Paschke

  4. Department of Environmental Microbiology, Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany

    Denny Popp

  5. Max Planck Institute for Marine Microbiology, Bremen, Germany

    Ulrike Jaekel, Friedrich Widdel & Florin Musat

  6. Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China

    Yong-Guan Zhu

  7. Department of Marine Sciences, University of Georgia, Athens, GA, USA

    Samantha B. Joye

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Contributions

S.-C.C., H.-H.R., F.W. and F.M. designed the research. S.B.J. retrieved the original sediment sample and contributed to establishment of the enrichment. U.J. and F.M. performed cultivation and physiology experiments. N.M. designed CARD–FISH probes and performed CARD–FISH and fluorescence microscopy. M.S., N.S. and N.M. designed and performed helium ion microscopy analyses. O.J.L. and H.P. performed FT–ICR–MS analyses, and LC–MS/MS method development and analyses. S.-C.C., D.P., Y.-G.Z. and F.M. performed metagenomics analyses. S.-C.C. performed phylogenetic and proteomics analyses. F.C., H.S. and N.M. designed and performed nanoSIMS analyses. S.-C.C., F.W. and F.M. wrote the manuscript with contributions from all co-authors.

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Correspondence to Florin Musat.

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Extended data figures and tables

Extended Data Fig. 1 Helium ion microscopy images showing vesicular structures interpreted as budding of Ca. A. ethanivorans.

Budding cells remained loosely attached to each other, leading to formation of small clusters or aggregates. To avoid false stacking of cells, centrifugation was avoided during sample preparation. The samples were fixed and filtered on gold–palladium-sputtered polycarbonate filters. All subsequent procedures (dehydration and critical point drying) were done with filter pieces. Images are representative of n = 20 recorded images of samples from n = 3 independent cultures.

Extended Data Fig. 2 Proposed pathway for ethane oxidation by Ca. Argoarchaeum based on proteogenomics analyses.

a, Candidatus Argoarchaeum uses an MCR-like enzyme (alkyl-CoM reductase (‘ACR’)) to activate ethane to ethyl-CoM. Reactions converting the alkyl thioether to the acyl thioester are currently unknown: we hypothesize an involvement of the detected methyl-transferase (mtr; see b) in these reactions. The proposed acetyl-CoA is oxidized to CO2 through the reverse (oxidative) Wood–Ljungdahl pathway. The physiological role of acetyl-CoA synthetase (Acs) and the acetate/cation symporter (ActP) is presently unclear. All enzymes depicted are encoded by the Ca. Argoarchaeum genome. Enzymes depicted in green were fully or partly detected in protein extracts (see b). Fpo, F420H2 dehydrogenase; Ftr, formylmethanofuran:tetrahydromethanopterin formyltransferase; Fwd, formylmethanofuran dehydrogenase; Hdr, heterodisulfide reductase; Mch, methenyltetrahydromethanopterin cyclohydrolase; Mer, 5,10-methylenetetrahydromethanopterin reductase; MF, methanofuran; Mnh, multicomponent Na+:H+ antiporter; MPT, methanopterin; Mtd, methylenetetrahydromethanopterin dehydrogenase; NAD, nicotinamide adenine dinucleotide; Ntp, vacuolar/archaea (V/A)-type H+/Na+-transporting ATPase; Nuo, NADH-quinone oxidoreductase. b, Organization of the genes that encode enzymes for the pathway proposed in a. Genes for which products were detected in protein extracts are depicted in green, all other genes are shown in yellow and genes unrelated to ethane oxidation are shown in grey.

Extended Data Fig. 3 NanoSIMS analysis of the Ethane12 enrichment culture.

a–f, Ion images of analysed areas (representative of n = 6 recorded fields of view). b, The cell types shown in b are Ca. Argoarchaeum (cocci; indicated by the arrows), Eth-SRB1 (curved rods; indicated by small arrowheads) and Eth-SRB2 (large, oval; indicated by large arrowheads). a, d, The 12C14N− ion image was used as indicator of biomass (all cell types). b, c, e, f, Images of 32S− (b, e) and 32S−:12C14N− ratios (c, f) show that cells of Ca. Argoarchaeum are enriched in sulfur, compared with bacterial cells—similar to AOM consortia16. Regions of interest used to define cells were drawn based on the single ion images (12C14N− and 32S−) and superimposed on the ratio images. g, Relative abundance of sulfur in Ca. Argoarchaeum compared to the sulfate-reducing bacteria at three different incubation times (95, 110 and 120 days). The average relative sulfur content of Ca. Argoarchaeum was more than twofold higher than in Eth-SRB1 and Eth-SRB2. Each dot represents the S:CN ion ratio of a single cell; in total, over 650 cells were analysed (517 of Ca. Argoarchaeum, 58 of Eth-SRB1 and 105 of Eth-SRB2). The box plots show the total ion ratio range (vertical line with whiskers), the clustering of 50% of all cells analysed (box) and the mean value for all cells of each strain. To calculate the ratio values in g, regions of interest were drawn in the LOOK@NanoSIMS software (not shown); these were smaller than those displayed in a–f, to avoid inclusion of filter material in the calculation. Scale bars, 2 μm (a–f).

Extended Data Fig. 4 Homology models of MCR from Ca. A. ethanivorans and Ca. S butanivorans.

a, Sequence alignment of the α subunit (McrA) and β subunit (McrB) of MCR from methanogens or ANME-1 methanotrophs (green), Ca. A. ethanivorans (AEth_00344, red) and Ca. S. butanivorans (SBU_000314, SBU_000718, SBU_001343 and SBU_001328; red); the functionally conserved residues in McrA and McrB are highlighted (yellow). The numbers below the alignment indicate the residue position in M. marburgensis MCR29. M. barkeri, Methanosarcina barkeri; M. formicicus, Methanotorris formicicus; M. kandleri, Methanopyrus kandleri; M. thermauto, Methanothermobacter thermautotrophicus; M. thermolitho, Methanothermococcus thermolithotrophicus; M. wolfeii, Methanothermobacter wolfeii. b. Crystal structure of M. marburgensis MCR (Protein Data Bank (PDB) accession 1MRO) bound to coenzyme B (CoB) and coenzyme M (CoM). c–g, Modelled active site regions in the MCR-like enzymes of Ca. A. ethanivorans (c) and Ca. S. butanivorans (d–g). The predicted structure was superimposed on M. marburgensis MCR (blue wireframes in c–g). Residues in McrA and McrB are indicated as green and cyan sticks, respectively; CoB and CoM are shown as yellow sticks, coenzyme F430 as pale yellow sticks and the arginine residue coordinating CoM as grey sticks (b–g).

Extended Data Table 1 Quantification of the anaerobic consumption of ethane, and sulfate reduction to sulfide in the Ethane12 enrichment culture
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Extended Data Table 2 Genes and proteins involved in ethane activation and complete oxidation by Ca. A. ethanivorans
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Extended Data Table 3 Genes and proteins involved in the energy metabolism of Ca. A. ethanivorans
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Extended Data Table 4 Genes that encode type IV pili in the genomes of Eth-SRB1 and Eth-SRB2
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Extended Data Table 5 Genes that encode cytochromes in the genomes of Eth-SRB1 and Eth-SRB2
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Extended Data Table 6 Environmental distribution of phylotypes related to Ca. A. ethanivorans
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Chen, SC., Musat, N., Lechtenfeld, O.J. et al. Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep. Nature 568, 108–111 (2019). https://doi.org/10.1038/s41586-019-1063-0

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