Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

A conspicuous nickel protein in microbial mats that oxidize methane anaerobically


Anaerobic oxidation of methane (AOM) in marine sediments is an important microbial process in the global carbon cycle and in control of greenhouse gas emission. The responsible organisms supposedly reverse the reactions of methanogenesis1,2,3,4,5,6,7,8, but cultures providing biochemical proof of this have not been isolated. Here we searched for AOM-associated cell components in microbial mats from anoxic methane seeps in the Black Sea9,10,11. These mats catalyse AOM rather than carry out methanogenesis. We extracted a prominent nickel compound displaying the same absorption spectrum as the nickel cofactor F430 of methyl-coenzyme M reductase, the terminal enzyme of methanogenesis12; however, the nickel compound exhibited a higher molecular mass than F430. The apparent variant of F430 was part of an abundant protein that was purified from the mat and that consists of three different subunits. Determined amino-terminal amino acid sequences matched a gene locus cloned from the mat. Sequence analyses revealed similarities to methyl-coenzyme M reductase from methanogenic archaea. The abundance of the nickel protein (7% of extracted proteins) in the mat suggests an important role in AOM.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it


Prices may be subject to local taxes which are calculated during checkout

Figure 1: Biochemical analysis of a microbial mat that oxidizes methane anaerobically.
Figure 2: Identification of the genes encoding the dominant protein, Ni-protein I, in the mat with the capacity for anaerobic oxidation of methane.
Figure 3: Phylogenetic relationships between Ni-protein I and MCR, and between the ANME-1 cluster and methanogenic archaea.


  1. Zehnder, A. J. B. & Brock, T. D. Methane formation and methane oxidation by methanogenic bacteria. J. Bacteriol. 137, 420–432 (1979)

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Hoehler, T. M., Alperin, M. J., Albert, D. B. & Martens, C. S. Field and laboratory studies of methane oxidation in an anoxic marine sediment: evidence for a methanogen-sulfate reducer consortium. Global Biogeochem. Cycles 8, 451–463 (1994)

    Article  ADS  CAS  Google Scholar 

  3. Harder, J. Anaerobic methane oxidation by bacteria employing 14C-methane uncontaminated with 14C-carbon monoxide. Mar. Geol. 137, 13–23 (1997)

    Article  ADS  CAS  Google Scholar 

  4. Hansen, L. B., Finster, K., Fossing, H. & Iversen, N. Anaerobic methane oxidation in sulfate depleted sediments: effects of sulfate and molybdate additions. Aquat. Microbial Ecol. 14, 195–204 (1998)

    Article  Google Scholar 

  5. Hinrichs, K. U., Hayes, J. M., Sylva, S. P., Brewer, P. G. & DeLong, E. F. Methane-consuming archaebacteria in marine sediments. Nature 398, 802–805 (1999)

    Article  ADS  CAS  Google Scholar 

  6. Valentine, D. L. & Reeburgh, W. S. New perspectives on anaerobic methane oxidation. Environ. Microbiol. 2, 477–484 (2000)

    Article  CAS  Google Scholar 

  7. Boetius, A. et al. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407, 623–626 (2000)

    Article  ADS  CAS  Google Scholar 

  8. Hallam, S. J., Girguis, P. G., Preston, C. M., Richardson, P. M. & DeLong, E. Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Appl. Environ. Microbiol. 69, 5483–5491 (2003)

    Article  CAS  Google Scholar 

  9. Pimenov, N. V. et al. Bacterial mats on coral-like structures at methane seeps in the Black Sea. Mikrobiologiya (Moscow) 66, 354–360 (1997)

    CAS  Google Scholar 

  10. Tourova, T. P., Kolganova, T. V., Kuznetsov, B. B. & Pimenov, N. V. Phylogenetic diversity of the archaeal component in microbial mats on coral-like structures associated with methane seeps in the Black Sea. Mikrobiologiya (Moscow) 71, 196–201 (2002)

    Article  CAS  Google Scholar 

  11. Michaelis, W. et al. Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane. Science 297, 1013–1015 (2002)

    Article  ADS  CAS  Google Scholar 

  12. Thauer, R. K. Biochemistry of methanogenesis: a tribute to Marjory Stephenson. Microbiology 144, 2377–2406 (1998)

    Article  CAS  Google Scholar 

  13. Elvert, M. & Suess, E. Anaerobic methane oxidation associated with marine gas hydrates: Superlight C-isotopes from saturated and unsaturated C20 and C25 irregular isoprenoids. Naturwissenschaften 86, 295–300 (1999)

    Article  ADS  CAS  Google Scholar 

  14. Orphan, V. J., House, C. H., Hinrichs, K. U., McKeegan, K. D. & DeLong, E. F. Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proc. Natl Acad. Sci. USA 99, 7663–7668 (2002)

    Article  ADS  CAS  Google Scholar 

  15. Martens, C. S. & Berner, R. A. Methane production in the interstitial waters of sulfate-depleted marine sediments. Science 185, 1167–1169 (1974)

    Article  ADS  CAS  Google Scholar 

  16. Barnes, R. & Goldberg, E. Methane production and consumption inanoxic marine sediments. Geology 4, 297–300 (1976)

    Article  ADS  CAS  Google Scholar 

  17. Reeburgh, W. Methane consumption in Cariaco Trench waters and sediments. Earth Planet. Sci. Lett. 28, 345–352 (1976)

    Article  ADS  Google Scholar 

  18. Iversen, N. & Jørgensen, B. B. Anaerobic methane oxidation rates at the sulfate-methane transition in marine sediments from Kattegat and Skagerrak (Denmark). Limnol. Oceanogr. 30, 944–955 (1985)

    Article  ADS  CAS  Google Scholar 

  19. Niewohner, C., Hensen, C., Kasten, S., Zabel, M. & Schulz, H. D. Deep sulfate reduction completely mediated by anaerobic methane oxidation in sediments of the upwelling area off Namibia. Geochim. Cosmochim. Acta 62, 455–464 (1998)

    Article  ADS  CAS  Google Scholar 

  20. Pancost, R. D., Hopmans, E. C. & Damste, J. S. S. Archaeal lipids in Mediterranean sold seeps: Molecular proxies for anaerobic methane oxidation. Geochim. Cosmochim. Acta 65, 1611–1627 (2001)

    Article  ADS  CAS  Google Scholar 

  21. Bian, L. et al. Algal and archaeal polyisoprenoids in a recent marine sediment: molecular-isotopic evidence for anaerobic oxidation of methane. Geochem. Geophys. Geosyst. 2, 1–22 (2001)

    Article  Google Scholar 

  22. Orphan, V. J., House, C. H., Hinrichs, K. U., McKeegan, K. D. & DeLong, E. F. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293, 484–487 (2001)

    Article  CAS  Google Scholar 

  23. Nauhaus, K., Boetius, A., Krüger, M. & Widdel, F. In vitro demonstration of anaerobic oxidation of methane coupled to sulphate reduction in sediment from a marine gas hydrate area. Environ. Microbiol. 4, 296–305 (2002)

    Article  CAS  Google Scholar 

  24. Sørensen, K. B., Finster, K. & Ramsing, N. B. Thermodynamic and kinetic requirements in anaerobic methane oxidizing consortia exclude hydrogen, acetate, and methanol as possible electron shuttles. Microbial Ecol. 42, 1–10 (2001)

    Google Scholar 

  25. Lynn, D. J., Singer, G. A. & Hickey, D. A. Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res. 30, 4272–4277 (2002)

    Article  CAS  Google Scholar 

  26. Pride, D. T., Meinersmann, R. J., Wassenaar, T. M. & Blaser, M. J. Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res. 13, 145–158 (2003)

    Article  CAS  Google Scholar 

  27. Schbath, S. An efficient statistic to detect over- and under-represented words in DNA sequences. J. Comput. Biol. 4, 189–192 (1997)

    Article  CAS  Google Scholar 

  28. Zhou, J., Bruns, M. A. & Tiedje, J. M. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62, 316–322 (1996)

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Lueders, T., Chin, K.-J., Conrad, R. & Friedrich, M. Molecular analyses of methyl-coenzyme M reductase alpha-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environ. Microbiol. 3, 194–204 (2001)

    Article  CAS  Google Scholar 

  30. Meyer, F. et al. GenDB—an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 31, 2187–2195 (2003)

    Article  CAS  Google Scholar 

Download references


We are particularly grateful to W. Michaelis, K. Nauhaus, R. Seifert and the Professor Logachev shipboard party for providing microbial mat samples, and to A. Boetius for coordination work and advice. We thank J. Moll, R. Appel and M. Sordel-Klippert for technical assistance; J. Knecht for the chemical analyses; D. Linder for N-terminal sequencing; and H. Teeling and T. Lombardot for help with bioinformatics. This work is part of the projects MUMM, GHOSTDABS and the GenoMic network Göttingen, supported by the Federal Ministry of Education and Research (Germany). Further support came from the Max Planck Society. This is a publication of GHOSTDABS and of the programme GEOTECHNOLOGIEN of the Federal Ministry of Education and Research and the Deutsche Forschungsgemeinschaft.

Author information

Authors and Affiliations


Corresponding authors

Correspondence to Friedrich Widdel or Rudolf K. Thauer.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Krüger, M., Meyerdierks, A., Glöckner, F. et al. A conspicuous nickel protein in microbial mats that oxidize methane anaerobically. Nature 426, 878–881 (2003).

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing