Skip to main content
SpringerLink
Log in

Detection of methanotrophic archaea in pockmark sediments (Gdansk Deep, Baltic Sea) by sequence analysis of the gene encoding the α subunit of methyl-coenzyme M reductase

  • Short Communications
  • Published:
Microbiology Aims and scope Submit manuscript

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

References

  1. Thauer, R.K., Biochemistry of Methanogenesis: a Tribute to Marjory Stephenson, Microbiology (UK), 1998, vol. 144, pp. 2377–2406.

    Article  CAS  Google Scholar 

  2. Shima, S. and Thauer, R.K., Methyl-Coenzyme M Reductase and the Anaerobic Oxidation of Methane in Methanotrophic Archaea, Curr. Opin. Microbiol., 2005, vol. 8, pp. 643–648.

    Article  CAS  PubMed  Google Scholar 

  3. Hallam, S.J., Girguis, P.R., Preston, C.M., Richardson, P.M., and DeLong, E.F., Identification of Methyl Coenzyme M Reductase A (mcrA) Genes Associated with Methane-Oxidizing Archaea, Appl. Environ. Microbiol., 2003, vol. 69, pp. 5483–5491.

    Article  CAS  PubMed  Google Scholar 

  4. Hallam, S.J., Putnam, N., Preston, C.M., Detter, J.C., Rokhsar, D., Richardson, P.M., and DeLong, E.F., Reverse Methanogenesis: Testing the Hypothesis with Environmental Genomics, Science, 2004, vol. 305, pp. 1457–1462.

    Article  CAS  PubMed  Google Scholar 

  5. Inagaki, F., Tsunogai, U., Suzuki, M., Kosaka, A., Machiyama, H., Takai, K., Nunoura, T., Nealson, K.H., and Horikoshi, K., Characterization of C1-Metabolizing Prokaryotic Communities in Methane Seep Habitats at the Kuroshima Knoll, Southern Ryukyu Arc, by Analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA Genes, Appl. Environ. Microbiol., 2004, vol. 70, pp. 7445–7455.

    Article  CAS  PubMed  Google Scholar 

  6. Krüger, M., Meyerdierks, A., Glöckner, F.O., Amann, R., Widdel, F., Kube, M., Reinhardt, R., Kahnt, J., Böcher, R., Thauer, R.K., and Shima, S., A Conspicuous Nickel Protein in Microbial Mats That Oxidize Methane Anaerobically, Nature, 2003, vol. 426, pp. 878–881.

    Article  PubMed  Google Scholar 

  7. Mayr, S., Latkoczy, C., Krüger, M., Günther, D., Shima, S., Thauer, R.K., Widdel, F., and Bernhard, J., Structure of an F430 Variant from Archaea Associated with Anaerobic Oxidation of Methane, J. Am. Chem. Soc., 2008, vol. 130, pp. 10758–10767.

    Article  CAS  PubMed  Google Scholar 

  8. Chistoserdova, L., Vorholt, J.A., Thauer, R.K., and Lidstrom, M.E., C-1 Transfer Enzymes and Coenzymes Linking Methylotrophic Bacteria and Methanogenic Archaea, Science, 1998, vol. 281, pp. 99–102.

    Article  CAS  PubMed  Google Scholar 

  9. Friedrich, M.W., Methyl-Coenzyme M Reductase Genes: Unique Functional Markers for Methanogenic and Anaerobic Methane-Oxidizing Archaea, Meth. Enzymol., 2005, vol. 397, pp. 428–442.

    Article  CAS  PubMed  Google Scholar 

  10. Hales, B.A., Edwards, C., Ritchi, D.A., Hal, G., Pickup, R.W., and Saunders, J.R., Isolation and Identification of Methanogen-Specific DNA from Blanket Bog Peat by PCR Amplification and Sequence Analysis, Appl. Environ. Microbiol., 1996, vol. 62, pp. 668–675.

    CAS  PubMed  Google Scholar 

  11. Lueders, T., Chin, K.J., Conrad, R., and Friedrich, M., Molecular Analyses of Methyl-coenzyme M Reductase α Subunit (mcrA) Genes in Rice Field Soil and Enrichment Cultures Reveal the Methanogenic Phenotype of a Novel Archaeal Lineage, Environ. Microbiol., 2001, vol. 3, pp. 194–204.

    Article  CAS  PubMed  Google Scholar 

  12. Springer, E., Sachs, M.S., Woese, C.R., and Boone, D.R., Partial Gene Sequences for the a Subunit of Methyl-Coenzyme M Reductase (mcrA) as a Phylogenetic Tool for the Family Methanosarcinaceae, Int. J. Syst. Bacteriol., 1995, vol. 45, pp. 554–559.

    Article  CAS  PubMed  Google Scholar 

  13. Valentine, D.L. and Reeburgh, W.S., New Perspectives on Anaerobic Methane Oxidation, Environ. Microbiol., 2000, vol. 2, pp. 477–484.

    Article  CAS  PubMed  Google Scholar 

  14. Knittel, K. and Boetius, A., Anaerobic Methane Oxidizers, in Handbook of Hydrocarbon and Lipid Microbiology, Timmis, K.N., Ed., Berlin: Springer, 2010.

    Google Scholar 

  15. Lösekann, T., Knittel, K., Nadalig, T., Fuchs, B., Niemann, H., Boetius, A., and Amann, R., Diversity and Abundance of Aerobic and Anaerobic Methane Oxidizers at the Haakon Mosby Mud Volcano, Barents Sea, Appl. Environ. Microbiol., 2007, vol. 73, pp. 3348–3362.

    Article  PubMed  Google Scholar 

  16. Geokhimiya vod i donnykh osadkov Baltiiskogo morya v raionakh razvitiya gazovykh kraterov i geoakusticheskikh anomalii (Geochemistry of Waters and Bottom Sediments of the Baltic Sea in the Regions of Development of Gas Craters and Geoacoustic Anomalies), Geodekyan, A.A, Romankevich, E.A, and Trotsyuk, V.Ya., Eds., Moscow: IO RAN, 1997.

    Google Scholar 

  17. Pimenov, N.V., Ul’yanova, M.O., Kanapatskii, T.A., Sivkov, V.V., and Ivanov, M.V., Microbiological and Biogeochemical Processes in a Pockmark of the Gdansk Depression, Baltic Sea, Mikrobiologiya, 2008, vol. 77, no. 5, pp. 651–659 [Microbiology (Engl. Transl.), vol. 77, no. 5, pp. 579–586].

    CAS  Google Scholar 

  18. Perevalova, A.A., Lebedinskii, A.V., Bonch-Osmolovskaya, E.A., and Chernykh, N.A., Detection of Hyperthermophilic Archaea of the Genus Desulfurococcus by Hybridization with Oligonucleotide Probes, Mikrobiologiya, 2003, vol. 72, no. 3, pp. 383–389 [Microbiology (Engl. Transl.), vol. 72, no. 3, pp. 340–346].

    CAS  Google Scholar 

  19. Luton, P.E., Wayne, J.M., Sharp, R.J., and Riley, P.W., The mcrA Gene as an Alternative to 16S rRNA in the Phylogenetic Analysis of Methanogen Populations in Landfill, Microbiology (UK), 2002, vol. 148, pp. 3521–3530.

    CAS  Google Scholar 

  20. Nunoura, T., Oida, H., Miyazaki, J., Miyashita, A., Imachi, H., and Takai, K., Quantification of mcrA by Fluorescent PCR in Methanogenic and Methanotrophic Microbial Communities, FEMS Microbiol. Ecol., 2008, vol. 64, pp. 240–247.

    Article  CAS  PubMed  Google Scholar 

  21. Kowalchuk, G.A., Stephen, J.R., De Boer, W., Prosser, J.I., Embley, T.M., and Woldendorp, J.W., Analysis of Ammonia-Oxidizing Bacteria of the Beta Subdivision of the Class Proteobacteria in Coastal Sand Dunes by Denaturing Gradient Gel Electrophoresis and Sequencing of PCR-Amplified 16S Ribosomal DNA Fragments, Appl. Environ. Microbiol., 1997, vol. 63, no. 4, pp. 1489–1497.

    CAS  PubMed  Google Scholar 

  22. Beal, E.J., House, C.H., and Orphan, V.J., Manganese- and Iron-Dependent Marine Methane Oxidation, Science, 2009, vol. 325, pp. 184–187.

    Article  CAS  PubMed  Google Scholar 

  23. Nunoura, T., Oida, H., Toki, T., Ashi, J., Takai, K., and Horikoshi, K., Quantification of mcrA by Quantitative Fluorescent PCR in Sediments from Methane Seep of the Nankai Trough, FEMS Microbiol. Ecol., 2006, vol. 57, no. 1, pp. 149–157.

    Article  CAS  PubMed  Google Scholar 

  24. Dang, H., Luan, X., Zhao, J., and Li, J., Diverse and Novel nifH and nifH-Like Gene Sequences in the Deep-Sea Methane Seep Sediments of the Okhotsk Sea, Appl. Environ. Microbiol., 2009, vol. 75, no. 7, pp. 2238–2245.

    Article  CAS  PubMed  Google Scholar 

  25. Treude, T., Krger, M., Boetius, A., and Jörgensen, B.B., Environmental Control on Anaerobic Oxidation of Methane in the Gassy Sediments of Eckernförde Bay (German Baltic), Limnol. Oceanogr., 2005, vol. 50, pp. 1771–1786.

    Article  CAS  Google Scholar 

  26. Steinberg, L.M. and Regan, J.M., mcrA-Targeted Real-Time Quantitative PCR Method to Examine Methanogen Communities, Appl. Environ. Microbiol., 2009, vol. 75, pp. 4435–4442.

    Article  CAS  PubMed  Google Scholar 

  27. Juottonen, H., Galand, P.E., and Yrälä, K., Detection of Methanogenic Archaea in Peat: Comparison of PCR Primers Targeting the mcrA Gene, Res. Microbiol., 2006, vol. 157, pp. 914–921.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Winogradsky Institute of Microbiology, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7, k. 2, Moscow, 117312, Russia

    A. Yu. Merkel, N. A. Chernykh, T. A. Kanapatskii & N. V. Pimenov

Authors
  1. A. Yu. Merkel
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. N. A. Chernykh
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. T. A. Kanapatskii
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. N. V. Pimenov
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to N. V. Pimenov.

Additional information

Original Russian Text © A.Yu. Merkel, N.A. Chernykh, T.A. Kanapatskii, N.V. Pimenov, 2010, published in Mikrobiologiya, 2010, Vol. 79, No. 6, pp. 852–855.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Merkel, A.Y., Chernykh, N.A., Kanapatskii, T.A. et al. Detection of methanotrophic archaea in pockmark sediments (Gdansk Deep, Baltic Sea) by sequence analysis of the gene encoding the α subunit of methyl-coenzyme M reductase. Microbiology 79, 849–852 (2010). https://doi.org/10.1134/S0026261710060196

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0026261710060196

Keywords

Search

Navigation