SEARCH

SEARCH BY CITATION

References

  • Amann, R.I., Binder, B.J., Olson, R.J., Chisholm, S.W., Devereux, R., and Stahl, D.A. (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56: 19191925.
  • Boetius, A., Ravenschlag, K., Schubert, C.J., Rickert, D., Widdel, F., Gieseke, A., et al. (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407: 623626.
  • Bohrmann, G., and Schenck, S. (2004) RV SONNE cruise report SO174, OTEGA II, Balboa – Corpus Christi – Miami (1 October–12 November, 2003). GEOMAR Rep 117: 130.
  • Daims, H., Bruhl, A., Amann, R., Schleifer, K.H., and Wagner, M. (1999) The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 22: 434444.
  • Devereux, R., Kane, M.D., Winfrey, J., and Stahl, D.A. (1992) Genus- and group-specific hybridization probes for determinative and environmental studies of sulfate-reducing bacteria. Syst Appl Microbiol 15: 601609.
  • Felden, J., and Boetius, A. (2009) Mud Volcanism Related Investigations of Sediment Core M70/2b_812_PUC-36, Unpublished Dataset #713379. Bremen, Germany: Max-Planck-Institut für Marine Mikrobiologie.
  • Fuchs, B.M., Glöckner, F.O., Wulf, J., and Amann, R. (2000) Unlabelled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labelled oligonucleotide probes. Appl Environ Microbiol 66: 36033607.
  • Guindon, S., Lethiec, F., Duroux, P., and Gascuel, O. (2005) PHYML Online – a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33: W557W559.
  • Hallam, S.J., Girguis, P.R., Preston, C.M., Richardson, P.M., and DeLong, E.F. (2003) Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Appl Environ Microbiol 69: 54835491.
  • Hallam, S.J., Putnam, N., Preston, C.M., Detter, J.C., Rokhsar, D., Richardson, P.M., and DeLong, E.F. (2004) Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305: 14571462.
  • Hinrichs, K.U., and Boetius, A. (2002) The anaerobic oxidation of methane: new insights in microbial ecology and biogeochemistry. In Ocean Margin Systems. Wefer, G., Billett, D., Hebbeln, D., Jørgensen, B.B., Schlüter, M., and Van Weering, T. (eds). Heidelberg, Germany: Springer-Verlag, pp. 457477.
  • Hinrichs, K., Hayes, J., Sylva, S., Brewer, P., and DeLong, E. (1999) Methane-consuming archaebacteria in marine sediments. Nature 398: 802805.
  • Hoehler, T.M., Alperin, M.J., Albert, D.B., and Martens, C.S. (1994) Field and laboratory studies of methane oxidation in anoxic marine sediment: evidence for a methanogenic-sulfate reducer consortium. Glob Biogeochem Cycles 8: 451463.
  • Holler, T., Wegener, G., Knittel, K., Boetius, A., Brunner, B., Kuypers, M.M.M., and Widdel, F. (2009) Substantial 13C/12C and D/H fractionation during anaerobic oxidation of methane by marine consortia enriched in vitro. Environ Microbiol Rep 1: 370376.
  • Ishii, K., Mussmann, M., MacGregor, B., and Amann, R. (2004) An improved fluorescence in situ hybridization protocol for the identification of bacteria and archaea in marine sediments. FEMS Microbiol Ecol 50: 203213.
  • Kniemeyer, O., Musat, F., Sievert, S.M., Knittel, K., Wilkes, H., Blumenberg, M., et al. (2007) Anaerobic oxidation of short-chain hydrocarbons by marine sulphate-reducing bacteria. Nature 449: 898901.
  • Knittel, K., and Boetius, A. (2009) Anaerobic oxidation of methane: progress with an unknown process. Annu Rev Microbiol 63: 311334.
  • Knittel, K., Boetius, A., Lemke, A., Eilers, H., Lochte, K., Pfannkuche, O., et al. (2003) Activity, distribution, and diversity of sulfate reducers and other bacteria in sediments above gas hydrate (Cascadia Margin, Oregon). Geomicrobiol J 20: 269294.
  • Knittel, K., Lösekann, T., Boetius, A., Kort, R., and Amann, R. (2005) Diversity and distribution of methanotrophic archaea at cold seeps. Appl Environ Microbiol 71: 467479.
  • Krüger, M., Meyerdierks, A., Glockner, F.O., Amann, R., Widdel, F., Kube, M., et al. (2003) A conspicuous nickel protein in microbial mats that oxidize methane anaerobically. Nature 426: 878881.
  • Linke, P., and Suess, E. (2001) R.V. SONNE cruise report SO148 TECFLUX-II-2000 (Victoria-Victoria; July 20-Agust 12, 2000). GEOMAR Rep 98: 122.
  • Lösekann, T., Knittel, K., Nadalig, T., Fuchs, B., Niemann, H., Boetius, A., and Amann, R. (2007) Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea. Appl Environ Microbiol 73: 33483362.
  • Loy, A., Lehner, A., Lee, N., Adamczyk, J., Meier, H., Ernst, J., et al. (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68: 50645081.
  • Lücker, S., Steger, D., Kjeldsen, K., MacGregor, B., Wagner, M., and Loy, A. (2007) Improved 16S rRNA-targeted probe set for analysis of sulfate-reducing bacteria by fluorescence in situ hybridization. J Microbiol Methods 69: 523528.
  • Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 13631371.
  • Macalady, J.L., Lyon, E.H., Koffman, B., Albertson, L.K., Meyer, K., Galdenzi, S., and Mariani, S. (2006) Dominant microbial populations in limestone-corroding stream biofilms, Frasassi Cave System, Italy. Appl Environ Microbiol 72: 55965609.
  • Manz, W., Amann, R., Ludwig, W., Wagner, M., and Schleifer, K.H. (1992) Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions. Syst Appl Microbiol 15: 593600.
  • Manz, W., Eisenbrecher, M., Neu, T.R., and Szewzyk, U. (1998) Abundance and spatial organization of Gram-negative sulfate-reducing bacteria in activated sludge investigated by in situ probing with specific 16S rRNA targeted oligonucleotides. FEMS Microbiol Ecol 25: 4361.
  • Meyerdierks, A., Kube, M., Lombardot, T., Knittel, K., Bauer, M., Glöckner, F.O, et al. (2005) Insights into the genomes of archaea mediating the anaerobic oxidation of methane. Environ Microbiol 7: 19371951.
  • Meyerdierks, A., Kube, M., Kostadinov, I., Teeling, H., Glöckner, F.O., Reinhardt, R., and Amann, R. (2010) Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group. Environ Microbiol 12: 422439.
  • Moran, J.J., Beal, E.J., Vrentas, J.M., Orphan, V.J., Freeman, K.H., and House, C.H. (2008) Methyl sulfides as intermediates in the anaerobic oxidation of methane. Environ Microbiol 10: 162173.
  • Muyzer, G., Teske, A., Wirsen, C., and Jannasch, H. (1995) Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 164: 165172.
  • Nauhaus, K., Boetius, A., Krüger, M., and Widdel, F. (2002) In vitro demonstration of anaerobic oxidation of methane coupled to sulphate reduction in sediment from a marine gas hydrate area. Environ Microbiol 4: 296305.
  • Nauhaus, K., Treude, T., Boetius, A., and Krüger, M. (2005) Environmental regulation of the anaerobic oxidation of methane: a comparison of ANME-I and ANME-II communities. Environ Microbiol 7: 98106.
  • Nauhaus, K., Albrecht, M., Elvert, M., Boetius, A., and Widdel, F. (2007) In vitro cell growth of marine archaeal-bacterial consortia during anaerobic oxidation of methane with sulfate. Environ Microbiol 9: 187196.
  • Neef, A. (1997) Anwendung der in situ Einzelzell-Identifizierung von Bakterien zur Populations analyse in komplexen mikrobiellen Biozönosen. PhD Thesis. Munich, Germany: Technical University Munich.
  • Niemann, H., Lösekann, T., De Beer, D., Elvert, M., Nadalig, T., Knittel, K., et al. (2006) Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink. Nature 443: 854858.
  • Omoregie, E., Niemann, H., Mastalerz, V., De Lange, G., Stadnitskaia, A., Mascle, J., et al. (2009) Microbial methane oxidation and sulfate reduction at cold seeps of the deep Eastern Mediterranean Sea. Mar Geol 261: 114127.
  • Orcutt, B., Samarkin, V., Boetius, A., and Joye, S.B. (2008) On the relationship between methane production and oxidation by anaerobic methanotrophic communities from cold seeps of the Gulf of Mexico. Environ Microbiol 10: 11081117.
  • Orphan, V.J., Hinrichs, K.U., Ussler, W., 3rd, Paull, C.K., Taylor, L.T., Sylva, S.P, et al. (2001) Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl Environ Microbiol 67: 19221934.
  • Orphan, V.J., House, C.H., Hinrichs, K.U., McKeegan, K.D., and DeLong, E.F. (2002) Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proc Natl Acad Sci USA 99: 76637668.
  • Pernthaler, A., Pernthaler, J., and Amann, R. (2004) Sensitive multi-color fluorescence in situ hybridization for the identification of environmental microorganisms. Mol Microbial Ecol Manual 1 and 2: 711725.
  • Pernthaler, A., Dekas, A.E., Brown, C.T., Goffredi, S.K., Embaye, T., and Orphan, V.J. (2008) Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics. Proc Natl Acad Sci USA 105: 70527057.
  • Pruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W., Peplies, J., and Glöckner, F.O. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 71887196.
  • Reeburgh, W.S. (2007) Oceanic methane biogeochemistry. Chem Rev 107: 486513.
  • Reitner, J., Peckmann, J., Blumenberg, M., Michaelis, W., Reimer, A., and Thiel, V. (2005) Concretionary methane-seep carbonates and associated microbial communities inBlack Sea sediments. Palaeogeogr Palaeoclimatol Palaeoecol 227: 1830.
  • Rossel, P.E., Lipp, J.S., Fredricks, H.F., Arnds, J., Boetius, A., Elvert, M., and Hinrichs, K.U. (2008) Intact polar lipids of anaerobic methanotrophic archaea and associated bacteria. Org Geochem 39: 992999.
  • Schramm, A., Fuchs, B.M., Nielsen, J.L., Tonolla, M., and Stahl, D.A. (2002) Fluorescence in situ hybridization of 16S rRNA gene clones (Clone-FISH) for probe validation and screening of clone libraries. Environ Microbiol 4: 713720.
  • Schubert, C.J., Durisch-Kaiser, E., Holzner, C.P., Klauser, L., Wehrli, B., Schmale, O., et al. (2006) Methanotrophic microbial communities associated with bubble plumes above gas seeps in the Black Sea. Geochem Geophys Geosys 7: Q04002.
  • Snaidr, J., Amann, R., Huber, I., Ludwig, W., and Schleifer, K.H. (1997) Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl Environ Microbiol 63: 28842896.
  • Stamatakis, A., Ludwig, T., and Meier, H. (2005) RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21: 456463.
  • Treude, T., Knittel, K., Blumenberg, M., Seifert, R., and Boetius, A. (2005) Subsurface microbial methanotrophic mats in the Black Sea. Appl Environ Microbiol 71: 63756378.
  • Treude, T., Orphan, V.J., Knittel, K., Gieseke, A., House, C.H., and Boetius, A. (2007) Consumption of methane and CO2 by methanotrophic microbial mats from gas seeps of the anoxic Black Sea. Appl Environ Microbiol 73: 22712283.
  • Wegener, G., Niemann, H., Elvert, M., Hinrichs, K.-U., and Boetius, A. (2008a) Assimilation of methane and inorganic carbon by microbial communities mediating the anaerobic oxidation of methane. Environ Microbiol 10: 22872298.
  • Wegener, G., Shovitri, M., Knittel, K., Niemann, H., Hovland, M., and Boetius, A. (2008b) Biogeochemical processes and microbial diversity of the Gullfaks and Tommeliten methane seeps (Northern North Sea). Biogeosciences 5: 11271144.
  • Widdel, F., and Hansen, T. (1992) The dissimilatory sulfate- and sulfur-reducing bacteria. In The Prokaryotes. Balows, A., Trüper, H.G., Dworkin, M., Harder, W., and Schleifer, K.H. (eds). New York, NY, USA: Springer-Verlag, pp. 583624.
  • Zhou, J., Bruns, M.A., and Tiedje, J.M. (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62: 316322.