Distribution and in situ abundance of sulfate-reducing bacteria in diverse marine hydrocarbon seep sediments

Environmental Microbiology

Volumn 14, Issue 10, 2012, Pages 2689-2710

  Kleindienst, Sara ^a   Ramette, Alban ^a   Amann, Rudolf ^a   Knittel, Katrin ^a  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

ARCHAEON; ARTICLE; BACTERIAL LOAD; BIODIVERSITY; CLASSIFICATION; DELTAPROTEOBACTERIA; ECOSYSTEM; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; MICROBIOLOGY; PHYLOGENY; PHYSIOLOGY; SEDIMENT;

ARCHAEA; BACTERIAL LOAD; BIODIVERSITY; DELTAPROTEOBACTERIA; ECOSYSTEM; GEOLOGIC SEDIMENTS; IN SITU HYBRIDIZATION, FLUORESCENCE; PHYLOGENY; RNA, RIBOSOMAL, 16S;

ARCHAEA; BACTERIA (MICROORGANISMS); DELTAPROTEOBACTERIA;

EID: 84867206624     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2012.02832.x     Document Type: Article

References (78)

1. 2 by a new type of sulfate-reducing bacterium. Arch Microbiol 156: 5-14.
2. Aharon, P., and Fu, B. (2000) Microbial sulfate reduction rates and sulfur and oxygen isotope fractionations at oil and gas seeps in deepwater Gulf of Mexico. Geochim Cosmochim Acta 64: 233-246.
3. Alperin, M.J., and Hoehler, T.M. (2009) Anaerobic methane oxidation by archaea/sulfate-reducing bacteria aggregates: 1. Thermodynamic and physical constraints. Am J Sci 309: 869-957.
4. Bazylinski, D.A., Farrington, J.W., and Jannasch, H.W. (1988) Hydrocarbons in surface sediments from a Guaymas Basin hydrothermal vent site. Org Geochem 12: 547-558.
5. Boetius, A., and Suess, E. (2004) Hydrate Ridge: a natural laboratory for the study of microbial life fueled by methane from near-surface gas hydrates. Chem Geol 205: 291-310.
6. Boetius, A., Ravenschlag, K., Schubert, C.J., Rickert, D., Widdel, F., Gieseke, A., etal. (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407: 623-626.
7. Borcard, D., Legendre, P., and Drapeau, P. (1992) Partialling out the spatial component of ecological variation. Ecology 73: 1045-1055.
8. Bowles, M.W., Samarkin, V.A., Bowles, K.M., and Joye, S.B. (2011) Weak coupling between sulfate reduction and the anaerobic oxidation of methane in methane-rich seafloor sediments during ex situ incubation. Geochim Cosmochim Acta 75: 500-519.
9. Brüning, M., Sahling, H., MacDonald, I.R., Ding, F., and Bohrmann, G. (2010) Origin, distribution, and alteration of asphalts at Chapopote Knoll, Southern Gulf of Mexico. Mar Petrol Geol 27: 1093-1106.
10. Chomczynski, P., and Sacchi, N. (2006)) The single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction: twenty-something years on. Nat Protoc 1: 581-585.
11. Claypool, G.E., and Kvenvolden, K.A. (1983) Methane and other hydrocarbon gases in marine sediment. Ann Rev Earth Planet Sci 11: 299-327.
12. Cravo-Laureau, C., Matheron, R., Cayol, J., Joulian, C., and Hirschler-Re'a, A. (2004) Desulfatibacillum aliphaticivorans gen. nov., sp. nov., an n-alkane- and n-alkene-degrading, sulfate-reducing bacterium. Int J Syst Evol Microbiol 54: 77-83.
13. Davidova, I.A., Duncan, K.E., Choi, O.K., and Suflita, J.M. (2006) Desulfoglaeba alkanexedens gen. nov., sp. nov., an n-alkane-degrading, sulfate-reducing bacterium. Int J Syst Evol Microbiol 56: 2737-2742.
14. De Beer, D., Sauter, E., Niemann, H., Kaul, N., Foucher, J.P., Witte, U., etal. (2006) In situ fluxes and zonation of microbial activity in surface sediments of the Haakon Mosby Mud Volcano. Limnol Oceanogr 51: 1315-1331.
15. Felden, J. (2009) Methane fluxes and associated biogeochemical processes in cold seep ecosystems. Doctoral Thesis. Jacobs University, Bremen.
16. Galushko, A., Minz, D., Schink, B., and Widdel, F. (1999) Anaerobic degradation of naphthalene by a pure culture of a novel type of marine sulphate-reducing bacterium. Environ Microbiol 1: 415-420.
17. Grünke, S., Felden, J., Lichtschlag, A., Girnth, A.C., de Beer, D., Wenzhöfer, F., and Boetius, A. (2011) Niche differentiation among mat-forming, sulfide-oxidizing bacteria at cold seeps of the Nile Deep Sea Fan (Eastern Mediterranean Sea). Geobiology 9: 330-348.
18. Harms, G., Zengler, K., Rabus, R., Aeckersberg, F., Minz, D., Rossello-Mora, R., and Widdel, F. (1999) Anaerobic oxidation of o-xylene, m-xylene, and homologous alkylbenzenes by new types of sulfate-reducing bacteria. Appl Environ Microbiol 65: 999-1004.
19. Hinrichs, K.U., Hayes, J.M., Sylva, S.P., Brewer, P.G., and DeLong, E.F. (1999) Methane-consuming archaebacteria in marine sediments. Nature 398: 802-805.
20. 12C and D/H fractionation during anaerobic oxidation of methane by marine consortia enriched in vitro. Environ Microbiol Rep 1: 370-376.
21. Holler, T., Widdel, F., Knittel, K., Amann, R., Kellerman, M.Y., Hinrichs, K., etal. (2011) Thermophilic anaerobic oxidation of methane by marine microbial consortia. ISME J 5: 1946-1956.
22. Hovland, M., Judd, A.G., and Burke, R.A. (1993) The global flux of methane from shallow submarine sediments. Chemosphere 26: 559-578.
23. Jagersma, C.G., Meulepas, R.J.W., Timmers, P.H.A., Szperl, A., Lens, P.N.L., and Stams, A.J.M. (2012) Enrichment of ANME-1 from Eckernförde Bay sediment on thiosulate, methane, and short-chain fatty acids. J Biotechnol 157: 482-489.
24. Joye, S.B., Boetius, A., Orcutt, B.N., Montoya, J.P., Schulz, H.N., Erickson, M.J., and Lugo, S.K. (2004) The anaerobic oxidation of methane and sulfate reduction in sediments from Gulf of Mexico cold seeps. Chem Geol 205: 219-238.
25. Joye, S.B., Samarkin, V.A., Orcutt, B.N., MacDonald, I.R., Hinrichs, K., Elvert, M., etal. (2009) Metabolic variability in seafloor brines revealed by carbon and sulphur dynamics. Nat Geosci 2: 349-354.
26. Kennicutt, M.C., Brooks, J.M., and Denoux, G.J. (1988) Leakage of deep, reservoired petroleum to the near-surface on the Gulf of Mexico continental-slope. Mar Chem 24: 39-59.
27. Kniemeyer, O., Fischer, T., Wilkes, H., Glöckner, F.O., and Widdel, F. (2003) Anaerobic degradation of ethylbenzene by a new type of marine sulfate-reducing bacterium. Appl Environ Microbiol 69: 760-768.
28. Kniemeyer, O., Musat, F., Sievert, S.M., Knittel, K., Wilkes, H., Blumenberg, M., etal. (2007) Anaerobic oxidation of short-chain hydrocarbons by marine sulphate-reducing bacteria. Nature 449: 898-910.
29. Knittel, K., Boetius, A., Lemke, A., Eilers, H., Lochte, K., Pfannkuche, O., etal. (2003) Activity, distribution, and diversity of sulfate reducers and other bacteria in sediments above gas hydrate (Cascadia margin, Oregon). Geomicrobiol J 20: 269-294.
30. 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: 467-479.
31. Kubo, K., Knittel, K., Amann, R., Fukui, M., and Matsuura, K. (2011) Sulfur-metabolizing bacterial populations in microbial mats of the Nakabusa hot spring, Japan. Syst Appl Microbiol 34: 293-302.
32. Legendre, P., and Gallagher, E. (2001) Ecologically meaningful transformations for ordination of species data. Oecologia 129: 271-280.
33. Liu, A., Garcia-Dominguez, E., Rhine, E.D., and Young, L.Y. (2004) A novel arsenate respiring isolate that can utilize aromatic substrates. FEMS Microbiol Ecol 48: 323-332.
34. Lloyd, K.G., Alperin, M.J., and Teske, A. (2011) Environmental evidence for net methane production and oxidation in putative ANaerobic MEthanotrophic (ANME) archaea. Environ Microbiol 13: 2548-2564.
35. 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: 3348-3362.
36. Lovley, D. (2006) Dissimilatory Fe(III)- and Mn(IV)-reducing prokaryotes. Prokaryotes 2: 635-658.
37. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, etal. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
38. MacDonald, I.R., Bohrmann, G., Escobar, E., Abegg, F., Blanchon, P., Blinova, V., etal. (2004) Asphalt volcanism and chemosynthetic life in the Campeche Knolls, Gulf of Mexico. Science 304: 999-1002.
39. Manz, W., Amann, R., Ludwig, W., Wagner, M., and Schleifer, K. (1992) Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions. Syst Appl Microbiol 15: 593-600.
40. 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: 43-61.
41. Mastalerz, V., de Lange, G.J., and Dahlmann, A. (2009) Differential aerobic and anaerobic oxidation of hydrocarbon gases discharged at mud volcanoes in the Nile deep-sea fan. Geochim Cosmochim Acta 73: 3849-3863.
42. Meyer, B., and Kuever, J. (2007) Phylogeny of the alpha and beta subunits of the dissimilatory adenosine-5′-phosphosulfate (APS) reductase from sulfate-reducing prokaryotes - origin and evolution of the dissimilatory sulfate-reduction pathway. Microbiology 153: 2026-2044.
43. Meyer-Reil, L.A. (1983) Benthic response to sedimentation events during autumn to spring at a shallow-water station in the western Kiel bight. Mar Biol 77: 247-256.
44. Michaelis, W., Seifert, R., Nauhaus, K., Treude, T., Thiel, V., Blumenberg, M., etal. (2002) Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane. Science 297: 1013-1015.
45. Morasch, B., Schink, B., Tebbe, C.C., and Meckenstock, R.U. (2004) Degradation of o-xylene and m-xylene by a novel sulfate-reducer belonging to the genus Desulfotomaculum. Arch Microbiol 181: 407-417.
46. Musat, F., Galushko, A., Jacob, J., Widdel, F., Kube, M., Reinhardt, R., etal. (2009) Anaerobic degradation of naphthalene and 2-methylnaphthalene by strains of marine sulfate-reducing bacteria. Environ Microbiol 11: 209-219.
47. Musat, N., Werner, U., Knittel, K., Kolb, S., Dodenhof, T., van Beusekom, J.E.E., etal. (2006) Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea. Syst Appl Microbiol 29: 333-348.
48. Mussmann, M., Ishii, K., Rabus, R., and Amann, R. (2005) Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea. Environ Microbiol 7: 405-418.
49. Muyzer, G., Dewaal, E.C., and Uitterlinden, A.G. (1993) Profiling of complex microbial-populations by denaturing gradient gel-electrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16S ribosomal-RNA. Appl Environ Microbiol 59: 695-700.
50. Muyzer, G., Teske, A., Wirsen, C.O., and Jannasch, H.W. (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: 165-172.
51. Niemann, H., Elvert, M., Hovland, M., Orcutt, B., Judd, A., Suck, I., etal. (2005) Methane emission and consumption at a North Sea gas seep (Tommeliten area). Biogeosciences 2: 335-351.
52. Niemann, H., Lösekann, T., de Beer, D., Elvert, M., Nadalig, T., Knittel, K., etal. (2006) Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink. Nature 443: 854-858.
53. Ommedal, H., and Torsvik, T. (2007) Desulfotignum toluenicum sp. nov., a novel toluene-degrading, sulphate-reducing bacterium isolated from an oil-reservoir model column. Int J Syst Evol Microbiol 57: 2865-2869.
54. Omoregie, E.O., Niemann, H., Mastalerz, V., de Lange, G.J., Stadnitskaia, A., Mascle, J., etal. (2009) Microbial methane oxidation and sulfate reduction at cold seeps of the deep Eastern Mediterranean Sea. Mar Geol 261: 114-127.
55. Orcutt, B., Boetius, A., Elvert, M., Samarkin, V., and Joye, S.B. (2005) Molecular biogeochemistry of sulfate reduction, methanogenesis and the anaerobic oxidation of methane at Gulf of Mexico cold seeps. Geochim Cosmochim Acta 69: 4267-4281.
56. Orcutt, B.N., Boetius, A., Lugo, S.K., MacDonald, I.R., Samarkin, V.A., and Joye, S.B. (2004) Life at the edge of methane ice: microbial cycling of carbon and sulfur in Gulf of Mexico gas hydrates. Chem Geol 205: 239-251.
57. Orcutt, B.N., Joye, S.B., Kleindienst, S., Knittel, K., Ramette, A., Reitz, A., etal. (2010) Impact of natural oil and higher hydrocarbons on microbial diversity, distribution, and activity in Gulf of Mexico cold-seep sediments. Deep Sea Res II 57: 2008-2021.
58. Orphan, V.J., Hinrichs, K.U., Ussler, W., Paull, C.K., Taylor, L.T., Sylva, S.P., etal. (2001) Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl Environ Microbiol 67: 1922-1934.
59. 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: 7663-7668.
60. Otte, S., Kuenen, J.G., Nielsen, L.P., Paerl, H.W., Zopfi, J., Schulz, H.N., etal. (1999) Nitrogen, carbon, and sulfur metabolism in natural Thioploca samples. Appl Environ Microbiol 65: 3148-3157.
61. Paull, C.K., Hecker, B., Commeau, R., Freeman-Lynde, R.P., Neumann, C., Corso, W.P., etal. (1984) Biological communities at the Florida escarpment resemble hydrothermal vent taxa. Science 226: 965-967.
62. Pernthaler, A., Pernthaler, J., and Amann, R. (2002) Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 68: 3094-3101.
63. 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: 7052-7057.
64. 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: 7188-7196.
65. Rabus, R., Nordhaus, R., Ludwig, W., and Widdel, F. (1993) Complete oxidation of toluene under strictly anoxic conditions by a new sulfate-reducing bacterium. Appl Environ Microbiol 59: 1444-1451.
66. Ramette, A. (2007) Multivariate analyses in microbial ecology. FEMS Microbiol Ecol 62: 142-160.
67. Rao, C.R. (1964) The use and interpretation of principal component analysis in applied research. Sankhya A 26: 329-358.
68. Ravenschlag, K., Sahm, K., Knoblauch, C., Jørgensen, B.B., and Amann, R. (2000) Community structure, cellular rRNA content and activity of sulfate-reducing bacteria in marine Arctic sediments. Appl Environ Microbiol 66: 3592-3602.
69. Rossel, P.E., Lipp, J.S., Fredricks, H.F., Arnds, J., Boetius, A., Elvert, M., etal. (2008) Intact polar lipids of anaerobic methanotrophic archaea and associated bacteria. Org Geochem 39: 992-999.
70. Schreiber, L., Holler, T., Knittel, K., Meyerdierks, A., and Amann, R. (2010) Identification of the dominant sulfate-reducing bacterial partner of anaerobic methanotrophs of the ANME-2 clade. Environ Microbiol 12: 2327-2340.
71. Schubotz, F., Lipp, J.S., Elvert, M., Kasten, S., Mollar, X.P., Zabel, M., etal. (2011) Petroleum degradation and associated microbial signatures at the Chapopote asphalt volcano, Southern Gulf of Mexico. Geochim Cosmochim Acta 75: 4377-4398.
72. Simoneit, B.R.T., and Lonsdale, P.F. (1982) Hydrothermal petroleum in mineralized mounds at the seabed of Guaymas Basin. Nature 295: 198-202.
73. Teske, A., Hinrichs, K., Edgcomb, V., Gomez, A., Kysela, D., Sylva, S.P., etal. (2002) Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl Environ Microbiol 68: 1994-2007.
74. Treude, T., Boetius, A., Knittel, K., Wallmann, K., and Jørgensen, B.B. (2003) Anaerobic oxidation of methane above gas hydrates at Hydrate Ridge, NE Pacific Ocean. Mar Ecol Prog Ser 264: 1-14.
75. Weber, A., and Jørgensen, B.B. (2002) Bacterial sulfate reduction in hydrothermal sediments of the Guaymas Basin, Gulf of California, Mexico. Deep Sea Res I 49: 827-841.
76. Wegener, G., Shovitri, M., Knittel, K., Niemann, H., Hovland, M., and Boetius, A. (2008) Biogeochemical processes and microbial diversity of the Gullfaks and Tommeliten methane seeps (Northern North Sea). Biogeosciences 5: 1127-1144.
77. Widdel, F., Knittel, K., and Galushko, A. (2010) Anaerobic hydrocarbon-degrading microorganisms: an overview. In Handbook of Hydrocarbon and Lipid Microbiology. Timmis, K.N., McGenity, T., van der Meer, J.R., and de Lorenzo, V. (eds). Berlin, Heidelberg: Springer, pp. 1997-2021.
78. Yarza, P., Ludwig, W., Euzéby, J., Amann, R., Schleifer, K., Glöckner, F.O., and Rosselló-Móra, R. (2010) Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 33: 291-299.