Microbial community structure in three deep-sea carbonate crusts

Microbial Ecology

Volumn 52, Issue 3, 2006, Pages 451-462

  Heijs, S K ^a   Aloisi, G ^b,e   Bouloubassi, I ^c   Pancost, R D ^d,f   Pierre, C ^b   Sinninghe Damste J S ^d   Gottschal, J C ^a   Van Elsas, J D ^a   Forney, L J ^a,g  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITÉ PIERRE ET MARIE CURIE   (France)

^c LABORATOIRE D OCÉANOGRAPHIE DE VILLEFRANCHE   (France)

^d ROYAL NETHERLANDS INSTITUTE FOR SEA RESEARCH   (Netherlands)

^e UNIVERSITÉ LYON 1   (France)

^f UNIVERSITY OF BRISTOL   (United Kingdom)

^g UNIVERSITY OF IDAHO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CARBON DIOXIDE; CARBONIC ACID DERIVATIVE; LIPID; METHANE; RNA 16S; SEA WATER;

BACTERIUM; CARBONATE; COMMUNITY STRUCTURE; DNA; GENETIC ANALYSIS; LIPID; MARINE ENVIRONMENT; MICROBIAL COMMUNITY; MUD VOLCANO; OCEANIC CRUST; PROKARYOTE; RNA;

ANAEROBIC GROWTH; ARCHAEBACTERIUM; ARTICLE; BIODIVERSITY; CHEMISTRY; CLASSIFICATION; GENETICS; GREENHOUSE EFFECT; METABOLISM; MICROBIOLOGY; PHYLOGENY; PROTEOBACTERIA; SEDIMENT; VOLCANO;

ANAEROBIOSIS; ARCHAEA; BIODIVERSITY; CARBON DIOXIDE; CARBONATES; DNA, BACTERIAL; GEOLOGIC SEDIMENTS; GREENHOUSE EFFECT; LIPIDS; METHANE; PHYLOGENY; PROTEOBACTERIA; RNA, RIBOSOMAL, 16S; SEAWATER; VOLCANIC ERUPTION; WATER MICROBIOLOGY;

ARCHAEA; BACTERIA (MICROORGANISMS); DELTAPROTEOBACTERIA; HALOMONAS; PROKARYOTA; PROTEOBACTERIA;

EID: 33845412481     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-006-9099-8     Document Type: Article

References (57)

1. Aharon, P (1994) Carbon and oxygen isotope tracers of submarine hydrocarbon emissions: Northern Gulf of Mexico. Israel J Earth Sci 43: 157-164
2. Aloisi, G, Pierre, C, Rouchy, JM, Foucher, JP, Woodside, J (2000) Methane-related authigenic carbonates of eastern Mediterranean Sea mud volcanoes and their possible relation to gas hydrate destabilisation. Earth Planet Sci Lett 184: 321-338
3. 4-consuming microorganisms and the formation of carbonate crusts at cold seeps. Earth Planet Sci Lett 203: 195-203
4. Altschul, SF, Gish, W, Miller, W, Myers, EW, Lipman, DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410
5. Barnes, RO, Goldberg, ED (1976) Methane production and consumption in anoxic marine sediments. Geology 4: 297-300
6. Boetius, A, Ravenschlag, K, Schubert, CJ, Rickert, D, Widdel, F, Gieseke, A, Amann, R, Jorgensen, BB, Witte, U, Pfannkuche, O (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407: 623-626
7. Burton, EA (1993) Controls on marine carbonate cement mineralogy: review and reassessment. Chem Geol 105: 163-179
8. Chandler, DP, Li, SM, Spadoni, CM, Drake, GR, Balkwill, DL, Fredrickson, JK, Brockman, FJ (1997) A molecular comparison of culturable aerobic heterotrophic bacteria and 16S rDNA clones derived from a deep subsurface sediment. FEMS Microbiol Ecol 23: 131-144
9. Coleman, ML (1993) Microbial processes: controls on the shape and composition of carbonate concretions. Mar Geol 113: 127-140
10. Costello, AM, Lidstrom, ME (1999) Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments. Appl Environ Microbiol 65:5066-5074
11. DeLong, EF (2003) Oceans of Archaea. ASM News 69: 503-511
12. Deppenmeier, U (2002) The unique biochemistry of methanogenesis. Prog Nucleic Acid Res Mol Biol 71: 223-283
13. Diekmann, OE, Bak, RPM, Tonk, L, Stam, WT, Olsen, JL (2002) No habitat correlation of zooxanthellae in the coral genus Madracis on a Curaçao reef. Mar Ecol Prog Ser 227: 221-232
14. Doronina, NV, Trotsenko, YA, Tourova, TP (2000) Methylarcula marina gen. nov., sp. nov. and Methylarcula terricola sp. nov.: novel aerobic, moderately halophilic, facultatively methylotrophic bacteria from coastal saline environments. Int J Syst Evol Microbiol 50: 1849-1859
15. Girguis, PR, Orphan, VJ, Hallam, SJ, DeLong, EF (2003) Growth and methane oxidation rates of anaerobic methanotrophic archaea in a continuous-flow bioreactor. Appl Environ Microbiol 69:5472-5482
16. Gray, ND, Head, IM (2001) Linking genetic identity and function in communities of uncultured bacteria. Environ Microbiol 3: 481-492
17. Greinert, J, Bohrmann, G, Elvert, M (2002) Stromatolitic fabric of authigenic carbonate crusts: result of anaerobic methane oxidation at cold seeps in 4,850 m water depth. Int J Earth Sci 91: 698-711
18. Hansen, LB, Finster, K, Fossing, H, Iversen, N (1998) Anaerobic methane oxidation in sulfate depleted sediments: effects of sulfate and molybdate additions. Aquat Microb Ecol 14: 195-204
19. Hanson, RS, Hanson, TE (1996) Methanotrophic bacteria. Microbiol Rev 60(2): 439-471
20. Harder, J (1997) Anaerobic methane oxidation by bacteria employing C-14-methane uncontaminated with C-14-carbon monoxide. Mar Geol 137: 13-23
21. Hinrichs, KU, Hayes, JM, Sylva, SP, Brewer, PG, DeLong, EF (1999) Methane-consuming archaebacteria in marine sediments. Nature 398: 802-805
22. Hinrichs, KU, Summons, RE, Orphan, VJ, Sylva, SP, Hayes, JM (2000) Molecular and isotopic analysis of anaerobic methaneoxidizing communities in marine sediments. Org Geochem 31:1685-1701
23. Hoehler, TM, Alperin, MJ, Albert, DB, Martens, CS (1994) Field and laboratory studies of methane oxidation in an anoxic marine sediment: evidence for a methanogen-sulfate reducer consortium. Global Biogeochem Cy 8: 451-463
24. Hoehler, TM, Alperin, MJ, Albert, DB, Martens, CS (2001) Apparent minimum free energy requirements for methanogenic Archaea and sulfate-reducing bacteria in an anoxic marine sediment. FEMS Microbiol Ecol 38: 33-41
25. Holmes, AJ, Owens, NJ, Murrell, JC (1995) Detection of novel marine methanotrophs using phylogenetic and functional gene probes after methane enrichment. Microbiology 141: 1947-1955
26. Hopmans, EC, Schouten, S, Pancost, RD, van der Meer, MJT, Sinninghe, Damsté, JS (2000) Analysis of intact tetraether lipids in archaeal cell material and sediments by high performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry. Rapid Commun Mass Spectrom 14: 585-589
27. Inagaki, F, Takai, K, Komatsu, T, Sakihama, Y, Inoue, A, Horikoshi, K (2002) Profile of microbial community structure and presence of endolithic microorganisms inside a deep-sea rock. Geomicrobiol J 19: 535-552
28. Kato, C, Nogi, Y (2001) Correlation between phylogenetic structure and function: examples from deep-sea Shewanella. FEMS Microbiol Ecol 35: 223-230
29. Lein, A, Pimenov, N, Guillou, C, Martin, JM, Lancelot, C, Rusanov, I, Yusupov, S, Miller, Y, Ivanov, M (2002) Seasonal dynamics of the sulphate reduction rate on the north-western Black Sea shelf. Estuar Coast Shelf Sci 54: 385-401
30. Lein, AY, Ivanov, MV, Pimenov, NV, Gulin, MB (2002) Geochemical peculiarities of the carbonate constructions formed during microbial oxidation of methane under anaerobic conditions. Microbiology 71: 78-90
31. Lein, AY, Pimenov, NV, Savvichev, AS, Pavlova, GA, Vogt, PR, Bogdanov, YA, Sagalevich, AM, Ivanov, MV (2000) Methane as a source of organic matter and carbon dioxide of carbonates at a cold seep in the Norway sea. Geochem Int 38: 232-245
32. Ludwig, W, Strunk, O, Westram, R, Richter, L, Meier, H, Yadhukumar, Buchner, A, Lai, T, Steppi, S, Jobb, G, Forster, W, Brettske, I, Gerber, S, Ginhart, AW, Gross, O, Grumann, S, Hermann, S, Jost, R, Konig, A, Liss, T, Lussmann, R, May, M, Nonhoff, B, Reichel, B, Strehlow, R, Stamatakis, A, Stuckmann, N, Vilbig, A, Lenke, M, Ludwig, T, Bode, A, Schleifer, KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363-1371
33. MEDINAUT, MEDINETH Shipboard Scientific Parties, Aloisi, G, Asjes, S, Bakker, K, Bakker, M, Charlou, J-L, De Lange, G, Donval, J-P, Fiala-Medioni, A, Foucher, J-P, Haanstra, R, Haese, R, Heijs, S, Henry, P, Huguen, C, Jelsma, B, de Lint, S, van der Maarel, M, Mascle, J, Muzet, S, Nobbe, G, Pancost, R, Pelle, H, Pierre, C, Polman, W, de Senerpont, Domis, L, Sibuet, M, Woodside, J, Zitter, T (2000) Linking Mediterranean brine pools and mud volcanism. Eos Trans AGU 81: 625, 631-633
34. Michaelis, W, Seifert, R, Nauhaus, K, Treude, T, Thiel, V, Blumenberg, M, Knittel, K, Gieseke, A, Peterknecht, K, Pape, T, Boetius, A, Amann, R, Jorgensen, BB, Widdel, F, Peckmann, J, Pimenov, NV, Gulin, MB (2002) Microbial reefs in the Black Sea fueled by anaerobic oxidation of methane. Science 297: 1013
35. Morita, RY (1980) Calcite precipitation by marine bacteria. Geomicrobiol J 2: 63-82
36. Orphan, VJ, Hinrichs, KU, Ussler, W III, Paull, CK, Taylor, LT, Sylva, SP, Hayes, JM, DeLong, EF (2001) Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl Environ Microbiol 67: 1922-1934
37. Orphan, VJ, House, CH, Hinrichs, KU, McKeegan, KD, DeLong, EF (2002) Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proc Natl Acad Sci USA 99: 7663-7668
38. Ouverney, CC, Fuhrman, JA (2000) Marine planktonic archaea take up amino acids. Appl Environ Microbiol 66: 4829-4833
39. Pancost, RD, Damste, JSS, de Lint, S, van der Maarel, MJEC, Gottschal, JC (2000) Biomarker evidence for widespread anaerobic methane oxidation in Mediterranean sediments by a consortium of methanogenic archaea and bacteria. Appl Environ Microbiol 66:1126-1132
40. Petit, JR, Jouzel, J, Raynaud, D, Barkov, NI, Barnola, J-M, Basile, I, Chappellaz, J, Davis, M, Delaygue, G, Delmotte, M, Kotlyakov, VM, Legrand, M, Lipenkov, VY, Lorius, C, Pépin, L, Ritz, C, Saltzman, E, Stievenard, M (1999) Climate and atmospheric history of the past 420,000 years from the Vostok ice core, Antarctica. Nature 399: 429-436
41. Pimenov, NV, Rusanov, II, Poglazova, MN, Mityushina, LL, Sorokin, DYu, Khmelenina, VN, Trotsenko, Yu A (1997) Corallike structures at methane seeps in the Black Sea. Microbiology 66:354-360
42. Purdy, KJ, Munson, MA, Cresswell, MT, Nedwell, DB, Embley, TM (2003) Use of 16S rRNA-targeted oligonucleotide probes to investigate function and phylogeny of sulphate-reducing bacteria and methanogenic archaea in a UK estuary. FEMS Microbiol Ecol 44: 361-371
43. Reeburgh, WS (1976) Methane consumption in Cariaco Trench waters and sediments. Earth Planet Sci Lett 28: 337-344
44. Ritger, S, Carson, B, Suess, E (1987) Methane-derived authigenic carbonates formed by subduction induced pore-water expulsion along the Oregon/Washington margin. Geol Soc Am Bull 98:147-156
45. Rivadeneyra, MA, Delgado, G, Ramos-Cormenzana, A, Delgado, R (1998) Biomineralization of carbonates by Halomonas eurihalina in solid and liquid media with different salinities: crystal formation sequence. Res Microbiol 149: 277-287
46. Schoell, M (1983) Genetic characterisation of natural gases. AAPG Bull 67: 2225-2238
47. Teske, A, Hinrichs, KU, Edgcomb, V, Vera Gomez, A, Kysela, D, Sylva, SP, Sogin, ML, Jannasch, HW (2002) Microbial diversity of hydrothermal sediments in the Guaymas basin: evidence for anaerobic methanotrophic communities. Appl Environ Microbiol 68: 1994-2007
48. Thomsen, TR, Finster, K, Ramsing, NB (2001) Biogeochemical and molecular signatures of anaerobic methane oxidation in a marine sediment. Appl Environ Microbiol 67: 1646-1656
49. Torsvik, V, Øvreås, L (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5: 240-245
50. Valentine, DL (2002) Biogeochemistry and microbial ecology of methane oxidation in anoxic environments: a review. Anton Leeuwenhoek Int J G 81: 271-282
51. Valentine, DL, Reeburgh, WS (2000) New perspectives on anaerobic methane oxidation: minireview. Environ Microbiol 2: 477
52. Van de Peer, Y, De Wachter, R (1994) TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comp Appl Biosci 10: 569-570
53. Vasconcelos, C, McKenzie, JA, Rujic, D, Tien, AJ (1995) Microbial mediation as a possible mechanism for natural dolomite formation at low temperatures. Nature 377: 220-222
54. Vetriani, C, Jannasch, HW, MacGregor, BJ, Stahl, DA, Reysenbach, AL (1999) Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments. Appl Environ Microbiol 65: 4375-4384
55. Wolda, H (1981) Similarity indices, sample size and diversity. Oecologia 50: 296-302
56. Wuchter, C, Schouten, S, Boschker, HTS, Sinninghe Damste, JS (2003) Bicarbonate uptake by marine Crenarchaeota. FEMS Microbiol Lett 219: 203-207
57. Zehnder, AJB, Brock, TD (1979) Methane formation and methane oxidation by methanogenic bacteria. J Bacteriol 137: 420-432