Microbial community structures of methane hydrate-bearing sediments in the Ulleung Basin, East Sea of Korea

Marine and Petroleum Geology

Volumn 47, Issue , 2013, Pages 136-146

  Lee, Jin Woo ^a,d   Kwon, Kae Kyoung ^a,b   Azizi, Aqil ^a,b   Oh, Hyun Myung ^a   Kim, Wonduck ^a   Bahk, Jang Jun ^c   Lee, Dong Hun ^d   Lee, Jung Hyun ^a,b  

^a Korea Research Institute of Ships and Ocean Engineering   (South Korea)

^b University of Science and Technology (UST)   (South Korea)

^c Korea Institute of Geosceince and Mineral Resources   (South Korea)

^d Chungbuk National University   (South Korea)

Author keywords

ANME 1b; Candidate division JS1 (JS1); Marine benthic group B (MBGB); Methane hydrate; Sulfate methane transition zone (SMTZ); The Ulleung Basin

Indexed keywords

ANME-1B; CANDIDATE DIVISION JS1 (JS1); MARINE BENTHIC GROUP B (MBGB); METHANE HYDRATES; SULFATE-METHANE TRANSITIONS; ULLEUNG BASIN;

BACTERIA; CLONING; HYDRATION; METHANE; RNA; SEDIMENTS; SULFUR COMPOUNDS;

GAS HYDRATES;

BENTHOS; COMMUNITY STRUCTURE; GAS HYDRATE; GENETIC ANALYSIS; MARINE SEDIMENT; METHANE; MICROBIAL COMMUNITY; OXIDATION; PHYLOGENETICS; RNA; SEDIMENT CORE; SULFATE; SULFATE-REDUCING BACTERIUM;

PACIFIC OCEAN; SEA OF JAPAN; ULLEUNG BASIN;

ARCHAEA; BACTERIA (MICROORGANISMS); DELTAPROTEOBACTERIA;

EID: 84883456203     PISSN: 02648172     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.marpetgeo.2013.06.002     Document Type: Article

References (65)

1. Beal E.J., House C.H., Orphan V.J. Manganese- and iron-dependent marine methane oxidation. Science 2009, 325:184-187.
2. Biddle J.F., Lipp J.S., Lever M.A., Lloyd K.G., Sorensen K.B., Anderson R., Fredricks H.F., Elvert M., Kelly T.J., Schrag D.P., Sogin M.L., Brenchley J.E., Teske A., House C.H., Hinrichs K.U. Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:3846-3851.
3. Boetius A., Ravenschlag K., Schubert C.J., Rickert D., Widdel F., Gieseke A., Amann R., Jorgensen B.B., Witte U., Pfannkuche O. Amarine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 2000, 407:623-626.
4. Briggs B.R., Pohlman J.W., Torres M., Riedel M., Brodie E.L., Colwell F.S. Macroscopic biofilms in fracture-dominated sediment that anaerobically oxidize methane. Appl. Environ. Microb. 2011, 77:6780-6787.
5. Chao A. Non-parametric estimation of the number of classes in a population. Scand. J. Stat. 1984, 11:783-791.
6. Chao A., Ma M.C., Yang M.C.K. Stopping rules and estimation for recapture debugging with unequal failure rates. Biometrika 1993, 80:193-201.
7. Chun J. Computer-assisted Classification and Identification of Actinomycetes 1995, Ph.D. thesis, University of Newcastle, Newcastle upon Tyne, United Kingdom.
8. Colwell F.S., Boyd S., Delwiche M.E., Reed D.W., Phelps T.J., Newby D.T. Estimates of biogenic methane production rates in deep marine sediments at Hydrate Ridge, Cascadia margin. Appl. Environ. Microb. 2008, 74:3444-3452.
9. Dang H.Y., Li T.G., Chen M.N., Huang G.Q. Cross-Ocean distribution of Rhodobacterales bacteria as primary surface colonizers in temperate coastal marine waters. Appl. Environ. Microb. 2008, 74:52-60.
10. Dang H.Y., Luan X.W., Chen R.P., Zhang X.X., Guo L.Z., Klotz M.G. Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea. Fems Microbiol. Ecol. 2010, 72:370-385.
11. Dang H.Y., Luan X.W., Zhao J.Y., Li J. Diverse and novel nifH and nifH-like gene sequences in the deep-sea methane seep sediments of the Okhotsk Sea. Appl. Environ. Microb. 2009, 75:2238-2245.
12. DeLong E.F. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. U. S. A. 1992, 89:5685-5689.
13. DeLong E.F. Everything in moderation: archaea as 'non-extremophiles'. Curr. Opin. Genet. Dev. 1998, 8:649-654.
14. Dhillon A., Teske A., Dillon J., Stahl D.A., Sogin M.L. Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin. Appl. Environ. Microb. 2003, 69:2765-2772.
15. Edlund A., Hardeman F., Jansson J.K., Sjoling S. Active bacterial community structure along vertical redox gradients in Baltic Sea sediment. Environ. Microbiol. 2008, 10:2051-2063.
16. Felsenstein J. Confidence-limits on phylogenies - an approach using the bootstrap. Evolution 1985, 39:783-791.
17. Fry J.C., Parkes R.J., Cragg B.A., Weightman A.J., Webster G. Prokaryotic biodiversity and activity in the deep subseafloor biosphere. Fems Microbiol. Ecol. 2008, 66:181-196.
18. Giovannoni S.J. The polymerase chain reaction. Nucleic Acid Techniques in Bacterial Systematics 1991, 177-203. John Wiley and Sons Ltd., Chichester, United Kingdom. E. Stackebrandt, M. Goodfellow (Eds.).
19. Hallam S.J., Putnam N., Preston C.M., Detter J.C., Rokhsar D., Richardson P.M., DeLong E.F. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 2004, 305:1457-1462.
20. Harrison B.K., Zhang H., Berelson W., Orphan V.J. Variations in archaeal and bacterial diversity associated with the sulfate-methane transition zone in continental margin sediments (Santa Barbara Basin, California). Appl. Environ. Microbiol. 2009, 75:1487-1499.
21. Heijs S.K., Haese R.R., van der Wielen P.W.J.J., Forney L.J., van Elsas J.D. Use of 16S rRNA gene based clone libraries to assess microbial communities potentially involved in anaerobic methane oxidation in a Mediterranean cold seep. Microb. Ecol. 2007, 53:384-398.
22. 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. Glob. Biogeochem. Cy. 1994, 8:451-463.
23. Inagaki F., Nunoura T., Nakagawa S., Teske A., Lever M., Lauer A., Suzuki M., Takai K., Delwiche M., Colwell F.S., Nealson K.H., Horikoshi K., D'Hondt S., Jorgensen B.B. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments, on the Pacific Ocean Margin. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:2815-2820.
24. Inagaki F., Suzuki M., Takai K., Oida H., Sakamoto T., Aoki K., Nealson K.H., Horikoshi K. Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl. Environ. Microb. 2003, 69:7224-7235.
25. Jeong I.S., Cho J.C., Bahk J.J., Hyun S.M., Kwon K.K., Le J.H., Kang S.G., Lee S.H., Lee J.H. Vertical profile of bacterial community in the sediment of Ulleung Basin: implication of the presence of methane-driven community. Microorganisms in Industry and Environment 2010, 219-229. World Scientific, Singapore. Mendez-Vilas (Ed.).
26. Jukes T.H., Cantor C.R. Evolution of protein molecules. Mammalian Protein Metabolism 1969, 21-132. Academic Press, New York. H.N. Munro (Ed.).
27. Kim B.B., Cho H.Y., Hyun J.H. Community structure, diversity, and vertical distribution of archaea revealed by 16S rRNA gene analysis in the deep sea sediment of Ulleung Basin, East Sea. Ocean Polar Res. 2010, 32:309-319.
28. Kim O.S., Cho Y.J., Lee K., Yoon S.H., Kim M., Na H., Park S.C., Jeon Y.S., Lee J.H., Yi H., Won S., Chun J. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbiol. 2012, 62:716-721.
29. Knittel K., Boetius A. Anaerobic oxidation of methane: progress with an unknown process. Annu. Rev. Microbiol. 2009, 63:311-334.
30. Knittel K., Losekann T., Boetius A., Kort R., Amann R. Diversity and distribution of methanotrophic archaea at cold seeps. Appl. Environ. Microb. 2005, 71:467-479.
31. Kuehl S.A., Nittrouer C.A., Allison M.A., Faria L.E.C., Dukat D.A., Jaeger J.M., Pacioni T.D., Figueiredo A.G., Underkoffler E.C. Sediment deposition, accumulation, and seabed dynamics in are energetic fine-grained coastal environment. Cont Shelf Res. 1996, 16:787-815.
32. Kvenvolden K.A. Methane hydrate - a major reservoir of carbon in the shallow geosphere. Chem. Geol. 1988, 71:41-51.
33. Kuever J., Rainey F.A., Widdel F. Family II. Syntrophaceae fam. nov. Bergey's Manual of Systematic Bacteriology 2005, 1033. Springer, New York. second ed. D.J. Brenner, N.R. Krieg, J.T. Staley, G.M. Garrity (Eds.).
34. Lee S.H., Chough S.K. Distribution and origin of shallow gas in deep-sea sediments of the Ulleung Basin, East Sea (Sea of Japan). Geo-Mar Lett. 2003, 22:204-209.
35. Leloup J., Fossing H., Kohls K., Holmkvist L., Borowski C., Jorgensen B.B. Sulfate-reducing bacteria in marine sediment (Aarhus Bay, Denmark): abundance and diversity related to geochemical zonation. Environ. Microbiol. 2009, 11:1278-1291.
36. Liao L., Xu X.W., Wang C.S., Zhang D.S., Wu M. Bacterial and archaeal communities in the surface sediment from the northern slope of the South China Sea. J.Zhejiang Univ. Sci. B 2009, 10:890-901.
37. Lipp J.S., Morono Y., Inagaki F., Hinrichs K.U. Significant contribution of archaea to extant biomass in marine subsurface sediments. Nature 2008, 454:991-994.
38. Lloyd K.G., Schreiber L., Petersen D.G., Kjeldsen K.U., Lever M.A., Steen A.D., Stepanauskas R., Richter M., Kleindienst S., Lenk S., Schramm A., Jorgensen B.B. Predominant archaea in marine sediments degrade detrital proteins. Nature 2013, 496:215-218.
39. Maymo-Gatell X., Chien Y., Gossett J.M., Zinder S.H. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 1997, 276:1568-1571.
40. Nunoura T., Oida H., Toki T., Ashi J., Takai K., Horikoshi K. Quantification of mcrA by quantitative fluorescent PCR in sediments from methane seep of the Nankai Trough. Fems Microbiol. Ecol. 2006, 57:149-157.
41. Orcutt B., Meile C. Constraints on mechanisms and rates of anaerobic oxidation of methane by microbial consortia: process-based modeling of ANME-2 archaea and sulfate reducing bacteria interactions. Biogeosciences 2008, 5:1587-1599.
42. Orcutt B.N., Joye S.B., Kleindienst S., Knittel K., Ramette A., Reitz A., Samarkin V., Treude T., Boetius A. Impact of natural oil and higher hydrocarbons on microbial diversity, distribution, and activity in Gulf of Mexico cold-seep sediments. Deep-Sea Res. Pt. 2010, 57:2008-2021.
43. 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 2001, 293:484-487.
44. Reeburgh W.S. Oceanic methane biogeochemistry. Chem. Rev. 2007, 107:486-513.
45. Reed D.W., Fujita Y., Delwiche M.E., Blackwelder D.B., Sheridan P.P., Uchida T., Colwell F.S. Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl. Environ. Microb. 2002, 68:3759-3770.
46. Roalkvam I., Jorgensen S.L., Chen Y.F., Stokke R., Dahle H., Hocking W.P., Lanzen A., Haflidason H., Steen I.H. New insight into stratification of anaerobic methanotrophs in cold seep sediments. Fems Microbiol. Ecol. 2011, 78:233-243.
47. Rochelle P.A., Cragg B.A., Fry J.C., Parkes R.J., Weightman A.J. Effect of sample handling on estimation of bacterial diversity in marine-sediments by 16s ribosomal-RNA gene sequence-analysis. Fems Microbiol. Ecol. 1994, 15:215-225.
48. Ryu B.J., Riedel M., Kim J.H., Hyndman R.D., Lee Y.J., Chung B.H., Kim I.S. Gas hydrates in the western deep-water Ulleung Basin, East Sea of Korea. Mar Petrol Geol. 2009, 26:1483-1498.
49. Saitou N., Nei M. The neighbor-joining method - a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
50. Schauer R., Bienhold C., Ramette A., Harder J. Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean. Isme J. 2010, 4:159-170.
51. Schloss P.D., Handelsman J. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microb. 2005, 71:1501-1506.
52. Sekiguchi Y., Yamada T., Hanada S., Ohashi A., Harada H., Kamagata Y. Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain bacteria at the subphylum level. Int. J. Syst. Evol. Microbiol. 2003, 53:1843-1851.
53. Siegl A., Kamke J., Hochmuth T., Piel J., Richter M., Liang C.G., Dandekar T., Hentschel U. Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J. 2011, 5:61-70.
54. Sorensen K.B., Teske A. Stratified communities of active archaea in deep marine subsurface sediments. Appl. Environ. Microbiol. 2006, 72:4596-4603.
55. Steven B., Chen M.O., Greer C.W., Whyte L.G., Niederberger T.D. Tumebacillus permanentifrigoris gen. nov., sp nov., an aerobic, spore-forming bacterium isolated from Canadian high Arctic permafrost. Int. J. Syst. Evol. Micr 2008, 58:1497-1501.
56. Takano Y., Chikaraishi Y., Ogawa N.O., Nomaki H., Morono Y., Inagaki F., Kitazato H., Hinrichs K.U., Ohkouchi N. Sedimentary membrane lipids recycled by deep-sea benthic archaea. Nat. Geosci. 2010, 3:858-861.
57. Thauer R.K., Kaster A.K., Seedorf H., Buckel W., Hedderich R. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat. Rev. Microbiol. 2008, 6:579-591.
58. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25:4876-4882.
59. Valentine D.L. Biogeochemistry and microbial ecology of methane oxidation in anoxic environments: a review. Anton Leeuw Int. J. G. 2002, 81:271-282.
60. Valentine D.L., Reeburgh W.S. New perspectives on anaerobic methane oxidation. Environ. Microbiol. 2000, 2:477-484.
61. Vetriani C., Jannasch H.W., MacGregor B.J., Stahl D.A., Reysenbach A.L. Population structure and phylogenetic characterization of marine benthic archaea in deep-sea sediments. Appl. Environ. Microb. 1999, 65:4375-4384.
62. Wang P., Li T., Hu A.Y., Wei Y.L., Guo W.T., Jiao N.Z., Zhang C.L. Community structure of archaea from deep-sea sediments of the South China Sea. Microb. Ecol. 2010, 60:796-806.
63. Webster G., Parkes R.J., Fry J.C., Weightman A.J. Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments. Appl. Environ. Microb. 2004, 70:5708-5713.
64. Webster G., Yarram L., Freese E., Koster J., Sass H., Parkes R.J., Weightman A.J. Distribution of candidate division JS1 and other Bacteria in tidal sediments of the German Wadden Sea using targeted 16S rRNA gene PCR-DGGE. Fems Microbiol. Ecol. 2007, 62:78-89.
65. Yumoto I., Nakamura A., Iwata H., Kojima K., Kusumoto K., Nodasaka Y., Matsuyama H. Dietzia psychralcaliphila sp nov., a novel, facultatively psychrophilic alkaliphile that grows on hydrocarbons. Int. J. Syst. Evol. Micr 2002, 52:85-90.