Culture-Independent Characterization of Microbial Diversity in Selected Deep-Sea Sediments

Chiaki Kato; Shizuka Arakawa; Takako Sato; Xiang Xiao

doi:10.1128/9781555815646.ch13

Chapter 13 : Culture-Independent Characterization of Microbial Diversity in Selected Deep-Sea Sediments

Authors: Chiaki Kato¹, Shizuka Arakawa², Takako Sato³, Xiang Xiao⁴

VIEW AFFILIATIONS HIDE AFFILIATIONS

Affiliations: 1: Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology, Yokosuka 237-0061, Japan; 2: Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology, Yokosuka 237-0061, Japan; 3: Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology, Yokosuka 237-0061, Japan; 4: Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, People’s Republic of China

Content Type: Monograph

Publication Year: 2008

Category: Applied and Industrial Microbiology

Book DOI: 10.1128/9781555815646

Chapter DOI: 10.1128/9781555815646.ch13

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:

Culture-Independent Characterization of Microbial Diversity in Selected Deep-Sea Sediments, Page 1 of 2

< Previous page | Next page > /docserver/preview/fulltext/10.1128/9781555815646/9781555814236_Chap13-1.gif /docserver/preview/fulltext/10.1128/9781555815646/9781555814236_Chap13-2.gif

Abstract:

This chapter focuses on studies of the microbial diversity in deep-sea methane-impacted sediments using culture-independent procedures. It discusses sulfur and carbon cycling ecosystems in chemosynthetic pathways which are independent of solar-power-dependent energy-generating systems. Microbial diversity studies in deep-sea sediments have been performed at depths ranging from ~1,000 m, in Sagami Bay, to ~11,000 m, in the Mariana Trench Challenger Deep. To study the different cold-seep microbial ecosystems present between the Japan Trench land slope and the Nankai Trough, the microbial diversity of Nankai Trough cold-seep sites at different depths was investigated and correlations were sought between the microbial communities and their geological settings. Methylotrophs are a group of bacteria which can utilize methane (methanotrophs) and/or a variety of other one-carbon (C1) compounds more reduced than formic acid, such as methanol and methylated amines, as sole carbon and energy sources. The levels of methylotrophs in the sediments of the tropical West Pacific Warm Pool (WP) were semiquantified by quantitative competitive PCR. It was found that the WP contained around 3 * 104 to 3 * 105 molecules of mxaF gene copy per gram of sediment. Using this method, the distribution and abundance of methylotrophs in deep-sea sediments from the West Pacific WP were compared with those in east and middle Pacific deep-sea sediments, seashore sediments, and flower garden and rice field soils.

Citation: Kato C, Arakawa S, Sato T, Xiao X. 2008. Culture-Independent Characterization of Microbial Diversity in Selected Deep-Sea Sediments, p 219-236. In Michiels C, Bartlett D, Aersten A (ed), High-Pressure Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555815646.ch13

Key Concept Ranking

Microbial Ecology: 0.52517456
Bacteria and Archaea: 0.4605939
Restriction Fragment Length Polymorphism: 0.4428227

0.52517456

Highlighted Text: Show | Hide

Full text loading...

Figures

Culture-Independent Characterization of Microbial Diversity in Selected Deep-Sea Sediments

[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555815646.ch13-1,webId=/content/author/10.1128/9781555815646.ch13-1,properties={foaf_givenname=Chiaki, foaf_name=Chiaki Kato, foaf_surname=Kato, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555815646.ch13-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555815646.ch13-2,webId=/content/author/10.1128/9781555815646.ch13-2,properties={foaf_givenname=Shizuka, foaf_name=Shizuka Arakawa, foaf_surname=Arakawa, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555815646.ch13-aff2]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555815646.ch13-3,webId=/content/author/10.1128/9781555815646.ch13-3,properties={foaf_givenname=Takako, foaf_name=Takako Sato, foaf_surname=Sato, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555815646.ch13-aff3]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555815646.ch13-4,webId=/content/author/10.1128/9781555815646.ch13-4,properties={foaf_givenname=Xiang, foaf_name=Xiang Xiao, foaf_surname=Xiao, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555815646.ch13-aff4]]}]]

/content/10.1128/9781555815646.ch13.ch13fig01

Figure 1.

Comparison of the microbial abundance of the Japan Trench cold-seep sediments at different depths (JT58, 5,791 m; JT64, 6,367 m; and JT75, 7,434 m) calculated from the numbers of 16S rRNA gene clones. (A) Bacterial diversity; (B) archaeal diversity.

10.1128/9781555815646/f0221-01_thmb.gif

10.1128/9781555815646/f0221-01.gif

Figure 1.

/content/10.1128/9781555815646.ch13.ch13fig02

Figure 2.

t-RFLP profiles of bacterial (A) and archaeal (B) community structures of the NT06, NT20, and NT33 sites. γ,δ, and ε indicate the corresponding proteobacterial groups. SYM, symbiotic bacteria related to SOx; Met, methanogenic archaea; Uk, unknown. The lengths of fragments (x axis) and relative fluorescence intensities of peaks (y axis) are also displayed.

10.1128/9781555815646/f0223-01_thmb.gif

10.1128/9781555815646/f0223-01.gif

Figure 2.

/content/10.1128/9781555815646.ch13.ch13fig03

Figure 3.

t-RFLP profiles of bacterial (A) and archaeal (B) community structures of the SBC and SBM. Abbreviations are the same as in Fig. 2 .

10.1128/9781555815646/f0224-01_thmb.gif

10.1128/9781555815646/f0224-01.gif

Figure 3.

t-RFLP profiles of bacterial (A) and archaeal (B) community structures of the SBC and SBM. Abbreviations are the same as in Fig. 2 .

/content/10.1128/9781555815646.ch13.ch13fig04

Figure 4.

Comparison of t-RFLP profiles of bacterial (A) and archaeal (B) communities between the microbial mats at the M1 and M2 sites. Abbreviations are the same as in Fig. 2 .

10.1128/9781555815646/f0226-01_thmb.gif

10.1128/9781555815646/f0226-01.gif

Figure 4.

Comparison of t-RFLP profiles of bacterial (A) and archaeal (B) communities between the microbial mats at the M1 and M2 sites. Abbreviations are the same as in Fig. 2 .

/content/10.1128/9781555815646.ch13.ch13fig05

Figure 5.

Sulfur and carbon cycling ecosystems within the microbial community in the cold-seep environment.

10.1128/9781555815646/f0227-01_thmb.gif

10.1128/9781555815646/f0227-01.gif

Figure 5.

Sulfur and carbon cycling ecosystems within the microbial community in the cold-seep environment.

/content/10.1128/9781555815646.ch13.ch13fig06

Figure 6.

Phylogenetic tree constructed based on deduced partial MxaF amino acid sequences. The MxaF sequences retrieved from the sediment of tropical West Pacific WP and from the cultured representative methylotrophs, including type I and type II methanotrophs, are involved in the tree construction. Only bootstrap values above 90 from 1,000 replicates are shown. The scale bar represents 0.05 substitution per amino acid site. The environmental mxaF clones from the Pacific WP sediment are designated by “wp”; the numbers in parentheses are the numbers of clones with identical sequences in the 90 sequenced clones.

10.1128/9781555815646/f0230-01_thmb.gif

10.1128/9781555815646/f0230-01.gif

Figure 6.

/content/10.1128/9781555815646.ch13.ch13fig07

Figure 7.

Phylogenetic tree constructed based on 16S rRNA gene sequences of archaea. Archaeal 16S rRNA gene clones retrieved from the Pacific WP sediments were named AW. Nine AW> clones together with relative clones in the data bank were used for phylogenetic tree construction. The phylogenetic tree was constructed from a matrix by least-squares distance matrix analysis and the neighbor-joining method using the DNAMAN program. One thousand trials of bootstrap analysis were used to provide confident estimates for phylogenetic tree topologies. Only bootstrap values above 50 are shown. The scale bar represents 0.05 substitution per nucleic acid site.

10.1128/9781555815646/f0231-01_thmb.gif

10.1128/9781555815646/f0231-01.gif

Figure 7.

/content/10.1128/9781555815646.ch13.ch13fig08

Figure 8.

Phylogenetic tree showing the relationship of WPA and related clones and strains. Archaeal 16S rRNA gene clones retrieved by PCR using primers ANMEF and 907R from the Pacific WP sediment were named WPA. Fifteen sequences representing 15 different RFLP types of WPA and 16S rRNA gene sequences of reference clones or strains in the data bank were used for dendrogram construction. The phylogenetic tree was constructed from a matrix by least-squares distance matrix analysis and the neighbor-joining method using the DNAMAN program, and 1,000 trials of bootstrap analysis were used to provide confident estimates for phylogenetic tree topologies. Only bootstrap values above 50 are shown. The scale bar represents 0.05 substitution per nucleic acid site.

10.1128/9781555815646/f0232-01_thmb.gif

10.1128/9781555815646/f0232-01.gif

Figure 8.

References

/content/book/10.1128/9781555815646.ch13

1. Arakawa, S.,, C. Kato,, T. Sato,, Y. Nogi,, Y. Yoshida,, R. Usami, and, K. Horikoshi. 2004. Microbial diversity of bacterial mat samples collected at a depth of 3,100 m in the Japan Sea. Mar. Biotechnol. 6: s185– s189.

2. Arakawa, S.,, M. Mori,, L. Li,, Y. Nogi,, T. Sato,, Y. Yoshida,, R. Usami, and, C. Kato. 2005. Cold-seep microbial communities are more abundant at deeper depths in the Japan Trench land slope. J. Jpn. Soc. Extremophiles 4: 50– 55.

3. Arakawa, S.,, T. Sato,, R. Sato,, J. Zhang,, T. Gamo,, U. Tsunogai,, A. Hirota,, Y. Yoshida,, R. Usami,, F. Inagaki, and, C. Kato. 2006. Molecular phylogenetic and chemical analyses of the microbial mats in deep-sea cold seep sediments at the northeastern Japan Sea. Extremophiles 10: 311– 319.

4. Arakawa, S.,, T. Sato,, Y. Yoshida,, R. Usami, and, C. Kato. 2006. Comparison of the microbial diversity in cold-seep sediments from the different water depths in the Nankai Trough. J. Gen. Appl. Microbiol. 52: 47– 54.

5. Ashi, J. 1997. Distribution of cold seepage at the fault scarp of the eastern Nankai accretionary prism. JAMSTEC J. Deep Sea Res. 13: 495– 501.

6. Barry, J. P.,, R. E. Kochevar, and, C. H. Baxter. 1997. The influence of pore-water chemistry and physiology on the distribution of vesicomyid clams at cold seeps in Monterey Bay: implications for patterns of chemosynthetic community organization. Limnol. Oceanogr. 42: 318– 328.

7. Boetius, A.,, K. Ravenschlag,, C. J. Schubert,, D. Ricket,, F. Widdel,, A. Gieseke,, R. Amann,, B. B. Jorgensen,, U. Witte, and, O. Pfannkuche. 2000. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407: 623– 626.

8. Bourne, D. B.,, I. R. Mcdonald, and, J. C. Murrell. 2001. Comparison of pmoA PCR primer sets as tools for investigating methanotroph diversity in three Danish soils. Appl. Environ. Microbiol. 67: 3802– 3809.

9. Cavanaugh, C. M. 1994. Microbial symbiosis: patterns of diversity in the marine environment. Am. Zool. 34: 79– 89.

10. DeLong, E. F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89: 5685– 5689.

11. D’Hondt, S.,, S. Rutherford, and, A. J. Spivack. 2002. Metabolic activity of subsurface life in deep-sea sediments. Science 295: 2067– 2070.

12. Fang, J.,, A. Shizuka,, C. Kato, and, S. Schouten. 2006. Microbial diversity of cold-seep sediments in Sagami Bay, Japan, as determined by 16S rRNA gene and lipid analyses. FEMS Microbiol. Ecol. 57: 429– 441.

13. Fujikura, K.,, Y. Fujiwara,, S. Kojima, and, T. Okutani. 2002. Micro-scale distribution of mollusks occurring in deep-sea chemosynthesis-based communities in the Japan Trench. Venus 60: 225– 236.

14. Fujikura, K.,, S. Kojima,, K. Tamaki,, Y. Maki,, J. Hunt, and, T. Okutani. 1999. The deepest chemosynthesis-based community yet discovered from the hadal zone, 7326m deep, in the Japan Trench. Mar. Ecol. Prog. Ser. 190: 17– 26.

15. Fujiwara, Y.,, C. Kato,, N. Masui,, K. Fujikura, and, S. Kojima. 2001. Dual symbiosis in the cold-seep thyasirid clam Maorithyas hadalis from the hadal zone in the Japan Trench, western Pacific. Mar. Ecol. Prog. Ser. 214: 151– 159.

16. Gamo, T.,, J. Ishibashi,, K. Shitashima,, T. Nakatsuka,, U. Tsunogai,, T. Masuzawa,, H. Sakai, and, K. Mitsuzawa. 1994. Chemical characteristics of cold seepage at the eastern Nankai Trough accretionary prism (KAIKO-TOKAI Program): a preliminary report of the dive 113 of “Shinkai 6500.” JAMSTEC J. Deep Sea Res. 10: 343– 352.

17. Hanson, R. S., and, T. E. Hanson. 1996. Methanotrophic bacteria. Microbiol. Rev. 60: 439– 471.

18. Hashimoto, J.,, S. Ohta,, K. Fujikura,, Y. Fujiwara, and, S. Sukizaki. 1995. Life habit of vesicomyid clam, Calyptogena soyoae, and hydrogen sulfide concentration in interstitial waters in Sagami Bay, Japan. J. Oceanogr. 51: 341– 350.

19. Hashimoto, J.,, S. Ohta,, T. Tanaka,, H. Hotta,, S. Matsuzawa, and, H. Sakai. 1989. Deep-sea communities dominated by the giant clam, Calyptogena soyoae, along the slope foot of Hatsushima island, Sagami Bay, central Japan. Paleogeogr. Paleoclimatol. Palaeoecol. 71: 179– 192.

20. Henckel, T.,, M. Friedrich, and, R. Conrad. 1999. Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase. Appl. Environ. Microbiol. 65: 1980– 1990.

21. Henry, P.,, S. Lallemant,, K. Nakamura,, U. Tsunogai,, S. Mazzotti, and, K. Kobayashi. 2002. Surface expression of fluid venting at the toe of the Nanakai wedge and implication for flow paths. Mar. Geol. 187: 119– 143.

22. Horz, H. P.,, M. T. Yimga, and, W. Liesack. 2001. Detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoA, mmoX, mxaF, and 16S rRNA and ribosomal DNA, including pmoA-based terminal restriction fragment length polymorphism profiling. Appl. Environ. Microbiol. 67: 4177– 4185.

23. Inagaki, F.,, Y. Sakihama,, A. Inoue,, C. Kato, and, K. Horikoshi. 2002. Molecular phylogenetic analyses of reverse transcripted bacterial rRNA obtained from deep-sea cold seep sediments. Environ. Microbiol. 4: 277– 286.

24. Inagaki, F.,, U. Tsunogai,, M. Suzuki,, A. Kosaka,, H. Machiyama,, K. Takai,, T. Nunoura,, K. H. Nealson, and, K. Horikoshi. 2004. Characterization of C1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, the Southern Ryukyu arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes. Appl. Environ. Microbiol. 70: 7445– 7455.

25. Kato, C., and, S. Arakawa. 2004. Microbial diversity and uncultivable microorganisms in deep-sea environment, p. 132– 147. In T. Kudo and, M. Ohkuma (ed.), Novel Technology for Uncultivable Microorganisms— Approach to Unused Bio-Resources. CMC Press, Tokyo, Japan. (In Japanese.)

26. Kato, C.,, S. Arakawa,, R. Usami, and, T. Sato. 2005. Microbial diversity in the cold seep sediments and sulfur circulation. Gekkan Chikyu 27: 939– 948. (In Japanese.)

27. Kato, C.,, L. Li,, J. Tamaoka, and, K. Horikoshi. 1997. Molecular analyses of the sediment of the 11000 m deep Mariana Trench. Extremophiles 1: 117– 123.

28. Kennicutt, M. C., II,, J. M. Brooks,, R. R. Bridigare,, R. R. Fay,, T. L. Wade, and, S. J. McDonald. 1985. Vent-type taxa in a hydrocarbon seep region on the Louisiana slope. Nature 317: 351– 353.

29. Kennicutt, M. C., II,, J. M. Brooks,, R. R. Bridigare,, S. J. McDonald, and, D. L. Adkison. 1989. An upper slope “cold” seep community: Northern California. Limnol. Oceanogr. 34: 635– 640.

30. Kobayashi, K. 2002. Tectonic significance of the cold seepage zones in the eastern Nankai accretionary wedge—an outcome of the 15 years’ KAIKO projects. Mar. Geol. 187: 3– 30.

31. Kodaira, S.,, T. Iidaka,, A. Kato,, J. O. Park,, T. Iwasaki, and, Y. Kaneda. 2004. High pore fluid pressure may cause silent slip in the Nankai Trough. Science 304: 1295– 1298.

32. Kojima, S.,, K. Fujikura, and, T. Okutani. 2004. Multiple trans-Pacific migrations of deep-sea vent/seependemic bivalves in the family Vesicomyidae. Mol. Phylogenet. Evol. 32: 396– 406.

33. Kulm, L. D.,, E. Suess,, J. C. Moore,, B. Carson,, B. T. Lewis,, S. D. Ritger,, D. C. Kadko,, T. M. Thornburg,, R. W. Embly,, W. D. Rugh,, G. J. Massoth,, M. G. Langseth,, G. R. Cochrane, and, R. L. Scamman. 1986. Oregon subduction zone: venting, fauna, and carbonates. Science 231: 561– 566.

34. Kuramoto, S.,, J. Ashi,, J. Greinert,, S. Gulic,, T. Ishimura,, S. Morita,, K. Nakamura,, M. Okada,, T. Okamoto,, D. Rickert,, S. Saiyo,, E. Suess,, U. Tsunogai, and, T. Tomosugi. 2001. Surface observations of subduction related mud volcanoes and large thrust sheets in the Nankai subduction margin; report on YK0010 and YK01-04 cruises. JAMSTEC J. Deep Sea Res. 19: 131– 139.

35. Kuramoto, S., and, M. Joshima. 1998. Precise gravity measurements for gas hydrate layer. JAMSTEC J. Deep Sea Res. 14: 371– 377.

36. LePichon, X.,, T. Iiyama,, J. Boulegue,, J. Charvet,, M. Faure,, K. Kano,, S. Lallemant,, H. Okada,, C. Ran-gin,, A. Taira,, T. Urabe, and, S. Uyeda. 1987. Nankai Trough and Zenisu Ridge: a deep-sea submersible survey. Earth Planet Sci. Lett. 83: 285– 299.

37. Li, L.,, J. Guenzennec,, P. Nichols,, P. Henry,, M. Yanagibayashi, and, C. Kato. 1999. Microbial diversity in Nankai Trough sediments at a depth of 3843 m. J. Oceanogr. 55: 635– 642.

38. Li, L., and, C. Kato. 1999. Microbial diversity in the sediments collected from cold-seep areas and from different depths of the deep-sea, p. 55– 58. In K. Horikoshi and, K. Tsujii (ed.), Extremophiles in Deep-Sea Environments. Springer-Verlag, Tokyo, Japan.

39. Li, L.,, C. Kato, and, K. Horikoshi. 1999. Bacterial diversity in deep-sea sediments from different depths. Biodivers. Conserv. 8: 659– 677.

40. Li, L.,, C. Kato, and, K. Horikoshi. 1999. Microbial communities in the world’s deepest ocean bottom, the Mariana Trench, p. 17– 20. In H. Ludwig (ed.), Advances in High Pressure Bioscience and Biotechnology. Springer-Verlag, Heidelberg, Germany.

41. Li, L.,, C. Kato, and, K. Horikoshi. 1999. Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench. Mar. Biotechnol. 1: 391– 400.

42. Massana, R.,, E. F. DeLong, and, C. Pedrós-Alió. 2000. A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl. Environ. Microbiol. 66: 1777– 1787.

43. Masuzawa, T.,, N. Handa,, H. Kitagawa, and, M. Kusakabe. 1992. Sulfate reduction using methane in sediments beneath a bathyal “cold seep” giant clam community off Hatsushima Island, Sagami Bay, Japan. Earth Planet Sci. Lett. 110: 39– 50.

44. Mcdonald, I. R., and, J. C. Murrell. 1997. The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs. Appl. Environ. Microbiol. 63: 3218– 3224.

45. Momma, H.,, R. Iwase,, K. Mitsuzawa,, Y. Kaiho, and, Y. Fujiwara. 1998. Preliminary results of a three-year continuous observation by a deep seafloor in Sagami Bay, central Japan. Phys. Earth Planet. Interiors 108: 263– 274.

46. Ogawa, Y.,, K. Fujioka,, K. Fujikura, and, Y. Iwabuchi. 1996. En echelon patterns of Calyptogena colonies in the Japan Trench. Geology 24: 807– 810.

47. Ohta, S., and, L. Laubier. 1987. Deep biological communities in the subduction zone of Japan from bottom photographs taken during “Nautile” dives in the Kaiko project. Earth Planet Sci. Lett. 83: 329– 342.

48. Ohta, S.,, H. Sakai,, A. Taira,, K. Ohwada,, T. Ishii,, M. Maeda,, K. Fujioka,, Y. Saino,, K. Kogure,, T. Gamo,, Y. Shirayama,, T. Furuta,, T. Ishizuka,, K. Endow,, T. Sumi,, H. Hotta,, J. Hashimoto,, N. Handa,, T. Masuzawa, and, M. Horikoshi. 1987. Multidisciplinary investigation of the Calyptogena communities at the Hatsushima site, Sagami Bay, central Japan. JAMSTEC J. Deep-Sea Res. 3: 51– 60.

49. Ohtake, M. 1995. A seismic gap in the eastern margin of the Sea of Japan as inferred from the time-space distribution of past seismicity. Island Arc 4: 156– 165.

50. Okamura, Y.,, K. Satake,, A. Takeuchi,, T. Gamo,, C. Kato,, Y. Sasayama,, F. Nakayama,, K. Ikehara, and, T. Kodera. 2002. Techtonic, geochemical and biological studies in the eastern margin of the Japan Sea—preliminary results of Yokosuka/Shinkai 6500 YK01-06 Cruise. JAMSTEC J. Deep Sea Res. 20: 77– 114.

51. Orphan, V. J.,, K. U. Hinrichs,, W. Ussler III,, C. K. Paull,, L. T. Taylor,, S. P. Sylva,, J. M. Hayes, and, E. F. DeLong. 2001. Comparative analysis of methane-oxidizing archaea and sulfate-reducing bacteria in anoxic marine sediments. Appl. Environ. Microbiol. 67: 1922– 1934.

52. Orphan, V. J.,, C. H. House,, K. U. Hinrichs,, K. D. McKeegan, and, E. F. DeLong. 2001. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293: 484– 487.

53. Park, J. O.,, T. Tsuru,, S. Kodaira,, P. R. Cummins, and, Y. Kaneda. 2002. Splay fault branching along the Nankai subduction zone. Science 297: 1157– 1160.

54. Paull, C. K.,, B. Hecker,, R. Commeau,, R. P. Freeman-Lynde,, C. Neumann,, W. P. Corso,, S. Golubic,, J. E. Hook,, E. Sikes, and, J. Curray. 1984. Biological communities at the Florida Escarpment resemble hydrothermal vent taxa. Science 226: 965– 967.

55. Sibuet, M.,, S. K. Juniper, and, G. Pautot. 1988. Cold-seep benthic communities in the Japan subduction zones: geological control of community development. J. Mar. Res. 46: 333– 348.

56. Sieburth, J. M.,, P. W. Johnson,, M. A. Eberhardt,, M. E. Sieracki,, M. Lidstrom, and, D. Laux. 1987. The first methane-oxidizing bacterium from the upper mixing layer of the deep ocean: Methylomonas pelagica sp. nov. Curr. Microbiol. 14: 285– 293.

57. Stott, L.,, C. Poulsen,, S. Lund, and, R. Thunell. 2002. Super ENSO and global climate oscillations at millennial time scales. Science 297: 222– 226.

58. Takai, K.,, H. Oida,, Y. Suzuki,, H. Hirayama,, S. Nakagawa,, T. Nunoura,, F. Inagaki,, K. H. Nealson, and, K. Horikoshi. 2004. Spatial distribution of marine Crenarchaeota group I in the vicinity of deep-sea hydrothermal systems. Appl. Environ. Microbiol. 70: 2404– 2413.

59. Takeuchi, A.,, Y. Okamura,, Y. Kato,, K. Ikehara,, J. Zhang,, K. Satake,, T. Nagao,, M. Hirano, and, M. Watanabe. 2000. Large earthquakes and bottom disturbances in the Okushiri ridge along the eastern margin of Japan Sea. JAMSTEC J. Deep Sea Res. 16: 29– 46.

60. Thomsen, T. R.,, K. Finster, and, E. B. Ramsing. 2001. Biochemical and molecular signatures of anaerobic methane oxidation in a marine sediment. Appl. Environ. Microbiol. 67: 1646– 1656.

61. Tsunogai, U.,, J. Ishibashi,, H. Wakita,, T. Gamo,, T. Masuzawa,, T. Natatsuka,, Y. Nojiri, and, T. Nakamura 1996. Freshwater seepage and pore water recycling on the seafloor: Sagami Trough subduction zone. Earth Planet Sci. Lett. 138: 157– 168.

62. Vetriani, C.,, H. W. Jannasch,, B. J. MacGregor,, D. A. Stahl, and, A. L. Reysenbach. 1999. Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Appl. Environ. Microbiol. 65: 4375– 4384.

63. Visser, K.,, R. Thunell, and, L. Stott. 2003. Magnitude and timing of temperature change in the indo-Pacific Warm Pool during deglaciation. Nature 421: 152– 155.

64. Wang, P.,, F. Wang,, M. Xu, and, X. Xiao. 2004. Molecular phylogeny of methylotrophs in a deep-sea sediment from a tropical west Pacific Warm Pool. FEMS Microbiol. Ecol. 47: 77– 84.

65. Wang, P.,, X. Xiao, and, F. P. Wang. 2005. Phylogenetic analysis of Archaea in the deep-sea sediments of west Pacific Warm Pool. Extremophiles 9: 209– 217.

66. Wei, D., and, T. Seno. 1998. Determination of the Amurian Plate motion, p. 337– 346. In M. J. Flower et al. (ed.), Mantle Dynamics and Plate Interactions in East Asia. Geodynamics series, vol. 27. American Geophysical Union, Washington, DC.