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標題: 台灣西南海域深水盆地區底泥微生物相結構分析
Microbial community structure in the deep-basin area SW offshore of Taiwan
作者: 陳丁濡
Chen, Ding-Ju
關鍵字: 16S rRNA gene
16S rRNA基因
Deep sea sediment
Microbial community
出版社: 生命科學系所
引用: 賴美津。2008。台灣西南海域新興能源-天然氣水合物資源調查與評估地球化學調查研究:台灣西南海域地質微生物(細菌與太古生物)多樣性調查與天然氣水合物形成與分解機制探討 (1/4)。中央地質調查所報告第97-29B號,委辦計畫編號(97-5226903000-02-03)。 賴美津。2009。台灣西南海域新興能源-天然氣水合物資源調查與評估地球化學調查研究:台灣西南海域地質微生物(細菌與太古生物)多樣性調查與天然氣水合物形成與分解機制探討 (2/4)。中央地質調查所報告第98-27-B號,委辦計畫編號(98-5226904000-04-03)。 賴美津。2010。台灣西南海域新興能源—天然氣水合物資源調查與評估:地球化學調查研究(3/4)。中央地質調查所報告第99-26-B 號,委辦計畫編號 (99-5226904000-04-03) 賴美津。2011。台灣西南海域新興能源—天然氣水合物資源調查與評估:地球化學調查研究(4/4)。中央地質調查所報告第100-25-B號,委辦計畫編號(100-5226904000-02-03)。 肯奈特(Kennett, J. P.)著,陳民本譯。1986。海洋地質學。國立編譯館主編。南山堂,台北。 楊燦堯。2010。台灣西南海域新興能源—天然氣水合物資源調查與評估:地球化學調查研究(3/4)。中央地質調查所報告第99-26-A號,委辦計畫編號(99-5226904000-04-03)。 徐春田。2010。台灣西南海域新興能源-天然氣水合物資源調查與評估:震測及地熱調查(3/4)。中央地質調查所報告第99-25-E 號,委辦計畫編號(99-5226904000-04-02)。 林曉武。2010。台灣西南海域新興能源-天然氣水合物資源調查與評估地球化學調查研究(3/4)。中央地質調查所報告第99-26-C 號,委辦計畫編號(99-5226904000-04-03)。 林曉武。2010。台灣西南海域新興能源-天然氣水合物資源調查與評估地球化學調查研究(3/4)。中央地質調查所報告第99-26 號,委辦計畫編號(99-5226904000-04-03)。 孫文惠。2008。高美濕地太古生物與細菌相。中興大學生命科學系碩士論文。 Anderson, I., O. D. N. Djao, M. Misra, O. Chertkov, M. Nolan, S. Lucas, A. Lapidus, T. G. Del Rio, H. Tice, J.-F. Cheng, R. Tapia, C. Han, L. Goodwin, S. Pitluck, K. Liolios, N. Ivanova, K. Mavromatis, N. Mikhailova, A. Pati, E. Brambilla, A. Chen, K. Palaniappan, M. Land, L. Hauser, Y.-J. Chang, C. D. Jeffries, J. Sikorski, S. Spring, M. Rohde, K. Eichinger, H. Huber, R. Wirth, M. Göker, J. C. Detter, T. Woyke, J. Bristow, J. A. Eisen, V. Markowitz, P. Hugenholtz, H.-P. Klenk and N. C. Kyrpides. 2010. Complete genome sequence of Methanothermus fervidus type strain (V24S). Stand Genomic Sci. 3:315-24. Arrigo, K. R. 2007. CARBON CYCLE: Marine manipulations. Nature 450:491-492. Baldauf, S. L., D. Bhattacharya, J. Cockrill, P. Hugenholtz, J. Pawlowski and A. G. B. Simpson. 2004. The tree of life: An overview. p. 43-75. In J. Cracraft and M. J. Donoghue (ed.), Oxford University Press, UK. Barns, S. M. and S. A. Nierzwicki-Bauer. 1997. Microbial diversity in ocean, surface, and subsurface environments. Rev. Mineral. 35:35-79. Barns, S. M., C. F. Delwiche, J. D. Palmer and N. R. Pace. 1996. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. PNAS 93:9188-9193. Barns, S. M., R. E. Fundyga, M. W. Jeffries and N. R. Pace. 1994. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. PNAS 91:1609-1613. Biddle, J. F., J. S. Lipp, M. A. Lever, K. G. Lloyd, K. B. Sørensen, R. Anderson, H. F. Fredricks, M. Elvert, T. J. Kelly, D. P. Schrag, M. L. Sogin, J. E. Brenchley, A. Teske, C. H. House and K.-U. Hinrichs. 2006. Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. PNAS 103:3846-3851. Blazejak, A., and A. Schippers. 2010. High abundance of JS-1- and Chloroflexi –related Bacteria in deeply buried marine sediments revealed by quantitative, real-time PCR. FEMS Microbiol. Ecol. 72:198-207. Blazejak, A., C. Erséus, R. Amann and N. Dubilier. Coexistence of Bacterial Sulfide Oxidizers, Sulfate Reducers, and Spirochetes in a Gutless Worm (Oligochaeta) from the Peru Margin. 2005. Appl. Environ. Microbiol. 71: 1553-1561. Boetius A., K. Ravenschlag, C. Schubert, D. Rickert, F. Widdel, A. Gieseke, R. Amann, B. B. Jørgensen, U. Witte and O. Pfannkuche. 2000. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623-626 Bonch-Osmolovskaya, E. A., A. I. Slesarev, M. L. Miroshnichenko, T. P. Svetlichnaya and V. A. Alekseev. 1988. Characteristics of Desulfurococcus amylolyticus n. sp.: a new extremely thermophilic archaebacterium isolated from thermal springs of Kamchatka and Kunashir Island. Mikrobiologiya 57:94-101. Briggs, B. R., J. W. Pohlman, M. Torres, M. Riedel, E. L. Brodie and F. S. Colwell. 2011. Macroscopic biofilms in fracture-dominated sediment that anaerobically oxidize methane. Appl. Environ. Microbiol. 77:6780-6787. Brochier-Armanet, C., B. Boussau, S. Gribaldo and P. Forterre. 2008. Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat. Rev. Microbiol. 6:245-252. Brochier, C., S. Gribaldo, Y. Zivanovic, F. Confalonieri and P. Forterre. 2005. Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Genome Biol. 6:R42. Chao, H. C. and C. F. You. 2006. Distribution of B, Cl and their isotopes in pore waters separated from gas hydrate potential areas, offshore southwestern Taiwan. Terr. Atmos. Ocean. Sci. 17:961-979. Chen, C. T. and H. C. Tseng. 2006. Abnormally high CH4 concentrations in seawater at mid-depths on the continental slopes of the northern South China Sea. Terr. Atmos. Ocean. Sci. 17:951-959. Chong, S. C., Y. Liu, M. Cummins, D. L. Valentine and D. R. Boone. 2002. Methanogenium marinum sp. nov., a H2-using methanogen from Skan Bay, Alaska, and kinetics of H2 utilization. Anton. Van Leeuw. 81:263-270. Chuang, P. C., T. F. Yang, S. Lin, H. F. Lee, T. F. Lan, W. L. Hong, C. S. Liu, J. C. Chen, and Y. Wang. 2006. Extremely high methane concentration in bottom water and cored sediments from offshore southwestern Taiwan. Terr. Atmos. Ocean. Sci. 17:903-920. Coolen, M. J. L., H. Cypionka, A. M. Sass, H. Sass and J. Overmann. 2002. Ongoing modification of mediterranean pleistocene sapropels mediated by prokaryotes. Science 296:2407-2410. Cragg, B. A., R. J. Parkes, J. C. Fry, A. J. Weightman, P. A. Rochelle, and J. R. Maxwell. 1996. Bacterial populations and processes in sediments containing gas hydrates (ODP leg 146: Cascadia margin). Earth Planet. Sci. Lett. 139:497–507. Dang, H., X. Luan, J. Zhao and J. Li. 2009. Diverse and Novel nifH and nifH-Like Gene Sequences in the Deep-Sea Methane Seep Sediments of the Okhotsk Sea. Appl. Environ. Microbiol. 75:2238-2245. Dang, H., X.-W. Luan, R. Chen, X. Zhang, L. Guo and M. G. Klotz. 2010. Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea. FEMS Microbiol. Ecol. 72:370-385. de la Torre, J. R., C. B. Walker, A. E. Ingalls, M. Könneke and D. A. Stahl. 2008. Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol. Environ. Microbiol. 10:810-818. DeLong, E. F. 1998. Everything in moderation: archaea as ‘non-extremophiles’. Curr. Opin. Genet. Devel. 8:649-654. Dhillon, A., M. Lever, K. G. Lloyd, D. B. Albert, M. L. Sogin and A. Teske. 2005. Methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A (mcrA) genes in hydrothermal sediments of the Guaymas Basin. Appl Environ. Microbiol. 71:4592-4601. Di, H. J., K. C. Cameron, J.-P. Shen, C. S. Winefield, M. O’Callaghan, S. Bowatte and J.-Z. He. 2010. Ammonia-oxidizing bacteria and archaea growunder contrasting soil nitrogen conditions. FEMS Microbiol Ecol 72:386–394. D’Hondt, S., S. Rutherford, and A. J. Spivack. 2002. Metabolic activity of subsurface life in deep-sea sediments. Science 295:2067-2070. Dimitrov L. I. 2002. Mud volcanoes—the most important pathway for degassing deeply buried sediments. Earth-Sci. Rev. 59:49-76. Elkins, J. G., M. Podar, D. E. Graham, K. S. Makarova, Y. Wolf, L. Ranau, B. P. Hedlund, C. Brochier-Armanet, V. Kunin, I. Anderson, A. Lapidus, E. Goltsman, K. Barry, E. V. Koonin, P. Hugenholtz, N. Kyrpides, G. Wanner, P. Richardson, M. Keller and K. O. Stetter. 2008. A korarchaeal genome reveals insights into the evolution of the Archaea. PNAS 105:8102-8107. Ferrer, M., O. V. Golyshina, T. N. Chernikova, A. N. Khachane, V. A. Martins Dos Santos, M. M. Yakimov, K. N. Timmis and P. N. Golyshin. 2005. Microbial enzymes mined from the Urania deepsea hypersaline anoxic basin. Chem. Biol. 12:895-904. Fiala, G. and K. O. Stetter. 1986. Pyrococcus furiosus sp. nov. represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100°C. Arch. Microbiol. 145:56- 61. Fry, J. C., J. R. Parkes, B. A. Cragg, A. J. Weightman and G. Webster. 2008. Prokaryotic biodiversity and activity in the deep subseafloor biosphere. FEMS Microbiol. Ecol. 66:181–196. Gabor, E. M., E. J. de Vries and D. B. Janssen. 2004. Construction, characterization, and use of small-insert gene banks of DNA isolated from soil and enrichment cultures for the recovery of novel amidases. Environ. Microbiol. 6:948-958. Giulio M.D. 2007. The tree of life might be rooted in the branch leading to Nanoarchaeota. Gene 401:108-113. Grossman, E. L., L. A. Cifuentes and I. M. Cozzarelli. 2002. Anaerobic methane oxidation in a landfill-leachate plume. Environ. Sci. Technol. 36:2436-2442. Gruber, N. 2008. The marine nitrogen cycle: Overview and challenges, p. 1-50. In D. G. Capone, D. A. Bronk, M. R. Mulholland and E. J. Carpenter (ed.), Amsterdam, The Netherlands: Elsevier Inc. Harris, J. K., S. T. Kelley and N. R. Pace. 2004. New Perspective on Uncultured Bacterial Phylogenetic Division OP11. Appl. Environ. Microbiol. 70:845-849. Hershberger, K. L., S. M. Barns, A.-L. Reysenbach, S. C. Dowson and N. R. Pace. 1996. Wide diversity of Creanarchaeota. Nature 384-420. Hinrichs, K.-U., J. M. Hayes, S. P. Sylva, P. G. Brewer, E. F. DeLong. 1999. Methane-consuming Archaebacteria in marine sediments. Nature 398:802–805. Hofmann, E. E., B. Cahill, K. Fennel, M. A. M. Friedrichs, K. Hyde, C. Lee, A. Mannino, R. G. Najjar, J. E. O’Reilly, J. Wilkin and J. Xue. 2011. Modeling the Dynamics of Continental Shelf Carbon. Annu. Rev. Mar. Sci. 3:93–122. Huang, C. Y., C. W. Chien, M. Zhao, H. C. Li and Y. Iizuka. 2006. Geological study of active cold seeps in the syn-collision accretionary prism Kaoping slope off SW Taiwan. Terr. Atmos. Ocean. Sci. 17: 679-702. Huber, H., S. Burggraf, T. Mayer, I. Wyschkony, R. Rachel and K. O. Stetter. 2000. Ignicoccus gen. nov., a novel genus of hyperthermophilic, chemolithoautotrophic Archaea, represented by two new species, Ignicoccus islandicus sp. nov. and Ignicoccus pacificus sp. nov.Int. J. Syst. Evol. Micr. 50;2093–2100. Huber, J. A., H. P. Johnson, D. A. Butterfield and J. A. Baross. 2006. Microbial life in ridge flank crustal fluids. Environ. Microbiol. 8:88-99. Hugenholtz, P., C. Pitulle, K. L. Hershberger and N. R. Pace. 1998. Novel Division Level Bacterial Diversity in a Yellowstone Hot Spring. J. Bacteriol. 180:366-376. Inagaki, F., M. Suzuki, K. Takai, H. Oida, T. Sakamoto, K. Aoki, K. H. Nealson and K. Horikoshi. 2003. Microbial communities associated with geological horizons in coastal subseafloor sediments from the sea of Okhotsk. Appl. Environ. Microbiol. 69:7224-7235. Inagaki, F., T. Nunoura, S. Nakagawa, A. Teske, M. Lever, A. Lauer, M. Suzuki, K. Takai, M. Delwiche, F. S. Colwell, K. H. Nealson, K. Horikoshi, S. D’Hondt and B. B. Jørgensen. 2006. Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. PNAS 103:2815-2820. Jarrell, K. F., G. D. Sprott and A. T. Matheson. 1984. Intracellular potassium concentration and relative acidity of the ribosomal proteins of methanogenic bacteria. Can. J. Microbiol. 30:663-668 Javor, B. 1989. Hypersaline environments: microbiology and biogeochemistry, p101-124. Springer-Verlag, New York. Jeon, J. H., J. T. Kim, Y. J. Kim, H. K. Kim, H. S. Lee, S. G. Kang, S. J. Kim and J. H. Lee. 2009. Cloning and characterization of a new cold-active lipase from a deep-sea sediment metagenome. Appl. Microbiol. Biotechnol. 81:865-874. Kato, S., K. Yanagawa, M. Sunamura, Y. Takano, J. Ishibashi, T. Kakegawa, M. Utsumi, T. Yamanaka, T. Toki, T. Noguchi, K. Kobayashi, A. Moroi, H. Kimura, Y. Kawarabayasi, K. Marumo, T. Urabe and A. Yamagishi. 2009. Abundance of ZetaProteobacteria within crustal fluids in back-arc hydrothermal fields of the Southern Mariana Trough. Environ. Microbiol. 11:3210-3222. Kendall, M. M., and D. R. Boone. 2006. Cultivation of methanogens from shallow marine sediments at Hydrate Ridge, Oregon. Archaea 2:31–38. Kendall, M. M., G. D. Wardlaw, C. F. Tang, A. S. Bonin, Y. Liu and D. L. Valentine. 2007. Diversity of Archaea in Marine Sediments from Skan Bay, Alaska, Including Cultivated Methanogens, and Description of Methanogenium boonei sp. nov. Appl. Environ. Microbiol. 73: 407-414. Kennedy, J., B. Flemer, S. A. Jackson, D. P. H. Lejon, J. P. Morrissey, F. O’Gara and A. D. W. Dobson. 2010. Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism. Mar. Drugs 8:608-628. Kim, B. S., H. M. Oh, H. Kang and J. Chun. 2005. Archaeal diversity in tidal flat sediment as revealed by 16S rDNA analysis. J. Microbiol. 43:144-151. Kletzin, A. 2007. General characteristics and important model organism, p. 14-92. In R. Cavicchioli (ed.), ASM Press, Washington, DC. Knittel, K. and A. Boetius. 2009. Anaerobic Oxidation of Methane: Progress with an Unknown Process. Annu. Rev. Microbiol. 63:311-34. Knittel, K., T. Losekann, A. Boetius, R. Kort and R. Amann. 2005. Diversity and distribution of methanotrophic archaea at cold seeps. Appl. Environ. Microbiol. 71:467-479. Kormas, K. A., A. Meziti, A. Dählmann, G. J. De Lange and V. Lykousis. 2008. Characterization of methanogenic and prokaryotic assemblages based on mcrA and 16S rRNA gene diversity in sediments of the Kazan mud volcano (Mediterranean Sea). Geobiology 6:450-460. Lai, M. C., T. Y. Hong and R. P. Gunsalus. 2000. Glycine betaine transport in the obligate halophilic archaeon Methanohalophilus portucalensis. J. Bacteriol. 182:5020-5024. LaMontagne, M. G., I. Leifer, S. Bergmann, L. C. Van De Werfhorst, and P. A. Holden. 2004. Bacterial diversity in marine hydrocarbon seep sediments. Environ. Microbiol. 6: 799–808. Lanoil, B. D., M. T. La Duc, M. Wright, M. Kastner, K. H. Nealson, and D. H. Bartlett. 2005. Archaeal diversity in ODP legacy borehole 892b and associated seawater and sediments of the Cascadia Margin. FEMS Microbiol. Ecol. 54:167–177. Lanoil, B. D., R. Sassen, M. T. LaDuc, S. T. Sweet, and K. H. Nealson. 2001. Bacteria and Archaea physically associated with Gulf of Mexico gas hydrates. Appl. Environ. Microbiol. 67:5143–5153. Lin, S., W. C. Hsieh, Y. C. Lim, T. F. Yang, C. S. Liu, and Y. Wang. 2006. Methane migration and its influence on sulfate reduction in the Good Weather Ridge region, South China Sea continental margin sediments. Terr. Atmos. Ocean. Sci. 17:883-902. Lipp, J. S., Y. Morono, F. Inagaki and K.-U. Hinrichs. 2008. Significant contribution of Archaea to extant biomass in marine subsurface sediments. Nature 454:991-994. Liu, C. S., P. Schnürle, Y. Wang, S. H. Chung, S. C. Chen, and T. H. Hsiuan. 2006. Distribution and characters of gas hydrate offshore of southwestern Taiwan. Terr. Atmos. Ocean. Sci. 17:615-644. Lloyd, K. G., L. Lapham and A. Teske. 2006. An Anaerobic Methane-Oxidizing Community of ANME-1b Archaea in Hypersaline Gulf of Mexico Sediments. Appl. Environ. Microbiol. 72:7218-7230. Martens-Habbena, W., P. M. Berube, H. Urakawa, J. R. de la Torre and D. A. Stahl. 2009. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 461:976-979. Maslin, M., M. Owen, R. Betts, S. Day, T. D. Jones and A. Ridgwell. 2010. Gas hydrates: past and future geohazard? Phil. Trans. R. Soc. A. 368:2369-2393. Mathur, E. J., G. Toledo, B. D. Green, M. Podar, T. H. Richardson, M. Kulwiec and H. W. Chang. 2005. A biodiversity-based approach to development of performance enzymes: applied metagenomics and directed evolution. Ind. Biotechnol. 4:283-287. Matsutani, N., T. Nakagawa, K. Nakamura, R. Takahashi, K. Yoshihara and T. Tokuyama. 2011. Enrichment of a novel marine ammonia-oxidizing archaeon obtained from sand of an eelgrass zone. Microbes Environ. 26:23-29. Milkov, A.V. 2004. Global estimates of hydrate-bound gas in marine sediment: how much is really out there? Earth-Sci. Rev. 66:183-197. Mills, H. J., C. Hodges, K. Wilson, I. R. MacDonald and P. A. Sobecky. 2003. Microbial diversity in sediments associated with surface-breaching gas hydrate mounds in the Gulf of Mexico. FEMS Microbiol. Ecol. 46:39-52. Mori, K., K. Yamaguchi, Y. Sakiyama, T. Urabe and K.-I. Suzuki. 2009. Caldisericum exile gen. nov., sp. nov., an anaerobic, thermophilic, filamentous bacterium of a novel bacterial phylum, Caldiserica phyl. nov., originally called the candidate phylum OP5, and description of Caldisericaceae fam. nov., Caldisericales ord. nov. and Caldisericia classis nov. Int. J. Syst. Evol. Micr. 59:2894–2898. Mori, K., M. Sunamura, K. Yanagawa, J.-I. Ishibashi, Y. Miyoshi, T. Iino, K.-I. Suzuki, and T. Urabe. 2008. First Cultivation and Ecological Investigation of a Bacterium Affiliated with the Candidate Phylum OP5 from Hot Springs. Appl. Environ. Microb. 74:6223–6229. Morikawa, M., Y. Izawa, N. Rashid, T. Hoaki and T. Imanaka. 1994. Purification and characterization of a thermostable thiol protease from a newly isolated hyperthermophilic Pyrococcus sp. Appl. Environ. Microbiol. 60:4559-4566. Nealson, K. H. and D. A. Stahl. 1997. Microorganisms and biogeochemical cycles: what can we learn from layered microbial communities? p. 5-34. In P. H. Ribbe (ed.), Mineralogical Society of America, Washington, D. C. Newberry, C. J., G. Webster, A. J. Weightman and J. C. Fry. 2004. Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190. Environ. Microbiol. 6:274-287. Nunoura T., Y. Takaki, J. Kakuta, S. Nishi, J. Sugahara, H. Kazama, G. J. Chee, M. Hattori, A. Kanai, H. Atomi, K. Takai and H. Takami. 2011. Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res. 39:3204-3223. Omoregie, E. O., H. Niemann, V. Mastalerz, G. J. de Lange, A. Stadnitskaia, J. Mascle, J.-P. Foucher, A. Boetius. 2009. Microbial methane oxidation and sulfate reduction at cold seeps of the deep Eastern Mediterranean Sea. Mar. Geol. 261:114-127. Orcutt, B. N., J. B. Sylvan, N. J. Knab and K. J. Edwards. 2011. Microbial Ecology of the Dark Ocean above, at, and below the Seafloor. Microbiol. Mol. Biol. R. 75:361-422. 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 Orphan, V. J., C. H. House, K.-U. Hinrichs, K. D. McKeegan, and E. F. DeLong. 2002. Multiple archaeal groups mediate methane oxidation in anoxic cold seep sedimets. PNAS 99:7663-7668. Oung, J. N., C. Y. Lee, C. S. Lee, and C. L. Kuo. 2006. Geochemical study on hydrocarbon gases in seafloor sediments, southwestern offshore Taiwan - implications in the potential occurrence of gas hydrates. Terr. Atmos. Ocean. Sci. 17:921-931. Pachiadaki, M. G., V. Lykousis, E. G. Stefanou and K. A. Kormas. 2010. Prokaryotic communitystructure and diversity in the sediments of an active submarine mud volcano (Kazanmudvolcano, East Mediterranean Sea). FEMS Microbiol. Ecol. 72:429-444. Parkes, R. J., B. A. Cragg, and P. Wellsbury. 2000. Recent studies on bacterial populations and processes in sub seafloor sediments: a review. Hydrogeol. J. 8:11-28. Parkes, R. J., G. Webster, B. A. Cragg, A. J. Weightman, C. J. Newberry, T. G. Ferdelman, J. Kallmeyer, B. B. Jørgensen, I. W. Aiello and J. C. Fry. 2005. Deep subseafloor prokaryotes stimulated at interfaces over geological time. Nature 436:390-394. Pester, M., C. Schleper and M. Wagner. 2011. The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Curr. Opin. Microbiol. 14:300–306. Raghoebarsing A. A., A. Pol, K. T. van de Pas-Schoonen, A. J. P. Smolders, K. F. Ettwig, W. I. C. Rijpstra, S. Schouten, J. S. S. Damsté, H. J. M. Op den Camp, M. S. M. Jetten and M. Strous. 2006. A microbial consortium couples anaerobic methane oxidation to denitrification. Nature 440:918-21. Ravin, N. V., A. V. Mardanov, A. V. Beletsky, I. V. Kublanov, T. V. Kolganova, A. V. Lebedinsky, N. A. Chernyh, E. A. Bonch-Osmolovskaya and K. G. Skryabin. 2009. Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis. J. Bacteriol. 191:2371-2379. Reeburgh W. S. 2007. Oceanic methane biogeochemistry. Chem. Rev. 107:486-513. Reed, A. J., R. A. Lutz, and C. Vetriani. 2006. Vertical distribution and diversity of bacteria and archaea in sulfide and methane-rich cold seep sediments located at the base of the Florida Escarpment. Extremophiles 10: 199-211. Reed, D. W., Y. Fujita, M. E. Delwiche, D. B. Blackwelder, P. P. Sheridan, T. Uchida and F. S. Colwell. 2002. Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin. Appl. Environ. Microbiol. 68:3759-3770. Rochelle, P. A., B. A. Cragg, J. C. Fry, R. J. Parkes and A. J. Weightman. 1994. Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rRNA gene sequence analysis. FEMS Microbiol. Ecol. 15:215-225 Santelli, C. M., B. N. Orcutt, E. Banning, W. Bach, C. L. Moyer, M. L. Sogin, H. Staudigel and K. J. Edwards. 2008. Abundance and diversity of microbial life in ocean crust. Nature 453:653-656. Schauer, R., C. Bienhold, A. Ramette and J. Harder. 2010. Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean. ISME J. 4:159-170. Schubert, C. J., F. Vazquez, T. Lösekann-Behrens, K. Knittel, M. Tonolla and A. Boetius. 2011. Evidence for anaerobic oxidation of methane in sediments of a freshwater system (Lago diCadagno). FEMS. Microbiol. Ecol. 76:26-38. Sievert, S. M., R. P. Kiene and H. N. Schulz-Vogt. 2007. The Sulfur Cycle. Oceanography 20:117-123. Sørensen, K. B. and A. Teske. 2006. Stratified communities of active archaea in deep marine subsurface sediments. Appl. Environ. Microbiol. 72:4596-4603. Takai, K. and K. Horikoshi. 1999. Genetic diversity of Archaea in deep-sea hydrothermal vent environments. Genetics 152:1285-1297. Takai, K. and K. Nakamura. 2011. Archaeal diversity and community development in deep-sea hydrothermal vents. Curr. Opin. Microbiol. 14:282-291. Takai, K. and Y. Sako. 1999. A molecular view of archaeal diversity in marine and terrestrial hot water environments. FEMS Microbiol. Ecol. 28:177-188. Takai, K., D. P. Moser, M. DeFlaun, T. C. Onstott and J. K. Fredrickson. 2001. Archaeal diversity in waters from deep South African gold mines. Appl. Environ. Microbiol. 67:5750-5760. Takai, K., S. Nakagawa, A.-L. Reysenbach and J. Hoek. 2006. Microbial ecology of Mid-Ocean Ridges and Back-Arc Basins. Geophysical Monograph Series 166: Back Arc Spreading Systems, Geological, Biological, Chemical and Physical Interactions 185-213. Takai, K., T. Nunoura, J. Ishibashi, J. Lupton, R. Suzuki, H. Hamasaki, Y. Ueno, S. Kawagucci, T. Gamo, Y. Suzuki, H. Hirayama and K. Horikoshi. 2008. Variability in the microbial communities and hydrothermal fluid chemistry at the newly-discovered Mariner hydrothermal field, southern Lau Basin. J. Geophys. Res. 113:G02031. Takai, K., T. Nunoura, K. Horikoshi, T. Shibuya, K. Nakamura, Y. Suzuki, M. Stott, G. J. Massoth, B. W. Christenson, C. E. J. deRonde, D. A. Butterfield, J. Ishibashi, J. E. Lupton and L. J. Evans. 2009. Variability in Microbial Communities in Black Smoker Chimneys at the NW Caldera Vent Field, Brothers Volcano, Kermadec Arc. Geomicrobiol. J. 26:552-569. Tamaki, H., Y. Tanaka, H. Matsuzawa, M. Muramatsu, X.-Y. Meng, S. Hanada, K. Mori and Y. Kamagata. 2011. Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10. Int. J. Syst. Evol. Micr. 61:1442–1447. Teske, A. 2006. Microbial communities of deep marine subsurface sediments: molecular and cultivation surveys. Geomicrobiol. J. 23:357-368. Teske, A. and K. B. Sørensen. 2008. Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME J. 2:3-18. Teske, A., K.-U. Hinrichs, V. Edgcomb, A. D. V. Gomez, D. Kysela, S. P. Sylva, M. L. Sogin and H. W. Jannasch. 2002. Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl. Environ. Microbiol. 68:1994-2007. Thornburg, C. C., T. M. Zabriskie and K. L. McPhail. 2010. Deep-Sea Hydrothermal Vents: Potential Hot Spots for Natural Products Discovery? J. Nat. Prod. 73:489-499. Thrash, J. C., J. C. Cho, K. L. Vergin, R. M. Morris, S. J. Giovannoni. 2010. Genome sequence of Lentisphaera araneosa HTCC2155T, the type species of the order Lentisphaerales in the phylum Lentisphaerae. J. Bacteriol. 192:2938-2939. Tivey, M. K. 2007. Generation of Seafloor Hydrothermal Vent Fluids and Associated Mineral Deposits. Oceanography 20:50-65. Ueno, Y., K. Yamada, N. Yoshida1, S. Maruyama1 and Y. Isozaki. 2006. Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era. Nature 440:516-519. van de Vossenberg, J. L. C. M., A. J. M. Driessen and W. N. Konings. 2000. The special composition of the cell membrane allows Archaea to live in extreme environments, p. 303. In K. B. Storey and J. M. Storey (ed.), Elsevier Science Ltd., Amsterdam, The Netherlands. van Passel, M. W., R. Kant, A. Palva, S. Lucas, A. Copeland, A. Lapidus, T. Glavina del Rio, E. Dalin, H. Tice, D. Bruce, L. Goodwin, S. Pitluck, K. W. Davenport, D. Sims, T. S. Brettin, J. C. Detter, S. Han, F. W. Larimer, M. L. Land, L. Hauser, N. Kyrpides, G. Ovchinnikova, P. P. Richardson, W. M. de Vos, H. Smidt and E. G. Zoetendal. 2011. Genome sequence of Victivallis vadensis ATCC BAA-548, an anaerobic bacterium from the phylum Lentisphaerae, isolated from the human gastrointestinal tract. J. Bacteriol. 193:2373-2374. 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. Wang, X. and W. E. Müller. 2009. Marine biominerals: perspectives and challenges for polymetallic nodules and crusts. Trends Biotechnol. 27:375-83. Ward, N., F. A. Rainey, E. Stackebrandt and H. Schlesner. 1995. Unraveling the Extent of Diversity within the Order Planctomycetales. Appl. Environ. Microbiol. 61:2270-2275. Wasmund, K., K. A. Burns, D. I. Kurtboke and D. G. Bourne. 2009. Novel alkane hydroxylase gene (alkB) diversity in sediments associated with hydrocarbon seeps in the Timor Sea, Australia. Appl. Environ. Microbiol. 75:7391-7398. Waters, E., M. J. Hohn, I. Ahel, D. E. Graham, M. D. Adams, M. Barnstead, K. Y. Beeson, L. Bibbs, R. Bolanos, M. Keller, K. Kretz, X. Lin, E. Mathur, J. Ni, M. Podar, T. Richardson, G. G. Sutton, M. Simon, D. Söll, K. O. Stetter, J. M. Short and M. Noordewier. 2003. The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. PNAS 100:12984-12988. Webster, G., R. J. Parkes, B. A. Cragg, C. J. Newberry, A. J. Weightman and J. C. Fry. 2006. Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin. FEMS Microbiol. Ecol. 58:65-85. Webster, G., R. J. Parkes, J. C. Fry and A. J. Weightman. 2004. Widespread occurrence of a novel division of bacteria identified by 16S rRNA gene sequences originally found in deep marine sediments. Appl Environ. Microb. 70:5708-5713. Webster, G., L. Yarram, E. Freese, J. Köster, H. Sass, R. J. Parkes and A. J. Weightman. 2007. 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. 62:78-89. Woese, C. R., O. Kandler and M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. PNAS. 87:4576-4579. Xu, M., X. Xiao and F. Wang. 2008. Isolation and characterization of alkane hydroxylases from a metagenomic library of Pacific deep-sea sediment. Extremophiles 12:255-262. Yanagawa, K., M. Sunamura, M. A. Lever, Y. Morono, A. Hiruta, O. Ishizaki, R. Matsumoto, T. Urabe and F. Inagaki. 2011. Niche Separation of Methanotrophic Archaea (ANME-1and -2) in Methane-Seep Sediments of the Eastern Japan Sea Offshore Joetsu. Geomicrobiol. J. 28:118-129. Yang, T. F., P. C. Chuang, S. Lin, J. C. Chen, Y. Wang and S. H. Chung. 2006. Methane Venting in Gas Hydrate Potential Area Offshore of SWTaiwan: Evidence of Gas Analysis of Water Column Samples. Terr. Atmos. Ocean. Sci. 17:933-950. Ying J.-Y., B.-J. Wang, S.-S. Yang and S.-J. Liu. 2006. Cyclobacterium lianum sp. nov., a marine bacterium isolated from sediment of an oilfield in the South China Sea, and emended description of the genus Cyclobacterium. Int. J. Syst. Evol. Microbiol. 56:2927-2930. Ying J.-Y., B.-J. Wang, X. Dai, S.-S. Yang, S.-J. Liu and Z.-P. Liu. 2007. Wenxinia marina gen. nov., sp. nov., a novel member of the Roseobacter clade isolated from oilfield sediments of the South China Sea. Int. J. Syst. Evol. Microbiol. 57:1711-1716.
摘要: 具豐富儲藏量的甲烷水合物為各國致力於發展的石油替代能源之ㄧ。自然界中甲烷水合物大多分布於板塊交界處以及永凍土之中,經地物學者發現屬於活動以及被動大陸邊緣交界處之台灣西南海域賦存甲烷水合物的可能性極高。甲烷水合物賦存區的微生物活動相當特殊,自然界中的甲烷大多是由甲烷太古生物所生成,因此賦存區通常具有許多的甲烷太古生物,並促使許多能提供甲烷化作用基質的甲烷生成共棲菌及以甲烷為能量來源的微生物如厭氧甲烷氧化太古生物親緣型(ANME)與好氧甲烷氧化細菌共存於此特殊棲地。此特殊棲地的微生物群落架構能夠作為甲烷水合物存在與否的依據。為了藉由微生物群落架構得知台灣西南海域賦存甲烷水合物的可能性,於2010年由Marion Dufresne研究船第178 航次利用巨型箱型岩心進行採樣。於深水盆地區(21°32.490’N, 119°19.640’E)取得的巨型箱型岩心共獲得16個不同深度的土樣,由樣品的太古生物與細菌16S rRNA 基因庫分析樣區微生物群落架構。194個太古生物16S rDNA轉殖株中,優勢群為SAGMEG (34%)以及MBG-D/MGIII (33%)親緣型,204個細菌16S rDNA轉殖株中,優勢群為Candidate Division JS1 (36%)以及Chloroflexi (22%)親緣型。此區域也發現到能進行厭氧降解提供甲烷化基質的細菌如Firmicutes、Chloroflexi、Proteobacteria、Bacteroidetes 及JS1,以及甲烷太古生物相關親緣型MBGD、GEG、SAGMEG以及Methanomicrobiales,應有許多甲烷生成作用,此外也發現到屬於高溫菌的TMEG、SAGMEG及DHVC親緣型。經由生物資訊分析比對得知,此區域所獲得的轉殖株與泥火山、甲烷冷泉及甲烷水合物賦存區等甲烷量較高的轉殖株關係較為密切,也發現到在甲烷水合物賦存區域分別屬於太古生物及細菌優勢群的DSAG以及JS1親緣型的存在,因此台灣西南海域深水盆地區域可能是甲烷水合物賦存潛力區。
The deep sea microbial community investigation can conjecture the marine associated environments, like oilfield, gas hydrate-buried site and hydrothermal vent, for further understanding the ecosystem and treasures of the natural resources. The CASQ box core MD178-3263C was obtained during the Marion Dufresne cruise (MD-178) at May 28, 2010. The sampling site of core MD178-3263C (8.52 meters) was located at the deep-basin area (21°32.490'N, 119°19.640'E) SW offshore Taiwan with water depth of 2819 meters. Both archaeal and bacterial 16S rRNA gene libraries were constructed from every 0.5 meter of core sections. Phylogenetic analysis indicated that the SAGMEG (34%) and MBG-D (33%) were dominant archaeal phylotypes, and the candidate division JS1 (36%) and Chloroflexi (22%) were dominant bacterial phylotypes. The occurrence of methanogenesis substrate- producing bacteria Firmicutes, Chloroflexi, Proteobacteria, Bacteroidetes and JS1, and methane producing archaea MBGD, GEG, SAGMEG and Methanomicrobiales, revealed the active methanogenesis process in this site. Thermophilic TMEG, SAGMEG and DHVC also present in this site. Additionally, the representative OTUs from most archaeal and bacterial phylotypes are close related with clones from deep sea sediments of active submarine mud volcano at East Mediterranean Sea, gas hydrate-bearing site and cold seep, which suggested that this habitat are potential gas hydrate-bearing site.
其他識別: U0005-0802201212482600
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