深海微生物多样性和嗜盐古菌乙醇代谢相关酶基因研究
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摘要
极端微生物能够在普通微生物无法生存的极端环境中良好生长。深海和盐湖是典型的极端生境,孕育了嗜热、嗜冷、嗜压、嗜盐、嗜碱等多种极端微生物。本论文以“非培养-可培养-功能基因”为研究线索,从三个不同方面,围绕生活在深海和盐湖中的极端微生物展开研究。
首先,针对采集自西南印度洋洋中脊2951米深的深海热液区沉积物样品,通过构建16SrRNA和nifH基因文库,对原核微生物的种群多样性进行分析。结果表明,古菌种系型主要分布在广古菌门的MBGE类群和Thaumarchaeota门的MGI类群。大约60%的细菌种系型属于于变形菌门,其余细菌种系型分布于放线菌门、拟杆菌门、浮霉菌门、酸杆菌门、硝化螺旋菌门、绿弯菌门、绿菌门、衣原体门、疣微菌门以及未分类类群OD1、OP11、WS3和TM6。nifH基因的发现说明西南印度洋洋中脊深海热液区存在生物固氮作用,系统发育分析表明只存在Ⅰ型和Ⅲ型微生物nifH基因,说明在此深海热液区环境中细菌发挥主要的固氮作用。
其次,从波多黎各海沟6000米深处海水样品中分离到一株专性嗜压疑似新种细菌YC-1并进行多相分类学研究。结果表明,菌株YC-1能在8℃和50 MPa的条件下最适生长,在标准大气压下无法生长。主要的脂肪酸成分为C16:1、C18：1和C10：03-OH。基因组G+C mol%含量为44.6 mmol%。菌株YC-1为革兰氏阴性细菌,无鞭毛,兼性厌氧,营异养生活。16S rRNA基因的序列与深海非培养细菌Oseda_syml最为相近,序列相似性为97.2%；最近缘的可培养标准菌株属于Neptunomonas属,16SrRNA基因序列相似性介于92.7-93.2%。根据多相分类的差异,建议定义菌株YC-1为海洋螺菌科新的分类单元,命名为"Profundimonas piezophila gen. nov., sp. nov."。
最后,对模式嗜盐碱古菌Natronomonas pharaonis的乙醇代谢及其功能酶进行研究。结果表明,N. pharaonis的乙醇代谢是应对环境中乙醇胁迫的一种应激机制。作为N. pharaonis乙醇代谢过程中两个关键酶,编码乙醇脱氢酶的adh基因不受乙醇的诱导表达,而编码乙醛脱氢酶的aldH2基因则受乙醇的诱导表达,说明乙醛脱氢酶对N. pharaonis的乙醇耐受性具有主要贡献,而乙醇脱氢酶可能还参与了其它代谢途径。大肠杆菌异源表达的N. pharaonis乙醇脱氢酶具有嗜盐、嗜碱和嗜热的性质,而乙醛脱氢酶则体现嗜碱、嗜热和非嗜盐的性质。
Extremophiles live well in several extreme environments, where normal microorganisms cannot survive. Typical extreme habitats as Deep Ocean and Salt Lake give birth to many thermophilic, psychrophilic, piezophilic, halophilic and alkaliphilic microorganisms. Focus on the microbial life living in Deep Ocean and Salt Lake, three different studies were presented in this thesis.
Firstly, a sediment sample collected from a deep-sea hydrothermal vent field located at a depth of 2,951 m on the Southwest Indian Ridge. Phylogenetic analyses were performed on the prokaryotic community and diversity based on the 16S rRNA and nifH genes libraries. Within the Archaea, the dominant clones belonged to the groups of MBGE and MGI within the phyla Euryarchaeota and Thaumarchaeota, respectively. About 60% of the bacterial clones belonged to the Proteobacteria. Additional bacterial phyla detected included the Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Nitrospirae, Chloroflexi, Chlorobi, Chlamydiae, Verrucomicrobia, and candidate divisions OD1, OP11, WS3, and TM6. The detection of nifH genes suggests that biological nitrogen fixation occurred in the hydrothermal vent field of the Southwest Indian Ridge. Phylogenetic analysis shown that only cluster I and cluster III NifH are present, indicating that Bacteria play the main role in nitrogen fixation in this hydrothermal vent environment.
Secondly, a novel obligately piezophilic bacterium was isolated from seawater collected from Puerto Rico Trench at a depth of 6,000 m. The isolated strain YC-1 grew well with an optimal growth hydrostatic pressure of 50 MPa at 8℃, and no growth was observed at atmospheric pressure. The predominant cellular fatty acids are C16:1, C18:1 and C10:0 3-OH. The G+C content was 44.6 mol%. Strain YC-1 is Gram-negative, non-flagellum forming, and facultative anaerobic heterotroph. The 16S rRNA gene sequence of strain YC-1 was closely similar to the uncultured deep-sea bacterial clone Osedax_syml (97.2%), and was closely related to cultivated members of the genus Neptunomonas (92.7-93.2%). Based on taxonomic and phenotypic differences observed, the strain YC-1 appears to represent a new species within the family Oceanospirillaceae, which named Profundimonas piezophila gen. nov., sp. nov.
Thirdly, we have studied the role of functional genes within ethanol metabolism of haloalkaliphilic Archaea Natronomonas pharaonis. It indicated that ethanol oxidation by N. pharaonis may be one of the mechanisms to degrade toxic compounds found in its habitat. In N. pharaonis, the adh gene and aldH2 gene encode alcohol dehydrogenase and aldehyde dehydrogenase, respectively, they are key enzymes involved in alcohol metabolism. Reverse transcription-PCR analysis showed that the aldH2 gene was inducible by ethanol, but the adh gene transcription was not affected by ethanol. It indicated that aldehyde dehydrogenase of N. pharaonis possibly contribute to the alcohol resistance, and alcohol dehydrogenase may play other physiological roles in addition to ethanol degradation. The recombinant alcohol dehydrogenase was haloalkaliphilic and thermophilic, and the recombinant aldehyde dehydrogenase was thermophilic, alkaliphilic and salt independent.
首先,针对采集自西南印度洋洋中脊2951米深的深海热液区沉积物样品,通过构建16SrRNA和nifH基因文库,对原核微生物的种群多样性进行分析。结果表明,古菌种系型主要分布在广古菌门的MBGE类群和Thaumarchaeota门的MGI类群。大约60%的细菌种系型属于于变形菌门,其余细菌种系型分布于放线菌门、拟杆菌门、浮霉菌门、酸杆菌门、硝化螺旋菌门、绿弯菌门、绿菌门、衣原体门、疣微菌门以及未分类类群OD1、OP11、WS3和TM6。nifH基因的发现说明西南印度洋洋中脊深海热液区存在生物固氮作用,系统发育分析表明只存在Ⅰ型和Ⅲ型微生物nifH基因,说明在此深海热液区环境中细菌发挥主要的固氮作用。
其次,从波多黎各海沟6000米深处海水样品中分离到一株专性嗜压疑似新种细菌YC-1并进行多相分类学研究。结果表明,菌株YC-1能在8℃和50 MPa的条件下最适生长,在标准大气压下无法生长。主要的脂肪酸成分为C16:1、C18：1和C10：03-OH。基因组G+C mol%含量为44.6 mmol%。菌株YC-1为革兰氏阴性细菌,无鞭毛,兼性厌氧,营异养生活。16S rRNA基因的序列与深海非培养细菌Oseda_syml最为相近,序列相似性为97.2%；最近缘的可培养标准菌株属于Neptunomonas属,16SrRNA基因序列相似性介于92.7-93.2%。根据多相分类的差异,建议定义菌株YC-1为海洋螺菌科新的分类单元,命名为"Profundimonas piezophila gen. nov., sp. nov."。
最后,对模式嗜盐碱古菌Natronomonas pharaonis的乙醇代谢及其功能酶进行研究。结果表明,N. pharaonis的乙醇代谢是应对环境中乙醇胁迫的一种应激机制。作为N. pharaonis乙醇代谢过程中两个关键酶,编码乙醇脱氢酶的adh基因不受乙醇的诱导表达,而编码乙醛脱氢酶的aldH2基因则受乙醇的诱导表达,说明乙醛脱氢酶对N. pharaonis的乙醇耐受性具有主要贡献,而乙醇脱氢酶可能还参与了其它代谢途径。大肠杆菌异源表达的N. pharaonis乙醇脱氢酶具有嗜盐、嗜碱和嗜热的性质,而乙醛脱氢酶则体现嗜碱、嗜热和非嗜盐的性质。
Extremophiles live well in several extreme environments, where normal microorganisms cannot survive. Typical extreme habitats as Deep Ocean and Salt Lake give birth to many thermophilic, psychrophilic, piezophilic, halophilic and alkaliphilic microorganisms. Focus on the microbial life living in Deep Ocean and Salt Lake, three different studies were presented in this thesis.
Firstly, a sediment sample collected from a deep-sea hydrothermal vent field located at a depth of 2,951 m on the Southwest Indian Ridge. Phylogenetic analyses were performed on the prokaryotic community and diversity based on the 16S rRNA and nifH genes libraries. Within the Archaea, the dominant clones belonged to the groups of MBGE and MGI within the phyla Euryarchaeota and Thaumarchaeota, respectively. About 60% of the bacterial clones belonged to the Proteobacteria. Additional bacterial phyla detected included the Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Nitrospirae, Chloroflexi, Chlorobi, Chlamydiae, Verrucomicrobia, and candidate divisions OD1, OP11, WS3, and TM6. The detection of nifH genes suggests that biological nitrogen fixation occurred in the hydrothermal vent field of the Southwest Indian Ridge. Phylogenetic analysis shown that only cluster I and cluster III NifH are present, indicating that Bacteria play the main role in nitrogen fixation in this hydrothermal vent environment.
Secondly, a novel obligately piezophilic bacterium was isolated from seawater collected from Puerto Rico Trench at a depth of 6,000 m. The isolated strain YC-1 grew well with an optimal growth hydrostatic pressure of 50 MPa at 8℃, and no growth was observed at atmospheric pressure. The predominant cellular fatty acids are C16:1, C18:1 and C10:0 3-OH. The G+C content was 44.6 mol%. Strain YC-1 is Gram-negative, non-flagellum forming, and facultative anaerobic heterotroph. The 16S rRNA gene sequence of strain YC-1 was closely similar to the uncultured deep-sea bacterial clone Osedax_syml (97.2%), and was closely related to cultivated members of the genus Neptunomonas (92.7-93.2%). Based on taxonomic and phenotypic differences observed, the strain YC-1 appears to represent a new species within the family Oceanospirillaceae, which named Profundimonas piezophila gen. nov., sp. nov.
Thirdly, we have studied the role of functional genes within ethanol metabolism of haloalkaliphilic Archaea Natronomonas pharaonis. It indicated that ethanol oxidation by N. pharaonis may be one of the mechanisms to degrade toxic compounds found in its habitat. In N. pharaonis, the adh gene and aldH2 gene encode alcohol dehydrogenase and aldehyde dehydrogenase, respectively, they are key enzymes involved in alcohol metabolism. Reverse transcription-PCR analysis showed that the aldH2 gene was inducible by ethanol, but the adh gene transcription was not affected by ethanol. It indicated that aldehyde dehydrogenase of N. pharaonis possibly contribute to the alcohol resistance, and alcohol dehydrogenase may play other physiological roles in addition to ethanol degradation. The recombinant alcohol dehydrogenase was haloalkaliphilic and thermophilic, and the recombinant aldehyde dehydrogenase was thermophilic, alkaliphilic and salt independent.
引文
Abe, F., and Horikoshi, K. The biotechnological potential of piezophiles. Trends Biotechnol (2001) 19:102-108.
Alain, K., Marteinsson, V. T., Miroshnichenko, M. L., Bonch-Osmolovskaya, E. A., Prieur, D., and Birrien, J. L. Marinitoga piezophila sp. nov., a rod-shaped, thermo-piezophilic bacterium isolated under high hydrostatic pressure from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol (2002) 52:1331-1339.
Alazard, D., Dukan, S., Urios, A., Verhe, F., Bouabida, N., Morel, F., Thomas, P., Garcia, J. L., and Ollivier, B. Desulfovibrio hydrothermalis sp nov., a novel sulfate-reducing bacterium isolated from hydrothermal vents. Int J Syst Evol Microbiol (2003) 53:173-178.
Allen, E. E., Facciotti, D., and Bartlett, D. H. Monounsaturated but not polyunsaturated fatty acids are required for growth of thedeep-sea bacterium Photobacterium profundum SS9 at high pressure and low temperature. Appl Environ Microbiol (1999) 65:1710-1720.
Allen, E. E., and Bartlett, D. H. Structure and regulation of the omega-3 polyunsaturated fatty acid synthase genes from the deep-sea bacterium Photobacterium profundum strain SS9. Microbiology (2002) 148:1903-1913.
Arakawa, S., Sato, T., Yoshida, Y., Usami, R., and Kato, C. Comparison of the microbial diversity in cold-seep sediments from different depths in the Nankai Trough. J Gen Appl Microbiol (2006) 52:47-54.
Azam, F., and Malfatti, F. Microbial structuring of marine ecosystems. Nat Rev Microbiol (2007) 5:782-791.
Baker, G. C., Smith, J. J., and Cowan, D. A. Review and re-analysis of domain-specific 16S primers. J Microbiol Methods (2003) 55:541-555.
Bale, S. J., Goodman, K., Rochelle, P. A., Marchesi, J. R., Fry, J. C., Weightman, A. J., and Parkes, R. J. Desulfovibrio profundus sp nov, a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea. Int J Syst Bacteriol (1997) 47:515-521.
Baltar, F., Aristegui, J., Gasol, J. M., Sintes, E., and Herndl, G. J. Evidence of prokaryotic metabolism on suspended particulate organic matter in the dark waters of the subtropical North Atlantic. Limnol Oceanogr (2009) 54:182-193.
Bartlett, D. H., Wright, M., Yayanos, A. A., and Silverman, M. Isolation of a gene regulated by hydrostatic pressure in a deepsea bacterium. Nature (1989) 342: 572-574.
Bartlett, D. H. Microbial life at high-pressures. Sci Prog (1992) 76:479-496.
Bonete, M. J., Camacho, M. L., and Cadenas, E. Purification and properties of NAD+-dependent glutamate dehydrogenase from Halobacterium halobium. Int J Biochem (1986) 18:785-789.
Bonete, M. J., Camacho, M. L., and Cadenas, E. A new glutamate dehydrogenase from Halobacterium halobium with different coenzyme specificity. Int J Biochem (1987) 19:1149-1155.
Brandt, A., Gooday, A. J., Brandao, S. N., Brix, S., Brokeland, W., Cedhagen, T., Choudhury, M., Cornelius, N., Danis, B., De Mesel, I., Diaz, R. J., Gillan, D. C., Ebbe, B., Howe, J. A., Janussen, D., Kaiser, S., Linse, K., Malyutina, M., Pawlowski, J., Raupach, M., and Vanreusel, A. First insights into the biodiversity and biogeography of the Southern Ocean deep sea. Nature (2007) 447:307-311.
Brochier-Armanet, C., Boussau, B., Gribaldo, S., and Forterre, P. Mesophilic Crenarchaeota:proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol (2008) 6:245-252.
Bruun, A. F. Deep sea and abyssal depths. Geol Soc Am Mem (1957) 67:641-672.
Canganella, F., Gonzalez, J. M., Yanagibayashi, M., Kato, C., and Horikoshi, K. Pressure and temperature effects on growth and viability of the hyperthermophilic archaeon Thermococcus peptonophilus. Arch Microbiol (1997) 168:1-7.
Charlou, J. L., Donval, J. P., Fouquet, Y., Jean-Baptiste, P., and Holm, N. Geochemistry of high H2 and CH4 vent fluids issuing from ultramafic rocks at the Rainbow hydrothermal field (36°14'N, MAR) Chem Geol (2002) 191: 345-359.
Chien, Y. T., and Zinder, S. H. Cloning, functional organization, transcript studies, and phylogenetic analysis of the complete nitrogenase structural genes (nifHDK2) and associated genes in the archaeon Methanosarcina barkeri 227. J Bacteriol (1996)178:143-148.
Chilukuri, L. N., and Bartlett, D. H. Isolation and characterization of the gene encoding single-stranded-DNA-binding protein (SSB) from four marine Shewanella strains that differ in their temperature and pressure optima for growth. Microbiology (1997) 143:1163-1174.
Corliss, J. B., Dymond, J., Gordon, L. I., Edmond, J. M., von Herzen, R. P., Ballard, R. D., Green, K., Williams, D., Bainbridge, A., Crane, K., and van Andel, T. H. Submarine Thermal Sprirngs on the Galapagos Rift. Science (1979) 203:1073-1083.
Daniel, I., Oger, P., and Winter, R. Origins of life and biochemistry under high-pressure conditions. Chem Soc Rev (2006) 35:858-875.
Danovaro, R., Dell'Anno, A., Fabiano, M., Pusceddu, A., and Tselepides, A. Deep-sea ecosystem response to climate changes:The eastern Mediterranean case study. Trends Ecol Evol (2001) 16:505-510.
DeLong, E. F., and Yayanos, A. A. Biochemical function and ecological significance of novel bacterial lipids in deep-sea procaryotes. Appl Environ Microbiol (1986) 51:730-737.
DeLong, E. F. Archaea in coastal marine environments. Proc Natl Acad Sci USA (1992)89:5685-5689.
DeLong, E. F., Franks, D. G., and Yayanos, A. A. Evolutionary relationships of cultivated psychrophilic and barophilic deep-sea bacteria. Appl Environ Microbiol (1997) 63:2105-2108.
DeLong, E. F., Preston, C. M., Mincer, T., Rich, V., Hallam, S. J., Frigaard, N. U., Martinez, A., Sullivan, M. B., Edwards, R., Brito, B. R., Chisholm, S. W., and Karl, D. M. Community genomics among stratified microbial assemblages in the ocean's interior. Science (2006) 311:496-503.
Deming, J. W., Somers, L. K., Straube, W. L., Swartz, D. G., and MacDonell, M. T. Isolation of an obligately barophilic bacterium and description of a new genus, Colwellia gen. nov. Syst Appl Microbiol (1988) 10:152-160.
Dietz, A. S., and Yayanos, A. A. Silica gel media for isolating and studying bacteria under hydrostatic pressure. Appl Environ Microbiol (1978) 36:966-968.
Di Giulio, M. A comparison of proteins from Pyrococcus furiosus and Pyrococcus abyssi:barophily in the physicochemical properties of amino acids and in the genetic code. Gene (2004) 346:1-6.
Emerson, D., Rentz, J. A., Lilburn, T. G., Davis, R. E., Aldrich, H., Chan, C., and Moyer, C. L. A novel lineage of Proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities. PLoS ONE (2007) 2:e667.
Falb, M., Pfeiffer, F., Palm, P., Rodewald, K., Hickmann, V., Tittor, J., and Oesterhelt, D. Living with two extremes:conclusions from the genome sequence of Natronomonas pharaonis. Genome Res (2005) 15:1336-1343.
Felsenstein, J. PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics (1989)5:164-166.
Foustoukos, D. I., and Seyfried, W. E. Hydrocarbons in hydrothermal vent fluids: The role of chromium-bearing catalysts. Science (2004) 304:1002-1005.
Fry, J. C., Parkes, R. J., Cragg, B. A., Weightman, A. J., and Webster, G. Prokaryotic biodiversity and activity in the deep subseafloor biosphere. FEMS Microbiol Ecol (2008) 66:181-196.
Fuhrman, J. A., McCallum, K., and Davis, A. A. Novel major archaebacterial group from marine plankton. Nature (1992) 356:148-149.
Garnova, E. S., and Krasil'nikova, E. N. Carbohydrate metabolism of the saccharolytic alkaliphilic anaerobes Halonatronum saccharophilum, Amphibacillus fermentum, and Amphibacillus tropicus. Microbiology (Moscow) (2003) 72:558-563.
Handelsman, J., Rondon, M. R., Brady, S. F., Clardy, J., and Goodman, R. M. Molecular biological access to the chemistry of unknown soil microbes:a new frontier for natural products. Chem Biol (1998) 5:245-249.
Hashimoto, J., Ohta, S., Gamo, T., Chiba, H., Yamaguchi, T., Tsuchida, S., Okudaira, T., Watabe, H., Yamanaka, T., and Kitazawa, M. First hydrothermal vent communities from the Indian Ocean discovered. Zool Sci (2001)18:717-721.
Heijs, S. K., Laverman, A. M., Forney, L. J., Hardoim, P. R., and van Elsas, J. D. Comparison of deep-sea sediment microbial communities in the Eastern Mediterranean. FEMS Microbiol Ecol (2008) 64:362-377.
Herndl, G. J., Reinthaler, T., Teira, E., Aken, H. M. V., Veth, C., Pernthaler, A., and Pernthaler, J. Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean. Appl Environ Microbiol (2005) 72:2303-2309.
Hess, M., and Antranikian, G Archaeal alcohol dehydrogenase active at increased temperatures and in the presence of organic solvents. Appl Microbiol Biotechnol (2008) 77:1003-1013.
Jergensen, B. B., and Boetius, A. Feast and famine-microbial life in the deep-sea bed. Nat Rev Microbiol (2007) 5:770-781.
Jukes, T. H., and Cantor, C. R. Evolution of protein molecules. In Mammalian Protein Metabolism (Munro, H. N., ed), New York:Academic Press (1969) pp. 21-132.
Karl, D. M. Ecology of free-hydrothermal vent microbial communities. In The Microbiology of Deep-sea Hydrothermal Vents (Karl, D. M., ed), Boca Raton: CRC Press Inc (1995) pp.35-124.
Kato, C., and Bartlett, D. H. The molecular biology of barophilic bacteria. Extremophiles (1997) 1:111-116.
Kato, C., Li, L., Nogi, Y., Nakamura, Y., Tamaoka, J., and Horikoshi, K. Extremely barophilic bacteria isolated from the Mariana Trench, Challenger Deep, at a depth of 11,000 m. Appl Environ Microbiol (1998) 64:1510-1513.
Kato, C. Handling of piezophilic microorganisms. In Extremophiles. Methods in Microbiology, vol.35 (Rainey, F. A., and Oren, A., eds), Amsterdam:Elsevier (2006) pp.733-741.
Kato, S., Kobayashi, C., Kakegawa, T., and Yamagishi, A. Microbial communities in iron-silica-rich microbial mats at deep-sea hydrothermal fields of the Southern Mariana Trough. Environ Microbiol (2009) 11:2094-2111.
Kato, S., Takano, Y., Kakegawa, T., Oba, H., Inoue, K., Kobayashi, C., Utsumi, M., Marumo, K., Kobayashi, K., Ito, Y., Ishibashi, J. I., and Yamagishi, A. Biogeography and biodiversity in sulfide structures of active and inactive vents at deep-sea hydrothermal fields of the Southern Mariana Trough. Appl Environ Microbiol (2010) doi:10.1128/AEM.00478-10.
Kennedy, S. P., Ng, W. V., Salzberg, S. L., Hood, L., and DasSarma, S. Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res(2001)11:1641-1650.
Kim, H., Joo, W., Cho, C., and Kim, C. Halophile aldehyde dehydrogenase from Halobacterium salinarum. JProteome Res (2006) 5:192-195
Kimura, M. A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J Mol Evol (1980) 16: 111-120.
Konneke, M., Bernhard, A. E., de la Torre, J. R., Walker, C. B., Waterbury, J. B., and Stahl, D. A. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature (2005) 437:543-546.
Konstantinidis, K., Tebbe, A., Klein, C., Scheffer, B., Aivaliotis, M., Bisle, B., Falb, M., Pfeiffer, F., Siedler, F., and Oesterhelt, D. Genome-wide proteomics of Natronomonas pharaonis. J Proteome Res (2007) 6:185-193.
Kyo, M., Tsuji, T., Usui, H., and Itoh, T. Collection, isolation and cultivation system for deep-sea microbes study:concept and design. Oceans (1991) 1:419-423.
Lampitt, R. S., and Antia, A.N. Particle flux in deep seas:regional characteristics and temporal variability. Deep Sea Res I (1997) 44:1377-1403.
Lauro, F. M., Chastain, R. A., Blankenship, L. E., Yayanos, A. A., and Bartlett, D. H. The unique 16S rRNA genes of piezophiles reflect both phylogeny and adaptation. Appl Environ Microbiol (2007) 73:838-845.
Lauro, F. M., and Bartlett, D. H. Prokaryotic lifestyles in deep sea habitats. Extremophiles (2008) 12:15-25.
Li, Y., Li, F., Zhang, X., Qin, S., Zeng, Z., Dang, H., and Qin, Y. Vertical distribution of bacterial and archaeal communities along discrete layers of a deep-sea cold sediment sample at the East Pacific Rise (～13°N). Extremophiles (2008) 12:573-585.
Lopez-Garcia, P., Duperron, S., Philippot, P., Foriel, J., Susini, J., and Moreira, D. Bacterial diversity in hydrothermal sediment and epsilonproteobacterial dominance in experimental microcolonizers at the Mid-Atlantic Ridge. Environ Microbiol (2003) 5:961-976.
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, A. W., 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., and Schleifer, K. H. ARB:a software environment for sequence data. Nucleic Acids Res (2004) 32:1363-1371.
Macdonald, A. G., and Gilchrist, I. Recovery of deep seawater at constant pressure. Nature (1969) 222:71-72.
Margesin, R., and Nogi, Y. Psychropiezophilic microorganisms. Cell Mol Biol (2004) 50:429-436.
Marteinsson, V. T., Moulin, P., Birrien, J. L., Gambacorta, A., Vernet, M., and Prieur, D. Physiological responses to stress conditions and barophilic behaviour of the hyperthermophilic archaeon Pyrococcus abyssi. Appl Environ Microbiol (1997)93:1230-1236.
Marteinsson, V. T., Birrien, J. L., Reysenbach, A. L., Venet, M., Marie, D., Gambacorta, A., Messner, P., Sleytr, U. B., and Prieur, D. Thermococcus barophilus sp. nov., a new barophilic and hyperthermophilic archaeon isolated under high hydrostatic pressure from a deep-sea hydrothermal vent. Int J Syst Bacteriol (1999) 49:351-359.
Martin, D. D., Bartlett, D. H., and Roberts, M. F. Solute accumulation in the deep-sea bacterium Photobacterium profundum. Extremophiles (2002) 6: 507-514.
Martin-Cuadrado, A. B., Lopez-Garcia, P., Alba, J. C., Moreira, D., Monticelli, L., Strittmatter, A., Gottschalk, G., and Rodriguez-Valera, F. Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS One (2007) 2: e914.
Mason, O. U., Stingl, U., Wilhelm, L. J., Moeseneder, M. M., DiMeo-Savoie, C. A., Fisk, M. R., and Giovannoni, S. J. The phylogeny of endolithic microbes associated with marine basalts. Environ Microbiol (2007) 9:2539-2550.
McCollom, T. M., and Shock, E. L. Geochemical constraints on Chemolithoautotrophic metabolism by microorganisms in seafloor hydrothermal systems. Geochim Cosmochim Acta (1997) 61:4375-4391.
Mehta, M. P., Butterfield, D. A., and Baross, J. A. Phylogenetic diversity of nitrogenase (nifH) genes in deep-sea and hydrothermal vent environments of the Juan de Fuca Ridge. Appl Environ Microbiol (2003) 69:960-970.
Mehta, M. P., and Baross, J. A. Nitrogen fixation at 92 ℃ by a hydrothermal vent archaeon. Science (2006) 314:1783-1786.
Miyazaki, M., Nogi, Y., Fujiwara, Y., Kawato, M., Kubokawa, K., and Horikoshi, K. Neptunomonas japonica sp. nov., an Osedax japonicus symbiont-like bacterium isolated from sediment adjacent to sperm whale carcasses off Kagoshima, Japan. Int J Syst Evol Microbiol (2008) 58:866-871.
Morita, R. Y. Psychrophilic bacteria. Bacteriol Rev (1975) 39:144-167.
Nagata, T., Tamburini, C., Aristegui, J., Baltar, F., Bochdansky, A., Fonda-Umani, S., Fukuda, H., Gogou, A., Hansell, D. A., Hansman, R. L., Herndl, G. J., Panagiotopoulos, C., Reinthaler, T., Sohrin, R., Verdugo, P., Yamada, N., Yamashita, Y., Yokokawa, T., and Bartlett, D. H. Emerging concepts on microbial processes in the bathypelagic ocean-ecology, biogeochemistry, and genomics. Deep-Sea Res Ⅱ(2010) doi:10.1016/j.dsr2.2010.02.019.
Nakagawa, S., Takai, K., Horikoshi, K., and Sako, Y. Persephonella hydrogeniphila sp. nov., a novel thermophilic, hydrogen-oxidizing bacterium from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol (2003) 53: 863-869.
Nakagawa, S., Takai, K., Inagaki, F., Hirayama, H., Nunoura, T., Horikoshi, K., and Sako, Y. Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field. Environ Microbiol (2005) 7:1619-1632.
Nakagawa, S., and Takai, K. Methods for the isolation of thermophiles from deep-sea hydrothermal environments. In Extremophiles. Methods in Microbiology, vol.35 (Rainey, F. A., and Oren, A., eds), Amsterdam:Elsevier (2006) pp.55-91.
Nakagawa, S., and Takai, K. Deep-sea vent chemoautotrophs:diversity, biochemistry and ecological significance. FEMS Microbiol Ecol (2008) 65:1-14.
Naqvi, W., and Gattuso, J. Marine nitrogen cycle. In Encyclopedia of Earth. (Cleveland, C. J., eds) Washington, DC:Environmental Information Coalition, National Council for Science and the Environment (2006).
Nercessian, O., Fouquet, Y., Pierre, C., Prieur, D., and Jeanthon, C. Diversity of Bacteria and Archaea associated with a carbonate-rich metalliferous sediment sample from the Rainbow vent field on the Mid-Atlantic Ridge. Environ Microbiol (2005) 7:698-714.
Ng, W. V., Kennedy, S. P., Mahairas, G. G., Berquist, B., Pan, M., Shukla, H. D., Lasky, S. R., Baliga, N. S., Thorsson, V., Sbrogna, J., Swartzell, S., Weir, D., Hall, J., Dahl, T. A., Welti, R., Goo, Y. A., Leithauser, B., Keller, K., Cruz, R., Danson, M. J., Hough, D. W., Maddocks, D. G., Jablonski, P. E., Krebs, M. P., Angevine, C. M., Dale, H., Isenbarger, T. A., Peck, R. F., Pohlschroder, M., Spudich, J. L., Jung, K. W., Alam, M., Freitas, T., Hou, S., Daniels, C. J., Dennis, P. P., Omer, A. D., Ebhardt, H., Lowe, T. M., Liang, P., Riley, M., Hood, L., and DasSarma, S. Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A (2000) 97:12176-12181.
Nogi, Y., Kato, C., and Horikoshi, K. Moritella japonica sp. nov., a novel barophilic bacterium isolated from a Japan Trench sediment. J Gen Appl Microbiol (1998a) 44:289-295.
Nogi, Y., Kato, C., and Horikoshi, K. Taxonomic studies of deep-sea barophilic Shewanella strains and description of Shewanella violacea sp. nov. Arch Microbiol (1998b) 170:331-338.
Nogi, Y., Masui, N., and Kato, C. Photobacterium profundum sp. nov., a new, moderately barophilic bacterial species isolated from a deep-sea sediment. Extremophiles (1998c) 2:1-7.
Nogi, Y., and Kato, C. Taxonomic studies of extremely barophilic bacteria isolated from the Mariana Trench and description of Moritella yayanosii sp. nov., a new barophilic bacterial isolate. Extremophiles (1999) 3:71-77.
Nogi, Y., Kato, C., and Horikoshi, K. Psychromonas kaikoae sp. nov., a novel piezophilic bacterium from the deepest cold-seep sediments in the Japan Trench. Int J Syst Evol Microbiol (2002) 52:1527-1532.
Nogi, Y., Hosoya, S., Kato, C., and Horikoshi, K. Colwellia piezophila sp. nov., a novel piezophilic species from deep-sea sediments of the Japan Trench. Int J Syst Evol Microbiol (2004) 54:1627-1631.
Nogi, Y., Hosoya, S., Kato, C., and Horikoshi, K. Psychromonas hadalis sp. nov., a novel piezophilic bacterium isolated from the bottom of the Japan Trench. Int J Syst Evol Microbiol (2007) 57:1360-1364.
Oesterhelt, D., and Stoeckenius, W. Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nat New Biol (1971) 233:149-152.
Olsen, G. J., Lane, D. J., Giovannoni, S. J., Pace, N. R., and Stahl, D. A. Microbial ecology and evolution:a ribosomal RNA approach. Annu Rev Microbiol (1986) 40:337-365.
Olu-LeRoy, K., Sibuet, M., Fiala-Medioni, A., Gofas, S., Salas, C., Mariotti, A., Foucher, J., and Woodside, J. Cold seep communities in the deep eastern Mediterranean Sea:composition, symbiosis, and spatial distribution on mud volcanoes. Deep-Sea Res Ⅰ(2004) 51:1915-1936.
Oren, A. A thermophilic amyloglucosidase from Halobacterium sodomense, a halophilic bacterium from the Dead Sea. Curr Microbiol (1973) 8:225-230.
Park, C. B., Boonyaratanakornkit, B. B., and Clark, D. S. Toward the large scale cultivation of hyperthermophiles at high-temperature and high-pressure. In Extremophiles. Methods in Microbiology, vol.35 (Rainey, F. A., and Oren, A., eds), Amsterdam:Elsevier (2006) pp.109-126.
Parkes, R. J., Sellek, G, Webster, G., Martin, D., Anders, E., Weightman, A. J., and Sass, H. Culturable prokaryotic diversity of deep, gas hydrate sediments: first use of a continuous high-pressure, anaerobic, enrichment and isolation system for subseafloor sediments (DeepIsoBUG). Environ Microbiol (2009) 11: 3140-3153.
Pham, V. D., Konstantinidis, K. T., Palden, T., and DeLong, E. F. Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre. Environ Microbiol (2008) 10:2313-2330.
Price, M. N., Dehal, P. S., and Arkin, A. P. FastTree:Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix. Mol Biol Evol (2009) 26:1641-1650.
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., and Glockner, F. O. SILVA:a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res (2007) 35:7188-7196.
Rainey, F. A., and Oren, A. Extremophile microorganisms and the methods to handle them. In Extremophiles. Methods in Microbiology, vol.35 (Rainey, F. A., and Oren, A., eds), Amsterdam:Elsevier (2006) pp.1-25.
Rappe, M. S., and Giovannoni, S. J. The uncultured microbial majority. Annu Rev Microbiol (2003) 57:369-394.
Reid, M. F., and Fewson, C. A. Molecular characterization of microbial alcohol dehydrogenase. Crit Rev Microbiol (1994) 20:13-56.
Reysenbach, A. L., and Shock, E. Merging genomes with geochemistry in hydrothermal ecosystems. Science (2002) 296:1077-1082.
Reysenbach, A. L., Liu, Y., Banta, A. B., Beveridge, T. J., Kirshtein, J. D., Schouten, S., Tivey, M. K., Von Damm, K. L., and Voytek, M. A. A ubiquitous thermoacidophilic archaeon from deep-sea hydrothermal vents. Nature (2006) 442:444-447.
Royer, C. A. Application of pressure to biochemical equilibria:the other thermodynamic variable. Methods Enzymol (1995) 259:357-377.
Saitou, N., and Nei, M. The neighbour joining method:a new tool for reconstructing phylogenetic trees. Mol Biol Evol (1987) 4:406-425.
Santelli, C. M., Orcutt, B. N., Banning, E., Bach, W., Moyer, C. L., Sogin, M. L., Staudigel, H., and Edwards, K. J. Abundance and diversity of microbial life in ocean crust. Nature (2008) 453:653-656.
Schrenk, M. O., Kelley, D. S., Delaney, J. R., and Baross, J. A. Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney. Appl Environ Microbiol (2003) 69:3580-3592.
Schrenk, M. O., Kelley, D. S., Bolton, S. A., and Baross, J. A. Low archaeal diversity linked to subseafloor geochemical processes at the Lost City Hydrothermal Field, Mid-Atlantic Ridge. Environ Microbiol (2004) 6: 1086-1095.
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., Sahl, J. W., Stres, B., Thallinger, G G., Van Horn, D. J., and Weber, C. F. Introducing Mothur:open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol (2009) 75:7537-7541.
Simonato, F., Campanaro, S., Lauro, F. M., Vezzi, A., D'Angelo, M., Vitulo, N., Valle, G, and Bartlett, D. H. Piezophilic adaptation:a genomic point of view. J Biotechnol (2006) 126:11-25.
Sogin, M. L., Morrison, H. G., Huber, J. A., Welch, D. M., Huse, S. M., Neal, P. R., Arrieta, J. M., and Herndl, G. J. Microbial diversity in thedeep sea and the underexplored "rare biosphere". Proc Natl Acad Sci USA (2006) 103: 12115-12120.
Soliman, G. S. H., and Truper, H. G. Halobacterium pharaonis sp.nov., a new, extremely haloalkaliphilic archaebacterium with low magnesium requirement. Zbl Bakt Hyg I Abt Orig C (1982) 3:318-329.
Steinberg, D. K., Van Mooy, B. A. S., Buesseler, K. O., Boyd, P. W., Kobari, T., and Karl, D. M. Bacterial vs. zooplankton control of sinking particle flux in the ocean's twilight zone. Limnol Oceanogr (2008) 53:1327-1338.
Suzuki, Y., Inagaki, F., Takai, K., Nealson, K. H., and Horikoshi, K. Microbial diversity in inactive chimney structures from deep-sea hydrothermal systems. Microb Ecol (2004) 47:186-196.
Takai, K., and Horikoshi, K. Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics (1999) 152:1285-1297.
Takai, K., and Horikoshi, K. Thermosipho japonicus sp. nov., an extremely thermophilic bacterium isolated from a deep-sea hydrothermal vent in Japan. Extremophiles (2000) 4:9-17.
Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol (2000) 50:489-500.
Takai, K., Nakagawa, S., Sako, Y., and Horikoshi K. Balnearium lithotrophicum gen. nov., sp. nov., a novel thermophilic, strictly anaerobic, hydrogen-oxidizing chemolithoautotroph isolated from a black smoker chimney in the Suiyo Seamount hydrothermal system. Int J Syst Evol Microbiol (2003) 53:1947-1954.
Takai, K., Gamo, T., Tsunogai, U., Nakayama, N., Hirayama, H., Nealson, K. H., and Horikoshi, K. Geochemical and microbiological evidence for a hydrogen-based, hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) beneath an active deep-sea hydrothermal field. Extremophiles (2004a) 8:269-282.
Takai, K., Oida, H., Suzuki, Y., Hirayama, H., Nakagawa, S., Nunoura, T., Inagaki, F., Nealson, K. H., and Horikoshi, K. Spatial distribution of marine Crenarchaeota group I in the vicinity of deep-sea hydrothermal systems. Appl Environ Microbiol (2004b) 70:2404-2413.
Takai, K., Nakagawa, S., Reysenbach, A. L., and Hoek, J. Microbial ecology of Mid-Ocean Ridges and Back-arc Basins. In Back-Arc Spreading Systems: Geological, Biological, Chemical and Physical Interactions (Christie, D. M., Fisher, C. R., Lee, S., and Givens, S., eds), Washington, DC:American Geophysical Union (2006) pp.185-214.
Takai, K., Miyazaki, M., Hirayama, H., Nakagawa, S., Querellou, J., and Godfroy, A. Isolation and physiological characterization of two novel, piezophilic, thermophilic chemolithoautotrophs from a deep-sea hydrothermal vent chimney. Environ Microbiol (2009) 11:1983-1997.
Tamura, K., Dudley, J., Nei, M., and Kumar, S. MEGA 4:Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol (2007) 24: 1596-1599.
Tindall, B. J., Ross, H. N. M., and Grant, W. D. Natronobacterium gen. nov. and Natronococcus gen. nov., two new genera of haloalkaliphilic archaebacteria. System Appl Microbiol (1984) 5:41-57.
Van Dover, C. L., Humphris, S. E., Fornari, D., Cavanaugh, C. M., Collier, R., Goffredi, S. K., Hashimoto, J., Lilley, M. D., Reysenbach, A. L., Shank, T. M., Von Damm, K. L., Banta, A., Gallant, R. M., Gotz, D., Green, D., Hall, J., Harmer, T. L., Hurtado, L. A., Johnson, P., McKiness, Z. P., Meredith, C., Olson, E., Pan, I. L., Turnipseed, M., Won, Y., Young Ⅲ, C. R., and Vrijenhoek, R. C. Biogeography and ecological setting of Indian Ocean hydrothermal vents. Science (2001) 294:818-823.
Varela, M. M., van Aken, H. M., Sintes, E., and Herndl, G. J. Latitudinal trends of Crenarchaeota and Bacteria in the meso-and bathypelagic water masses of the Eastern North Atlantic. Environ Microbiol (2008) 10:110-124.
Vetriani, C., Jannasch, H. W., MacGregor, B. J., Stahl, D. A., and Reysenbach, A. L. Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Appl Environ Microbiol (1999) 65:4375-4384.
Vezzi, A., Campanaro, S., D'Angelo, M., Simonato, F., Vitulo, N., Lauro, F. M., Cestaro, A., Malacrida, G., Simionati, B., Cannata, N., Romualdi, C., Bartlett, D. H., and Valle, G. Life at depth:Photobacterium profundum genome sequence and expression analysis. Science (2005) 307:1459-1461.
Wang, F., Zhou, H., Meng, J., Peng, X., Jiang, L., Sun, P., Zhang, C., Van Nostrand, J. D., Deng, Y., He, Z., Wu, L., Zhou, J., and Xiao, X. GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proc Natl Acad Sci U S A. (2009) 106: 4840-4845.
Wasmund, K., Kurtboke, D. I., Burns, K. A., and Bourne, D. G. Microbial diversity in sediments associated with a shallow methane seep in the tropical Timor Sea of Australia reveals a novel aerobic methanotroph diversity. FEMS Microbiol Ecol (2009) 68:142-151.
Wenzhofer, F., and Glud, R. N. Benthic carbon mineralization in the Atlantic:a synthesis based on in situ data from the last decade. Deep-Sea Res I (2002) 49: 1255-1279.
Welch, T. J., and Bartlett, D. H. Isolation and characterization of the structural gene for OmpL, a pressure-regulated porin-like protein from the deep-sea bacterium Photobacterium species strain SS9. JBacteriol (1996) 178:5027-5031.
Whitman, W. B., Coleman, D. C., and Wiebe, W. J. Prokaryotes:the unseen majority. Proc Natl Acad Sci U S A (1998) 95:6578-6583.
Wirsen, C. O., Jannasch, H. W., Wakeham, S. G., and Canuel, E. A. Membrane lipids of a psychrophilic and barophilic deep-sea bacterium. Curr Microbiol (1987) 14:319-322.
Witte, U., Wenzhofer, F., Sommer, S., Boetius, A., Heinz, P., Aberle, N., Sand, M., Cremer, A., Abraham, W. R., Jergensen, B. B., and Pfannkuche, O. In situ experimental evidence of the fate of a phytodetritus pulse at the abyssal sea floor. Nature (2003) 424:763-766.
Xu, Y., Nogi, Y., Kato, C., Liang, Z., Ruger, H. J., De Kegel, D., and Glansdorff, N. Psychromonas profunda sp. nov., a psychropiezophilic bacterium from deep Atlantic sediments. Int JSyst Evol Microbiol (2003a) 53:527-532.
Xu, Y., Nogi, Y., Kato, C., Liang, Z., Ruger, H. J., De Kegel, D., and Glansdorff, N. Moritella profunda sp. nov. and Moritella abyssi sp. nov., two psychropiezophilic organisms isolated from deep Atlantic sediments. Int J Syst Evol Microbiol (2003b) 53:533-538.
Yanagibayashi, M., Nogi, Y., Li, L., and Kato, C. Changes in the microbial community in Japan Trench sediment from a depth of 6292 m during cultivation without decompression. FEMS Microbiol Lett (1999) 170:271-279.
Yayanos, A. A. Simply actuated closure for a pressure vessel:design for use to trap deep-sea animals. Rev Sci Instrum (1977) 48:786-789.
Yayanos, A. A., Dietz, A. S., and Vanboxtel, R. Isolation of a deepsea barophilic bacterium and some of its growth characteristics. Science (1979) 205:808-810.
Yayanos, A. A., Dietz, A. S., and Van Boxtel, R. Obligately barophilic bacterium from the Mariana Trench. Proc Natl Acad Sci USA (1981) 78:5212-5215.
Yayanos, A. A., and Van Boxtel, R. Coupling device for quick high-pressure connections to 100 MPa. Rev Sci Instrum (1982) 53:704-705.
Yayanos, A. A., and Dietz, A. S. Death of a hadal deep-sea bacterium after decompression. Science (1983) 220:497-498.
Yayanos, A. A. Evolutional and ecological implications of the properties of deep-sea barophilic bacteria. Proc Natl Acad Sci USA (1986) 83:9542-9546.
Yayanos, A. A. Microbiology to 10,500 meters in the deep sea. Annu Rev Microbiol (1995)49:777-805.
Zehr, J. P., and McReynoIds, L. A. Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol (1989) 55:2522-2526.
Zehr, J. P., Jenkins, B. D., Short, S. M., and Steward, G. F. Nitrogenase gene diversity and microbial community structure:a cross-system comparison. Environ Microbiol (2003) 5:539-554.
Zeng, X., Birrien, J. L., Fouquet, Y., Cherkashov, G., Jebbar, M., Querellou, J., Oger, P., Cambon-Bonavita, M. A., Xiao, X., and Prieur, D. Pyrococcus CHI, an obligate piezophilic hyperthermophile:extending the upper pressure-temperature limits for life. ISME J (2009) 3:873-876.
Zhang, X. Y., Zhang, Y. J., Yu, Y., Li, H. J., Gao, Z. M., Chen, X. L., Chen, B., and Zhang, Y. Z. Neptunomonas antarctica sp. nov., isolated from Antarctic marine sediment. Int JSyst Evol Microbiol (2009) doi:10.1099/ijs.0.017756-0.
Zhilina, T. N., Garnova, E. S., Tourova, T. P., Kostrikina, N. A., and Zavarzin, G. A. Halonatronum saccharophilum gen. nov. sp. nov.:a new haloalkaliphilic bacterium of the order Haloanaerobiales from Lake Magadi. Microbiology (Moscow) (2001) 70:64-72.
ZoBell, C. E. Studies on marine bacteria. I. The cultural requirements of the heterotrophic aerobes. Jour Marine Research (1941) 4:42-75.
ZoBell, C. E., and Johnson, F. H. The influence of hydrostatic pressure on the growth and viability of terrestrial and marine bacteria. J Bacteriol (1949) 57: 179-189.
ZoBell, C. E. Bacterial life at the bottom of the Philippine trench. Science (1952) 115: 507-508.
ZoBell, C. E., and Morita, R. Y. Barophilic bacteria in some deep-sea sediments. J Bacteriol (1957) 73:563-568.
Alain, K., Marteinsson, V. T., Miroshnichenko, M. L., Bonch-Osmolovskaya, E. A., Prieur, D., and Birrien, J. L. Marinitoga piezophila sp. nov., a rod-shaped, thermo-piezophilic bacterium isolated under high hydrostatic pressure from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol (2002) 52:1331-1339.
Alazard, D., Dukan, S., Urios, A., Verhe, F., Bouabida, N., Morel, F., Thomas, P., Garcia, J. L., and Ollivier, B. Desulfovibrio hydrothermalis sp nov., a novel sulfate-reducing bacterium isolated from hydrothermal vents. Int J Syst Evol Microbiol (2003) 53:173-178.
Allen, E. E., Facciotti, D., and Bartlett, D. H. Monounsaturated but not polyunsaturated fatty acids are required for growth of thedeep-sea bacterium Photobacterium profundum SS9 at high pressure and low temperature. Appl Environ Microbiol (1999) 65:1710-1720.
Allen, E. E., and Bartlett, D. H. Structure and regulation of the omega-3 polyunsaturated fatty acid synthase genes from the deep-sea bacterium Photobacterium profundum strain SS9. Microbiology (2002) 148:1903-1913.
Arakawa, S., Sato, T., Yoshida, Y., Usami, R., and Kato, C. Comparison of the microbial diversity in cold-seep sediments from different depths in the Nankai Trough. J Gen Appl Microbiol (2006) 52:47-54.
Azam, F., and Malfatti, F. Microbial structuring of marine ecosystems. Nat Rev Microbiol (2007) 5:782-791.
Baker, G. C., Smith, J. J., and Cowan, D. A. Review and re-analysis of domain-specific 16S primers. J Microbiol Methods (2003) 55:541-555.
Bale, S. J., Goodman, K., Rochelle, P. A., Marchesi, J. R., Fry, J. C., Weightman, A. J., and Parkes, R. J. Desulfovibrio profundus sp nov, a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea. Int J Syst Bacteriol (1997) 47:515-521.
Baltar, F., Aristegui, J., Gasol, J. M., Sintes, E., and Herndl, G. J. Evidence of prokaryotic metabolism on suspended particulate organic matter in the dark waters of the subtropical North Atlantic. Limnol Oceanogr (2009) 54:182-193.
Bartlett, D. H., Wright, M., Yayanos, A. A., and Silverman, M. Isolation of a gene regulated by hydrostatic pressure in a deepsea bacterium. Nature (1989) 342: 572-574.
Bartlett, D. H. Microbial life at high-pressures. Sci Prog (1992) 76:479-496.
Bonete, M. J., Camacho, M. L., and Cadenas, E. Purification and properties of NAD+-dependent glutamate dehydrogenase from Halobacterium halobium. Int J Biochem (1986) 18:785-789.
Bonete, M. J., Camacho, M. L., and Cadenas, E. A new glutamate dehydrogenase from Halobacterium halobium with different coenzyme specificity. Int J Biochem (1987) 19:1149-1155.
Brandt, A., Gooday, A. J., Brandao, S. N., Brix, S., Brokeland, W., Cedhagen, T., Choudhury, M., Cornelius, N., Danis, B., De Mesel, I., Diaz, R. J., Gillan, D. C., Ebbe, B., Howe, J. A., Janussen, D., Kaiser, S., Linse, K., Malyutina, M., Pawlowski, J., Raupach, M., and Vanreusel, A. First insights into the biodiversity and biogeography of the Southern Ocean deep sea. Nature (2007) 447:307-311.
Brochier-Armanet, C., Boussau, B., Gribaldo, S., and Forterre, P. Mesophilic Crenarchaeota:proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol (2008) 6:245-252.
Bruun, A. F. Deep sea and abyssal depths. Geol Soc Am Mem (1957) 67:641-672.
Canganella, F., Gonzalez, J. M., Yanagibayashi, M., Kato, C., and Horikoshi, K. Pressure and temperature effects on growth and viability of the hyperthermophilic archaeon Thermococcus peptonophilus. Arch Microbiol (1997) 168:1-7.
Charlou, J. L., Donval, J. P., Fouquet, Y., Jean-Baptiste, P., and Holm, N. Geochemistry of high H2 and CH4 vent fluids issuing from ultramafic rocks at the Rainbow hydrothermal field (36°14'N, MAR) Chem Geol (2002) 191: 345-359.
Chien, Y. T., and Zinder, S. H. Cloning, functional organization, transcript studies, and phylogenetic analysis of the complete nitrogenase structural genes (nifHDK2) and associated genes in the archaeon Methanosarcina barkeri 227. J Bacteriol (1996)178:143-148.
Chilukuri, L. N., and Bartlett, D. H. Isolation and characterization of the gene encoding single-stranded-DNA-binding protein (SSB) from four marine Shewanella strains that differ in their temperature and pressure optima for growth. Microbiology (1997) 143:1163-1174.
Corliss, J. B., Dymond, J., Gordon, L. I., Edmond, J. M., von Herzen, R. P., Ballard, R. D., Green, K., Williams, D., Bainbridge, A., Crane, K., and van Andel, T. H. Submarine Thermal Sprirngs on the Galapagos Rift. Science (1979) 203:1073-1083.
Daniel, I., Oger, P., and Winter, R. Origins of life and biochemistry under high-pressure conditions. Chem Soc Rev (2006) 35:858-875.
Danovaro, R., Dell'Anno, A., Fabiano, M., Pusceddu, A., and Tselepides, A. Deep-sea ecosystem response to climate changes:The eastern Mediterranean case study. Trends Ecol Evol (2001) 16:505-510.
DeLong, E. F., and Yayanos, A. A. Biochemical function and ecological significance of novel bacterial lipids in deep-sea procaryotes. Appl Environ Microbiol (1986) 51:730-737.
DeLong, E. F. Archaea in coastal marine environments. Proc Natl Acad Sci USA (1992)89:5685-5689.
DeLong, E. F., Franks, D. G., and Yayanos, A. A. Evolutionary relationships of cultivated psychrophilic and barophilic deep-sea bacteria. Appl Environ Microbiol (1997) 63:2105-2108.
DeLong, E. F., Preston, C. M., Mincer, T., Rich, V., Hallam, S. J., Frigaard, N. U., Martinez, A., Sullivan, M. B., Edwards, R., Brito, B. R., Chisholm, S. W., and Karl, D. M. Community genomics among stratified microbial assemblages in the ocean's interior. Science (2006) 311:496-503.
Deming, J. W., Somers, L. K., Straube, W. L., Swartz, D. G., and MacDonell, M. T. Isolation of an obligately barophilic bacterium and description of a new genus, Colwellia gen. nov. Syst Appl Microbiol (1988) 10:152-160.
Dietz, A. S., and Yayanos, A. A. Silica gel media for isolating and studying bacteria under hydrostatic pressure. Appl Environ Microbiol (1978) 36:966-968.
Di Giulio, M. A comparison of proteins from Pyrococcus furiosus and Pyrococcus abyssi:barophily in the physicochemical properties of amino acids and in the genetic code. Gene (2004) 346:1-6.
Emerson, D., Rentz, J. A., Lilburn, T. G., Davis, R. E., Aldrich, H., Chan, C., and Moyer, C. L. A novel lineage of Proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities. PLoS ONE (2007) 2:e667.
Falb, M., Pfeiffer, F., Palm, P., Rodewald, K., Hickmann, V., Tittor, J., and Oesterhelt, D. Living with two extremes:conclusions from the genome sequence of Natronomonas pharaonis. Genome Res (2005) 15:1336-1343.
Felsenstein, J. PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics (1989)5:164-166.
Foustoukos, D. I., and Seyfried, W. E. Hydrocarbons in hydrothermal vent fluids: The role of chromium-bearing catalysts. Science (2004) 304:1002-1005.
Fry, J. C., Parkes, R. J., Cragg, B. A., Weightman, A. J., and Webster, G. Prokaryotic biodiversity and activity in the deep subseafloor biosphere. FEMS Microbiol Ecol (2008) 66:181-196.
Fuhrman, J. A., McCallum, K., and Davis, A. A. Novel major archaebacterial group from marine plankton. Nature (1992) 356:148-149.
Garnova, E. S., and Krasil'nikova, E. N. Carbohydrate metabolism of the saccharolytic alkaliphilic anaerobes Halonatronum saccharophilum, Amphibacillus fermentum, and Amphibacillus tropicus. Microbiology (Moscow) (2003) 72:558-563.
Handelsman, J., Rondon, M. R., Brady, S. F., Clardy, J., and Goodman, R. M. Molecular biological access to the chemistry of unknown soil microbes:a new frontier for natural products. Chem Biol (1998) 5:245-249.
Hashimoto, J., Ohta, S., Gamo, T., Chiba, H., Yamaguchi, T., Tsuchida, S., Okudaira, T., Watabe, H., Yamanaka, T., and Kitazawa, M. First hydrothermal vent communities from the Indian Ocean discovered. Zool Sci (2001)18:717-721.
Heijs, S. K., Laverman, A. M., Forney, L. J., Hardoim, P. R., and van Elsas, J. D. Comparison of deep-sea sediment microbial communities in the Eastern Mediterranean. FEMS Microbiol Ecol (2008) 64:362-377.
Herndl, G. J., Reinthaler, T., Teira, E., Aken, H. M. V., Veth, C., Pernthaler, A., and Pernthaler, J. Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean. Appl Environ Microbiol (2005) 72:2303-2309.
Hess, M., and Antranikian, G Archaeal alcohol dehydrogenase active at increased temperatures and in the presence of organic solvents. Appl Microbiol Biotechnol (2008) 77:1003-1013.
Jergensen, B. B., and Boetius, A. Feast and famine-microbial life in the deep-sea bed. Nat Rev Microbiol (2007) 5:770-781.
Jukes, T. H., and Cantor, C. R. Evolution of protein molecules. In Mammalian Protein Metabolism (Munro, H. N., ed), New York:Academic Press (1969) pp. 21-132.
Karl, D. M. Ecology of free-hydrothermal vent microbial communities. In The Microbiology of Deep-sea Hydrothermal Vents (Karl, D. M., ed), Boca Raton: CRC Press Inc (1995) pp.35-124.
Kato, C., and Bartlett, D. H. The molecular biology of barophilic bacteria. Extremophiles (1997) 1:111-116.
Kato, C., Li, L., Nogi, Y., Nakamura, Y., Tamaoka, J., and Horikoshi, K. Extremely barophilic bacteria isolated from the Mariana Trench, Challenger Deep, at a depth of 11,000 m. Appl Environ Microbiol (1998) 64:1510-1513.
Kato, C. Handling of piezophilic microorganisms. In Extremophiles. Methods in Microbiology, vol.35 (Rainey, F. A., and Oren, A., eds), Amsterdam:Elsevier (2006) pp.733-741.
Kato, S., Kobayashi, C., Kakegawa, T., and Yamagishi, A. Microbial communities in iron-silica-rich microbial mats at deep-sea hydrothermal fields of the Southern Mariana Trough. Environ Microbiol (2009) 11:2094-2111.
Kato, S., Takano, Y., Kakegawa, T., Oba, H., Inoue, K., Kobayashi, C., Utsumi, M., Marumo, K., Kobayashi, K., Ito, Y., Ishibashi, J. I., and Yamagishi, A. Biogeography and biodiversity in sulfide structures of active and inactive vents at deep-sea hydrothermal fields of the Southern Mariana Trough. Appl Environ Microbiol (2010) doi:10.1128/AEM.00478-10.
Kennedy, S. P., Ng, W. V., Salzberg, S. L., Hood, L., and DasSarma, S. Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res(2001)11:1641-1650.
Kim, H., Joo, W., Cho, C., and Kim, C. Halophile aldehyde dehydrogenase from Halobacterium salinarum. JProteome Res (2006) 5:192-195
Kimura, M. A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J Mol Evol (1980) 16: 111-120.
Konneke, M., Bernhard, A. E., de la Torre, J. R., Walker, C. B., Waterbury, J. B., and Stahl, D. A. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature (2005) 437:543-546.
Konstantinidis, K., Tebbe, A., Klein, C., Scheffer, B., Aivaliotis, M., Bisle, B., Falb, M., Pfeiffer, F., Siedler, F., and Oesterhelt, D. Genome-wide proteomics of Natronomonas pharaonis. J Proteome Res (2007) 6:185-193.
Kyo, M., Tsuji, T., Usui, H., and Itoh, T. Collection, isolation and cultivation system for deep-sea microbes study:concept and design. Oceans (1991) 1:419-423.
Lampitt, R. S., and Antia, A.N. Particle flux in deep seas:regional characteristics and temporal variability. Deep Sea Res I (1997) 44:1377-1403.
Lauro, F. M., Chastain, R. A., Blankenship, L. E., Yayanos, A. A., and Bartlett, D. H. The unique 16S rRNA genes of piezophiles reflect both phylogeny and adaptation. Appl Environ Microbiol (2007) 73:838-845.
Lauro, F. M., and Bartlett, D. H. Prokaryotic lifestyles in deep sea habitats. Extremophiles (2008) 12:15-25.
Li, Y., Li, F., Zhang, X., Qin, S., Zeng, Z., Dang, H., and Qin, Y. Vertical distribution of bacterial and archaeal communities along discrete layers of a deep-sea cold sediment sample at the East Pacific Rise (～13°N). Extremophiles (2008) 12:573-585.
Lopez-Garcia, P., Duperron, S., Philippot, P., Foriel, J., Susini, J., and Moreira, D. Bacterial diversity in hydrothermal sediment and epsilonproteobacterial dominance in experimental microcolonizers at the Mid-Atlantic Ridge. Environ Microbiol (2003) 5:961-976.
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, A. W., 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., and Schleifer, K. H. ARB:a software environment for sequence data. Nucleic Acids Res (2004) 32:1363-1371.
Macdonald, A. G., and Gilchrist, I. Recovery of deep seawater at constant pressure. Nature (1969) 222:71-72.
Margesin, R., and Nogi, Y. Psychropiezophilic microorganisms. Cell Mol Biol (2004) 50:429-436.
Marteinsson, V. T., Moulin, P., Birrien, J. L., Gambacorta, A., Vernet, M., and Prieur, D. Physiological responses to stress conditions and barophilic behaviour of the hyperthermophilic archaeon Pyrococcus abyssi. Appl Environ Microbiol (1997)93:1230-1236.
Marteinsson, V. T., Birrien, J. L., Reysenbach, A. L., Venet, M., Marie, D., Gambacorta, A., Messner, P., Sleytr, U. B., and Prieur, D. Thermococcus barophilus sp. nov., a new barophilic and hyperthermophilic archaeon isolated under high hydrostatic pressure from a deep-sea hydrothermal vent. Int J Syst Bacteriol (1999) 49:351-359.
Martin, D. D., Bartlett, D. H., and Roberts, M. F. Solute accumulation in the deep-sea bacterium Photobacterium profundum. Extremophiles (2002) 6: 507-514.
Martin-Cuadrado, A. B., Lopez-Garcia, P., Alba, J. C., Moreira, D., Monticelli, L., Strittmatter, A., Gottschalk, G., and Rodriguez-Valera, F. Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS One (2007) 2: e914.
Mason, O. U., Stingl, U., Wilhelm, L. J., Moeseneder, M. M., DiMeo-Savoie, C. A., Fisk, M. R., and Giovannoni, S. J. The phylogeny of endolithic microbes associated with marine basalts. Environ Microbiol (2007) 9:2539-2550.
McCollom, T. M., and Shock, E. L. Geochemical constraints on Chemolithoautotrophic metabolism by microorganisms in seafloor hydrothermal systems. Geochim Cosmochim Acta (1997) 61:4375-4391.
Mehta, M. P., Butterfield, D. A., and Baross, J. A. Phylogenetic diversity of nitrogenase (nifH) genes in deep-sea and hydrothermal vent environments of the Juan de Fuca Ridge. Appl Environ Microbiol (2003) 69:960-970.
Mehta, M. P., and Baross, J. A. Nitrogen fixation at 92 ℃ by a hydrothermal vent archaeon. Science (2006) 314:1783-1786.
Miyazaki, M., Nogi, Y., Fujiwara, Y., Kawato, M., Kubokawa, K., and Horikoshi, K. Neptunomonas japonica sp. nov., an Osedax japonicus symbiont-like bacterium isolated from sediment adjacent to sperm whale carcasses off Kagoshima, Japan. Int J Syst Evol Microbiol (2008) 58:866-871.
Morita, R. Y. Psychrophilic bacteria. Bacteriol Rev (1975) 39:144-167.
Nagata, T., Tamburini, C., Aristegui, J., Baltar, F., Bochdansky, A., Fonda-Umani, S., Fukuda, H., Gogou, A., Hansell, D. A., Hansman, R. L., Herndl, G. J., Panagiotopoulos, C., Reinthaler, T., Sohrin, R., Verdugo, P., Yamada, N., Yamashita, Y., Yokokawa, T., and Bartlett, D. H. Emerging concepts on microbial processes in the bathypelagic ocean-ecology, biogeochemistry, and genomics. Deep-Sea Res Ⅱ(2010) doi:10.1016/j.dsr2.2010.02.019.
Nakagawa, S., Takai, K., Horikoshi, K., and Sako, Y. Persephonella hydrogeniphila sp. nov., a novel thermophilic, hydrogen-oxidizing bacterium from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol (2003) 53: 863-869.
Nakagawa, S., Takai, K., Inagaki, F., Hirayama, H., Nunoura, T., Horikoshi, K., and Sako, Y. Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field. Environ Microbiol (2005) 7:1619-1632.
Nakagawa, S., and Takai, K. Methods for the isolation of thermophiles from deep-sea hydrothermal environments. In Extremophiles. Methods in Microbiology, vol.35 (Rainey, F. A., and Oren, A., eds), Amsterdam:Elsevier (2006) pp.55-91.
Nakagawa, S., and Takai, K. Deep-sea vent chemoautotrophs:diversity, biochemistry and ecological significance. FEMS Microbiol Ecol (2008) 65:1-14.
Naqvi, W., and Gattuso, J. Marine nitrogen cycle. In Encyclopedia of Earth. (Cleveland, C. J., eds) Washington, DC:Environmental Information Coalition, National Council for Science and the Environment (2006).
Nercessian, O., Fouquet, Y., Pierre, C., Prieur, D., and Jeanthon, C. Diversity of Bacteria and Archaea associated with a carbonate-rich metalliferous sediment sample from the Rainbow vent field on the Mid-Atlantic Ridge. Environ Microbiol (2005) 7:698-714.
Ng, W. V., Kennedy, S. P., Mahairas, G. G., Berquist, B., Pan, M., Shukla, H. D., Lasky, S. R., Baliga, N. S., Thorsson, V., Sbrogna, J., Swartzell, S., Weir, D., Hall, J., Dahl, T. A., Welti, R., Goo, Y. A., Leithauser, B., Keller, K., Cruz, R., Danson, M. J., Hough, D. W., Maddocks, D. G., Jablonski, P. E., Krebs, M. P., Angevine, C. M., Dale, H., Isenbarger, T. A., Peck, R. F., Pohlschroder, M., Spudich, J. L., Jung, K. W., Alam, M., Freitas, T., Hou, S., Daniels, C. J., Dennis, P. P., Omer, A. D., Ebhardt, H., Lowe, T. M., Liang, P., Riley, M., Hood, L., and DasSarma, S. Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A (2000) 97:12176-12181.
Nogi, Y., Kato, C., and Horikoshi, K. Moritella japonica sp. nov., a novel barophilic bacterium isolated from a Japan Trench sediment. J Gen Appl Microbiol (1998a) 44:289-295.
Nogi, Y., Kato, C., and Horikoshi, K. Taxonomic studies of deep-sea barophilic Shewanella strains and description of Shewanella violacea sp. nov. Arch Microbiol (1998b) 170:331-338.
Nogi, Y., Masui, N., and Kato, C. Photobacterium profundum sp. nov., a new, moderately barophilic bacterial species isolated from a deep-sea sediment. Extremophiles (1998c) 2:1-7.
Nogi, Y., and Kato, C. Taxonomic studies of extremely barophilic bacteria isolated from the Mariana Trench and description of Moritella yayanosii sp. nov., a new barophilic bacterial isolate. Extremophiles (1999) 3:71-77.
Nogi, Y., Kato, C., and Horikoshi, K. Psychromonas kaikoae sp. nov., a novel piezophilic bacterium from the deepest cold-seep sediments in the Japan Trench. Int J Syst Evol Microbiol (2002) 52:1527-1532.
Nogi, Y., Hosoya, S., Kato, C., and Horikoshi, K. Colwellia piezophila sp. nov., a novel piezophilic species from deep-sea sediments of the Japan Trench. Int J Syst Evol Microbiol (2004) 54:1627-1631.
Nogi, Y., Hosoya, S., Kato, C., and Horikoshi, K. Psychromonas hadalis sp. nov., a novel piezophilic bacterium isolated from the bottom of the Japan Trench. Int J Syst Evol Microbiol (2007) 57:1360-1364.
Oesterhelt, D., and Stoeckenius, W. Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nat New Biol (1971) 233:149-152.
Olsen, G. J., Lane, D. J., Giovannoni, S. J., Pace, N. R., and Stahl, D. A. Microbial ecology and evolution:a ribosomal RNA approach. Annu Rev Microbiol (1986) 40:337-365.
Olu-LeRoy, K., Sibuet, M., Fiala-Medioni, A., Gofas, S., Salas, C., Mariotti, A., Foucher, J., and Woodside, J. Cold seep communities in the deep eastern Mediterranean Sea:composition, symbiosis, and spatial distribution on mud volcanoes. Deep-Sea Res Ⅰ(2004) 51:1915-1936.
Oren, A. A thermophilic amyloglucosidase from Halobacterium sodomense, a halophilic bacterium from the Dead Sea. Curr Microbiol (1973) 8:225-230.
Park, C. B., Boonyaratanakornkit, B. B., and Clark, D. S. Toward the large scale cultivation of hyperthermophiles at high-temperature and high-pressure. In Extremophiles. Methods in Microbiology, vol.35 (Rainey, F. A., and Oren, A., eds), Amsterdam:Elsevier (2006) pp.109-126.
Parkes, R. J., Sellek, G, Webster, G., Martin, D., Anders, E., Weightman, A. J., and Sass, H. Culturable prokaryotic diversity of deep, gas hydrate sediments: first use of a continuous high-pressure, anaerobic, enrichment and isolation system for subseafloor sediments (DeepIsoBUG). Environ Microbiol (2009) 11: 3140-3153.
Pham, V. D., Konstantinidis, K. T., Palden, T., and DeLong, E. F. Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre. Environ Microbiol (2008) 10:2313-2330.
Price, M. N., Dehal, P. S., and Arkin, A. P. FastTree:Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix. Mol Biol Evol (2009) 26:1641-1650.
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., and Glockner, F. O. SILVA:a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res (2007) 35:7188-7196.
Rainey, F. A., and Oren, A. Extremophile microorganisms and the methods to handle them. In Extremophiles. Methods in Microbiology, vol.35 (Rainey, F. A., and Oren, A., eds), Amsterdam:Elsevier (2006) pp.1-25.
Rappe, M. S., and Giovannoni, S. J. The uncultured microbial majority. Annu Rev Microbiol (2003) 57:369-394.
Reid, M. F., and Fewson, C. A. Molecular characterization of microbial alcohol dehydrogenase. Crit Rev Microbiol (1994) 20:13-56.
Reysenbach, A. L., and Shock, E. Merging genomes with geochemistry in hydrothermal ecosystems. Science (2002) 296:1077-1082.
Reysenbach, A. L., Liu, Y., Banta, A. B., Beveridge, T. J., Kirshtein, J. D., Schouten, S., Tivey, M. K., Von Damm, K. L., and Voytek, M. A. A ubiquitous thermoacidophilic archaeon from deep-sea hydrothermal vents. Nature (2006) 442:444-447.
Royer, C. A. Application of pressure to biochemical equilibria:the other thermodynamic variable. Methods Enzymol (1995) 259:357-377.
Saitou, N., and Nei, M. The neighbour joining method:a new tool for reconstructing phylogenetic trees. Mol Biol Evol (1987) 4:406-425.
Santelli, C. M., Orcutt, B. N., Banning, E., Bach, W., Moyer, C. L., Sogin, M. L., Staudigel, H., and Edwards, K. J. Abundance and diversity of microbial life in ocean crust. Nature (2008) 453:653-656.
Schrenk, M. O., Kelley, D. S., Delaney, J. R., and Baross, J. A. Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney. Appl Environ Microbiol (2003) 69:3580-3592.
Schrenk, M. O., Kelley, D. S., Bolton, S. A., and Baross, J. A. Low archaeal diversity linked to subseafloor geochemical processes at the Lost City Hydrothermal Field, Mid-Atlantic Ridge. Environ Microbiol (2004) 6: 1086-1095.
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., Sahl, J. W., Stres, B., Thallinger, G G., Van Horn, D. J., and Weber, C. F. Introducing Mothur:open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol (2009) 75:7537-7541.
Simonato, F., Campanaro, S., Lauro, F. M., Vezzi, A., D'Angelo, M., Vitulo, N., Valle, G, and Bartlett, D. H. Piezophilic adaptation:a genomic point of view. J Biotechnol (2006) 126:11-25.
Sogin, M. L., Morrison, H. G., Huber, J. A., Welch, D. M., Huse, S. M., Neal, P. R., Arrieta, J. M., and Herndl, G. J. Microbial diversity in thedeep sea and the underexplored "rare biosphere". Proc Natl Acad Sci USA (2006) 103: 12115-12120.
Soliman, G. S. H., and Truper, H. G. Halobacterium pharaonis sp.nov., a new, extremely haloalkaliphilic archaebacterium with low magnesium requirement. Zbl Bakt Hyg I Abt Orig C (1982) 3:318-329.
Steinberg, D. K., Van Mooy, B. A. S., Buesseler, K. O., Boyd, P. W., Kobari, T., and Karl, D. M. Bacterial vs. zooplankton control of sinking particle flux in the ocean's twilight zone. Limnol Oceanogr (2008) 53:1327-1338.
Suzuki, Y., Inagaki, F., Takai, K., Nealson, K. H., and Horikoshi, K. Microbial diversity in inactive chimney structures from deep-sea hydrothermal systems. Microb Ecol (2004) 47:186-196.
Takai, K., and Horikoshi, K. Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics (1999) 152:1285-1297.
Takai, K., and Horikoshi, K. Thermosipho japonicus sp. nov., an extremely thermophilic bacterium isolated from a deep-sea hydrothermal vent in Japan. Extremophiles (2000) 4:9-17.
Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol (2000) 50:489-500.
Takai, K., Nakagawa, S., Sako, Y., and Horikoshi K. Balnearium lithotrophicum gen. nov., sp. nov., a novel thermophilic, strictly anaerobic, hydrogen-oxidizing chemolithoautotroph isolated from a black smoker chimney in the Suiyo Seamount hydrothermal system. Int J Syst Evol Microbiol (2003) 53:1947-1954.
Takai, K., Gamo, T., Tsunogai, U., Nakayama, N., Hirayama, H., Nealson, K. H., and Horikoshi, K. Geochemical and microbiological evidence for a hydrogen-based, hyperthermophilic subsurface lithoautotrophic microbial ecosystem (HyperSLiME) beneath an active deep-sea hydrothermal field. Extremophiles (2004a) 8:269-282.
Takai, K., Oida, H., Suzuki, Y., Hirayama, H., Nakagawa, S., Nunoura, T., Inagaki, F., Nealson, K. H., and Horikoshi, K. Spatial distribution of marine Crenarchaeota group I in the vicinity of deep-sea hydrothermal systems. Appl Environ Microbiol (2004b) 70:2404-2413.
Takai, K., Nakagawa, S., Reysenbach, A. L., and Hoek, J. Microbial ecology of Mid-Ocean Ridges and Back-arc Basins. In Back-Arc Spreading Systems: Geological, Biological, Chemical and Physical Interactions (Christie, D. M., Fisher, C. R., Lee, S., and Givens, S., eds), Washington, DC:American Geophysical Union (2006) pp.185-214.
Takai, K., Miyazaki, M., Hirayama, H., Nakagawa, S., Querellou, J., and Godfroy, A. Isolation and physiological characterization of two novel, piezophilic, thermophilic chemolithoautotrophs from a deep-sea hydrothermal vent chimney. Environ Microbiol (2009) 11:1983-1997.
Tamura, K., Dudley, J., Nei, M., and Kumar, S. MEGA 4:Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol (2007) 24: 1596-1599.
Tindall, B. J., Ross, H. N. M., and Grant, W. D. Natronobacterium gen. nov. and Natronococcus gen. nov., two new genera of haloalkaliphilic archaebacteria. System Appl Microbiol (1984) 5:41-57.
Van Dover, C. L., Humphris, S. E., Fornari, D., Cavanaugh, C. M., Collier, R., Goffredi, S. K., Hashimoto, J., Lilley, M. D., Reysenbach, A. L., Shank, T. M., Von Damm, K. L., Banta, A., Gallant, R. M., Gotz, D., Green, D., Hall, J., Harmer, T. L., Hurtado, L. A., Johnson, P., McKiness, Z. P., Meredith, C., Olson, E., Pan, I. L., Turnipseed, M., Won, Y., Young Ⅲ, C. R., and Vrijenhoek, R. C. Biogeography and ecological setting of Indian Ocean hydrothermal vents. Science (2001) 294:818-823.
Varela, M. M., van Aken, H. M., Sintes, E., and Herndl, G. J. Latitudinal trends of Crenarchaeota and Bacteria in the meso-and bathypelagic water masses of the Eastern North Atlantic. Environ Microbiol (2008) 10:110-124.
Vetriani, C., Jannasch, H. W., MacGregor, B. J., Stahl, D. A., and Reysenbach, A. L. Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Appl Environ Microbiol (1999) 65:4375-4384.
Vezzi, A., Campanaro, S., D'Angelo, M., Simonato, F., Vitulo, N., Lauro, F. M., Cestaro, A., Malacrida, G., Simionati, B., Cannata, N., Romualdi, C., Bartlett, D. H., and Valle, G. Life at depth:Photobacterium profundum genome sequence and expression analysis. Science (2005) 307:1459-1461.
Wang, F., Zhou, H., Meng, J., Peng, X., Jiang, L., Sun, P., Zhang, C., Van Nostrand, J. D., Deng, Y., He, Z., Wu, L., Zhou, J., and Xiao, X. GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proc Natl Acad Sci U S A. (2009) 106: 4840-4845.
Wasmund, K., Kurtboke, D. I., Burns, K. A., and Bourne, D. G. Microbial diversity in sediments associated with a shallow methane seep in the tropical Timor Sea of Australia reveals a novel aerobic methanotroph diversity. FEMS Microbiol Ecol (2009) 68:142-151.
Wenzhofer, F., and Glud, R. N. Benthic carbon mineralization in the Atlantic:a synthesis based on in situ data from the last decade. Deep-Sea Res I (2002) 49: 1255-1279.
Welch, T. J., and Bartlett, D. H. Isolation and characterization of the structural gene for OmpL, a pressure-regulated porin-like protein from the deep-sea bacterium Photobacterium species strain SS9. JBacteriol (1996) 178:5027-5031.
Whitman, W. B., Coleman, D. C., and Wiebe, W. J. Prokaryotes:the unseen majority. Proc Natl Acad Sci U S A (1998) 95:6578-6583.
Wirsen, C. O., Jannasch, H. W., Wakeham, S. G., and Canuel, E. A. Membrane lipids of a psychrophilic and barophilic deep-sea bacterium. Curr Microbiol (1987) 14:319-322.
Witte, U., Wenzhofer, F., Sommer, S., Boetius, A., Heinz, P., Aberle, N., Sand, M., Cremer, A., Abraham, W. R., Jergensen, B. B., and Pfannkuche, O. In situ experimental evidence of the fate of a phytodetritus pulse at the abyssal sea floor. Nature (2003) 424:763-766.
Xu, Y., Nogi, Y., Kato, C., Liang, Z., Ruger, H. J., De Kegel, D., and Glansdorff, N. Psychromonas profunda sp. nov., a psychropiezophilic bacterium from deep Atlantic sediments. Int JSyst Evol Microbiol (2003a) 53:527-532.
Xu, Y., Nogi, Y., Kato, C., Liang, Z., Ruger, H. J., De Kegel, D., and Glansdorff, N. Moritella profunda sp. nov. and Moritella abyssi sp. nov., two psychropiezophilic organisms isolated from deep Atlantic sediments. Int J Syst Evol Microbiol (2003b) 53:533-538.
Yanagibayashi, M., Nogi, Y., Li, L., and Kato, C. Changes in the microbial community in Japan Trench sediment from a depth of 6292 m during cultivation without decompression. FEMS Microbiol Lett (1999) 170:271-279.
Yayanos, A. A. Simply actuated closure for a pressure vessel:design for use to trap deep-sea animals. Rev Sci Instrum (1977) 48:786-789.
Yayanos, A. A., Dietz, A. S., and Vanboxtel, R. Isolation of a deepsea barophilic bacterium and some of its growth characteristics. Science (1979) 205:808-810.
Yayanos, A. A., Dietz, A. S., and Van Boxtel, R. Obligately barophilic bacterium from the Mariana Trench. Proc Natl Acad Sci USA (1981) 78:5212-5215.
Yayanos, A. A., and Van Boxtel, R. Coupling device for quick high-pressure connections to 100 MPa. Rev Sci Instrum (1982) 53:704-705.
Yayanos, A. A., and Dietz, A. S. Death of a hadal deep-sea bacterium after decompression. Science (1983) 220:497-498.
Yayanos, A. A. Evolutional and ecological implications of the properties of deep-sea barophilic bacteria. Proc Natl Acad Sci USA (1986) 83:9542-9546.
Yayanos, A. A. Microbiology to 10,500 meters in the deep sea. Annu Rev Microbiol (1995)49:777-805.
Zehr, J. P., and McReynoIds, L. A. Use of degenerate oligonucleotides for amplification of the nifH gene from the marine cyanobacterium Trichodesmium thiebautii. Appl Environ Microbiol (1989) 55:2522-2526.
Zehr, J. P., Jenkins, B. D., Short, S. M., and Steward, G. F. Nitrogenase gene diversity and microbial community structure:a cross-system comparison. Environ Microbiol (2003) 5:539-554.
Zeng, X., Birrien, J. L., Fouquet, Y., Cherkashov, G., Jebbar, M., Querellou, J., Oger, P., Cambon-Bonavita, M. A., Xiao, X., and Prieur, D. Pyrococcus CHI, an obligate piezophilic hyperthermophile:extending the upper pressure-temperature limits for life. ISME J (2009) 3:873-876.
Zhang, X. Y., Zhang, Y. J., Yu, Y., Li, H. J., Gao, Z. M., Chen, X. L., Chen, B., and Zhang, Y. Z. Neptunomonas antarctica sp. nov., isolated from Antarctic marine sediment. Int JSyst Evol Microbiol (2009) doi:10.1099/ijs.0.017756-0.
Zhilina, T. N., Garnova, E. S., Tourova, T. P., Kostrikina, N. A., and Zavarzin, G. A. Halonatronum saccharophilum gen. nov. sp. nov.:a new haloalkaliphilic bacterium of the order Haloanaerobiales from Lake Magadi. Microbiology (Moscow) (2001) 70:64-72.
ZoBell, C. E. Studies on marine bacteria. I. The cultural requirements of the heterotrophic aerobes. Jour Marine Research (1941) 4:42-75.
ZoBell, C. E., and Johnson, F. H. The influence of hydrostatic pressure on the growth and viability of terrestrial and marine bacteria. J Bacteriol (1949) 57: 179-189.
ZoBell, C. E. Bacterial life at the bottom of the Philippine trench. Science (1952) 115: 507-508.
ZoBell, C. E., and Morita, R. Y. Barophilic bacteria in some deep-sea sediments. J Bacteriol (1957) 73:563-568.