深海热液口微生物群落环境适应性及其基因资源研究
|
摘要
深海热液口烟囱是通过来自地壳的熔浆与海水交互作用而形成的特殊的地质结构,该环境被认为与地球早期环境相似,在热液口烟囱的喷口中,不断有气体、金属离子喷出,且形成了热量和化学物质浓度梯度。这些热量与化学物质浓度梯度为微生物的生存提供了保证,大量的化能自养微生物通过氧化这些无机物获取能量,将该环境中的无机碳转化为有机碳,从而为该环境丰富的生物群落提供大量初级营养物质。尽管对这些化能自养型微生物的多样性研究较为深入,但是对它们的代谢特征的研究才刚刚起步。我们对胡安得富卡洋中脊硫化物样品4143-1宏基因组文库的2880个Fosmid克隆子进行454高通量测序,一共获得308,034条序列,平均长度为227bp。对这些序列进行拼接后得到15.3 MB序列,包括31,405条拼接序列和22,968不能拼接的序列,其中21,836条序列能够与NCBI非冗余蛋白数据库在期望值为10-5下有较好的注释。所有注释序列中有70%能够分布在COG的分类项目中。
首先,我们利用双向聚类的方法对包括4143-1样品和Lost City热液口烟囱样品的18个环境宏基因组数据做比较分析发现,两个热液口烟囱能够聚为一支,且参与DNA错配修复和同源重组的基因序列丰度均显著高于其他环境,表明该环境微生物具备丰富的DNA修复系统以应对该环境下有毒物质对基因组的损伤。另外,两个热液口烟囱均含有丰度较高的化学趋化性和鞭毛运动相关基因,反应出这些微生物对于烟囱壁动态变化环境的一种适应性。
其次,通过对4143-1宏基因组数据分析发现,该环境微生物群落代谢方面具有以下特征:通过硫氧化物复合体依赖性途径或者腺苷-5'-磷酸硫酸酐依赖途径氧化硫化物提供电子,偶联硝酸盐还原提供能量,以卡尔文循环为主要途径进行二氧化碳固定。通过对代谢关键酶基因簇的分析发现,兼性厌氧和专性厌氧微生物均对该环境初级营养物质的产生发挥作用。
最后,通过高通量测序获取的基因片段信息,设计特异引物筛选对应的Fosmid克隆子,可获取对应基因或基因簇的全长信息,我们从宏基因文库中筛选到两个分别含聚酮合成酶基因簇和聚酮聚肽杂合型基因簇的克隆子,虽然两个克隆子对三种标准菌均未表现出抑菌活性,这些模块仍表现出一些与目前已知的PKS基因簇不同的特征,为组合生物合成研究增加了新的成员。
总而言之,我们的研究不仅在物质能量水平揭示了胡安得富卡洋中脊热液口烟囱壁微生物群落对该极端环境的适应性机制,也为进一步开发利用该环境的基因资源打下基础。
Deep-sea hydrothermal vent chimneys that form by interactions between hot fluids and cold seawater are regarded as primordial environments reminiscent of early Earth conditions, with reactive gases, dissolved elements, and thermal and chemical gradients operating over spatial scales of millimeters and centimeters up to meters. These chemical and thermal gradients along and inside the sulfide chimneys provide a wide range of microhabitats for chemolithoautotrophic microorganisms that fix inorganic carbon using chemical energy obtained through the oxidation of reduced inorganic compounds contained in the hydrothermal fluids, converting the geothermally derived energy into microbial biomass. Although the phylogenetic diversity of these microorganisms has been described previously, the adaptation and metabolic potential of the microbial communities is only beginning to be revealed. A pyrosequencing approach was utilized to directly obtain sequences from a fosmid library constructed from a black smoker chimney 4143-1 in the Mothra hydrothermal vent field at the Juan de Fuca Ridge. A total of 308,034 reads with an average sequence length of 227 bp were generated. The sequenced microbiome of the hydrothermal vent sample consisted of 31,405 contigs and 22,968 singletons, a total of 15.3 MB. A total of 21,836 open reading frames (ORFs) were predicted from the data set, more than 70% of which could be classified into function sets in the COG category.
Firstly, comparative genomic analyses of metagenomes from a variety of environments by two-way clustering of samples and functional gene categories demonstrated that the 4143-1 metagenome clustered most closely with that from a carbonate chimney from Lost City; both are highly enriched in genes for mismatch repair and homologous recombination, suggesting that the microbial communities have evolved extensive DNA repair systems to cope with the extreme conditions that have potential deleterious effects on the genomes. As previously reported for the Lost City microbiome, the metagenome of chimney 4143-1 exhibited a high proportion of transposases, implying that horizontal gene transfer may be a common occurrence in the deep-sea vent chimney biosphere. In addition, genes for chemotaxis and flagellar assembly were highly enriched in the chimney metagenomes, reflecting the adaptation of the organisms to the highly dynamic conditions present within the chimney walls.
Secondly, we reconstruct the metabolic pathways at the metegenome level. The result indicated that the microbial community in the wall of chimney 4143-1 was mainly fueled by sulfur oxidation through sulfur-compound oxidation (sox) dependent and adenosine-5'-phosphosulfate (APS) dependent pathways, putatively coupled to nitrate reduction to perform inorganic carbon fixation through the Calvin-Benson-Bassham cycle (CBB cycle). Based on the genomic organization of the key genes of the carbon fixation and sulfur oxidation pathways contained in the large genomic fragments, both obligate and facultative autotrophs appear to be present and contributing to biomass production.
Then, we screened the library with specific primers and got two fomsid containing PKS/NPRS gene fragments. Although neither of them had antimicrobial functions towards Escherichia coli, Bacillus subtilis or Saccharomyces cerevisiae. There are some characters of the two PKS/NPRS clusters, which are different from knows.
In summary, in addition to the understanding of novel mechanism for the formation of such unique environment driven by this special community of microbiota, the genetic resources from the deep-sea vent environments will be available for further functional analyses as gene treasure house through this novel approach.
首先,我们利用双向聚类的方法对包括4143-1样品和Lost City热液口烟囱样品的18个环境宏基因组数据做比较分析发现,两个热液口烟囱能够聚为一支,且参与DNA错配修复和同源重组的基因序列丰度均显著高于其他环境,表明该环境微生物具备丰富的DNA修复系统以应对该环境下有毒物质对基因组的损伤。另外,两个热液口烟囱均含有丰度较高的化学趋化性和鞭毛运动相关基因,反应出这些微生物对于烟囱壁动态变化环境的一种适应性。
其次,通过对4143-1宏基因组数据分析发现,该环境微生物群落代谢方面具有以下特征:通过硫氧化物复合体依赖性途径或者腺苷-5'-磷酸硫酸酐依赖途径氧化硫化物提供电子,偶联硝酸盐还原提供能量,以卡尔文循环为主要途径进行二氧化碳固定。通过对代谢关键酶基因簇的分析发现,兼性厌氧和专性厌氧微生物均对该环境初级营养物质的产生发挥作用。
最后,通过高通量测序获取的基因片段信息,设计特异引物筛选对应的Fosmid克隆子,可获取对应基因或基因簇的全长信息,我们从宏基因文库中筛选到两个分别含聚酮合成酶基因簇和聚酮聚肽杂合型基因簇的克隆子,虽然两个克隆子对三种标准菌均未表现出抑菌活性,这些模块仍表现出一些与目前已知的PKS基因簇不同的特征,为组合生物合成研究增加了新的成员。
总而言之,我们的研究不仅在物质能量水平揭示了胡安得富卡洋中脊热液口烟囱壁微生物群落对该极端环境的适应性机制,也为进一步开发利用该环境的基因资源打下基础。
Deep-sea hydrothermal vent chimneys that form by interactions between hot fluids and cold seawater are regarded as primordial environments reminiscent of early Earth conditions, with reactive gases, dissolved elements, and thermal and chemical gradients operating over spatial scales of millimeters and centimeters up to meters. These chemical and thermal gradients along and inside the sulfide chimneys provide a wide range of microhabitats for chemolithoautotrophic microorganisms that fix inorganic carbon using chemical energy obtained through the oxidation of reduced inorganic compounds contained in the hydrothermal fluids, converting the geothermally derived energy into microbial biomass. Although the phylogenetic diversity of these microorganisms has been described previously, the adaptation and metabolic potential of the microbial communities is only beginning to be revealed. A pyrosequencing approach was utilized to directly obtain sequences from a fosmid library constructed from a black smoker chimney 4143-1 in the Mothra hydrothermal vent field at the Juan de Fuca Ridge. A total of 308,034 reads with an average sequence length of 227 bp were generated. The sequenced microbiome of the hydrothermal vent sample consisted of 31,405 contigs and 22,968 singletons, a total of 15.3 MB. A total of 21,836 open reading frames (ORFs) were predicted from the data set, more than 70% of which could be classified into function sets in the COG category.
Firstly, comparative genomic analyses of metagenomes from a variety of environments by two-way clustering of samples and functional gene categories demonstrated that the 4143-1 metagenome clustered most closely with that from a carbonate chimney from Lost City; both are highly enriched in genes for mismatch repair and homologous recombination, suggesting that the microbial communities have evolved extensive DNA repair systems to cope with the extreme conditions that have potential deleterious effects on the genomes. As previously reported for the Lost City microbiome, the metagenome of chimney 4143-1 exhibited a high proportion of transposases, implying that horizontal gene transfer may be a common occurrence in the deep-sea vent chimney biosphere. In addition, genes for chemotaxis and flagellar assembly were highly enriched in the chimney metagenomes, reflecting the adaptation of the organisms to the highly dynamic conditions present within the chimney walls.
Secondly, we reconstruct the metabolic pathways at the metegenome level. The result indicated that the microbial community in the wall of chimney 4143-1 was mainly fueled by sulfur oxidation through sulfur-compound oxidation (sox) dependent and adenosine-5'-phosphosulfate (APS) dependent pathways, putatively coupled to nitrate reduction to perform inorganic carbon fixation through the Calvin-Benson-Bassham cycle (CBB cycle). Based on the genomic organization of the key genes of the carbon fixation and sulfur oxidation pathways contained in the large genomic fragments, both obligate and facultative autotrophs appear to be present and contributing to biomass production.
Then, we screened the library with specific primers and got two fomsid containing PKS/NPRS gene fragments. Although neither of them had antimicrobial functions towards Escherichia coli, Bacillus subtilis or Saccharomyces cerevisiae. There are some characters of the two PKS/NPRS clusters, which are different from knows.
In summary, in addition to the understanding of novel mechanism for the formation of such unique environment driven by this special community of microbiota, the genetic resources from the deep-sea vent environments will be available for further functional analyses as gene treasure house through this novel approach.
引文
A.R Miller, C. D. D., E.T Degens, J.C Hathaway, F.T Manheim, P.F McFarlin, R Pocklington and A Jokela (1966). Hot brines and recent iron deposits in deeps of the Red Sea[J]. Geochimica et Cosmochimica Acta 30(3): 341-350.
Alt, J. (1988). Hydrothermal oxide and nontronite deposits on seamounts in the eastern Pacific[J]. Marine Geology 81: 227-239.
Amann, R. I., W. Ludwig and K. H. Schleifer (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation[J]. Microbiol Rev 59(1): 143-169.
Antranikian, G., C. Herzberg and G. Gottschalk (1982). Characterization of ATP citrate lyase from Chlorobium limicola[J]. J Bacteriol 152(3): 1284-1287.
Baker, E. T., J. W. Lavelle, R. A. Feely, G. J. Massoth, S. L. Walker, and J. E. Lupton (1989). Episodic venting of hydrothermal fluids from the Juan de Fuca Ridge[J]. J. Geophys. Res. 94: 9237–9250.
Baker, S. L. W. a. E. T. (1988). Particle-size distributions within hydrothermal plumes over the Juan de Fuca Ridge[J]. Marine Geology 78: 217-226
Banchetti, R., D. Marsili and L. Galleni (2004). Ecological modelling: from the biosphere to the everyday data gathering; filling the gap[J]. Riv Biol 97(3): 469-482.
Becker, P. L. a. K. (1985). Hydrothermal plumes, hot springs, and conductive heat flow in the Southern Trough of Guaymas Basin [J]. Peter Lonsdalea and Keir Beckera 74(2): 211-225.
Bouvier, R. d. W. a. T. (2004). Everything is everywhere, but,the environment selects what did Baas Becking and Beijerinck really say?[J]. Environmental Microbiology.
Brock, T. D. (1975). Effect of water potential on growth and iron oxidation by Thiobacillus ferrooxidans[J]. Appl Microbiol 29(4): 495-501.
C. L. Van Dover, C. R. G., K. G. Speer, L. M. Parson, R. C. Vrijenhoek (2002). Evolution and Biogeography of Deep-Sea Vent and Seep Invertebrates[J]. science 295(1253-1257).
Campbell, B. J., J. L. Smith, T. E. Hanson, M. G. Klotz, L. Y. Stein, C. K. Lee, D. Wu, J. M. Robinson, H. M. Khouri, J. A. Eisen and S. C. Cary (2009). Adaptations tosubmarine hydrothermal environments exemplified by the genome of Nautilia profundicola[J]. PLoS Genet 5(2): e1000362.
Campbell, B. J., J. L. Stein and S. C. Cary (2003). Evidence of chemolithoautotrophy in the bacterial community associated with Alvinella pompejana, a hydrothermal vent polychaete[J]. Appl Environ Microbiol 69(9): 5070-5078.
Cavanaugh, C. M., S. L. Gardiner, M. L. Jones, H. W. Jannasch and J. B. Waterbury (1981). Prokaryotic Cells in the Hydrothermal Vent Tube Worm Riftia pachyptila Jones: Possible Chemoautotrophic Symbionts[J]. science 213(4505): 340-342.
Cavanaugh, C. M., C. O. Wirsen and H. W. Jannasch (1992). Evidence for Methylotrophic Symbionts in a Hydrothermal Vent Mussel (Bivalvia: Mytilidae) from the Mid-Atlantic Ridge[J]. Appl Environ Microbiol 58(12): 3799-3803.
Chadwick, W. W., Jr.; Embley, Robert W.; Fox, Christopher G. (1995). SeaBeam depth changes associated with recent lava flows, CoAxial segment, Juan de Fuca Ridge: Evidence for multiple eruptions between 1981-1993[J]. Geophysical Research Letters 22: 167-170.
Chu, X., H. He, C. Guo and B. Sun (2008). Identification of two novel esterases from a marine metagenomic library derived from South China Sea[J]. Appl Microbiol Biotechnol 80(4): 615-625.
Cornel E.J. de Ronde , E. T. B., Gary J. Massoth, John E. Lupton, Ian C. Wright, Richard A. Feely and Ronald R. Greene (2001). Intra-oceanic subduction-related hydrothermal venting, Kermadec volcanic arc, New Zealand [J]. Earth and Planetary Science Letters 194(3-3): 359-369.
Costello, E. K., C. L. Lauber, M. Hamady, N. Fierer, J. I. Gordon and R. Knight (2009). Bacterial Community Variation in Human Body Habitats Across Space and Time[J]. Science.
Courtois, S., C. M. Cappellano, M. Ball, F. X. Francou, P. Normand, G. Helynck, A. Martinez, S. J. Kolvek, J. Hopke, M. S. Osburne, P. R. August, R. Nalin, M.
Guerineau, P. Jeannin, P. Simonet and J. L. Pernodet (2003). Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products[J]. Appl Environ Microbiol 69(1): 49-55.
Cowan, D., Q. Meyer, W. Stafford, S. Muyanga, R. Cameron and P. Wittwer (2005). Metagenomic gene discovery: past, present and future[J]. Trends Biotechnol 23(6): 321-329.
Cowen, M. A. B., Edward T. Baker, Richard A. Feely, Gary J. Massoth and Melanie Summit (1998). Geomicrobial transformation of manganese in Gorda Ridge event plumes[J]. Deep-Sea Res II 45: 2713-2737
Cowen, X. W. a. B. N. P. (2002). Methane in aging hydrothermal plumes [J]. Geochimica et Cosmochimica Acta 66: 3563-3571
CR Fisher, K. T., N Le Bris (2007). Hydrothermal vent ecosystems[J]. Oceanography 20(1): 15-23.
de la Torre, J. R., C. B. Walker, A. E. Ingalls, M. Konneke and D. A. Stahl (2008). Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol[J]. Environ Microbiol 10(3): 810-818.
de Pascale, D., A. M. Cusano, F. Autore, E. Parrilli, G. di Prisco, G. Marino and M. L. Tutino (2008). The cold-active Lip1 lipase from the Antarctic bacterium
Pseudoalteromonas haloplanktis TAC125 is a member of a new bacterial lipolytic enzyme family[J]. Extremophiles 12(3): 311-323.
Dinsdale, E. A., R. A. Edwards, D. Hall, F. Angly, M. Breitbart, J. M. Brulc, M. Furlan, C. Desnues, M. Haynes, L. Li, L. McDaniel, M. A. Moran, K. E. Nelson, C. Nilsson,
R. Olson, J. Paul, B. R. Brito, Y. Ruan, B. K. Swan, R. Stevens, D. L. Valentine, R. V. Thurber, L. Wegley, B. A. White and F. Rohwer (2008). Functional metagenomic profiling of nine biomes[J]. nature 452(7187): 629-632.
Drakare, S., J. J. Lennon and H. Hillebrand (2006). The imprint of the geographical, evolutionary and ecological context on species-area relationships[J]. Ecol Lett 9(2): 215-227.
Eckburg, P. B., E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen, M. Sargent, S. R. Gill, K. E. Nelson and D. A. Relman (2005). Diversity of the human intestinal microbial flora[J]. science 308(5728): 1635-1638.
Edmonds, H. N., P. J. Michael, E. T. Baker, D. P. Connelly, J. E. Snow, C. H. Langmuir, H. J. Dick, R. Muhe, C. R. German and D. W. Graham (2003). Discovery of abundant hydrothermal venting on the ultraslow-spreading Gakkel ridge in the Arctic Ocean[J]. nature 421(6920): 252-256.
Edwards, K. J., W. Bach and T. M. McCollom (2005). Geomicrobiology in oceanography: microbe-mineral interactions at and below the seafloor[J]. Trends Microbiol 13(9): 449-456.
Elend, C., C. Schmeisser, C. Leggewie, P. Babiak, J. D. Carballeira, H. L. Steele, J. L.Reymond, K. E. Jaeger and W. R. Streit (2006). Isolation and biochemical characterization of two novel metagenome-derived esterases[J]. Appl Environ Microbiol 72(5): 3637-3645.
ET Baker, G. M., RA Feely (1987). Cataclysmic hydrothermal venting on the Juan de Fuca Ridge[J]. Natue 329: 149 - 151.
Fernandes, S., B. Geueke, O. Delgado, J. Coleman and R. Hatti-Kaul (2002). Beta-galactosidase from a cold-adapted bacterium: purification, characterization and application for lactose hydrolysis[J]. Appl Microbiol Biotechnol 58(3): 313-321.
Ferrer, M., O. V. Golyshina, T. N. Chernikova, A. N. Khachane, D. Reyes-Duarte, V. A. Santos, C. Strompl, K. Elborough, G. Jarvis, A. Neef, M. M. Yakimov, K. N. Timmis and P. N. Golyshin (2005). Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora[J]. Environ Microbiol 7(12): 1996-2010.
Funa, N., Y. Ohnishi, I. Fujii, M. Shibuya, Y. Ebizuka and S. Horinouchi (1999). A new pathway for polyketide synthesis in microorganisms[J]. nature 400(6747): 897-899.
FUSTEC A, D. D., JUNIPER S. K. (1987). Deep-sea hydrothermal vent communities at 13°N on the East Pacific Rise: microdistribution and temporal variations[J]. Biological oceanography 4: 121-164.
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[J]. Environ Microbiol 6(9): 948-958.
Gillespie, D. E., S. F. Brady, A. D. Bettermann, N. P. Cianciotto, M. R. Liles, M. R. Rondon, J. Clardy, R. M. Goodman and J. Handelsman (2002). Isolation of antibiotics turbomycin a and B from a metagenomic library of soil microbial DNA[J]. Appl Environ Microbiol 68(9): 4301-4306.
Green, J. L., B. J. Bohannan and R. J. Whitaker (2008). Microbial biogeography: from taxonomy to traits[J]. science 320(5879): 1039-1043.
Groudieva, T., M. Kambourova, H. Yusef, M. Royter, R. Grote, H. Trinks and G. Antranikian (2004). Diversity and cold-active hydrolytic enzymes of culturable bacteria associated with Arctic sea ice, Spitzbergen[J]. Extremophiles 8(6): 475-488.
Hatzenpichler, R., E. V. Lebedeva, E. Spieck, K. Stoecker, A. Richter, H. Daims and M. Wagner (2008). A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring[J]. Proc Natl Acad Sci U S A 105(6): 2134-2139.
He, Y. Z., K. Q. Fan, C. J. Jia, Z. J. Wang, W. B. Pan, L. Huang, K. Q. Yang and Z. Y. Dong (2007). Characterization of a hyperthermostable Fe-superoxide dismutase from hot spring[J]. Appl Microbiol Biotechnol 75(2): 367-376.
Henne, A., R. Daniel, R. A. Schmitz and G. Gottschalk (1999). Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4-hydroxybutyrate[J]. Appl Environ Microbiol 65(9): 3901-3907.
Henne, A., R. A. Schmitz, M. Bomeke, G. Gottschalk and R. Daniel (2000). Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli[J]. Appl Environ Microbiol 66(7): 3113-3116.
Hoffman, J. A. B. a. S. E. (1985). Submarine hydrothermal vents and associated gradient environments as sites for the origin and evolution of life [J]. Origins of Life and Evolution of Biospheres 35: 327-345.
Holden, J. F. and M. W. Adams (2003). Microbe-metal interactions in marine hydrothermal environments[J]. Curr Opin Chem Biol 7(2): 160-165.
Horst Felbeck, J. J. C., George N. Somero (1981). Calvin-Benson cycle and sulphide oxidation enzymes in animals from sulphide-rich habitats[J]. nature 293: 291-293.
Hourdez, S. and R. E. Weber (2005). Molecular and functional adaptations in deep-sea hemoglobins[J]. J Inorg Biochem 99(1): 130-141.
Hu, Y., C. Fu, Y. Huang, Y. Yin, G. Cheng, F. Lei, N. Lu, J. Li, E. J. Ashforth, L. Zhang and B. Zhu (2010). Novel lipolytic genes from the microbial metagenomic library of the South China Sea marine sediment[J]. FEMS Microbiol Ecol.
Hu, Y., G. Zhang, A. Li, J. Chen and L. Ma (2008). Cloning and enzymatic characterization of a xylanase gene from a soil-derived metagenomic library with an efficient approach[J]. Appl Microbiol Biotechnol 80(5): 823-830.
Huber, J. A., D. B. Mark Welch, H. G. Morrison, S. M. Huse, P. R. Neal, D. A. Butterfield and M. L. Sogin (2007). Microbial population structures in the deep marine biosphere[J]. Science 318(5847): 97-100.
J. E. Lupton, J. R. D., H. P.Johnson & M. K.Tivey (1985). Entrainment and verticaltransport of deep-ocean water by buoyant hydrothermal plumes[J]. Nature 316: 621 - 623
Jannasch H W, W. C. O. (1985). The biochemical versatility of chemosynthetic bacteria at deep-sea hydrothermal vents. [J]. Bulletin of the Biological Society of Washington 6: 325-334.
Jannasch, H. W. and M. J. Mottl (1985). Geomicrobiology of Deep-Sea Hydrothermal Vents[J]. science 229(4715): 717-725.
Jannasch, H. W. and C. D. Taylor (1984). Deep-sea microbiology[J]. Annu Rev Microbiol 38: 487-514.
Jin, D., W. Lu, S. Ping, W. Zhang, J. Chen, B. Dun, R. Ma, Z. Zhao, J. Sha, L. Li, Z. Yang, M. Chen and M. Lin (2007). Identification of a new gene encoding EPSPs with high glyphosate resistance from the metagenomic library[J]. Curr Microbiol 55(4): 350-355.
Kelley, D. S., J. A. Karson, D. K. Blackman, G. L. Fruh-Green, D. A. Butterfield, M. D. Lilley, E. J. Olson, M. O. Schrenk, K. K. Roe, G. T. Lebon and P. Rivizzigno (2001). An off-axis hydrothermal vent field near the Mid-Atlantic Ridge at 30 degrees N[J]. nature 412(6843): 145-149.
Kennedy, C. B., S. D. Scott and F. G. Ferris (2003). Ultrastructure and potential sub-seafloor evidence of bacteriogenic iron oxides from Axial Volcano, Juan de Fuca Ridge, north-east Pacific Ocean[J]. FEMS Microbiol Ecol 43(2): 247-254.
Khan, N. H., E. Roets, J. Hoogmartens and H. Vanderhaeghe (1987). Quantitative analysis of oxytetracycline and related substances by high-performance liquid chromatography[J]. J Chromatogr 405: 229-245.
Kim, H. K., S. Y. Park, J. K. Lee and T. K. Oh (1998). Gene cloning and characterization of thermostable lipase from Bacillus stearothermophilus L1[J]. Biosci Biotechnol Biochem 62(1): 66-71.
Kim, M. C., J. H. Ahn, H. C. Shin, T. Kim, T. H. Ryu, D. H. Kim, H. G. Song, G. H. Lee and J. O. Ka (2008). Molecular analysis of bacterial community structures in paddy soils for environmental risk assessment with two varieties of genetically modified rice, Iksan 483 and Milyang 204[J]. J Microbiol Biotechnol 18(2): 207-218.
Kim, T. K., A. K. Hewavitharana, P. N. Shaw and J. A. Fuerst (2006). Discovery of a new source of rifamycin antibiotics in marine sponge actinobacteria by phylogeneticprediction[J]. Appl Environ Microbiol 72(3): 2118-2125.
Kim, T. W., J. H. Lee, S. E. Kim, M. H. Park, H. C. Chang and H. Y. Kim (2009). Analysis of microbial communities in doenjang, a Korean fermented soybean paste, using nested PCR-denaturing gradient gel electrophoresis[J]. Int J Food Microbiol 131(2-3): 265-271.
Knietsch, A., T. Waschkowitz, S. Bowien, A. Henne and R. Daniel (2003). Construction and screening of metagenomic libraries derived from enrichment cultures: generation of a gene bank for genes conferring alcohol oxidoreductase activity on Escherichia coli[J]. Appl Environ Microbiol 69(3): 1408-1416.
Konhauser, K. O. (1998). Diversity of bacterial iron mineralization [J]. Earth-Science Reviews 43: 91-121
Konneke, M., A. E. Bernhard, J. R. de la Torre, C. B. Walker, J. B. Waterbury and D. A. Stahl (2005). Isolation of an autotrophic ammonia-oxidizing marine archaeon[J]. nature 437(7058): 543-546.
Kopczynski, E. D., M. M. Bateson and D. M. Ward (1994). Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms[J]. Appl Environ Microbiol 60(2): 746-748.
Krause, L., N. N. Diaz, A. Goesmann, S. Kelley, T. W. Nattkemper, F. Rohwer, R. A. Edwards and J. Stoye (2008). Phylogenetic classification of short environmental DNA fragments[J]. Nucleic Acids Res 36(7): 2230-2239.
Lammle, K., H. Zipper, M. Breuer, B. Hauer, C. Buta, H. Brunner and S. Rupp (2007). Identification of novel enzymes with different hydrolytic activities by metagenome expression cloning[J]. J Biotechnol 127(4): 575-592.
Lee, C. C., R. E. Kibblewhite-Accinelli, K. Wagschal, G. H. Robertson and D. W. Wong (2006). Cloning and characterization of a cold-active xylanase enzyme from an environmental DNA library[J]. Extremophiles 10(4): 295-300.
Lee, M. H., C. H. Lee, T. K. Oh, J. K. Song and J. H. Yoon (2006). Isolation and characterization of a novel lipase from a metagenomic library of tidal flat sediments: evidence for a new family of bacterial lipases[J]. Appl Environ Microbiol 72(11): 7406-7409.
Liesack, H. W. a. E. S. (1991). Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria [J]. Microbial Ecology 21: 191-198.
Lilley, D. A. B., E. J. Olson, J. E. Lupton, S. A. Macko,R. E. McDuff (1993). Anomalous CH4 and NH4+ concentrations at an unsedimented mid-ocean-ridge hydrothermal system[J]. Nature 364: 45-47.
Luther, G. W., 3rd, T. F. Rozan, M. Taillefert, D. B. Nuzzio, C. Di Meo, T. M. Shank, R. A.
Lutz and S. C. Cary (2001). Chemical speciation drives hydrothermal vent ecology[J]. nature 410(6830): 813-816.
Lydmark, P., R. Almstrand, K. Samuelsson, A. Mattsson, F. Sorensson, P. E. Lindgren and M. Hermansson (2007). Effects of environmental conditions on the nitrifying population dynamics in a pilot wastewater treatment plant[J]. Environ Microbiol 9(9): 2220-2233.
Majernik, A., G. Gottschalk and R. Daniel (2001). Screening of environmental DNA libraries for the presence of genes conferring Na(+)(Li(+))/H(+) antiporter activity on Escherichia coli: characterization of the recovered genes and the corresponding gene products[J]. J Bacteriol 183(22): 6645-6653.
Malin, C. and P. Illmer (2008). Ability of DNA content and DGGE analysis to reflect the performance condition of an anaerobic biowaste fermenter[J]. Microbiol Res 163(5): 503-511.
Marcel Margulies, M. E., William E. Altman1, Said Attiya1, Joel S. Bader1, Lisa A. Bemben1,, M. S. B. Jan Berka1, Yi-Ju Chen1, Zhoutao Chen1, Scott B. Dewell1, Lei Du1, Joseph M. Fierro1,, B. C. G. Xavier V. Gomes1, Wen He1, Scott Helgesen1, Chun He Ho1, Gerard P. Irzyk1,, M. L. I. A. Szilveszter C. Jando1, Thomas P. Jarvie1, Kshama B. Jirage1, Jong-Bum Kim1,, J. R. L. James R. Knight1, John H. Leamon1, Steven M. Lefkowitz1, Ming Lei1, Jing Li1, Kenton L. Lohman1,, V. B. M. Hong Lu1, Keith E. McDade1, Michael P. McKenna1, Eugene W. Myers2,, J. R. N. Elizabeth Nickerson1, Ramona Plant1, Bernard P. Puc1, Michael T. Ronan1, George T. Roth1,, J. F. S. Gary J. Sarkis1, John W. Simpson1, Maithreyan Srinivasan1, Karrie R. Tartaro1,, K. A. V. Alexander Tomasz3, Greg A. Volkmer1, Shally H. Wang1, Yong Wang1, Michael P. Weiner4, and R. F. B. J. M. R. Pengguang Yu1 (2005). Genome sequencing in microfabricated high-density picolitre reactors[J]. nature.
Margulies, M., M. Egholm, W. E. Altman, S. Attiya, J. S. Bader, L. A. Bemben, J. Berka, M. S. Braverman, Y. J. Chen, Z. Chen, S. B. Dewell, L. Du, J. M. Fierro, X. V. Gomes, B. C. Godwin, W. He, S. Helgesen, C. H. Ho, G. P. Irzyk, S. C. Jando, M.L. Alenquer, T. P. Jarvie, K. B. Jirage, J. B. Kim, J. R. Knight, J. R. Lanza, J. H. Leamon, S. M. Lefkowitz, M. Lei, J. Li, K. L. Lohman, H. Lu, V. B. Makhijani, K. E. McDade, M. P. McKenna, E. W. Myers, E. Nickerson, J. R. Nobile, R. Plant, B. P. Puc, M. T. Ronan, G. T. Roth, G. J. Sarkis, J. F. Simons, J. W. Simpson, M. Srinivasan, K. R. Tartaro, A. Tomasz, K. A. Vogt, G. A. Volkmer, S. H. Wang, Y. Wang, M. P. Weiner, P. Yu, R. F. Begley and J. M. Rothberg (2005). Genome sequencing in microfabricated high-density picolitre reactors[J]. nature 437(7057): 376-380.
Mark Hildebrand, Laura E. Waggoner, Haibin Liu, Sebastian Sudek and Scott Allen (2004). bryA: An Unusual Modular Polyketide Synthase Gene from the Uncultivated Bacterial Symbiont of the Marine Bryozoan Bugula neritina[J]. Chemistry & Biology,6.67 11(11): 1543-1552.
Martinez, A., S. J. Kolvek, C. L. Yip, J. Hopke, K. A. Brown, I. A. MacNeil and M. S. Osburne (2004). Genetically modified bacterial strains and novel bacterial artificial chromosome shuttle vectors for constructing environmental libraries and detecting heterologous natural products in multiple expression hosts[J]. Appl Environ Microbiol 70(4): 2452-2463.
Mayumi, D., Y. Akutsu-Shigeno, H. Uchiyama, N. Nomura and T. Nakajima-Kambe (2008). Identification and characterization of novel poly(DL-lactic acid) depolymerases from metagenome[J]. Appl Microbiol Biotechnol 79(5): 743-750.
Mehta, M. P., D. A. Butterfield and J. A. Baross (2003). Phylogenetic diversity of nitrogenase (nifH) genes in deep-sea and hydrothermal vent environments of the Juan de Fuca Ridge[J]. Appl Environ Microbiol 69(2): 960-970.
Meng, J., F. Wang, Y. Zheng, X. Peng, H. Zhou and X. Xiao (2009). An uncultivated crenarchaeota contains functional bacteriochlorophyll a synthase[J]. ISME J 3(1): 106-116.
Miller, S. L. and J. L. Bada (1988). Submarine hot springs and the origin of life[J]. nature 334(6183): 609-611.
Minic, Z. and G. Herve (2004). Biochemical and enzymological aspects of the symbiosis between the deep-sea tubeworm Riftia pachyptila and its bacterial endosymbiont[J]. Eur J Biochem 271(15): 3093-3102.
Mittelbach, G. G., D. W. Schemske, H. V. Cornell, A. P. Allen, J. M. Brown, M. B. Bush, S. P. Harrison, A. H. Hurlbert, N. Knowlton, H. A. Lessios, C. M. McCain, A. R.McCune, L. A. McDade, M. A. McPeek, T. J. Near, T. D. Price, R. E. Ricklefs, K. Roy, D. F. Sax, D. Schluter, J. M. Sobel and M. Turelli (2007). Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography[J]. Ecol Lett 10(4): 315-331.
MK, T. (2004). The remarkable diversity of seafloor vents[J]. Oceanus 42: 60-65.
Monika Beh, G. S., Robert Huber, Karl-Otto Stetter and Georg Fuchs (1977). Enzymes of the reductive citric acid cycle in the autotrophic eubacterium Aquifex pyrophilus and in the archaebacterium Thermoproteus neutrophilus [J]. Archives of Microbiology 160: 306-311.
Mootz, H. D., D. Schwarzer and M. A. Marahiel (2002). Ways of assembling complex natural products on modular nonribosomal peptide synthetases[J]. Chembiochem 3(6): 490-504.
Moyer, D. E. a. C. L. ( 2002). Neutrophilic Fe-Oxidizing Bacteria Are Abundant at the Loihi Seamount Hydrothermal Vents and Play a Major Role in Fe Oxide Deposition [J]. Applied and Environmental Microbiology 68: 3085-3093.
Murakami, T. K. a. T. (2001). The effect of microorganisms on Fe precipitation rates at neutral pH [J]. Chemical Geology 180: 117-128. Mussmann, M., F. Z. Hu, M. Richter, D. de Beer, A. Preisler, B. B. Jorgensen, M.
Huntemann, F. O. Glockner, R. Amann, W. J. Koopman, R. S. Lasken, B. Janto, J. Hogg, P. Stoodley, R. Boissy and G. D. Ehrlich (2007). Insights into the genome of large sulfur bacteria revealed by analysis of single filaments[J]. PLoS Biol 5(9): e230.
Nakagawa, S. and K. Takai (2008). Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance[J]. FEMS Microbiol Ecol 65(1): 1-14.
Nakagawa, S., Y. Takaki, S. Shimamura, A. L. Reysenbach, K. Takai and K. Horikoshi (2007). Deep-sea vent epsilon-proteobacterial genomes provide insights into emergence of pathogens[J]. Proc Natl Acad Sci U S A 104(29): 12146-12150.
Nakagawa, T., Y. Fujimoto, R. Ikehata, T. Miyaji and N. Tomizuka (2006). Purification and molecular characterization of cold-active beta-galactosidase from Arthrobacter psychrolactophilus strain F2[J]. Appl Microbiol Biotechnol 72(4): 720-725.
Nichols, C. A., J. Guezennec and J. P. Bowman (2005). Bacterial exopolysaccharides from extreme marine environments with special consideration of the southern ocean, sea ice, and deep-sea hydrothermal vents: a review[J]. Mar Biotechnol (NY) 7(4):253-271.
Pang, H., P. Zhang, C. J. Duan, X. C. Mo, J. L. Tang and J. X. Feng (2009). Identification of cellulase genes from the metagenomes of compost soils and functional characterization of one novel endoglucanase[J]. Curr Microbiol 58(4): 404-408.
Parkhill, J., B. W. Wren, K. Mungall, J. M. Ketley, C. Churcher, D. Basham, T. Chillingworth, R. M. Davies, T. Feltwell, S. Holroyd, K. Jagels, A. V. Karlyshev, S. Moule, M. J. Pallen, C. W. Penn, M. A. Quail, M. A. Rajandream, K. M.
Rutherford, A. H. van Vliet, S. Whitehead and B. G. Barrell (2000). The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences[J]. nature 403(6770): 665-668.
Piel, J., D. Hui, G. Wen, D. Butzke, M. Platzer, N. Fusetani and S. Matsunaga (2004). Antitumor polyketide biosynthesis by an uncultivated bacterial symbiont of the marine sponge Theonella swinhoei[J]. Proc Natl Acad Sci U S A 101(46): 16222-16227.
Pieper, R., G. Luo, D. E. Cane and C. Khosla (1995). Cell-free synthesis of polyketides by recombinant erythromycin polyketide synthases[J]. nature 378(6554): 263-266.
R. F. WEISS, P. L., J. E. LUPTON, A. E. BAINBRIDGE, H. CRAIG (1977). Hydrothermal plumes in the Galapagos Rift[J]. Nature 267: 600-603.
Ranjan, R., A. Grover, R. K. Kapardar and R. Sharma (2005). Isolation of novel lipolytic genes from uncultured bacteria of pond water[J]. Biochem Biophys Res Commun 335(1): 57-65.
Rashamuse, K., T. Ronneburg, F. Hennessy, D. Visser, E. van Heerden, L. Piater, D. Litthauer, C. Moller and D. Brady (2009). Discovery of a novel carboxylesterase through functional screening of a pre-enriched environmental library[J]. J Appl Microbiol 106(5): 1532-1539.
Rasmussen, B. (2000). Filamentous microfossils in a 3,235-million-year-old volcanogenic massive sulphide deposit[J]. nature 405(6787): 676-679.
Rhee, J. K., D. G. Ahn, Y. G. Kim and J. W. Oh (2005). New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library[J]. Appl Environ Microbiol 71(2): 817-825.
Rondon, M. R., P. R. August, A. D. Bettermann, S. F. Brady, T. H. Grossman, M. R. Liles, K. A. Loiacono, B. A. Lynch, I. A. MacNeil, C. Minor, C. L. Tiong, M. Gilman, M.S. Osburne, J. Clardy, J. Handelsman and R. M. Goodman (2000). Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms[J]. Appl Environ Microbiol 66(6): 2541-2547.
Siqueira, J. F., Jr., I. N. Rocas, G. J. Debelian, F. L. Carmo, S. S. Paiva, F. R. Alves and A. S. Rosado (2008). Profiling of root canal bacterial communities associated with chronic apical periodontitis from Brazilian and Norwegian subjects[J]. J Endod 34(12): 1457-1461.
Sirevag, R., B. B. Buchanan, J. A. Berry and J. H. Troughton (1977). Mechanisms of CO2 fixation in bacterial photosynthesis studied by the carbon isotope fractionation technique[J]. Arch Microbiol 112(1): 35-38. Spiess, F. N., K. C. Macdonald, T. Atwater, R. Ballard, A. Carranza, D. Cordoba, C. Cox,
V. M. Garcia, J. Francheteau, J. Guerrero, J. Hawkins, R. Haymon, R. Hessler, T. Juteau, M. Kastner, R. Larson, B. Luyendyk, J. D. Macdougall, S. Miller, W. Normark, J. Orcutt and C. Rangin (1980). East Pacific Rise: Hot Springs and Geophysical Experiments[J]. science 207(4438): 1421-1433.
Stokes, H. W., A. J. Holmes, B. S. Nield, M. P. Holley, K. M. Nevalainen, B. C. Mabbutt and M. R. Gillings (2001). Gene cassette PCR: sequence-independent recovery of entire genes from environmental DNA[J]. Appl Environ Microbiol 67(11): 5240-5246.
Summit, M. (2000). Ecology, physiology, and phylogeny of subseafloor thermophiles from mid-ocean ridge [J]. University of Washington.
Summit, M. and J. A. Baross (2001). A novel microbial habitat in the mid-ocean ridge subseafloor[J]. Proc Natl Acad Sci U S A 98(5): 2158-2163.
Susumu Mochizuki, K. H., Masanori Suwa (2003). The large linear plasmid pSLA2-L of Streptomyces rochei has an unusually condensed gene organization for secondary metabolism[J]. Molecular Microbiology 48: 1501-1510.
Szymanski, C. M., D. H. Burr and P. Guerry (2002). Campylobacter protein glycosylation affects host cell interactions[J]. Infect Immun 70(4): 2242-2244.
Tirawongsaroj, P., R. Sriprang, P. Harnpicharnchai, T. Thongaram, V. Champreda, S. Tanapongpipat, K. Pootanakit and L. Eurwilaichitr (2008). Novel thermophilic and thermostable lipolytic enzymes from a Thailand hot spring metagenomic library[J]. J Biotechnol 133(1): 42-49.
Tokuda, G., M. Miyagi, H. Makiya, H. Watanabe and G. Arakawa (2009). Digestivebeta-glucosidases from the wood-feeding higher termite, Nasutitermes takasagoensis: Intestinal distribution, molecular characterization, and alteration in sites of expression[J]. Insect Biochem Mol Biol.
Tringe, S. G. and E. M. Rubin (2005). Metagenomics: DNA sequencing of environmental samples[J]. Nat Rev Genet 6(11): 805-814.
Uchiyama, T., T. Abe, T. Ikemura and K. Watanabe (2005). Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes[J]. Nat Biotechnol 23(1): 88-93.
Venter, J. C., K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch, J. A. Eisen, D. Wu, I. Paulsen, K. E. Nelson, W. Nelson, D. E. Fouts, S. Levy, A. H. Knap, M. W. Lomas, K. Nealson, O. White, J. Peterson, J. Hoffman, R. Parsons, H. Baden-Tillson, C. Pfannkoch, Y. H. Rogers and H. O. Smith (2004). Environmental genome shotgun sequencing of the Sargasso Sea[J]. science 304(5667): 66-74.
Wacker, M., D. Linton, P. G. Hitchen, M. Nita-Lazar, S. M. Haslam, S. J. North, M. Panico, H. R. Morris, A. Dell, B. W. Wren and M. Aebi (2002). N-linked glycosylation in Campylobacter jejuni and its functional transfer into E. coli[J]. science 298(5599): 1790-1793.
Wagner, M., P. H. Nielsen, A. Loy, J. L. Nielsen and H. Daims (2006). Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays[J]. Curr Opin Biotechnol 17(1): 83-91.
Walsh, C. T., H. Chen, T. A. Keating, B. K. Hubbard, H. C. Losey, L. Luo, C. G. Marshall, D. A. Miller and H. M. Patel (2001). Tailoring enzymes that modify nonribosomal peptides during and after chain elongation on NRPS assembly lines[J]. Curr Opin Chem Biol 5(5): 525-534.
Weber, K. A., L. A. Achenbach and J. D. Coates (2006). Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction[J]. Nat Rev Microbiol 4(10): 752-764.
William W. Chadwick Jr, R. W. E. C. G. F. (1991). Evidence for volcanic eruption on the southern Juan de Fuca ridge between 1981 and 1987[J]. Nature 350 350: 416 - 418.
Xu, M., X. Xiao and F. Wang (2008). Isolation and characterization of alkanehydroxylases from a metagenomic library of Pacific deep-sea sediment[J]. Extremophiles 12(2): 255-262.
Young, N. M., J. R. Brisson, J. Kelly, D. C. Watson, L. Tessier, P. H. Lanthier, H. C. Jarrell, N. Cadotte, F. St Michael, E. Aberg and C. M. Szymanski (2002). Structure of the N-linked glycan present on multiple glycoproteins in the Gram-negative bacterium, Campylobacter jejuni[J]. J Biol Chem 277(45): 42530-42539.
Yukihiro Nojiri, J.-i. I., Takayoshi Kawai, Akira Otsuki & Hitoshi Sakai (1989). Hydrothermal plumes along the North Fiji Basin spreading axis[J]. Nature 342(667 - 670).
Zhou, J., M. A. Bruns and J. M. Tiedje (1996). DNA recovery from soils of diverse composition[J]. Appl Environ Microbiol 62(2): 316-322.
王淑芳(2008).深海热液口硫化物微生物群落多样性分析[D].厦门,厦门大学.
李慧;,何晶晶;,张颖;,徐慧; and陈冠雄(2008).宏基因组技术在开发未培养环境微生物基因资源中的应用[J].生态学报28: 1762-1773.
周怀阳,李江涛,彭晓彤(2010).海底热液活动与生命起源[J].自然杂志31: 207-212.
徐晓宇,刘和为(2009). 454测序法在环境微生物生态研究中的应用[J].生物技术通报1: 73-77.
魏曼曼,王玉光,郑甲,周洪波(2009).劳盆地深海热液喷口沉积物中细菌多样性研究[J].微生物学通报36(4): 538-543.
赵春华(2008).聚酮聚肽杂合抗生素垩唑霉素的生物合成机理与途径工程[D].上海,上海交通大学.
黄循柳,黄仕杰,郭丽琼,林俊芳(2009).宏基因组学研究进展[J].微生物学通报36 1058-1066.
Alt, J. (1988). Hydrothermal oxide and nontronite deposits on seamounts in the eastern Pacific[J]. Marine Geology 81: 227-239.
Amann, R. I., W. Ludwig and K. H. Schleifer (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation[J]. Microbiol Rev 59(1): 143-169.
Antranikian, G., C. Herzberg and G. Gottschalk (1982). Characterization of ATP citrate lyase from Chlorobium limicola[J]. J Bacteriol 152(3): 1284-1287.
Baker, E. T., J. W. Lavelle, R. A. Feely, G. J. Massoth, S. L. Walker, and J. E. Lupton (1989). Episodic venting of hydrothermal fluids from the Juan de Fuca Ridge[J]. J. Geophys. Res. 94: 9237–9250.
Baker, S. L. W. a. E. T. (1988). Particle-size distributions within hydrothermal plumes over the Juan de Fuca Ridge[J]. Marine Geology 78: 217-226
Banchetti, R., D. Marsili and L. Galleni (2004). Ecological modelling: from the biosphere to the everyday data gathering; filling the gap[J]. Riv Biol 97(3): 469-482.
Becker, P. L. a. K. (1985). Hydrothermal plumes, hot springs, and conductive heat flow in the Southern Trough of Guaymas Basin [J]. Peter Lonsdalea and Keir Beckera 74(2): 211-225.
Bouvier, R. d. W. a. T. (2004). Everything is everywhere, but,the environment selects what did Baas Becking and Beijerinck really say?[J]. Environmental Microbiology.
Brock, T. D. (1975). Effect of water potential on growth and iron oxidation by Thiobacillus ferrooxidans[J]. Appl Microbiol 29(4): 495-501.
C. L. Van Dover, C. R. G., K. G. Speer, L. M. Parson, R. C. Vrijenhoek (2002). Evolution and Biogeography of Deep-Sea Vent and Seep Invertebrates[J]. science 295(1253-1257).
Campbell, B. J., J. L. Smith, T. E. Hanson, M. G. Klotz, L. Y. Stein, C. K. Lee, D. Wu, J. M. Robinson, H. M. Khouri, J. A. Eisen and S. C. Cary (2009). Adaptations tosubmarine hydrothermal environments exemplified by the genome of Nautilia profundicola[J]. PLoS Genet 5(2): e1000362.
Campbell, B. J., J. L. Stein and S. C. Cary (2003). Evidence of chemolithoautotrophy in the bacterial community associated with Alvinella pompejana, a hydrothermal vent polychaete[J]. Appl Environ Microbiol 69(9): 5070-5078.
Cavanaugh, C. M., S. L. Gardiner, M. L. Jones, H. W. Jannasch and J. B. Waterbury (1981). Prokaryotic Cells in the Hydrothermal Vent Tube Worm Riftia pachyptila Jones: Possible Chemoautotrophic Symbionts[J]. science 213(4505): 340-342.
Cavanaugh, C. M., C. O. Wirsen and H. W. Jannasch (1992). Evidence for Methylotrophic Symbionts in a Hydrothermal Vent Mussel (Bivalvia: Mytilidae) from the Mid-Atlantic Ridge[J]. Appl Environ Microbiol 58(12): 3799-3803.
Chadwick, W. W., Jr.; Embley, Robert W.; Fox, Christopher G. (1995). SeaBeam depth changes associated with recent lava flows, CoAxial segment, Juan de Fuca Ridge: Evidence for multiple eruptions between 1981-1993[J]. Geophysical Research Letters 22: 167-170.
Chu, X., H. He, C. Guo and B. Sun (2008). Identification of two novel esterases from a marine metagenomic library derived from South China Sea[J]. Appl Microbiol Biotechnol 80(4): 615-625.
Cornel E.J. de Ronde , E. T. B., Gary J. Massoth, John E. Lupton, Ian C. Wright, Richard A. Feely and Ronald R. Greene (2001). Intra-oceanic subduction-related hydrothermal venting, Kermadec volcanic arc, New Zealand [J]. Earth and Planetary Science Letters 194(3-3): 359-369.
Costello, E. K., C. L. Lauber, M. Hamady, N. Fierer, J. I. Gordon and R. Knight (2009). Bacterial Community Variation in Human Body Habitats Across Space and Time[J]. Science.
Courtois, S., C. M. Cappellano, M. Ball, F. X. Francou, P. Normand, G. Helynck, A. Martinez, S. J. Kolvek, J. Hopke, M. S. Osburne, P. R. August, R. Nalin, M.
Guerineau, P. Jeannin, P. Simonet and J. L. Pernodet (2003). Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products[J]. Appl Environ Microbiol 69(1): 49-55.
Cowan, D., Q. Meyer, W. Stafford, S. Muyanga, R. Cameron and P. Wittwer (2005). Metagenomic gene discovery: past, present and future[J]. Trends Biotechnol 23(6): 321-329.
Cowen, M. A. B., Edward T. Baker, Richard A. Feely, Gary J. Massoth and Melanie Summit (1998). Geomicrobial transformation of manganese in Gorda Ridge event plumes[J]. Deep-Sea Res II 45: 2713-2737
Cowen, X. W. a. B. N. P. (2002). Methane in aging hydrothermal plumes [J]. Geochimica et Cosmochimica Acta 66: 3563-3571
CR Fisher, K. T., N Le Bris (2007). Hydrothermal vent ecosystems[J]. Oceanography 20(1): 15-23.
de la Torre, J. R., C. B. Walker, A. E. Ingalls, M. Konneke and D. A. Stahl (2008). Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol[J]. Environ Microbiol 10(3): 810-818.
de Pascale, D., A. M. Cusano, F. Autore, E. Parrilli, G. di Prisco, G. Marino and M. L. Tutino (2008). The cold-active Lip1 lipase from the Antarctic bacterium
Pseudoalteromonas haloplanktis TAC125 is a member of a new bacterial lipolytic enzyme family[J]. Extremophiles 12(3): 311-323.
Dinsdale, E. A., R. A. Edwards, D. Hall, F. Angly, M. Breitbart, J. M. Brulc, M. Furlan, C. Desnues, M. Haynes, L. Li, L. McDaniel, M. A. Moran, K. E. Nelson, C. Nilsson,
R. Olson, J. Paul, B. R. Brito, Y. Ruan, B. K. Swan, R. Stevens, D. L. Valentine, R. V. Thurber, L. Wegley, B. A. White and F. Rohwer (2008). Functional metagenomic profiling of nine biomes[J]. nature 452(7187): 629-632.
Drakare, S., J. J. Lennon and H. Hillebrand (2006). The imprint of the geographical, evolutionary and ecological context on species-area relationships[J]. Ecol Lett 9(2): 215-227.
Eckburg, P. B., E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen, M. Sargent, S. R. Gill, K. E. Nelson and D. A. Relman (2005). Diversity of the human intestinal microbial flora[J]. science 308(5728): 1635-1638.
Edmonds, H. N., P. J. Michael, E. T. Baker, D. P. Connelly, J. E. Snow, C. H. Langmuir, H. J. Dick, R. Muhe, C. R. German and D. W. Graham (2003). Discovery of abundant hydrothermal venting on the ultraslow-spreading Gakkel ridge in the Arctic Ocean[J]. nature 421(6920): 252-256.
Edwards, K. J., W. Bach and T. M. McCollom (2005). Geomicrobiology in oceanography: microbe-mineral interactions at and below the seafloor[J]. Trends Microbiol 13(9): 449-456.
Elend, C., C. Schmeisser, C. Leggewie, P. Babiak, J. D. Carballeira, H. L. Steele, J. L.Reymond, K. E. Jaeger and W. R. Streit (2006). Isolation and biochemical characterization of two novel metagenome-derived esterases[J]. Appl Environ Microbiol 72(5): 3637-3645.
ET Baker, G. M., RA Feely (1987). Cataclysmic hydrothermal venting on the Juan de Fuca Ridge[J]. Natue 329: 149 - 151.
Fernandes, S., B. Geueke, O. Delgado, J. Coleman and R. Hatti-Kaul (2002). Beta-galactosidase from a cold-adapted bacterium: purification, characterization and application for lactose hydrolysis[J]. Appl Microbiol Biotechnol 58(3): 313-321.
Ferrer, M., O. V. Golyshina, T. N. Chernikova, A. N. Khachane, D. Reyes-Duarte, V. A. Santos, C. Strompl, K. Elborough, G. Jarvis, A. Neef, M. M. Yakimov, K. N. Timmis and P. N. Golyshin (2005). Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora[J]. Environ Microbiol 7(12): 1996-2010.
Funa, N., Y. Ohnishi, I. Fujii, M. Shibuya, Y. Ebizuka and S. Horinouchi (1999). A new pathway for polyketide synthesis in microorganisms[J]. nature 400(6747): 897-899.
FUSTEC A, D. D., JUNIPER S. K. (1987). Deep-sea hydrothermal vent communities at 13°N on the East Pacific Rise: microdistribution and temporal variations[J]. Biological oceanography 4: 121-164.
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[J]. Environ Microbiol 6(9): 948-958.
Gillespie, D. E., S. F. Brady, A. D. Bettermann, N. P. Cianciotto, M. R. Liles, M. R. Rondon, J. Clardy, R. M. Goodman and J. Handelsman (2002). Isolation of antibiotics turbomycin a and B from a metagenomic library of soil microbial DNA[J]. Appl Environ Microbiol 68(9): 4301-4306.
Green, J. L., B. J. Bohannan and R. J. Whitaker (2008). Microbial biogeography: from taxonomy to traits[J]. science 320(5879): 1039-1043.
Groudieva, T., M. Kambourova, H. Yusef, M. Royter, R. Grote, H. Trinks and G. Antranikian (2004). Diversity and cold-active hydrolytic enzymes of culturable bacteria associated with Arctic sea ice, Spitzbergen[J]. Extremophiles 8(6): 475-488.
Hatzenpichler, R., E. V. Lebedeva, E. Spieck, K. Stoecker, A. Richter, H. Daims and M. Wagner (2008). A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring[J]. Proc Natl Acad Sci U S A 105(6): 2134-2139.
He, Y. Z., K. Q. Fan, C. J. Jia, Z. J. Wang, W. B. Pan, L. Huang, K. Q. Yang and Z. Y. Dong (2007). Characterization of a hyperthermostable Fe-superoxide dismutase from hot spring[J]. Appl Microbiol Biotechnol 75(2): 367-376.
Henne, A., R. Daniel, R. A. Schmitz and G. Gottschalk (1999). Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4-hydroxybutyrate[J]. Appl Environ Microbiol 65(9): 3901-3907.
Henne, A., R. A. Schmitz, M. Bomeke, G. Gottschalk and R. Daniel (2000). Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli[J]. Appl Environ Microbiol 66(7): 3113-3116.
Hoffman, J. A. B. a. S. E. (1985). Submarine hydrothermal vents and associated gradient environments as sites for the origin and evolution of life [J]. Origins of Life and Evolution of Biospheres 35: 327-345.
Holden, J. F. and M. W. Adams (2003). Microbe-metal interactions in marine hydrothermal environments[J]. Curr Opin Chem Biol 7(2): 160-165.
Horst Felbeck, J. J. C., George N. Somero (1981). Calvin-Benson cycle and sulphide oxidation enzymes in animals from sulphide-rich habitats[J]. nature 293: 291-293.
Hourdez, S. and R. E. Weber (2005). Molecular and functional adaptations in deep-sea hemoglobins[J]. J Inorg Biochem 99(1): 130-141.
Hu, Y., C. Fu, Y. Huang, Y. Yin, G. Cheng, F. Lei, N. Lu, J. Li, E. J. Ashforth, L. Zhang and B. Zhu (2010). Novel lipolytic genes from the microbial metagenomic library of the South China Sea marine sediment[J]. FEMS Microbiol Ecol.
Hu, Y., G. Zhang, A. Li, J. Chen and L. Ma (2008). Cloning and enzymatic characterization of a xylanase gene from a soil-derived metagenomic library with an efficient approach[J]. Appl Microbiol Biotechnol 80(5): 823-830.
Huber, J. A., D. B. Mark Welch, H. G. Morrison, S. M. Huse, P. R. Neal, D. A. Butterfield and M. L. Sogin (2007). Microbial population structures in the deep marine biosphere[J]. Science 318(5847): 97-100.
J. E. Lupton, J. R. D., H. P.Johnson & M. K.Tivey (1985). Entrainment and verticaltransport of deep-ocean water by buoyant hydrothermal plumes[J]. Nature 316: 621 - 623
Jannasch H W, W. C. O. (1985). The biochemical versatility of chemosynthetic bacteria at deep-sea hydrothermal vents. [J]. Bulletin of the Biological Society of Washington 6: 325-334.
Jannasch, H. W. and M. J. Mottl (1985). Geomicrobiology of Deep-Sea Hydrothermal Vents[J]. science 229(4715): 717-725.
Jannasch, H. W. and C. D. Taylor (1984). Deep-sea microbiology[J]. Annu Rev Microbiol 38: 487-514.
Jin, D., W. Lu, S. Ping, W. Zhang, J. Chen, B. Dun, R. Ma, Z. Zhao, J. Sha, L. Li, Z. Yang, M. Chen and M. Lin (2007). Identification of a new gene encoding EPSPs with high glyphosate resistance from the metagenomic library[J]. Curr Microbiol 55(4): 350-355.
Kelley, D. S., J. A. Karson, D. K. Blackman, G. L. Fruh-Green, D. A. Butterfield, M. D. Lilley, E. J. Olson, M. O. Schrenk, K. K. Roe, G. T. Lebon and P. Rivizzigno (2001). An off-axis hydrothermal vent field near the Mid-Atlantic Ridge at 30 degrees N[J]. nature 412(6843): 145-149.
Kennedy, C. B., S. D. Scott and F. G. Ferris (2003). Ultrastructure and potential sub-seafloor evidence of bacteriogenic iron oxides from Axial Volcano, Juan de Fuca Ridge, north-east Pacific Ocean[J]. FEMS Microbiol Ecol 43(2): 247-254.
Khan, N. H., E. Roets, J. Hoogmartens and H. Vanderhaeghe (1987). Quantitative analysis of oxytetracycline and related substances by high-performance liquid chromatography[J]. J Chromatogr 405: 229-245.
Kim, H. K., S. Y. Park, J. K. Lee and T. K. Oh (1998). Gene cloning and characterization of thermostable lipase from Bacillus stearothermophilus L1[J]. Biosci Biotechnol Biochem 62(1): 66-71.
Kim, M. C., J. H. Ahn, H. C. Shin, T. Kim, T. H. Ryu, D. H. Kim, H. G. Song, G. H. Lee and J. O. Ka (2008). Molecular analysis of bacterial community structures in paddy soils for environmental risk assessment with two varieties of genetically modified rice, Iksan 483 and Milyang 204[J]. J Microbiol Biotechnol 18(2): 207-218.
Kim, T. K., A. K. Hewavitharana, P. N. Shaw and J. A. Fuerst (2006). Discovery of a new source of rifamycin antibiotics in marine sponge actinobacteria by phylogeneticprediction[J]. Appl Environ Microbiol 72(3): 2118-2125.
Kim, T. W., J. H. Lee, S. E. Kim, M. H. Park, H. C. Chang and H. Y. Kim (2009). Analysis of microbial communities in doenjang, a Korean fermented soybean paste, using nested PCR-denaturing gradient gel electrophoresis[J]. Int J Food Microbiol 131(2-3): 265-271.
Knietsch, A., T. Waschkowitz, S. Bowien, A. Henne and R. Daniel (2003). Construction and screening of metagenomic libraries derived from enrichment cultures: generation of a gene bank for genes conferring alcohol oxidoreductase activity on Escherichia coli[J]. Appl Environ Microbiol 69(3): 1408-1416.
Konhauser, K. O. (1998). Diversity of bacterial iron mineralization [J]. Earth-Science Reviews 43: 91-121
Konneke, M., A. E. Bernhard, J. R. de la Torre, C. B. Walker, J. B. Waterbury and D. A. Stahl (2005). Isolation of an autotrophic ammonia-oxidizing marine archaeon[J]. nature 437(7058): 543-546.
Kopczynski, E. D., M. M. Bateson and D. M. Ward (1994). Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms[J]. Appl Environ Microbiol 60(2): 746-748.
Krause, L., N. N. Diaz, A. Goesmann, S. Kelley, T. W. Nattkemper, F. Rohwer, R. A. Edwards and J. Stoye (2008). Phylogenetic classification of short environmental DNA fragments[J]. Nucleic Acids Res 36(7): 2230-2239.
Lammle, K., H. Zipper, M. Breuer, B. Hauer, C. Buta, H. Brunner and S. Rupp (2007). Identification of novel enzymes with different hydrolytic activities by metagenome expression cloning[J]. J Biotechnol 127(4): 575-592.
Lee, C. C., R. E. Kibblewhite-Accinelli, K. Wagschal, G. H. Robertson and D. W. Wong (2006). Cloning and characterization of a cold-active xylanase enzyme from an environmental DNA library[J]. Extremophiles 10(4): 295-300.
Lee, M. H., C. H. Lee, T. K. Oh, J. K. Song and J. H. Yoon (2006). Isolation and characterization of a novel lipase from a metagenomic library of tidal flat sediments: evidence for a new family of bacterial lipases[J]. Appl Environ Microbiol 72(11): 7406-7409.
Liesack, H. W. a. E. S. (1991). Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria [J]. Microbial Ecology 21: 191-198.
Lilley, D. A. B., E. J. Olson, J. E. Lupton, S. A. Macko,R. E. McDuff (1993). Anomalous CH4 and NH4+ concentrations at an unsedimented mid-ocean-ridge hydrothermal system[J]. Nature 364: 45-47.
Luther, G. W., 3rd, T. F. Rozan, M. Taillefert, D. B. Nuzzio, C. Di Meo, T. M. Shank, R. A.
Lutz and S. C. Cary (2001). Chemical speciation drives hydrothermal vent ecology[J]. nature 410(6830): 813-816.
Lydmark, P., R. Almstrand, K. Samuelsson, A. Mattsson, F. Sorensson, P. E. Lindgren and M. Hermansson (2007). Effects of environmental conditions on the nitrifying population dynamics in a pilot wastewater treatment plant[J]. Environ Microbiol 9(9): 2220-2233.
Majernik, A., G. Gottschalk and R. Daniel (2001). Screening of environmental DNA libraries for the presence of genes conferring Na(+)(Li(+))/H(+) antiporter activity on Escherichia coli: characterization of the recovered genes and the corresponding gene products[J]. J Bacteriol 183(22): 6645-6653.
Malin, C. and P. Illmer (2008). Ability of DNA content and DGGE analysis to reflect the performance condition of an anaerobic biowaste fermenter[J]. Microbiol Res 163(5): 503-511.
Marcel Margulies, M. E., William E. Altman1, Said Attiya1, Joel S. Bader1, Lisa A. Bemben1,, M. S. B. Jan Berka1, Yi-Ju Chen1, Zhoutao Chen1, Scott B. Dewell1, Lei Du1, Joseph M. Fierro1,, B. C. G. Xavier V. Gomes1, Wen He1, Scott Helgesen1, Chun He Ho1, Gerard P. Irzyk1,, M. L. I. A. Szilveszter C. Jando1, Thomas P. Jarvie1, Kshama B. Jirage1, Jong-Bum Kim1,, J. R. L. James R. Knight1, John H. Leamon1, Steven M. Lefkowitz1, Ming Lei1, Jing Li1, Kenton L. Lohman1,, V. B. M. Hong Lu1, Keith E. McDade1, Michael P. McKenna1, Eugene W. Myers2,, J. R. N. Elizabeth Nickerson1, Ramona Plant1, Bernard P. Puc1, Michael T. Ronan1, George T. Roth1,, J. F. S. Gary J. Sarkis1, John W. Simpson1, Maithreyan Srinivasan1, Karrie R. Tartaro1,, K. A. V. Alexander Tomasz3, Greg A. Volkmer1, Shally H. Wang1, Yong Wang1, Michael P. Weiner4, and R. F. B. J. M. R. Pengguang Yu1 (2005). Genome sequencing in microfabricated high-density picolitre reactors[J]. nature.
Margulies, M., M. Egholm, W. E. Altman, S. Attiya, J. S. Bader, L. A. Bemben, J. Berka, M. S. Braverman, Y. J. Chen, Z. Chen, S. B. Dewell, L. Du, J. M. Fierro, X. V. Gomes, B. C. Godwin, W. He, S. Helgesen, C. H. Ho, G. P. Irzyk, S. C. Jando, M.L. Alenquer, T. P. Jarvie, K. B. Jirage, J. B. Kim, J. R. Knight, J. R. Lanza, J. H. Leamon, S. M. Lefkowitz, M. Lei, J. Li, K. L. Lohman, H. Lu, V. B. Makhijani, K. E. McDade, M. P. McKenna, E. W. Myers, E. Nickerson, J. R. Nobile, R. Plant, B. P. Puc, M. T. Ronan, G. T. Roth, G. J. Sarkis, J. F. Simons, J. W. Simpson, M. Srinivasan, K. R. Tartaro, A. Tomasz, K. A. Vogt, G. A. Volkmer, S. H. Wang, Y. Wang, M. P. Weiner, P. Yu, R. F. Begley and J. M. Rothberg (2005). Genome sequencing in microfabricated high-density picolitre reactors[J]. nature 437(7057): 376-380.
Mark Hildebrand, Laura E. Waggoner, Haibin Liu, Sebastian Sudek and Scott Allen (2004). bryA: An Unusual Modular Polyketide Synthase Gene from the Uncultivated Bacterial Symbiont of the Marine Bryozoan Bugula neritina[J]. Chemistry & Biology,6.67 11(11): 1543-1552.
Martinez, A., S. J. Kolvek, C. L. Yip, J. Hopke, K. A. Brown, I. A. MacNeil and M. S. Osburne (2004). Genetically modified bacterial strains and novel bacterial artificial chromosome shuttle vectors for constructing environmental libraries and detecting heterologous natural products in multiple expression hosts[J]. Appl Environ Microbiol 70(4): 2452-2463.
Mayumi, D., Y. Akutsu-Shigeno, H. Uchiyama, N. Nomura and T. Nakajima-Kambe (2008). Identification and characterization of novel poly(DL-lactic acid) depolymerases from metagenome[J]. Appl Microbiol Biotechnol 79(5): 743-750.
Mehta, M. P., D. A. Butterfield and J. A. Baross (2003). Phylogenetic diversity of nitrogenase (nifH) genes in deep-sea and hydrothermal vent environments of the Juan de Fuca Ridge[J]. Appl Environ Microbiol 69(2): 960-970.
Meng, J., F. Wang, Y. Zheng, X. Peng, H. Zhou and X. Xiao (2009). An uncultivated crenarchaeota contains functional bacteriochlorophyll a synthase[J]. ISME J 3(1): 106-116.
Miller, S. L. and J. L. Bada (1988). Submarine hot springs and the origin of life[J]. nature 334(6183): 609-611.
Minic, Z. and G. Herve (2004). Biochemical and enzymological aspects of the symbiosis between the deep-sea tubeworm Riftia pachyptila and its bacterial endosymbiont[J]. Eur J Biochem 271(15): 3093-3102.
Mittelbach, G. G., D. W. Schemske, H. V. Cornell, A. P. Allen, J. M. Brown, M. B. Bush, S. P. Harrison, A. H. Hurlbert, N. Knowlton, H. A. Lessios, C. M. McCain, A. R.McCune, L. A. McDade, M. A. McPeek, T. J. Near, T. D. Price, R. E. Ricklefs, K. Roy, D. F. Sax, D. Schluter, J. M. Sobel and M. Turelli (2007). Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography[J]. Ecol Lett 10(4): 315-331.
MK, T. (2004). The remarkable diversity of seafloor vents[J]. Oceanus 42: 60-65.
Monika Beh, G. S., Robert Huber, Karl-Otto Stetter and Georg Fuchs (1977). Enzymes of the reductive citric acid cycle in the autotrophic eubacterium Aquifex pyrophilus and in the archaebacterium Thermoproteus neutrophilus [J]. Archives of Microbiology 160: 306-311.
Mootz, H. D., D. Schwarzer and M. A. Marahiel (2002). Ways of assembling complex natural products on modular nonribosomal peptide synthetases[J]. Chembiochem 3(6): 490-504.
Moyer, D. E. a. C. L. ( 2002). Neutrophilic Fe-Oxidizing Bacteria Are Abundant at the Loihi Seamount Hydrothermal Vents and Play a Major Role in Fe Oxide Deposition [J]. Applied and Environmental Microbiology 68: 3085-3093.
Murakami, T. K. a. T. (2001). The effect of microorganisms on Fe precipitation rates at neutral pH [J]. Chemical Geology 180: 117-128. Mussmann, M., F. Z. Hu, M. Richter, D. de Beer, A. Preisler, B. B. Jorgensen, M.
Huntemann, F. O. Glockner, R. Amann, W. J. Koopman, R. S. Lasken, B. Janto, J. Hogg, P. Stoodley, R. Boissy and G. D. Ehrlich (2007). Insights into the genome of large sulfur bacteria revealed by analysis of single filaments[J]. PLoS Biol 5(9): e230.
Nakagawa, S. and K. Takai (2008). Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance[J]. FEMS Microbiol Ecol 65(1): 1-14.
Nakagawa, S., Y. Takaki, S. Shimamura, A. L. Reysenbach, K. Takai and K. Horikoshi (2007). Deep-sea vent epsilon-proteobacterial genomes provide insights into emergence of pathogens[J]. Proc Natl Acad Sci U S A 104(29): 12146-12150.
Nakagawa, T., Y. Fujimoto, R. Ikehata, T. Miyaji and N. Tomizuka (2006). Purification and molecular characterization of cold-active beta-galactosidase from Arthrobacter psychrolactophilus strain F2[J]. Appl Microbiol Biotechnol 72(4): 720-725.
Nichols, C. A., J. Guezennec and J. P. Bowman (2005). Bacterial exopolysaccharides from extreme marine environments with special consideration of the southern ocean, sea ice, and deep-sea hydrothermal vents: a review[J]. Mar Biotechnol (NY) 7(4):253-271.
Pang, H., P. Zhang, C. J. Duan, X. C. Mo, J. L. Tang and J. X. Feng (2009). Identification of cellulase genes from the metagenomes of compost soils and functional characterization of one novel endoglucanase[J]. Curr Microbiol 58(4): 404-408.
Parkhill, J., B. W. Wren, K. Mungall, J. M. Ketley, C. Churcher, D. Basham, T. Chillingworth, R. M. Davies, T. Feltwell, S. Holroyd, K. Jagels, A. V. Karlyshev, S. Moule, M. J. Pallen, C. W. Penn, M. A. Quail, M. A. Rajandream, K. M.
Rutherford, A. H. van Vliet, S. Whitehead and B. G. Barrell (2000). The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences[J]. nature 403(6770): 665-668.
Piel, J., D. Hui, G. Wen, D. Butzke, M. Platzer, N. Fusetani and S. Matsunaga (2004). Antitumor polyketide biosynthesis by an uncultivated bacterial symbiont of the marine sponge Theonella swinhoei[J]. Proc Natl Acad Sci U S A 101(46): 16222-16227.
Pieper, R., G. Luo, D. E. Cane and C. Khosla (1995). Cell-free synthesis of polyketides by recombinant erythromycin polyketide synthases[J]. nature 378(6554): 263-266.
R. F. WEISS, P. L., J. E. LUPTON, A. E. BAINBRIDGE, H. CRAIG (1977). Hydrothermal plumes in the Galapagos Rift[J]. Nature 267: 600-603.
Ranjan, R., A. Grover, R. K. Kapardar and R. Sharma (2005). Isolation of novel lipolytic genes from uncultured bacteria of pond water[J]. Biochem Biophys Res Commun 335(1): 57-65.
Rashamuse, K., T. Ronneburg, F. Hennessy, D. Visser, E. van Heerden, L. Piater, D. Litthauer, C. Moller and D. Brady (2009). Discovery of a novel carboxylesterase through functional screening of a pre-enriched environmental library[J]. J Appl Microbiol 106(5): 1532-1539.
Rasmussen, B. (2000). Filamentous microfossils in a 3,235-million-year-old volcanogenic massive sulphide deposit[J]. nature 405(6787): 676-679.
Rhee, J. K., D. G. Ahn, Y. G. Kim and J. W. Oh (2005). New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library[J]. Appl Environ Microbiol 71(2): 817-825.
Rondon, M. R., P. R. August, A. D. Bettermann, S. F. Brady, T. H. Grossman, M. R. Liles, K. A. Loiacono, B. A. Lynch, I. A. MacNeil, C. Minor, C. L. Tiong, M. Gilman, M.S. Osburne, J. Clardy, J. Handelsman and R. M. Goodman (2000). Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms[J]. Appl Environ Microbiol 66(6): 2541-2547.
Siqueira, J. F., Jr., I. N. Rocas, G. J. Debelian, F. L. Carmo, S. S. Paiva, F. R. Alves and A. S. Rosado (2008). Profiling of root canal bacterial communities associated with chronic apical periodontitis from Brazilian and Norwegian subjects[J]. J Endod 34(12): 1457-1461.
Sirevag, R., B. B. Buchanan, J. A. Berry and J. H. Troughton (1977). Mechanisms of CO2 fixation in bacterial photosynthesis studied by the carbon isotope fractionation technique[J]. Arch Microbiol 112(1): 35-38. Spiess, F. N., K. C. Macdonald, T. Atwater, R. Ballard, A. Carranza, D. Cordoba, C. Cox,
V. M. Garcia, J. Francheteau, J. Guerrero, J. Hawkins, R. Haymon, R. Hessler, T. Juteau, M. Kastner, R. Larson, B. Luyendyk, J. D. Macdougall, S. Miller, W. Normark, J. Orcutt and C. Rangin (1980). East Pacific Rise: Hot Springs and Geophysical Experiments[J]. science 207(4438): 1421-1433.
Stokes, H. W., A. J. Holmes, B. S. Nield, M. P. Holley, K. M. Nevalainen, B. C. Mabbutt and M. R. Gillings (2001). Gene cassette PCR: sequence-independent recovery of entire genes from environmental DNA[J]. Appl Environ Microbiol 67(11): 5240-5246.
Summit, M. (2000). Ecology, physiology, and phylogeny of subseafloor thermophiles from mid-ocean ridge [J]. University of Washington.
Summit, M. and J. A. Baross (2001). A novel microbial habitat in the mid-ocean ridge subseafloor[J]. Proc Natl Acad Sci U S A 98(5): 2158-2163.
Susumu Mochizuki, K. H., Masanori Suwa (2003). The large linear plasmid pSLA2-L of Streptomyces rochei has an unusually condensed gene organization for secondary metabolism[J]. Molecular Microbiology 48: 1501-1510.
Szymanski, C. M., D. H. Burr and P. Guerry (2002). Campylobacter protein glycosylation affects host cell interactions[J]. Infect Immun 70(4): 2242-2244.
Tirawongsaroj, P., R. Sriprang, P. Harnpicharnchai, T. Thongaram, V. Champreda, S. Tanapongpipat, K. Pootanakit and L. Eurwilaichitr (2008). Novel thermophilic and thermostable lipolytic enzymes from a Thailand hot spring metagenomic library[J]. J Biotechnol 133(1): 42-49.
Tokuda, G., M. Miyagi, H. Makiya, H. Watanabe and G. Arakawa (2009). Digestivebeta-glucosidases from the wood-feeding higher termite, Nasutitermes takasagoensis: Intestinal distribution, molecular characterization, and alteration in sites of expression[J]. Insect Biochem Mol Biol.
Tringe, S. G. and E. M. Rubin (2005). Metagenomics: DNA sequencing of environmental samples[J]. Nat Rev Genet 6(11): 805-814.
Uchiyama, T., T. Abe, T. Ikemura and K. Watanabe (2005). Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes[J]. Nat Biotechnol 23(1): 88-93.
Venter, J. C., K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch, J. A. Eisen, D. Wu, I. Paulsen, K. E. Nelson, W. Nelson, D. E. Fouts, S. Levy, A. H. Knap, M. W. Lomas, K. Nealson, O. White, J. Peterson, J. Hoffman, R. Parsons, H. Baden-Tillson, C. Pfannkoch, Y. H. Rogers and H. O. Smith (2004). Environmental genome shotgun sequencing of the Sargasso Sea[J]. science 304(5667): 66-74.
Wacker, M., D. Linton, P. G. Hitchen, M. Nita-Lazar, S. M. Haslam, S. J. North, M. Panico, H. R. Morris, A. Dell, B. W. Wren and M. Aebi (2002). N-linked glycosylation in Campylobacter jejuni and its functional transfer into E. coli[J]. science 298(5599): 1790-1793.
Wagner, M., P. H. Nielsen, A. Loy, J. L. Nielsen and H. Daims (2006). Linking microbial community structure with function: fluorescence in situ hybridization-microautoradiography and isotope arrays[J]. Curr Opin Biotechnol 17(1): 83-91.
Walsh, C. T., H. Chen, T. A. Keating, B. K. Hubbard, H. C. Losey, L. Luo, C. G. Marshall, D. A. Miller and H. M. Patel (2001). Tailoring enzymes that modify nonribosomal peptides during and after chain elongation on NRPS assembly lines[J]. Curr Opin Chem Biol 5(5): 525-534.
Weber, K. A., L. A. Achenbach and J. D. Coates (2006). Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction[J]. Nat Rev Microbiol 4(10): 752-764.
William W. Chadwick Jr, R. W. E. C. G. F. (1991). Evidence for volcanic eruption on the southern Juan de Fuca ridge between 1981 and 1987[J]. Nature 350 350: 416 - 418.
Xu, M., X. Xiao and F. Wang (2008). Isolation and characterization of alkanehydroxylases from a metagenomic library of Pacific deep-sea sediment[J]. Extremophiles 12(2): 255-262.
Young, N. M., J. R. Brisson, J. Kelly, D. C. Watson, L. Tessier, P. H. Lanthier, H. C. Jarrell, N. Cadotte, F. St Michael, E. Aberg and C. M. Szymanski (2002). Structure of the N-linked glycan present on multiple glycoproteins in the Gram-negative bacterium, Campylobacter jejuni[J]. J Biol Chem 277(45): 42530-42539.
Yukihiro Nojiri, J.-i. I., Takayoshi Kawai, Akira Otsuki & Hitoshi Sakai (1989). Hydrothermal plumes along the North Fiji Basin spreading axis[J]. Nature 342(667 - 670).
Zhou, J., M. A. Bruns and J. M. Tiedje (1996). DNA recovery from soils of diverse composition[J]. Appl Environ Microbiol 62(2): 316-322.
王淑芳(2008).深海热液口硫化物微生物群落多样性分析[D].厦门,厦门大学.
李慧;,何晶晶;,张颖;,徐慧; and陈冠雄(2008).宏基因组技术在开发未培养环境微生物基因资源中的应用[J].生态学报28: 1762-1773.
周怀阳,李江涛,彭晓彤(2010).海底热液活动与生命起源[J].自然杂志31: 207-212.
徐晓宇,刘和为(2009). 454测序法在环境微生物生态研究中的应用[J].生物技术通报1: 73-77.
魏曼曼,王玉光,郑甲,周洪波(2009).劳盆地深海热液喷口沉积物中细菌多样性研究[J].微生物学通报36(4): 538-543.
赵春华(2008).聚酮聚肽杂合抗生素垩唑霉素的生物合成机理与途径工程[D].上海,上海交通大学.
黄循柳,黄仕杰,郭丽琼,林俊芳(2009).宏基因组学研究进展[J].微生物学通报36 1058-1066.