深海热液口管状蠕虫Ridgeia picesae共生微生物的鉴定及代谢机制的初步研究
|
摘要
Ridgeia piscesae是热液口管状蠕虫的一种,主要分布于东北太平洋Explorer、Juan de Fuca及Gorda洋中脊。该类管状蠕虫具有形态多样性,按其形态主要可分为短胖型及细长型虫体。根据以往研究,管状蠕虫R. piscesae滋养体中的共生微生物类型被认为主要为γ-proteobacteria,但是也有很多研究报道反对这种“滋养体单一菌种”的假说。
本论文的主要目的是鉴定由深海热液口Juan de Fuca洋中脊Endeavor段采集的管状蠕虫R. piscesae的共生微生物类型,并进行相关代谢机制研究。实验中,我们运用差速离心的方法分离了该管状蠕虫共生微生物,并通过通用引物对该共生微生物的16S rDNA进行了扩增,建立了16S rDNA克隆文库并对该文库进行了限制性酶切片断多态性(RFLP)分析。RFLP分析及后续测序显示,该管状蠕虫共生微生物只包含一种类型的微生物,即ε-proteobacteria,与以往发现的共生微生物类型完全不同。为了鉴定该共生微生物的自养特性,我们通过PCR扩增了其固碳途径的关键酶D-ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO)基因。我们发现该共生微生物同时含有两种形式的RuBisCO基因(cbbL和cbbM),反应了其利用卡尔文循环固定无机碳的自养途径;另一方面,通过对硫氧化相关基因的筛选,我们证明该共生微生物自养代谢的能量来源于对环境中无机硫的氧化过程。
此外,为了便于活性物质基因簇的挖掘,我们建立了该管状蠕虫共生微生物大片断基因组DNA的cosmid文库并对文库中重金属抑制酶的克隆进行了筛选。通过对获得的抑制砷、铅及铜离子的活性克隆进行交叉检测后,砷抑制克隆表现较高抑制活性。因此,我们将该克隆进行了cosmid质粒测序。根据测序结果,我们鉴定了砷抑制酶的基因簇以待后续功能检测工作的进行。
Ridgeia piscesae is a vestimentiferan tubeworm that inhabits deep sea hydrothermal vents along Explorer, Juan de Fuca and Gorda Ridges in the northeastern Pacific Ocean. The known endosymbionts of R. piscesae at hydrothermal vents were within the subdivisionγ-proteobacteria. However, many studies were conducted against the hypothesis of“single taxon endosymbiont within the trophsome”.
The primary goal of this study was to phylogenetically characterize the endosymbionts in the trophosome of R. piscesae collected from Endeavor ventfield on Juan de Fuca Ridge. The endosymbionts were isolated from the tubeworm by differential centrifugation and their 16S rRNA genes were amplified with universal bacterial 16S rRNA primers. The genes were subsequently sequenced and the 16S rDNA clone library was screened by restriction fragment length polymorphism (RFLP) analysis to identify distinct clone types. The RFLP analysis identified only one clone family that fell within the subdivision ofε-proteobacteria. To confirm the autotrophy of the endosymbiont, the trophosome section of tubeworm were stained by haematoxylin/eosin dye mixture and only one type of coccoid cells was observed under microscope. Besides, the genes of RuBisCO formⅠ(cbbL) andⅡ(cbbM) were both detected from the endosymbiont DNA, indicating that this endosymbiont utilized a Calvin-Benson Cycle for carbon fixation. Detection of ATP sulfurylase gene and other sulfur metabolism related genes also suggested that this autotrophic symbiosis was mediated by sulfide oxidation process.
On the other hand, the cosmid library of genomic DNA extracted from R. piscesae endosymbionts was constructed. Clones resistant to heavy metal of arsenic, lead and copper were screened. The single clone that was resistant to arsenic revealed high enzyme activity and was subjected to cosmid vector sequencing. The gene cluster of arsenic resistance enzyme was then identified.
本论文的主要目的是鉴定由深海热液口Juan de Fuca洋中脊Endeavor段采集的管状蠕虫R. piscesae的共生微生物类型,并进行相关代谢机制研究。实验中,我们运用差速离心的方法分离了该管状蠕虫共生微生物,并通过通用引物对该共生微生物的16S rDNA进行了扩增,建立了16S rDNA克隆文库并对该文库进行了限制性酶切片断多态性(RFLP)分析。RFLP分析及后续测序显示,该管状蠕虫共生微生物只包含一种类型的微生物,即ε-proteobacteria,与以往发现的共生微生物类型完全不同。为了鉴定该共生微生物的自养特性,我们通过PCR扩增了其固碳途径的关键酶D-ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO)基因。我们发现该共生微生物同时含有两种形式的RuBisCO基因(cbbL和cbbM),反应了其利用卡尔文循环固定无机碳的自养途径;另一方面,通过对硫氧化相关基因的筛选,我们证明该共生微生物自养代谢的能量来源于对环境中无机硫的氧化过程。
此外,为了便于活性物质基因簇的挖掘,我们建立了该管状蠕虫共生微生物大片断基因组DNA的cosmid文库并对文库中重金属抑制酶的克隆进行了筛选。通过对获得的抑制砷、铅及铜离子的活性克隆进行交叉检测后,砷抑制克隆表现较高抑制活性。因此,我们将该克隆进行了cosmid质粒测序。根据测序结果,我们鉴定了砷抑制酶的基因簇以待后续功能检测工作的进行。
Ridgeia piscesae is a vestimentiferan tubeworm that inhabits deep sea hydrothermal vents along Explorer, Juan de Fuca and Gorda Ridges in the northeastern Pacific Ocean. The known endosymbionts of R. piscesae at hydrothermal vents were within the subdivisionγ-proteobacteria. However, many studies were conducted against the hypothesis of“single taxon endosymbiont within the trophsome”.
The primary goal of this study was to phylogenetically characterize the endosymbionts in the trophosome of R. piscesae collected from Endeavor ventfield on Juan de Fuca Ridge. The endosymbionts were isolated from the tubeworm by differential centrifugation and their 16S rRNA genes were amplified with universal bacterial 16S rRNA primers. The genes were subsequently sequenced and the 16S rDNA clone library was screened by restriction fragment length polymorphism (RFLP) analysis to identify distinct clone types. The RFLP analysis identified only one clone family that fell within the subdivision ofε-proteobacteria. To confirm the autotrophy of the endosymbiont, the trophosome section of tubeworm were stained by haematoxylin/eosin dye mixture and only one type of coccoid cells was observed under microscope. Besides, the genes of RuBisCO formⅠ(cbbL) andⅡ(cbbM) were both detected from the endosymbiont DNA, indicating that this endosymbiont utilized a Calvin-Benson Cycle for carbon fixation. Detection of ATP sulfurylase gene and other sulfur metabolism related genes also suggested that this autotrophic symbiosis was mediated by sulfide oxidation process.
On the other hand, the cosmid library of genomic DNA extracted from R. piscesae endosymbionts was constructed. Clones resistant to heavy metal of arsenic, lead and copper were screened. The single clone that was resistant to arsenic revealed high enzyme activity and was subjected to cosmid vector sequencing. The gene cluster of arsenic resistance enzyme was then identified.
引文
[1] Corliss JB, Dymond J, Gordon LI, Edmond JM, Herzen RPV, Ballard RD, Green K, Williams D, Bainbridge A, Crane K, Andel TH. Submarine thermal springs on the Galapagos Rift [J]. Science, 1979, 203: 1073–1083.
[2] Lonsdale P. Clustering of suspension-feeding macrobenthos near abyssal hydrothermal vents at oceanic spreading centers [J]. Deep Sea Res, 1977, 24: 857–863.
[3] Seyfried WF, Jr. Experimental and theoretical constraints on hydrothermal alteration processes at mid ocean ridges [J]. Ann. Rev. Earth Planet. Sci., 1987, 15: 317–335.
[4] MacDonald IR, Boland GS, Baker JS, Brooks JM, Kennicutt MC II, Bidigare RR. Gulf of Mexico hydrocarbon seep communities. II. Spatial distribution of seep organisms and hydrocarbons at Bush Hill [J]. Mar. Biol., 1989, 101: 235–247.
[5] Tunnicliffe V, McArthur A, McHugh D. A biogeographical perspective of the deep-sea hydrothermal vent fauna [J]. Adv. Mar. Biol., 1998, 34: 353–442.
[6] Zierenberg RA, Adams MW, Arp AJ. Life in extreme environments: hydrothermal vents [J]. Proc. Natl. Acad. Sci. USA, 2000, 97: 12961–12962.
[7] MacDonald IR, Guinasso NL, Reilly JF, Brooks JM, Callender WR, Gabrielle SG. Gulf of Mexico hydrocarbon seep communities. IV. Patterns in community structure and habitat [J]. Geo-Mar. Lett., 1990, 10: 244–252.
[8] Fisher CR. Chemoautotrophic and methanotrophic symbioses in marine inverterbrates [J]. Aquat. Sci., 1996, 2: 399–436.
[9] Arndt C, Gaill F, Felbeck H. Anaerobic sulfur metabolism in thiotrophic symbioses [J]. J. Exp. Biol., 2001, 204: 741–750.
[10] DoverCLV, Lutz RA. Experimental ecology at deep-sea hydrothermal vents: a perspective [J]. J. Exp. Mar. Biol. Ecol., 2004, 300: 273–307.
[11] Tunnicliffe V. The biology of hydrothermal vents: ecology and evolution [J]. Oceanogr. Mar. Biol. Annu. Rev., 1991, 29: 319–407.
[12] Blum J, Fridovich I. Enzymatic defenses against oxygen toxicity in thehydrothermal vent animals Riftia pachyptila and Calyptogena magnifica [J]. Arch. Biochem. Biophys., 1984, 228: 617–620.
[13] Kim YW, Yasuda M, Yamagishi A, Oshima T, Ohta, S. Characterization of the Endosymbiont of a Deep-Sea Bivalve, Calyptogena soyoae [J]. Appl. Environ. Microbiol., 1995, 61: 823–827.
[14] Dunlap PV, Ast JC. Genomic and phylogenetic characterization of luminous bacteria symbiotic with the deep-sea fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae) [J]. Appl. Environ. Microbiol., 2005, 71: 930–939.
[15] Campbell BJ, Cary SC. Characterization of a novel spirochete associated with the hydrothermal vent polychaete annelid, Alvinella pompejana [J]. Appl. Environ. Microbiol., 2001, 67: 110–117.
[16] Cottrell MT, Cary SC. Diversity of dissimilatory bisulfite reductase genes of bacteria associated with the deep-sea hydrothermal vent polychaete annelid Alvinella pompejana [J]. Appl. Environ. Microbiol., 1999, 65: 1127–1132.
[17] Fujiwara1 Y, Takai K, Uematsu K, Tsuchida1 S, Hunt JC, Hashimoto J. Phylogenetic characterization of endosymbionts in three hydrothermal vent mussels: influence on host distributions [J]. Mar. Ecol. Prog. Ser., 2000, 208: 147–155.
[18] Haddad A, Camacho F, Durand P, Cary SC. Phylogenetic Characterization of the epibiotic bacteria associated with the hydrothermal vent polychaete Alvinella pompejana [J]. Appl. Environ. Microbiol., 1995, 61: 1679–1687.
[19] Stein JL, Haygood M, Felbeck H. Nucleotide sequence and expression of a deep-sea ribulose-1,5-bisphosphate carboxylase gene cloned from a chemoautotrophic bacterial endosymbiont [J]. Proc. Nati. Acad. Sci. USA, 1990, 87: 8850–8854.
[20] Distel DL, Lee HKW, Cavanaugh CM. Intracellular coexistence of methano- and thioautotrophic bacteria in a hydrothermal vent mussel [J]. Proc. Natl. Acad. Sci. USA, 1995, 92: 9598–9602.
[21] Kasting JF. Earth’s early atmosphere [J]. Science, 1993, 259: 920–926.
[22] Baross JA, Hoffman SE. Submarine hydrothermal vents and associated gradient environments as sites for the origin and evolution of life [J]. Naval Res. Rev., 1986, 38: 2–12.
[23] Pace NR. Origin of life–facing up to the physical setting [J]. Cell, 1991, 65: 531–533.
[24] Vetriani C, Speck MD, Ellor SV, Lutz RA, Starovoytov V. Thermovibrio ammonificans sp. nov., a thermophilic, chemolithotrophic, nitrate-ammonifying bacterium from deep-sea hydrothermal vents [J]. Int. J. Syst. Evol. Microbiol., 2004, 54: 175–181.
[25] Reysenbach AL, Liu Y, Banta1 AB, Beveridge TJ, Kirshtein JD, Schouten S, Tivey MK, Von Damm KL, Voytek MA. A ubiquitous thermoacidophilic archaeon from deep-sea hydrothermal vents [J]. Nature, 2006, 442: 444–447.
[26] Takai K, Inagaki F, Nakagawa S, Hirayama H, Nunoura T, Sako Y, Nealson KH, Horikoshi K. Isolation and phylogenetic diversity of members of previously uncultivated ε-Proteobacteria in deep-sea hydrothermal fields [J]. FEMS Microbiol Lett, 2003, 218: 167–174.
[27] Black MB, Halanych KM, Maas PAY, Hoeh WR, Hashimoto J, Desbruyères D, Lutz RA, Vrijenhoek RC. Molecular systematics of vestimentiferan tubeworms from hydrothermal vents and cold-water seeps [J]. Mar. Biol., 1997, 130: 141–149.
[28] Jones ML. On the Vestimentifera, new phylum: six new species, and other taxa, from hydrothermal vents and elsewhere [J]. Bulletin of the Biological Society of Washington, 1985, 6: 117–158.
[29] Black MB, Trivedi A, Maas PAY, Lutz RA, Vrijenhoek RC. Population genetics and biogeography of vestimentiferan tube worms [J]. Deep-Sea Research, 1998, 45: 365–382.
[30] Southward EC, Tunnicliffe V, Black M. Revision of the species of Ridgeia from northeast Pacific hydrothermal vents, with a redescription of Ridgeia piscesae Jones (Pogonophora: Obturata
[31] Tunnicliffe V, Juniper SK. Dynamic character of the hydrothermal vent habitat and the nature of sulfide chimney fauna [J]. Progress in Oceanography, 1990, 24: 1–13.
[32] Arp AJ, Childress JJ, Fisher CR Jr. Blood gas transport in Riftia pachyptila [J]. Bull. Biol. Soc. Wash., 1985, 6: 289–300.
[33] Jones ML. The vestimentifera, their biology, systematic and evolutionary patterns [J]. Oceanol. Acta, 1988, 8: 69–82.
[34] Cavanaugh CM, Gardiner SL, Jons ML, Jannasch HW, Waterbury JB. Prokaryotic cells in the hydrothermal vent tube worm Riftia pachyptila Jones: Possible chemoautotrophic symbionts [J]. Science, 1981, 213: 340–342.
[35] Felbech H, Childress JJ, Somero GN. Calvin-Benson cycle and sulphide oxidation enzymes in animals from sulphide-rich habitats [J]. Nature, 1981, 293: 291–293.
[36] Felbeck H. Chemoautotrophic potential of the hydrothermal vent tube worm, Riftia pachyptila Jones (Vestimentifera) [J]. Science, 1981, 213: 336–338.
[37] Childress JJ, Arp AJ, Fisher CR. Metabolic and blood characteristics of the hydrothermal vent tube worm Riftia pachyptila [J]. Mar. Biol. (Berl.), 1984, 83: 109–124.
[38] Powell MA and Somero GN. Adaptations to sulfide by hydrothermal vent animals: sites and mechanisms of detoxification and metabolism [J]. Biol. Bull., 1986, 171: 274–290.
[39] Belkin S, Nelson DC, Jannasch HW. Symbiotic assimilation of CO2 in two hydrothermal vent animals, the mussel Bathymodiolus thermophilus and the tube worm Riftia pachyptil [J]. Biol. Bull., 1986, 170: 110–121.
[40] Fisher CR, Childress JJ, Minnich E. Autotrophic carbon fixation by the chemoautotrophic symbionts of Riftia pachyptila [J]. Biol. Bull., 1989, 177: 372–385.
[41] Arp AJ, Childress JJ. Blood function in the hydrothermal vent vestimentiferan tube worm [J]. Science, 1981, 213: 342–344.
[42] Felbeck H, Childress JJ. Riftia pachyptila: a highly integrated symbiosis [J].Oceanol. Acta, 1988, 8: 131–138.
[43] Minic Z, Simon V, Penverne B, Gaill F, Herve G. Contribution of the bacterial endosymbiont to the biosynthesis of pyrimidine nucleotides in the deep-sea tube worm Riftia pachyptila [J]. J. Biol. Chem., 2001, 276: 23777–23784.
[44] Elsaied H, Kimura H, Naganuma T. Molecular characterization and endosymbiotic localization of the gene encoding D-ribulose 1,5-bisphosphate carboxylase–oxygenase (RuBisCO) form II in the deep-sea vestimentiferan trophosome [J]. Microbiology, 2002, 148: 1947–1957.
[45] Hand SC. Trophosome ultrastructure and the characterization of isolated bacteriocytes from invertebrate-sulfur bacteria symbiosis [J]. Biol. Bull., 1987, 173: 260–276.
[46] Stahl D, Lane D, Olsen G, Pace N. Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences [J]. Science, 1984, 224: 409–411.
[47] Distel DL, Felbeck H, Cavanaugh CM. Evidence for phylogenetic congruence among sulfur-oxidizing chemoautotrophic bacterial endosymbionts and their bivalvia hosts [J]. J. Mol. Evol., 1994, 38: 533–542.
[48] DiMeo CA, Wilbur AE, Holben WE, Feldman RA, Vrijenhoek RC, Cary SC. Genetic variation among endosymbionts of widely distributed vestimentiferan tubeworms [J]. Appl. Environ. Microbiol., 2000, 66: 651–658.
[49] Felbeck H, Childress JH, Somero GN. Calvin-Benson cycle and sulfide oxidation enzymes in animals from sulfide-rich habitats [J]. Nature, 1981, 293: 291–293.
[50] Kellogg EA, Juliano ND. The structure and function of RuBisCO and their implications for systematic studies [J]. Am. J. Bot., 1997, 84: 413–428.
[51] Watson GM, Yu JP, Tabita FR. Unusual ribulose 1,5-bisphosphate carboxylase/oxygenase of anoxic Archaea [J]. J. Bacteriol., 1999, 181: 1569–1575.
[52] Elsaied H, Naganuma T. Phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes from deep-sea microorganisms [J]. Appl. Environ. Microbiol., 2001, 67: 1751–1765.
[53] Schwedock J, Harmer TL, Scott KM, Hektor HJ, Seitz AP, Fontana MC, DistelDL, Cavanaugh CM. Characterization and expression of genes from the RubisCO gene cluster of the chemoautotrophic symbiont of Solemya velum: cbbLSQO [J]. Arch Microbiol., 2004, 182: 18–29.
[54] Preuss A, Schauder R, Fuchs G, Stichler W. Carbon isotope fractionation by autotrophic bacteria with 3 different CO2 fixation pathways [J]. Z. Naturforsch. C, 1989, 44: 397–402.
[55] Hügler M, Wirsen CO, Fuchs G, Taylor GD, Sievert SM. Evidence for autotrophic CO2 fixation via the reductive tricarboxylic acid cycle by members of the ε subdivision of proteobacteria [J]. J. Bacteriol., 2005, 187: 3020–3027.
[56] Campbell BJ, Stein JL, Cary SC. Evidence of chemolithoautotrophy in the bacterial community associated with Alvinella pompejana, a hydrothermal vent polychaete [J]. Appl. Environ. Microbiol., 2003, 69: 5070–5078.
[57] Campbell BJ, Cary SC. Abundance of reverse tricarboxylic acid cycle genes in free-living microorganisms at deep-sea hydrothermal vents [J]. Appl. Environ. Microbiol., 2004, 70: 6282–6289.
[58] Distel DL, Lane DJ, Olsen GJ, Giovannoni SJ, Pace B, Pace NR, Stahl DA, Felbeck H. Sulfur-oxidizing bacterial endosymbionts: analysis of phylogeny and specificity by 16S rRNA sequences [J]. J. Bacteriol, 1988, 170: 2506–2510.
[59] Chao LSL, Davis RE, Moyer CL. Characterization of bacterial community structure in vestimentiferan tubeworm Ridgeia piscesae trophosomes [J]. Mar. Ecol, 2007, 28: 72–85.
[60] deBurgh ME, Juniper SK, Singla CL. Bacterial symbiosis in northeast Pacific vestimentifera: a TEM study [J]. Mar. Biol., 1989, 101: 97–105.
[61] Cavanaugh CM. Symbioses of chemoautotrophic bacteria and marine invertebrates from hydrothermal vents and reducing sediments [J]. Bull. Biol. Soc. Washington, 1985, 6: 373–388.
[62] Cavanaugh CM, Gardiner SL, Jones ML, Jannasch HW, Waterbury JB. Prokaryotic cells in the hydrothermal vent tube worm Riftia pachyptila Jones: possible chemoautotrophic symbionts [J]. Science, 1981, 213: 340–342.
[63] Fisher CR. Chemoautotrophic and methanotrophic symbiosis in marineinvertebrates [J]. Rev. Aquat. Sci., 1990, 2: 399–436.
[64] Naganuma T, Kato C, Hirayama H, Moriyama N, Hashimoto J, Horikoshi K. Intracellular occurrence of ε-proteobacterial 16S rDNA sequences in the vestimentiferan trophosome [J]. J. Oceanography, 1997, 53: 193–197.
[65] Naganuma T, Naka J, Okayama Y, Minami A, Horikoshi K. Morphological diversity of the microbial population in a vestimentiferan tubeworm [J]. J. Mar. Biotech., 1997, 5: 119–123.
[66] Arp AJ, Doyle ML, Di Cera E, Gill SJ. Oxygenation properties of the two co-occurring hemoglobins of the tube worm Riftia pachyptila [J]. Respir. Physiol., 1990, 80: 323–334.
[67] Goffredi SK, Childress JJ, Desaulniers NT, Lallier FJ. Sulfide acquisition by the vent worm Riftia pachyptila appears to be via uptake of HS–, rather than H2S [J]. J. Exp. Biol., 1997, 200: 2609–2616.
[68] Weber RE, Vinogradov SN. Nonvertebrate hemoglobins: functions and molecular adaptations [J]. Physiol. Rev., 2001, 81: 569–628.
[69] Zal F, Lallier FH, Wall JS, Vinogradov SN, Toulmond A. The multi-hemoglobin system of the hydrothermal vent tube worm Riftia pachyptila. I. Reexamination of the number and masses of its constituents [J]. J. Biol. Chem., 1996, 271: 8869–8874.
[70] Nicholls P. The effect of sulphide on cytochrome aa3. Isosteric and allosteric shifts of the reduced alpha-peak [J]. Biochim. Biophys. Acta, 1975, 396: 24–35.
[71] Suzuki T, Takagi T, Ohta S. Primary structure of a constituent polypeptide chain (AIII) of the giant haemoglobin from the deep-sea tube worm Lamellibrachia. A possible H2S-binding site [J]. Biochem. J., 1990, 266: 221–225.
[72] Zal F, Leize E, Lallier FH, Toulmond A, VanDorsselaer A, Childress JJ. S-Sulfohemoglobin and disulfide exchange: the mechanisms of sulfide binding by Riftia pachyptila hemoglobins [J]. Proc. Natl. Acad. Sci. USA, 1998, 95: 8997–9002.
[73] Bailly X, Jollivet D, Vanin S, Deutsch J, Zal F, Lallier F, Toulmond A. Evolution of the sulfide-binding function within the globin multigenic family of thedeep-sea hydrothermal vent tubeworm Riftia pachyptila [J]. Mol. Biol. Evol., 2002, 19: 1421–1433.
[74] Zal F, Suzuki T, Kawasaki Y, Childress JJ, Lallier FH, Toulmond A. Primary structure of the common polypeptide chain b from the multi-hemoglobin system of the hydrothermal vent tube worm Riftia pachyptila: an insight on the sulfide binding-site [J]. Proteins, 1997, 29: 562–574.
[75] Bailly X, Leroy R, Carney S, Collin O, Zal F, Toulmond A, Jollivet D. The loss of the hemoglobin H2S-binding function in annelids from sulfide-free habitats reveals molecular adaptation driven by Darwinian positive selection [J]. Proc. Natl. Acad. Sci. USA, 2003, 100: 5885–5890.
[76] Renosto F, Martin RL, Borrell JL, Nelson DC, Segel IH. ATP sulfurylase from trophosome tissue of Riftia pachyptila (hydrothermal vent tube worm) [J]. Arch. Biochem. Biophys., 1991, 290: 66–78.
[77] Smith DW, Strohl WR. Sulfur-oxidizing bacteria. In: Variations in autotrophic life (Shively JM, Barton LL, eds), 1991, pp. 121–146, Academic Press, San Diego, CA.
[78] Rau GH. Hydrothermal vent clam and tubeworm 13C/12C. Further evidence of nonphotosynthetic food sources [J]. Science, 1981, 213: 338–340.
[79] Beynon JD, MacRae IJ, Huston SL, Nelson DC, Segel IH, Fisher AJ. Crystal structure of ATP sulfurylase from the bacterial symbiont of the hydrothermal vent tubeworm Riftia pachyptila [J]. Biochemistry, 2001, 40, 14509–14517.
[80] Laue BE, Nelson DC. Characterization of the gene encoding the autotrophic ATP sulfurylase from the bacterial endosymbiont of the hydrothermal vent tubeworm Riftia pachyptila [J]. J. Bacteriol., 1994, 176: 3723–3729.
[81] Robinson JJ, Stein JL, Cavanaugh CM. Cloning and sequencing of a form II ribulose-1,5-biphosphate carboxylase/oxygenase from the bacterial symbiont of the hydrothermal vent tubeworm Riftia pachyptila [J]. J. Bacteriol., 1998, 180: 1596–1599.
[82] Williams CA, Nelson DC, Farah BA, Jannasch HW, Shively JM. Ribulose bisphosphate carboxylase of the prokaryotic symbiont of a hydrothermal vent tube worm: kinetics, activity and gene hybridization [J]. FEMS Microbiol. Lett., 1988, 50: 107–112.
[83] Minic Z, Hervé G. Biochemical and enzymological aspects of the symbiosis between the deep-sea tubeworm Riftia pachyptila and its bacterial endosymbiont [J]. Eur. J. Biochem., 2004, 271: 3093–3102.
[84] Childress JJ, Fisher CR. The biology of hydrothermal vent animals: physiology, biochemistry and autotrophic symbiosis [J]. Oceanogr. Mar. Biol. Annu. Rev., 1992, 30: 337–441.
[85] Childress JJ, Lee RW, Sanders NK, Felbeck H, Oros DR, Toulmond A, Desbruyeres A, Kennicutt MC, Brooks J. Inorganic carbon uptake in hydrothermal vent tubeworms facilitated by high environmental pC02 [J]. Nature, 1993, 362: 147–149.
[86] Scott KM, Fisher CR, Vodenichar JS, Nix ER, Minnich E. Inorganic carbon and temperature requirements for autotrophic carbon fixation by the chemoautotrophic symbionts of the giant hydrothermal vent tube worm, Riftia pachyptila [J]. Physiol. Zool., 1994, 67: 617–638.
[87] Felbeck H, Jarchow J. Carbon release from purified chemoautotrophic bacterial symbionts of the hydrothermal vent tubeworm Riftia pachyptila [J]. Physiol. Zool., 1998, 71: 294–302.
[88] Felbeck H. CO2 fixation in the hydrothermal vent tube worm Riftia pachyptila (Jones) [J]. Physiol. Zool., 1985, 58: 272–281.
[89] Lutz RA, Shank TM, Fornari DJ, Haymon RM, Lilley MD, Von Damm KL, Desbruyeres D. Rapid growth at deep-sea vents [J]. Nature, 1994, 371: 663–664.
[90] Nix ER, Fisher CR, Vodenichar J, Scott KM. Physiological ecology of a mussel with methanotrophic endosymbionts at three hydrocarbon seep sites in the Gulf of Mexico [J]. Mar. Biol., 1995, 122: 605–617.
[91] Lutz RA, Kennish MJ. Ecology of deep-sea hydrothermal vent communities: a review [J]. Rev. Geophys., 1993, 31: 211–242.
[92] Johnson KS, Childress JJ, Hessler RR, Sakamoto-Arnold CM, Beehler CL. Chemical and biological interactions in the Rose Garden hydrothermal vent field[J]. Deep-Sea Res., 1988, 35: 1723–1744.
[93] Lilley MD, Butterfield DA, Olson EJ, Lupton JE, Macko SA, McDuff RE. Anomalous CH4 and NH4+ concentrations at an unsedimented mid-ocean-ridge hydrothermal system [J]. Nature, 1993, 364: 45–47.
[94] Conway NM, Howes BL, McDowellcapuzzo JE, Turner RD, Cavanaugh CM. Characterization and site description of Solemya borealis (Bivalvia; Solemyidae), another bivalve-bacteria symbiosis [J]. Mar. Biol., 1992, 112: 601–613.
[95] Hentschel U, Felbeck H. Nitrate respiration in the hydrothermal vent tubeworm Riftia pachyptila [J]. Nature, 1993, 366: 338–340.
[96] Lee RW, Robinson JJ, Cavanaugh CM. Pathways of inorganic nitrogen assimilation in chemoautotrophic bacteria-marine invertebrate symbioses: expression of host and symbiont glutamine synthetase [J]. J. Exp. Biol., 1999, 202: 289-300.
[97] Girguis PR, Lee RW, Desaulniers N, Childress JJ, Pospesel M, Felbeck H, Zal F. Fate of nitrate acquired by the tubeworm Riftia pachyptila [J]. Appl. Environ. Microbiol., 2000, 66: 2783–2790.
[98] Minic Z, Simon V, Penverne B, Gaill F, Herve G. Contribution of the bacterial endosymbiont to the biosynthesis of pyrimidine nucleotides in the deep-sea tube worm Riftia pachyptila [J]. J. Biol. Chem., 2001, 276: 23777–23784.
[99] Markert S, Arndt C, Felbeck H, Becher D, Sievert SM, Hügler M, Albrecht D, Robidart J, Bench S, Feldman RA, Hecker M, Schweder T. Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila [J]. Science, 2007, 315: 247–250.
[100] Woese CR. Bacterial evolution [J]. Microbiol. Rev., 1987, 51: 221–271.
[101] Muyzer G. DGGE/TGGE a method for identifying genes from natural ecosystems [J]. Curr. Opini. in Microbiol., 1999, 2: 317–322.
[102] Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products [J]. Chem. Biol., 1998, 5: R245–R249.
[103] Corre E, Reysenbach AL, Prieur D. ε-Proteobacteria diversity from a deep-seahydrothermal vent on the Mid-Atlantic Ridge [J]. FEMS Microbiol. Lett., 2001, 205: 329–335.
[104] Huber JA, Butterfield DA, Baross JA. Bacterial diversity in a seafloor habitat following a deep-sea volcanic eruption [J]. FEMS Microbiol. Ecol., 2003, 43: 393–409.
[105] Campbell BJ, Engel AS, Porter ML, Takai K. The versatile ε-proteobacteria: key players in sulphidic habitats [J]. Nature, 2006, 4: 458–468.
[106] Haddad A, Camacho F, Durand P, Cary SC. Phylogenetic characterization of the epibiotic bacteria associated with the hydrothermal vent polychaete Alvinella pompejana [J]. Appl. Environ. Microbiol., 1995, 61: 1679-1687.
[107] López-García P, Gaill F, Moreira D. Wide bacterial diversity associated with tubes of the vent worm Riftia pachyptila [J]. Environ. Microbiol., 2002, 4: 204–215.
[108] Elsaied HE, Kaneko R, Naganuma T. Molecular characterization of a deep-sea methanotrophic mussel symbiont that carries a RuBisCO Gene [J]. Mar. Biotech., 2006, 8: 511–520.
[109] Griesbeck C, Hauska G, Schütz M. Biological sulfide-oxidation: sulfide-quinone reductase (SQR), the primary reaction [J]. Recent Res. Dev. Microbiol., 2000, 4: 179–203.
[110] Mussmann M, Richter M, Lombardot T, Meyerdierks A, Kuever J, Kube M, Gl?ckner FO. Clustered genes related to sulfate respiration in uncultured prokaryotes support the theory of their concomitant horizontal transfer [J]. J Bacteriol., 2005, 187: 7126–7137.
[111] Friedrich MW. Phylogenetic analysis reveals multiple lateral transfers of adenosine-5′-phosphosulfate reductase genes among sulfate-reducing microorganisms [J]. J. Bacteriol., 2002, 184: 278–289.
[112] Klein M, Friedrich M, Roger AJ, Hugenholtz P, Fishbain S, Abicht H, Blackall LL, Stahl DA, Wagner M. Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes [J]. J. Bacteriol., 2001, 183: 6028–6035.
[2] Lonsdale P. Clustering of suspension-feeding macrobenthos near abyssal hydrothermal vents at oceanic spreading centers [J]. Deep Sea Res, 1977, 24: 857–863.
[3] Seyfried WF, Jr. Experimental and theoretical constraints on hydrothermal alteration processes at mid ocean ridges [J]. Ann. Rev. Earth Planet. Sci., 1987, 15: 317–335.
[4] MacDonald IR, Boland GS, Baker JS, Brooks JM, Kennicutt MC II, Bidigare RR. Gulf of Mexico hydrocarbon seep communities. II. Spatial distribution of seep organisms and hydrocarbons at Bush Hill [J]. Mar. Biol., 1989, 101: 235–247.
[5] Tunnicliffe V, McArthur A, McHugh D. A biogeographical perspective of the deep-sea hydrothermal vent fauna [J]. Adv. Mar. Biol., 1998, 34: 353–442.
[6] Zierenberg RA, Adams MW, Arp AJ. Life in extreme environments: hydrothermal vents [J]. Proc. Natl. Acad. Sci. USA, 2000, 97: 12961–12962.
[7] MacDonald IR, Guinasso NL, Reilly JF, Brooks JM, Callender WR, Gabrielle SG. Gulf of Mexico hydrocarbon seep communities. IV. Patterns in community structure and habitat [J]. Geo-Mar. Lett., 1990, 10: 244–252.
[8] Fisher CR. Chemoautotrophic and methanotrophic symbioses in marine inverterbrates [J]. Aquat. Sci., 1996, 2: 399–436.
[9] Arndt C, Gaill F, Felbeck H. Anaerobic sulfur metabolism in thiotrophic symbioses [J]. J. Exp. Biol., 2001, 204: 741–750.
[10] DoverCLV, Lutz RA. Experimental ecology at deep-sea hydrothermal vents: a perspective [J]. J. Exp. Mar. Biol. Ecol., 2004, 300: 273–307.
[11] Tunnicliffe V. The biology of hydrothermal vents: ecology and evolution [J]. Oceanogr. Mar. Biol. Annu. Rev., 1991, 29: 319–407.
[12] Blum J, Fridovich I. Enzymatic defenses against oxygen toxicity in thehydrothermal vent animals Riftia pachyptila and Calyptogena magnifica [J]. Arch. Biochem. Biophys., 1984, 228: 617–620.
[13] Kim YW, Yasuda M, Yamagishi A, Oshima T, Ohta, S. Characterization of the Endosymbiont of a Deep-Sea Bivalve, Calyptogena soyoae [J]. Appl. Environ. Microbiol., 1995, 61: 823–827.
[14] Dunlap PV, Ast JC. Genomic and phylogenetic characterization of luminous bacteria symbiotic with the deep-sea fish Chlorophthalmus albatrossis (Aulopiformes: Chlorophthalmidae) [J]. Appl. Environ. Microbiol., 2005, 71: 930–939.
[15] Campbell BJ, Cary SC. Characterization of a novel spirochete associated with the hydrothermal vent polychaete annelid, Alvinella pompejana [J]. Appl. Environ. Microbiol., 2001, 67: 110–117.
[16] Cottrell MT, Cary SC. Diversity of dissimilatory bisulfite reductase genes of bacteria associated with the deep-sea hydrothermal vent polychaete annelid Alvinella pompejana [J]. Appl. Environ. Microbiol., 1999, 65: 1127–1132.
[17] Fujiwara1 Y, Takai K, Uematsu K, Tsuchida1 S, Hunt JC, Hashimoto J. Phylogenetic characterization of endosymbionts in three hydrothermal vent mussels: influence on host distributions [J]. Mar. Ecol. Prog. Ser., 2000, 208: 147–155.
[18] Haddad A, Camacho F, Durand P, Cary SC. Phylogenetic Characterization of the epibiotic bacteria associated with the hydrothermal vent polychaete Alvinella pompejana [J]. Appl. Environ. Microbiol., 1995, 61: 1679–1687.
[19] Stein JL, Haygood M, Felbeck H. Nucleotide sequence and expression of a deep-sea ribulose-1,5-bisphosphate carboxylase gene cloned from a chemoautotrophic bacterial endosymbiont [J]. Proc. Nati. Acad. Sci. USA, 1990, 87: 8850–8854.
[20] Distel DL, Lee HKW, Cavanaugh CM. Intracellular coexistence of methano- and thioautotrophic bacteria in a hydrothermal vent mussel [J]. Proc. Natl. Acad. Sci. USA, 1995, 92: 9598–9602.
[21] Kasting JF. Earth’s early atmosphere [J]. Science, 1993, 259: 920–926.
[22] Baross JA, Hoffman SE. Submarine hydrothermal vents and associated gradient environments as sites for the origin and evolution of life [J]. Naval Res. Rev., 1986, 38: 2–12.
[23] Pace NR. Origin of life–facing up to the physical setting [J]. Cell, 1991, 65: 531–533.
[24] Vetriani C, Speck MD, Ellor SV, Lutz RA, Starovoytov V. Thermovibrio ammonificans sp. nov., a thermophilic, chemolithotrophic, nitrate-ammonifying bacterium from deep-sea hydrothermal vents [J]. Int. J. Syst. Evol. Microbiol., 2004, 54: 175–181.
[25] Reysenbach AL, Liu Y, Banta1 AB, Beveridge TJ, Kirshtein JD, Schouten S, Tivey MK, Von Damm KL, Voytek MA. A ubiquitous thermoacidophilic archaeon from deep-sea hydrothermal vents [J]. Nature, 2006, 442: 444–447.
[26] Takai K, Inagaki F, Nakagawa S, Hirayama H, Nunoura T, Sako Y, Nealson KH, Horikoshi K. Isolation and phylogenetic diversity of members of previously uncultivated ε-Proteobacteria in deep-sea hydrothermal fields [J]. FEMS Microbiol Lett, 2003, 218: 167–174.
[27] Black MB, Halanych KM, Maas PAY, Hoeh WR, Hashimoto J, Desbruyères D, Lutz RA, Vrijenhoek RC. Molecular systematics of vestimentiferan tubeworms from hydrothermal vents and cold-water seeps [J]. Mar. Biol., 1997, 130: 141–149.
[28] Jones ML. On the Vestimentifera, new phylum: six new species, and other taxa, from hydrothermal vents and elsewhere [J]. Bulletin of the Biological Society of Washington, 1985, 6: 117–158.
[29] Black MB, Trivedi A, Maas PAY, Lutz RA, Vrijenhoek RC. Population genetics and biogeography of vestimentiferan tube worms [J]. Deep-Sea Research, 1998, 45: 365–382.
[30] Southward EC, Tunnicliffe V, Black M. Revision of the species of Ridgeia from northeast Pacific hydrothermal vents, with a redescription of Ridgeia piscesae Jones (Pogonophora: Obturata
[31] Tunnicliffe V, Juniper SK. Dynamic character of the hydrothermal vent habitat and the nature of sulfide chimney fauna [J]. Progress in Oceanography, 1990, 24: 1–13.
[32] Arp AJ, Childress JJ, Fisher CR Jr. Blood gas transport in Riftia pachyptila [J]. Bull. Biol. Soc. Wash., 1985, 6: 289–300.
[33] Jones ML. The vestimentifera, their biology, systematic and evolutionary patterns [J]. Oceanol. Acta, 1988, 8: 69–82.
[34] Cavanaugh CM, Gardiner SL, Jons ML, Jannasch HW, Waterbury JB. Prokaryotic cells in the hydrothermal vent tube worm Riftia pachyptila Jones: Possible chemoautotrophic symbionts [J]. Science, 1981, 213: 340–342.
[35] Felbech H, Childress JJ, Somero GN. Calvin-Benson cycle and sulphide oxidation enzymes in animals from sulphide-rich habitats [J]. Nature, 1981, 293: 291–293.
[36] Felbeck H. Chemoautotrophic potential of the hydrothermal vent tube worm, Riftia pachyptila Jones (Vestimentifera) [J]. Science, 1981, 213: 336–338.
[37] Childress JJ, Arp AJ, Fisher CR. Metabolic and blood characteristics of the hydrothermal vent tube worm Riftia pachyptila [J]. Mar. Biol. (Berl.), 1984, 83: 109–124.
[38] Powell MA and Somero GN. Adaptations to sulfide by hydrothermal vent animals: sites and mechanisms of detoxification and metabolism [J]. Biol. Bull., 1986, 171: 274–290.
[39] Belkin S, Nelson DC, Jannasch HW. Symbiotic assimilation of CO2 in two hydrothermal vent animals, the mussel Bathymodiolus thermophilus and the tube worm Riftia pachyptil [J]. Biol. Bull., 1986, 170: 110–121.
[40] Fisher CR, Childress JJ, Minnich E. Autotrophic carbon fixation by the chemoautotrophic symbionts of Riftia pachyptila [J]. Biol. Bull., 1989, 177: 372–385.
[41] Arp AJ, Childress JJ. Blood function in the hydrothermal vent vestimentiferan tube worm [J]. Science, 1981, 213: 342–344.
[42] Felbeck H, Childress JJ. Riftia pachyptila: a highly integrated symbiosis [J].Oceanol. Acta, 1988, 8: 131–138.
[43] Minic Z, Simon V, Penverne B, Gaill F, Herve G. Contribution of the bacterial endosymbiont to the biosynthesis of pyrimidine nucleotides in the deep-sea tube worm Riftia pachyptila [J]. J. Biol. Chem., 2001, 276: 23777–23784.
[44] Elsaied H, Kimura H, Naganuma T. Molecular characterization and endosymbiotic localization of the gene encoding D-ribulose 1,5-bisphosphate carboxylase–oxygenase (RuBisCO) form II in the deep-sea vestimentiferan trophosome [J]. Microbiology, 2002, 148: 1947–1957.
[45] Hand SC. Trophosome ultrastructure and the characterization of isolated bacteriocytes from invertebrate-sulfur bacteria symbiosis [J]. Biol. Bull., 1987, 173: 260–276.
[46] Stahl D, Lane D, Olsen G, Pace N. Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences [J]. Science, 1984, 224: 409–411.
[47] Distel DL, Felbeck H, Cavanaugh CM. Evidence for phylogenetic congruence among sulfur-oxidizing chemoautotrophic bacterial endosymbionts and their bivalvia hosts [J]. J. Mol. Evol., 1994, 38: 533–542.
[48] DiMeo CA, Wilbur AE, Holben WE, Feldman RA, Vrijenhoek RC, Cary SC. Genetic variation among endosymbionts of widely distributed vestimentiferan tubeworms [J]. Appl. Environ. Microbiol., 2000, 66: 651–658.
[49] Felbeck H, Childress JH, Somero GN. Calvin-Benson cycle and sulfide oxidation enzymes in animals from sulfide-rich habitats [J]. Nature, 1981, 293: 291–293.
[50] Kellogg EA, Juliano ND. The structure and function of RuBisCO and their implications for systematic studies [J]. Am. J. Bot., 1997, 84: 413–428.
[51] Watson GM, Yu JP, Tabita FR. Unusual ribulose 1,5-bisphosphate carboxylase/oxygenase of anoxic Archaea [J]. J. Bacteriol., 1999, 181: 1569–1575.
[52] Elsaied H, Naganuma T. Phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes from deep-sea microorganisms [J]. Appl. Environ. Microbiol., 2001, 67: 1751–1765.
[53] Schwedock J, Harmer TL, Scott KM, Hektor HJ, Seitz AP, Fontana MC, DistelDL, Cavanaugh CM. Characterization and expression of genes from the RubisCO gene cluster of the chemoautotrophic symbiont of Solemya velum: cbbLSQO [J]. Arch Microbiol., 2004, 182: 18–29.
[54] Preuss A, Schauder R, Fuchs G, Stichler W. Carbon isotope fractionation by autotrophic bacteria with 3 different CO2 fixation pathways [J]. Z. Naturforsch. C, 1989, 44: 397–402.
[55] Hügler M, Wirsen CO, Fuchs G, Taylor GD, Sievert SM. Evidence for autotrophic CO2 fixation via the reductive tricarboxylic acid cycle by members of the ε subdivision of proteobacteria [J]. J. Bacteriol., 2005, 187: 3020–3027.
[56] Campbell BJ, Stein JL, Cary SC. Evidence of chemolithoautotrophy in the bacterial community associated with Alvinella pompejana, a hydrothermal vent polychaete [J]. Appl. Environ. Microbiol., 2003, 69: 5070–5078.
[57] Campbell BJ, Cary SC. Abundance of reverse tricarboxylic acid cycle genes in free-living microorganisms at deep-sea hydrothermal vents [J]. Appl. Environ. Microbiol., 2004, 70: 6282–6289.
[58] Distel DL, Lane DJ, Olsen GJ, Giovannoni SJ, Pace B, Pace NR, Stahl DA, Felbeck H. Sulfur-oxidizing bacterial endosymbionts: analysis of phylogeny and specificity by 16S rRNA sequences [J]. J. Bacteriol, 1988, 170: 2506–2510.
[59] Chao LSL, Davis RE, Moyer CL. Characterization of bacterial community structure in vestimentiferan tubeworm Ridgeia piscesae trophosomes [J]. Mar. Ecol, 2007, 28: 72–85.
[60] deBurgh ME, Juniper SK, Singla CL. Bacterial symbiosis in northeast Pacific vestimentifera: a TEM study [J]. Mar. Biol., 1989, 101: 97–105.
[61] Cavanaugh CM. Symbioses of chemoautotrophic bacteria and marine invertebrates from hydrothermal vents and reducing sediments [J]. Bull. Biol. Soc. Washington, 1985, 6: 373–388.
[62] Cavanaugh CM, Gardiner SL, Jones ML, Jannasch HW, Waterbury JB. Prokaryotic cells in the hydrothermal vent tube worm Riftia pachyptila Jones: possible chemoautotrophic symbionts [J]. Science, 1981, 213: 340–342.
[63] Fisher CR. Chemoautotrophic and methanotrophic symbiosis in marineinvertebrates [J]. Rev. Aquat. Sci., 1990, 2: 399–436.
[64] Naganuma T, Kato C, Hirayama H, Moriyama N, Hashimoto J, Horikoshi K. Intracellular occurrence of ε-proteobacterial 16S rDNA sequences in the vestimentiferan trophosome [J]. J. Oceanography, 1997, 53: 193–197.
[65] Naganuma T, Naka J, Okayama Y, Minami A, Horikoshi K. Morphological diversity of the microbial population in a vestimentiferan tubeworm [J]. J. Mar. Biotech., 1997, 5: 119–123.
[66] Arp AJ, Doyle ML, Di Cera E, Gill SJ. Oxygenation properties of the two co-occurring hemoglobins of the tube worm Riftia pachyptila [J]. Respir. Physiol., 1990, 80: 323–334.
[67] Goffredi SK, Childress JJ, Desaulniers NT, Lallier FJ. Sulfide acquisition by the vent worm Riftia pachyptila appears to be via uptake of HS–, rather than H2S [J]. J. Exp. Biol., 1997, 200: 2609–2616.
[68] Weber RE, Vinogradov SN. Nonvertebrate hemoglobins: functions and molecular adaptations [J]. Physiol. Rev., 2001, 81: 569–628.
[69] Zal F, Lallier FH, Wall JS, Vinogradov SN, Toulmond A. The multi-hemoglobin system of the hydrothermal vent tube worm Riftia pachyptila. I. Reexamination of the number and masses of its constituents [J]. J. Biol. Chem., 1996, 271: 8869–8874.
[70] Nicholls P. The effect of sulphide on cytochrome aa3. Isosteric and allosteric shifts of the reduced alpha-peak [J]. Biochim. Biophys. Acta, 1975, 396: 24–35.
[71] Suzuki T, Takagi T, Ohta S. Primary structure of a constituent polypeptide chain (AIII) of the giant haemoglobin from the deep-sea tube worm Lamellibrachia. A possible H2S-binding site [J]. Biochem. J., 1990, 266: 221–225.
[72] Zal F, Leize E, Lallier FH, Toulmond A, VanDorsselaer A, Childress JJ. S-Sulfohemoglobin and disulfide exchange: the mechanisms of sulfide binding by Riftia pachyptila hemoglobins [J]. Proc. Natl. Acad. Sci. USA, 1998, 95: 8997–9002.
[73] Bailly X, Jollivet D, Vanin S, Deutsch J, Zal F, Lallier F, Toulmond A. Evolution of the sulfide-binding function within the globin multigenic family of thedeep-sea hydrothermal vent tubeworm Riftia pachyptila [J]. Mol. Biol. Evol., 2002, 19: 1421–1433.
[74] Zal F, Suzuki T, Kawasaki Y, Childress JJ, Lallier FH, Toulmond A. Primary structure of the common polypeptide chain b from the multi-hemoglobin system of the hydrothermal vent tube worm Riftia pachyptila: an insight on the sulfide binding-site [J]. Proteins, 1997, 29: 562–574.
[75] Bailly X, Leroy R, Carney S, Collin O, Zal F, Toulmond A, Jollivet D. The loss of the hemoglobin H2S-binding function in annelids from sulfide-free habitats reveals molecular adaptation driven by Darwinian positive selection [J]. Proc. Natl. Acad. Sci. USA, 2003, 100: 5885–5890.
[76] Renosto F, Martin RL, Borrell JL, Nelson DC, Segel IH. ATP sulfurylase from trophosome tissue of Riftia pachyptila (hydrothermal vent tube worm) [J]. Arch. Biochem. Biophys., 1991, 290: 66–78.
[77] Smith DW, Strohl WR. Sulfur-oxidizing bacteria. In: Variations in autotrophic life (Shively JM, Barton LL, eds), 1991, pp. 121–146, Academic Press, San Diego, CA.
[78] Rau GH. Hydrothermal vent clam and tubeworm 13C/12C. Further evidence of nonphotosynthetic food sources [J]. Science, 1981, 213: 338–340.
[79] Beynon JD, MacRae IJ, Huston SL, Nelson DC, Segel IH, Fisher AJ. Crystal structure of ATP sulfurylase from the bacterial symbiont of the hydrothermal vent tubeworm Riftia pachyptila [J]. Biochemistry, 2001, 40, 14509–14517.
[80] Laue BE, Nelson DC. Characterization of the gene encoding the autotrophic ATP sulfurylase from the bacterial endosymbiont of the hydrothermal vent tubeworm Riftia pachyptila [J]. J. Bacteriol., 1994, 176: 3723–3729.
[81] Robinson JJ, Stein JL, Cavanaugh CM. Cloning and sequencing of a form II ribulose-1,5-biphosphate carboxylase/oxygenase from the bacterial symbiont of the hydrothermal vent tubeworm Riftia pachyptila [J]. J. Bacteriol., 1998, 180: 1596–1599.
[82] Williams CA, Nelson DC, Farah BA, Jannasch HW, Shively JM. Ribulose bisphosphate carboxylase of the prokaryotic symbiont of a hydrothermal vent tube worm: kinetics, activity and gene hybridization [J]. FEMS Microbiol. Lett., 1988, 50: 107–112.
[83] Minic Z, Hervé G. Biochemical and enzymological aspects of the symbiosis between the deep-sea tubeworm Riftia pachyptila and its bacterial endosymbiont [J]. Eur. J. Biochem., 2004, 271: 3093–3102.
[84] Childress JJ, Fisher CR. The biology of hydrothermal vent animals: physiology, biochemistry and autotrophic symbiosis [J]. Oceanogr. Mar. Biol. Annu. Rev., 1992, 30: 337–441.
[85] Childress JJ, Lee RW, Sanders NK, Felbeck H, Oros DR, Toulmond A, Desbruyeres A, Kennicutt MC, Brooks J. Inorganic carbon uptake in hydrothermal vent tubeworms facilitated by high environmental pC02 [J]. Nature, 1993, 362: 147–149.
[86] Scott KM, Fisher CR, Vodenichar JS, Nix ER, Minnich E. Inorganic carbon and temperature requirements for autotrophic carbon fixation by the chemoautotrophic symbionts of the giant hydrothermal vent tube worm, Riftia pachyptila [J]. Physiol. Zool., 1994, 67: 617–638.
[87] Felbeck H, Jarchow J. Carbon release from purified chemoautotrophic bacterial symbionts of the hydrothermal vent tubeworm Riftia pachyptila [J]. Physiol. Zool., 1998, 71: 294–302.
[88] Felbeck H. CO2 fixation in the hydrothermal vent tube worm Riftia pachyptila (Jones) [J]. Physiol. Zool., 1985, 58: 272–281.
[89] Lutz RA, Shank TM, Fornari DJ, Haymon RM, Lilley MD, Von Damm KL, Desbruyeres D. Rapid growth at deep-sea vents [J]. Nature, 1994, 371: 663–664.
[90] Nix ER, Fisher CR, Vodenichar J, Scott KM. Physiological ecology of a mussel with methanotrophic endosymbionts at three hydrocarbon seep sites in the Gulf of Mexico [J]. Mar. Biol., 1995, 122: 605–617.
[91] Lutz RA, Kennish MJ. Ecology of deep-sea hydrothermal vent communities: a review [J]. Rev. Geophys., 1993, 31: 211–242.
[92] Johnson KS, Childress JJ, Hessler RR, Sakamoto-Arnold CM, Beehler CL. Chemical and biological interactions in the Rose Garden hydrothermal vent field[J]. Deep-Sea Res., 1988, 35: 1723–1744.
[93] Lilley MD, Butterfield DA, Olson EJ, Lupton JE, Macko SA, McDuff RE. Anomalous CH4 and NH4+ concentrations at an unsedimented mid-ocean-ridge hydrothermal system [J]. Nature, 1993, 364: 45–47.
[94] Conway NM, Howes BL, McDowellcapuzzo JE, Turner RD, Cavanaugh CM. Characterization and site description of Solemya borealis (Bivalvia; Solemyidae), another bivalve-bacteria symbiosis [J]. Mar. Biol., 1992, 112: 601–613.
[95] Hentschel U, Felbeck H. Nitrate respiration in the hydrothermal vent tubeworm Riftia pachyptila [J]. Nature, 1993, 366: 338–340.
[96] Lee RW, Robinson JJ, Cavanaugh CM. Pathways of inorganic nitrogen assimilation in chemoautotrophic bacteria-marine invertebrate symbioses: expression of host and symbiont glutamine synthetase [J]. J. Exp. Biol., 1999, 202: 289-300.
[97] Girguis PR, Lee RW, Desaulniers N, Childress JJ, Pospesel M, Felbeck H, Zal F. Fate of nitrate acquired by the tubeworm Riftia pachyptila [J]. Appl. Environ. Microbiol., 2000, 66: 2783–2790.
[98] Minic Z, Simon V, Penverne B, Gaill F, Herve G. Contribution of the bacterial endosymbiont to the biosynthesis of pyrimidine nucleotides in the deep-sea tube worm Riftia pachyptila [J]. J. Biol. Chem., 2001, 276: 23777–23784.
[99] Markert S, Arndt C, Felbeck H, Becher D, Sievert SM, Hügler M, Albrecht D, Robidart J, Bench S, Feldman RA, Hecker M, Schweder T. Physiological proteomics of the uncultured endosymbiont of Riftia pachyptila [J]. Science, 2007, 315: 247–250.
[100] Woese CR. Bacterial evolution [J]. Microbiol. Rev., 1987, 51: 221–271.
[101] Muyzer G. DGGE/TGGE a method for identifying genes from natural ecosystems [J]. Curr. Opini. in Microbiol., 1999, 2: 317–322.
[102] Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products [J]. Chem. Biol., 1998, 5: R245–R249.
[103] Corre E, Reysenbach AL, Prieur D. ε-Proteobacteria diversity from a deep-seahydrothermal vent on the Mid-Atlantic Ridge [J]. FEMS Microbiol. Lett., 2001, 205: 329–335.
[104] Huber JA, Butterfield DA, Baross JA. Bacterial diversity in a seafloor habitat following a deep-sea volcanic eruption [J]. FEMS Microbiol. Ecol., 2003, 43: 393–409.
[105] Campbell BJ, Engel AS, Porter ML, Takai K. The versatile ε-proteobacteria: key players in sulphidic habitats [J]. Nature, 2006, 4: 458–468.
[106] Haddad A, Camacho F, Durand P, Cary SC. Phylogenetic characterization of the epibiotic bacteria associated with the hydrothermal vent polychaete Alvinella pompejana [J]. Appl. Environ. Microbiol., 1995, 61: 1679-1687.
[107] López-García P, Gaill F, Moreira D. Wide bacterial diversity associated with tubes of the vent worm Riftia pachyptila [J]. Environ. Microbiol., 2002, 4: 204–215.
[108] Elsaied HE, Kaneko R, Naganuma T. Molecular characterization of a deep-sea methanotrophic mussel symbiont that carries a RuBisCO Gene [J]. Mar. Biotech., 2006, 8: 511–520.
[109] Griesbeck C, Hauska G, Schütz M. Biological sulfide-oxidation: sulfide-quinone reductase (SQR), the primary reaction [J]. Recent Res. Dev. Microbiol., 2000, 4: 179–203.
[110] Mussmann M, Richter M, Lombardot T, Meyerdierks A, Kuever J, Kube M, Gl?ckner FO. Clustered genes related to sulfate respiration in uncultured prokaryotes support the theory of their concomitant horizontal transfer [J]. J Bacteriol., 2005, 187: 7126–7137.
[111] Friedrich MW. Phylogenetic analysis reveals multiple lateral transfers of adenosine-5′-phosphosulfate reductase genes among sulfate-reducing microorganisms [J]. J. Bacteriol., 2002, 184: 278–289.
[112] Klein M, Friedrich M, Roger AJ, Hugenholtz P, Fishbain S, Abicht H, Blackall LL, Stahl DA, Wagner M. Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes [J]. J. Bacteriol., 2001, 183: 6028–6035.