Phylogenetic characterization of the bacterial assemblage associated with mucous secretions of the hydrothermal vent polychaete Paralvinella palmiformis

FEMS Microbiology Ecology

Volumn 42, Issue 3, 2002, Pages 463-476

  Alain, Karine ^a   Olagnon, Michel ^a   Desbruyères, Daniel ^a   Pagé, Antoine ^a,b   Barbier, Georges ^a   Juniper, S Kim ^b   Quérellou, Joël ^a   Cambon Bonavita, Marie Anne ^a  

^a IFREMER   (France)

^b UNIVERSITÉ DU QUÉBEC À MONTRÉAL   (Canada)

Author keywords

16S rRNA; Hydrothermal vent; Microbial diversity; Paralvinella palmiformis; Phylogeny; Proteobacteria

Indexed keywords

DNA 16S; ORGANIC MATTER;

HYDROTHERMAL VENT; MICROBIAL COMMUNITY; PHYLOGENETICS; POLYCHAETE; SECRETION; SPECIES DIVERSITY;

ARCHAEBACTERIUM; ARTICLE; BACTERIUM CULTURE; DNA LIBRARY; FUSOBACTERIUM; GENE CONSTRUCT; GRAM NEGATIVE BACTERIUM; HYDROTHERMAL VENT; MOLECULAR BIOLOGY; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PARAVINELLA PALMIFORMIS; PHYLOGENY; POLYCHAETA; PRIORITY JOURNAL; SAMPLING; SECRETION; SULFUR BACTERIUM; UNINDEXED SEQUENCE;

PACIFIC OCEAN;

ALVINELLIDAE; BACTERIA (MICROORGANISMS); CHLOROFLEXI; CYTOPHAGA; DELTAPROTEOBACTERIA; EPSILONPROTEOBACTERIA; FIRMICUTES; FLAVOBACTERIA; FUSOBACTERIA; PARALVINELLA PALMIFORMIS; POLYCHAETA; PROTEOBACTERIA; VERRUCOMICROBIA;

EID: 0036889705     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6496(02)00390-2     Document Type: Article

References (70)

1. Jeanthon C. Molecular ecology of hydrothermal vent microbial communities. Antonie van Leeuwenhoek. 77:2000;117-133.
2. Quérellou J., Alain K., Cambon-Bonavita M.-A. Thermophiles from deep-sea hydrothermal vents. Vie Milieu. 51:2001;161-172.
3. Haddad A., Camacho F., Durand P., Cary S.C. Phylogenetic association of the epibiotic bacteria associated with the hydrothermal vent polychaete Alvinella pompejana. Appl. Environ. Microbiol. 61:1995;1679-1687.
4. Longnecker K., Reysenbach A.L. Expansion of the geographic distribution of a novel lineage of ε-Proteobacteria to a hydrothermal vent site on the Southern East Pacific Rise. FEMS Microbiol. Ecol. 35:2001;287-293.
5. Moyer C.L., Dobbs F.C., Karl D.M. Phylogenetic diversity of the bacterial community from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl. Environ. Microbiol. 61:1995;1555-1562.
6. Polz M.F., Cavanaugh C.M. Dominance of one bacterial phylotype at a Mid-Atlantic Ridge hydrothermal vent site. Proc. Natl. Acad. Sci. USA. 92:1995;7232-7236.
7. Reysenbach A.L., Longnecker K., Kirshtein J. Novel bacterial and archaeal lineages from an in situ growth chamber deployed at a Mid-Atlantic Ridge hydrothermal vent. Appl. Environ. Microbiol. 66:2000;3798-3806.
8. Corre E., Reysenbach A.-L., Prieur D. ε-Proteobacterial diversity from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge. FEMS Microbiol. Lett. 205:2001;329-335.
9. Desbruyères D., Gaill F., Laubier L., Fouquet Y. Polychaetous annelids from hydrothermal vent ecosystems: an ecological overview. Biol. Soc. Wash. Bull. 6:1985;103-116.
10. Desbruyères, D. and Ségonzac, M. (Eds.) (1997) Handbook of Deep-Sea Hydrothermal Vent Fauna, pp. 1-279. IFREMER, Plouzané.
11. Desbruyères D., Chevaldonné P., Alayse A.-M., Jollivet D., Lallier F.H., Jouin-Toulmond C., Zal F., Sarradin P.-M., Cosson R., Caprais J.-C., Arndt C., O'Brien J., Guezennec J., Hourdez S., Riso R., Gaill F., Laubier L., Toulmond A. Biology and ecology of the 'Pompeii worm' (Alvinella pompejana Desbruyères and Laubier), a normal dweller of an extreme deep-sea environment: a synthesis of current knowledge and recent developments. Deep-Sea Res. 45:1998;383-422.
12. Tunnicliffe V., McArthur A.G., McHugh D. A biogeographical perspective of the deep-sea hydrothermal vent fauna. Adv. Mar. Biol. 34:1998;353-426.
13. Desbruyères D., Biscoito M., Caprais J.-C., Colaço A., Comtet T., Crassous P., Fouquet Y., Khripounoff A., Le Bris N., Olu K., Riso R., Sarradin P.-M., Segonzac M., Vangriesheim A. Variations in deep-sea hydrothermal vent communities on the mid-Atlantic ridge near the Azores plateau. Deep-Sea Res. 48:2001;1325-1346.
14. Sarrazin J., Robigou V., Juniper K.M., Delaney J.R. Biological and geological dynamics over four years on a high-temperature sulfide structure at the Juan de Fuca ridge hydrothermal observatory. Mar. Ecol. Prog. Ser. 153:1997;5-24.
15. Cavanaugh C.M. Symbiosis of chemoautotrophic bacteria and marine invertebrates from hydrothermal vents and reducing sediments. Bull. Biol. Soc. Wash. 6:1985;373-388.
16. Distel D.L., Lane D.J., Olsen G.J., Giovannoni S.J., Pace B., Pace N.R., Stahl D.A., Felbeck H. Sulfur-oxidizing bacterial endosymbionts: analysis of phylogeny and specificity by 16S rRNA sequences. J. Bacteriol. 170:1988;2506-2510.
17. Felbeck H., Childress J.J. Riftia pachyptila: a highly integrated symbiosis. Oceanol. Acta. 8:1988;131-138.
18. Feldman R.A., Black M.B., Cary C.S., Lutz R.A., Vrijenhoek R.C. Molecular phylogenetics of bacterial endosymbionts and their vestimentiferan hosts. Mol. Mar. Biol. Biotechnol. 6:1997;268-277.
19. Desbruyères D., Laubier L. Les Alvinellidae, une famille nouvelle d'annélides polychètes inféodées aux sources hydrothermales sous-marines: systématique, biologie et écologie. Can. J. Zool. 64:1986;2227-2245.
20. Tunnicliffe V., Desbruyères D., Jolivet D., Laubier L. Systematic and ecological characteristics of Paralvinella sulfincola Desbruyères and Laubier, a nex polychaete (family Alvinellidae) from northeast Pacific hydrothermal vents. Can. J. Zool. 71:1993;286-297.
21. e conférence internationale des polychètes (Dauvin, J.-C., Laubier, L. and Reish, D.H., Eds.), Mem. Mus. Natl. Hist. Nat. 162, 453-462. Paris.
22. Desbruyères D., Laubier L. Alvinella pompejana gen. sp. nov., aberrant Ampharetidae From east pacific rise hydrothermal vents. Oceanol. Acta. 3:1980;267-274.
23. Cary S.C., Cottrell M.T., Stein J.L., Camacho F., Desbruyères D. Molecular identification and localization of filamentous symbiotic bacteria associated with the hydrothermal vent annelid Alvinella pompejana. Appl. Environ. Microbiol. 63:1997;1124-1130.
24. Juniper S.K., Jonasson I.R., Tunnicliffe V., Southward A. Influence of a tube-building polychaete on hydrothermal chimney mineralization. Geology. 20:1992;895-898.
25. Juniper, K. (1988) Géochimie et écologie d'un microenvironnement hydrothermal: Les sécrétions de mucus de Paralvinella palmiformis. Oceanol. Acta, 167-172.
26. Juniper S.K., Cambon M.-A., Lesongeur F., Barbier G. Extraction and purification of DNA from organic rich subsurface sediments (ODP Leg 169S). Mar. Geol. 174:2001;241-247.
27. Leff L.G., Dana J.R., McAarthur J.V., Shimkets L.J. Comparisons of methods of DNA extraction from stream sediments. Appl. Environ. Microbiol. 61:1995;1141-1143.
28. Sanger F., Nicklen S., Coulson A.R. DNA sequencing with chain terminating inhibitors. Proc. Natl. Acad. Sci. USA. 74:1977;5467-5473.
29. Raguénès G., Pignet P., Gauthier G., Peres A., Christen R., Rougeaux H., Barbier G., Guezennec J. Description of a new polymer-secreting bacterium from a deep-sea hydrothermal vent, Alteromonas macleodii subsp. fijiensis, and preliminary characterization of the polymer. Appl. Environ. Microbiol. 62:1997;67-73.
30. Maidak B.L., Cole J.R., Lilburn T.G., Parker C.T., Saxman P.R., Stredwick J.M., Garrity G.M., Li B., Olsen G.J., Pramanik S., Schmidt T.M., Tiedje J.M. The RDP (Ribosomal Database Project) continues. Nucleic Acids Res. 28:2000;173-174.
31. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
32. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680.
33. Galtier N., Gouy M., Gautier C. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. CABIOS. 12:1996;543-548.
34. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425.
35. Felsentein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:1981;368-376.
36. Felsentein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 30:1985;783-791.
37. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparatives studies of nucleotide sequence. J. Mol. Evol. 16:1980;111-120.
38. Good I.J. The population frequencies of species and the estimation of population parameters. Biometrika. 40:1953;237-264.
39. Singleton D.R., Furlong M.A., Rathbun S.L., Whitman W.B. Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl. Environ. Microbiol. 67:2001;4374-4376.
40. Pettitt, A.N. (1982) Cramér-von Mises statistic. In: Encyclopedia of Statiscal Sciences (Kotz, S. and Johnson, N.L., Eds.), Wiley-Interscience, New York, pp. 220-221.
41. Hope A.C.A. A simplified Monte Carlo significance test procedure. J. R. Stat. Soc. B. 30:1968;582-598.
42. Sarrazin J., Juniper S.K. Biological characteristics of a hydrothermal edifice mosaic community. Mar. Ecol. Prog. Ser. 185:1999;1-19.
43. Moyer C.L., Dobbs F.C., Karl D.M. Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl. Environ. Microbiol. 60:1994;871-879.
44. Rossello-Mora R., Amann R. The species concept for prokaryotes. FEMS Microbiol. Rev. 25:2001;39-67.
45. Hugenholtz P., Goebel B.M., Pace N.R. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180:1998;4765-4774.
46. Nakagawa Y., Yamamoto S. Emendation of the genus Cytophaga and transfer of Cytophaga agarovorans and Cytophaga salmonicolor to Marinilabilia gen. nov. phylogenetic analysis of the Flavobacterium-Cytophaga complex. Int. J. Syst. Bacteriol. 46:1996;599-603.
47. Phelps C.D., Kerkhof L.J., Young L.Y. Molecular characterization of a sulfate-reducing consortium which mineralizes benzene. FEMS Microbiol. Ecol. 27:1998;269-279.
48. Hedlund B.P., Gosink J.J., Stanley J.T. Verrucomicrobia div. nov., a new division of the Bacteria containing three new species of Prosthecobacter. Antonie van Leeuwenhoek. 72:1997;29-38.
49. Wery N., Moricet J.M., Cueff V., Jean J., Pignet P., Lesongeur F., Cambon-Bonavita M.A., Barbier G. Caloranaerobacter azorensis gen. nov., sp. nov., an anaerobic thermophilic bacterium, isolated from a deep-sea hydrothermal vent. Int. J. Syst. Evol. Microbiol. 51:2001;1789-1796.
50. Miroshnichenko M.L., Rainey F.A., Rhode M., Bonch-Osmolovskaya E.A. Hippea maritima gen. nov., sp. nov., a new genus of thermophilic, sulfur-reducing bacterium from submarine hot vents. Int. J. Syst. Bacteriol. 49:1999;1033-1038.
51. Raguénès G., Christen R., Guézennec J., Pignet P., Barbier G. Vibrio diabolicus sp. nov., a new polysaccharide-secreting organism isolated from a deep-sea hydrothermal vent polychaete annelid, Alvinella pompejana. Int. J. Syst. Bacteriol. 47:1997;989-995.
52. Alain K., Pignet P., Zbinden M., Quillévéré M., Duchiron F., Donval J.-P., Lesongeur F., Raguénès G., Crassous P., Quérellou J., Cambon-Bonavita M.-A. Caminicella sporogenes, gen. nov., sp. nov., a novel thermophilic spore-forming bacterium isolated from an East-pacific rise hydrothermal vent. Int. J. Syst. Evol. Microbiol. 52:2002;1621-1628.
53. Lieasck W., Finster K. Phylogenetic analysis of five strains of Gram-negative, obligately anaerobic, sulfur-reducing bacteria and description of Desulfuromusa gen. nov., including Desulfuromusa kysingii sp. nov., Desulfuromusa bakii sp. nov., and Desulfuromusa succinoxidans sp. nov. Int. J. Syst. Bacteriol. 44:1994;753-758.
54. Suzuki M.T., Giovanonni S.J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:1996;625-630.
55. Farrelly V., Rainey F.A., Stackebrandt E. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61:1995;2798-2801.
56. Amann G., Stetter K.O., Llobet-Brossa E., Amann R., Anton J. Direct proof for the presence and expression of two 5% different 16S rRNA genes in individual cells of Haloarcula marismortui. Extremophiles. 4:2000;373-376.
57. Alain K., Quérellou J., Lesongeur F., Pignet P., Crassous P., Raguénès G., Cueff V., Cambon-Bonavita M.A. Caminibacter hydrogeniphilus, gen. nov., sp. nov., a novel thermophilic hydrogen-oxidising bacterium isolated from an East-Pacific rise hydrothermal vent. Int. J. Syst. Evol. Microbiol. 52:2002;1317-1323.
58. Tuttle J.H. The role of sulfur-oxidizing bacteria at deep-sea hydrothermal vents. Biol. Soc. Wash. Bull. 6:1985;335-343.
59. Alayse-Danet A.M., Gaill F., Desbruyères D. In situ bicarbonate uptake by bacteria-Alvinella associations. Mar. Ecol. 7:1986;233-240.
60. Campbell B.J., Jeanthon C., Kostka J.E., Luther III G.W., Cary C. Growth and phylogenetic properties of novel bacteria belonging to the epsilon subdivision of the Proteobacteria enriched from Alvinella pompejana and deep-sea hydrothermal vents. Appl. Environ. Microbiol. 67:2001;4566-4572.
61. Olsen G.J., Woese C.R., Overbeek R. The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176:1994;1-6.
62. Reichenbach, H. (1992) The order Cytophagales. In: The Prokaryotes (Balows, A., Truper, H.G., Dworkin, M., Harder, W. and Schleifer, K.H., Eds.), Vol. IV, chapter 199, pp. 3631-3675. Springer-Verlag, New York.
63. Schlesner, H. (1992) The genus Verrucomicrobium. In: The Prokaryotes (Balows, A., Truper, H.G., Dworkin, M., Harder, W. and Schleifer, K.H., Eds.), Vol. IV, chapter 210, pp. 3806-3808. Springer-Verlag, New York.
64. Woese C.R. Bacterial evolution. Microbiol. Rev. 51:1987;221-271.
65. Talmont F., Fournet B. Chemical composition of mucins from deep-sea hydrothermal vent tubiculous annelids worms. Comp. Biochem. Physiol. 96B:1990;753-759.
66. Mc Collom T.M., Shock E.L. Geochemical constraints on chemolithoautotrophic metabolism by microorganisms in seafloor hydrothermal systems. Geochim. Cosmochim. Acta. 61:1997;4375-4391.
67. Jannasch H.W., Mottl J.O. Geomicrobiology of deep-sea hydrothermal vents. Science. 229:1985;717-725.
68. Wirsen C.O., Sievert S.M., Cavanaugh C.M., Molyneaux S.J., Ahmad A., Taylor L.T., DeLong E.F., Taylor C.D. Characterization of an autotrophic sulfide-oxidizing marine Arcobacter sp. that produces filamentous sulfur. Appl. Environ. Microbiol. 68:2002;316-325.
69. Watson J.W., Matsui G.Y., Leaphart A., Wiegel J., Rainey F.A., Lovell C.R. Reductively debrominating strains of Propionigenium maris from burrows of bromophenol-producing marine infauna. Int. J. Syst. Evol. Microbiol. 50:2000;1035-1042.
70. López-García P., Gaill F., Moreira D. Wide bacterial diversity associated with tubes of the vent worm Riftia pachyptila. Environ. Microbiol. 4:2002;204-215.