Effect of variation of environmental conditions on the microbial communities of deep-sea vent chimneys, cultured in a bioreactor

Extremophiles

Volumn 13, Issue 4, 2009, Pages 595-608

  Byrne, Nathalie ^a   Lesongeur, Françoise ^a   Bienvenu, Nadège ^a   Geslin, Claire ^a   Alain, Karine ^a   Prieur, Daniel ^a   Godfroy, Anne ^a  

^a Centre National de la Recherche Scientifique   (France)

Author keywords

16S rRNA genes; Bioreactor; Continuous enrichment culture; Deep sea hydrothermal vent; Environmental condition; Microbial diversity; Oligotrophic condition

Indexed keywords

CARBON DIOXIDE; RNA 16S; SULFUR;

ARTICLE; BIODIVERSITY; BIOREACTOR; CHEMISTRY; CULTURE MEDIUM; CULTURE TECHNIQUE; DNA SEQUENCE; ELECTRON; ENVIRONMENT; GENETICS; METHODOLOGY; MICROBIOLOGY; PH; POLYMERASE CHAIN REACTION; SINGLE STRAND CONFORMATION POLYMORPHISM; TEMPERATURE;

BIODIVERSITY; BIOREACTORS; CARBON DIOXIDE; CELL CULTURE TECHNIQUES; CULTURE MEDIA; ELECTRONS; ENVIRONMENT; HYDROGEN-ION CONCENTRATION; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE-STRANDED CONFORMATIONAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SULFUR; TEMPERATURE; WATER MICROBIOLOGY;

ARCHAEA; BACTERIA (MICROORGANISMS); DEFERRIBACTERALES; PROKARYOTA; THERMALES; THERMOCOCCALES;

EID: 70349471028     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-009-0242-6     Document Type: Article

References (46)

1. Atomi H, Fukui T, Kanai T, Morikawa M, Imanaka T (2004) Description of Thermococcus kodakaraensis sp. nov., a well studied hyperthermophilic archaeon previously reported as Pyrococcus sp. KOD1. Archae 1:263-267
2. Campbell AC, Palmer MR, Klinkhammer GP, Bowers TS, Edmond JM, Lawrence JR, Casey JF, Thompson G, Humphris S, Rona P, Karson JA (1988) Chemistry of hot springs on the Mid-Atlantic Ridge. Nature 335:514-519
3. Charlou JL, Donval JP, Fouquet Y, Jean-Baptiste P, Holm N (2002) Geochemistry of high H2 and CH4 vent fluids issuing from ultramafic rocks at the Rainbow hydrothermal field (36[deg]14′N, MAR). Chem Geol 191:345-359
4. Corbari L, Cambon-Bonavita M-A, Long GJ, Grandjean F, Zbinden M, Gaill F, Compère P (2008) Iron oxide deposits associated with the ectosymbiotic bacteria in the hydrothermal vent shrimp Rimicaris exoculata. Biogeosciences 5:1295-1310
5. Delbes C, Moletta R, Godon JJ (2000) Monitoring of activity dynamics of an anaerobic digester bacterial community using 16S rRNA polymerase chain reaction single strand conformation polymorphism analysis. Environ Microbiol 2:506-515
6. Galtier N, Gouy M, Gautier C (1996) Seaview and Phylowin two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12:543-548
7. Geslin C, Le Romancer M, Erauso G, Gaillard M, Perrot G, Prieur D (2003) PAV1, the first virus-like particle isolated from a hyperthermophilic Euryarchaeote, Pyrococcus abyssi. J Bacteriol 185:3888-3894
8. Godfroy A, Meunier J-R, Guezennec J, Lesongeur F, Raguénès G, Rimbault A, Barbier G (1996) Thermococcus fumicolans sp. nov. a new hyperthermophilic archaeum isolated from deep-sea hydrothermal vent in North Fiji bassin. Int J Syst Bacteriol 46:1113-1119
9. Godfroy A, Lesongeur F, Raguénès G, Quérellou J, Antoine E, Meunier J-R, Guezennec J, Barbier G (1997) Thermococcus hydrothermalis sp. nov., a new hyperthermophilic archaeon isolated from deep-sea hydrothermal vent. Int J Syst Bacteriol 47:622-626
10. Godfroy A, Raven NDH, Sharp RJ (2000) Physiology and continuous culture of the hyperthermophilic deep-sea vent archaeon Pyrococcus abyssi ST549. FEMS Microbiol Lett 186:127-132
11. Haring M, Vestergaard G, Rachel R, Chen L, Garrett RA, Prangishvili D (2005) Virology: independent virus development outside a host. Nature 436:1101-1102
12. Houghton JL, Seyfried WE Jr, Banta A, Reysenbach A-L (2007) Continuous enrichment culturing of thermophiles under sulfate and nitrate-reducing conditions and at deep-sea hydrostatic pressures. Extremophiles 11:371-382
13. Huber R, Stoffers P, Cheminee JL, Richnow HH, Stetter KO (1990) Hyperthermophilic archaebacteria within the crater and open sea plume of erupting Macdonald seamount. Nature 345:179-182
14. Inagaki F, Takai K, Nealson KH, Horikoshi K (2004) Sulfurovum lithotrophicum gen. nov., sp. nov., a novel sulfur-oxidizing chemolithoautotroph within the {epsilon}-Proteobacteria isolated from Okinawa Trough hydrothermal sediments. Int J Syst Evol Microbiol 54:1477-1482
15. Kashefi K, Tor JM, Holmes DE, Gaw van Praagh CV, Reysenbach AL, Lovley DR (2002) Geoglobus ahangari gen. nov., sp. nov., a novel hyperthermophilic archaeon capable of oxidizing organic acids and growing autotrophically on hydrogen with Fe(III) serving as the sole electron acceptor. Int J Syst Evol Microbiol 52:719-728
16. Loisel P, Harmand J, Zemb O, Latrille E, Lobry C, Delgenès J-P, Godon J-J (2006) Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity. Environ Microbiol 8:720-731
17. Lopez-Garcia P, Gaill F, Moreira D (2002) Wide bacterial diversity associated with tubes of the vent worm Riftia pachyptila. Environ Microbiol 4:204-215
18. Losekann T, Knittel K, Nadalig T, Fuchs B, Niemann H, Boetius A, Amann R (2007) Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea. Appl Environ Microbiol 73:3348-3362
19. Marteinsson VT (1999) Isolation and characterization of Thermus thermophilus Gy1211 from a deep-sea hydrothermal vent. Extremophiles 3:247-251
20. McCliment EA, Voglesonger KM, O'Day PA, Dunn EE, Holloway JR, Cary SC (2006) Colonization of nascent, deep-sea hydrothermal vents by a novel Archaeal and Nanoarchaeal assemblage. Environ Microbiol 8:114-125
21. Miroshnichenko ML, Bonch-Osmolovskaya EA (2006) Recent developments in the thermophilic microbiology of deep sea hydrothermals vents. Extremophiles 10:85-96
22. Miroshnichenko ML, Slobodkin AI, Kostrikina NA, L'Haridon S, Nercessian O, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA, Jeanthon C (2003a) Deferribacter abyssi sp. nov., an anaerobic thermophile from deep-sea hydrothermal vents of the Mid-Atlantic Ridge. Int J Syst Evol Microbiol 53:1637-1641
23. Miroshnichenko ML, L'Haridon S, Nercessian O, Antipov AN, Kostrikina NA, Tindall BJ, Schumann P, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA, Jeanthon C (2003b) Vulcanithermus mediatlanticus gen. nov., sp. nov., a novel member of the family Thermaceae from a deep-sea hot vent. Int J Syst Evol Microbiol 53:1143-1148
24. Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek 73:127-141
25. Muyzer G, Teske A, Wirsen KO, Jannasch HW (1995) Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vents samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 164:165-172
26. Nadkarni MA, Martin FE, Jacques NA, Hunter N (2002) Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiol 148:257-266
27. Nakagawa S, Takai K, Horikoshi K, Sako Y (2004) Aeropyrum camini sp. nov., a strictly aerobic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol 54:329-335
28. Nercessian O, Fouquet Y, Pierre C, Prieur D, Jeanthon C (2005) Diversity of Bacteria and Archaea associated with a carbonate-rich metalliferous sediment sample from the Rainbow vent field on the Mid-Atlantic Ridge. Environ Microbiol 7:698-714
29. Page A, Tivey MK, Stakes DS, Reysenbach A-L (2008) Temporal and spatial archaeal colonization of hydrothermal vent deposits. Environ Microbiol 10:874-884
30. Postec A, Pignet P, Cueff-Gauchard V, Schmitt A, Querellou J, Godfroy A (2005a) Optimisation of growth conditions for continuous culture of the hyperthermophilic archaeon Thermococcus hydrothermalis and development of sulphur-free defined and minimal media. Res Microbiol 156:82-87
31. Postec A, Urios L, Lesongeur F, Ollivier B, Quérellou J, Godfroy A (2005b) Continuous enrichment culture and molecular monitoring to investigate the microbial diversity of thermophiles inhabiting the deep-sea hydrothermal ecosystems. Curr Microbiol 50:138-144
32. Postec A, Lesongeur F, Pignet P, Ollivier B, Quérellou J, Godfroy A (2007) Continuous enrichment cultures: insights into prokaryotic diversity and metabolic interactions in deep-sea vent chimneys. Extremophiles 11:747-757
33. Pukall R, Buntefuss D, Fruhling A, Rohde M, Kroppenstedt RM, Burghardt J, Lebaron P, Bernard L, Stackebrandt E (1999) Sulfitobacter mediterraneus sp. nov., a new sulphite-oxidizing member of the {alpha}-proteobacteria. Int J Syst Bacteriol 49:513-519
34. Raven N, Ladwa N, Sharp R (1992) Continuous culture of the hyperthermophilic archaeum Pyrococcus furiosus. Appl Microbiol Biotechnol 38:263-267
35. Sako Y, Nomura N, Ushida A, Ishida Y, Morii H, Hoaki T, Maruyama T (1996) Aeropyrum pernix, gen. nov; sp. nov., a novel aerobic hyperthermophilic archaeon growing at temperatures up to 100°C. Int J Syst Bacteriol 46:1070-1077
36. Schmidt C, Vuillemin R, Le Gall C, Gaill F, Le Bris N (2008) Geochemical energy sources for microbial primary production in the environment of hydrothermal vent shrimps. Mar Chem 108:18-31
37. Schrenk MO, Kelley DS, Delaney JR, Baross JA (2003) Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney. Appl Environ Microbiol 69:3580-3592
38. Slobodkin A, Campbell B, Cary SC, Bonch-Osmolovskaya E, Jeanthon C (2001) Evidence for the presence of thermophilic Fe(III)-reducing microorganisms in deep-sea hydrothermal vents at 13°N (East Pacific Rise). FEMS Microbiol Ecol 36:235-243
39. Sokolova TG, Jeanthon C, Kostrikina NA, Chernyh NA, Lebedinski AV, Stackebrandt E, Bonch-Osmolovkaya EA (2004) The first evidence of anaerobic CO oxidation coupled with H2 production by a hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent. Extremophiles 8:317-323
40. Takai K, Horikoshi K (1999) Molecular phylogenetic analysis of archaeal intron-containing genes coding for rRNA obtained from a deep-subsurface geothermal water pool. Appl Environ Microbiol 65:5586-5589
41. Takai K, Horikoshi K (2000) Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes. Appl Environ Microbiol 66:5066-5072
42. Takai K, Nunoura T, Ishibashi J-I, Lupton J, Suzuki R, Hamasaki H, Ueno Y, Kawagucci S, Gamo T, Suzuki Y, Hirayama H, Horikoshi K (2008) Variability in the microbial communities and hydrothermal fluid chemistry at the newly discovered Mariner hydrothermal field, southern Lau Basin. J Geophys Res 113. doi:10.1029/2007JG000521
43. Teske A, Sorensen KB (2007) Uncultured archaea in deep marine subsurface sediments: Have we caught them all? ISME J 2:3-18
44. Tor JM, Amend JP, Lovley DR (2003) Metabolism of organic compounds in anaerobic, hydrothermal sulphate-reducing marine sediments. Environ Microbiol 5:583-591
45. Webster G, Newberry CJ, Fry JC, Weightman AJ (2003) Assessment of bacterial community structure in the deep sub-seafloor biosphere by 16 s rDNA-based techniques: a cautionary tale. J Microbiol Methods 55:155-164
46. Zemb O, Haegeman B, Delgenes JP, Lebaron P, Godon JJ (2007) Safum: statistical analysis of SSCP fingerprints using PCA projections, dendrograms and diversity estimators. Mol Ecol Notes 7:767-770