Continuous enrichment cultures: Insights into prokaryotic diversity and metabolic interactions in deep-sea vent chimneys

Extremophiles

Volumn 11, Issue 6, 2007, Pages 747-757

  Postec, Anne ^a,c   Lesongeur, Françoise ^a   Pignet, Patricia ^a   Ollivier, Bernard ^b   Querellou, Joël ^a   Godfroy, Anne ^a  

^a Centre National de la Recherche Scientifique   (France)

^b AIX MARSEILLE UNIVERSITY   (France)

^c GEOLOGICAL INSTITUTE   (Switzerland)

Author keywords

16S rRNA gene; Bioreactor; Continuous enrichment cultures; Deep sea hydrothermal vent; Metabolic interactions; Microbial diversity; Thermophiles

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); CAMINICELLA; DEFERRIBACTER; MARINITOGA; PROKARYOTA; THERMOCOCCUS; THERMODESULFATATOR; THERMOSIPHO;

EID: 35748938437     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-007-0092-z     Document Type: Article

References (37)

1. Alain K, Olagnon M, Desbruyeres D, Page A, Barbier G, Juniper SK, Querellou J, Cambon-Bonavita MA (2002a) Phylogenetic characterization of the bacterial assemblage associated with mucous secretions of the hydrothermal vent polychaete Paralvinella palmiformis. FEMS Microbiol Ecol 42:463-476
2. Alain K, Pignet P, Zbinden M, Quillevere M, Duchiron F, Donval JP Lesongeur F, Raguenes G, Crassous P, Querellou J, Cambon-Bonavita MA (2002b) 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 52:1621-1628
3. Allen EE, Banfield JF (2005) Community genomics in microbial ecology and evolution. Nat Rev Microbiol 3:489-498
4. Altschul SF, Gish W, Miller W, Meyers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
5. Antoine E, Cilia V, Meunier J, Guezennec J, Lesongeur F, Barbier G (1997) Thermosipho melanesiensis sp. nov., a new thermophilic anaerobic bacterium belonging to the order Thermotogales, isolated from deep-sea hydrothermal vents in the southwestern Pacific Ocean. Int J Syst Bacteriol 47:1118-1123
6. DeChaine EG, Bates AE, Shank TM, Cavanaugh CM (2006) Off-axis symbiosis found: characterization and biogeography of bacterial symbionts of Bathymodiolus mussels from Lost City hydrothermal vents. Environ Microbiol 8:1902-1912
7. Galtier N, Gouy M, Gautier C (1996) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. CABIOS 12:543-548
8. Godfroy A, Meunier JR, 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 JR, 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. Godfroy A, Postec A, Raven NDH (2005) Growth of hyperthermophilic microorganisms for physiological and nutritional studies. In: Rainey FA, Oren A (eds) Methods in microbiology, extremophiles. Academic, Oxford, pp 91-106
12. Grote R, Li LN, Tamaoka J, Kato C, Horikoshi K, Antranikian G (1999) Thermococcus siculi sp. nov., a novel hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent at the Mid-Okinawa trough. Extremophiles 3:55-62
13. 2 lake of the southern Okinawa trough hydrothermal system. PNAS 103:14164-14169
14. Johnson MR, Conners SB, Montero CI, Chou CJ, Shockley KR, Kelly RM (2006) The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture. Appl Environ Microbiol 72:811-818
15. Karl DM (1995) Ecology of free-living hydrothermal vent microbial communities. In: Karl DM (ed) The microbiology of deep-sea hydrothermal vents. CRC Press, West Palm Beach, pp 35-125
16. Kormas KA, Tivey MK, Von Damm K, Teske A (2006) Bacterial and archaeal phylotypes associated with distinct mineralogical layers of a white smoker spire from a deep-sea hydrothermal vent site (9°N, East Pacific Rise). Environ Microbiol 8:909-920
17. Marteinsson V, Birrien J, Reysenbach A, Vernet M, Marie D, Gambacorta A, Messner P, Sleytr U, Prieur D (1999) Thermococcus barophilus sp. nov., a new barophilic and hyperthermophilic archaeon isolated under high hydrostatic pressure from a deep-sea hydrothermal vent. Int J Syst Bacteriol 49:351-359
18. 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
19. Miroshnichenko ML, Slobodkin AI, Kostrikina NA, L'Haridon S, Nercessian O, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA, Jeanthon C (2003) 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
20. Moussard H, L'Haridon S, Tindall BJ, Banta A, Schumann P, Stackebrandt E, Reysenbach AL, Jeanthon C (2004) Thermodesulfatator indicus gen. nov., sp. nov., a novel thermophilic chemolithoautotrophic sulfate-reducing bacterium isolated from the Central Indian Ridge. Int J Syst Evol Microbiol 54:227-233
21. Moussard H, Corre E, Cambon-Bonavita MA, Fouquet Y, Jeanthon C (2006) Novel uncultured Epsilonproteobacteria dominate a filamentous sulphur mat from the 13°N hydrothermal vent field, East Pacific Rise. FEMS Microbiol Ecol 58:449-463
22. Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Ant van Leeuw 73:127-141
23. Muyzer G, De Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695-700
24. Nercessian O, Reysenbach AL, Prieur D, Jeanthon C (2003) Archaeal diversity associated with in situ samplers deployed on hydrothermal vents on the East Pacific Rise (13°N). Environ Microbiol 5:492-502
25. 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
26. Postec A, Urios L, Lesongeur L, Ollivier B, Querellou 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
27. Postec A, Le Breton C, Fardeau ML, Lesongeur F, Pignet P, Querellou J, Ollivier B, Godfroy A (2005c) Marinitoga hydrogenitolerans sp. nov., a novel member of the order Thermotogales isolated from a black smoker chimney on the Mid-Atlantic Ridge. Int J Syst Evol Microbiol 55:1217-1221
28. Postec A (2005d) Diversité de populations microbiennes thermophiles d'une cheminée hydrothermale océanique: cultures d'enrichissement en bioréacteur et isolement d'espèces nouvelles. In: Thesis, Université de Provence, France
29. Raven N, Ladwa N, Sharp R (1992) Continuous culture of the hyperthermophilic archaeum Pyrococcus furiosus. Appl Microbiol Biotechnol 38:263-267
30. Raven NDH, Sharp RJ (1997) Development of defined and minimal media for the growth of the hyperthermophilic archaeon Pyrococcus furiosus Vc1. FEMS Microbiol Lett 146:135-141
31. Sharp RJ, Raven NDH (1997) Isolation and growth of hyperthermophiles. In: Rhodes PM, Stanbury PF (eds) Applied microbial physiology: a practical approach. IRL Press, Oxford, pp 23-51
32. Suzuki M, Giovannoni S (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625-630
33. Theron J, Cloete TE (2000) Molecular techniques for determining microbial diversity and community structure in natural environments. Crit Rev Microbiol 26:37-57
34. Thompson J, Higgins D, Gibson T (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nuc Acids Res 22:4673-4680
35. Tor JM, Amend JP, Lovley DR (2003) Metabolism of organic compounds in anaerobic, hydrothermal sulphate-reducing marine sediments. Environ Microbiol 5:583-591
36. Wery N, Cambon-Bonavita MA, Lesongeur F, Barbier G (2002) Diversity of anaerobic heterotrophic thermophiles isolated from deep-sea hydrothermal vents of the Mid-Atlantic Ridge. FEMS Microbiol Ecol 41:105-114
37. Wery N, Lesongeur F, Pignet P, Derennes V, Cambon-Bonavita MA, Godfroy A, Barbier G (2001) Marinitoga camini gen. nov., sp. nov., a rod-shaped bacterium belonging to the order Thermotogales, isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 51:495-504