Abstract
The prokaryotic diversity of culturable thermophilic communities of deep-sea hydrothermal chimneys was analysed using a continuous enrichment culture performed in a gas-lift bioreactor, and compared to classical batch enrichment cultures in vials. Cultures were conducted at 60°C and pH 6.5 using a complex medium containing carbohydrates, peptides and sulphur, and inoculated with a sample of a hydrothermal black chimney collected at the Rainbow field, Mid-Atlantic Ridge, at 2,275 m depth. To assess the relevance of both culture methods, bacterial and archaeal diversity was studied using cloning and sequencing, DGGE, and whole-cell hybridisation of 16S rRNA genes. Sequences of heterotrophic microorganisms belonging to the genera Marinitoga, Thermosipho, Caminicella (Bacteria) and Thermococcus (Archaea) were obtained from both batch and continuous enrichment cultures while sequences of the autotrophic bacterial genera Deferribacter and Thermodesulfatator were only detected in the continuous bioreactor culture. It is presumed that over time constant metabolite exchanges will have occurred in the continuous enrichment culture enabling the development of a more diverse prokaryotic community. In particular, CO2 and H2 produced by the heterotrophic population would support the growth of autotrophic populations. Therefore, continuous enrichment culture is a useful technique to grow over time environmentally representative microbial communities and obtain insights into prokaryotic species interactions that play a crucial role in deep hydrothermal environments.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
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
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
Allen EE, Banfield JF (2005) Community genomics in microbial ecology and evolution. Nat Rev Microbiol 3:489–498
Altschul SF, Gish W, Miller W, Meyers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
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
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
Galtier N, Gouy M, Gautier C (1996) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. CABIOS 12:543–548
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
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
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
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
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
Inagaki F, Kuypers MMM, Tsunogai U, Ishibashi JI, Nakamura KI, Treude T, Ohkubo S, Nakaseama M, Gena K, Chiba H, Hirayama H, Nunoura T, Takai K, Jorgensen BB, Horikoshi K, Boetius A (2006) From the cover: microbial community in a sediment-hosted CO2 lake of the southern Okinawa trough hydrothermal system. PNAS 103:14164–14169
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Raven N, Ladwa N, Sharp R (1992) Continuous culture of the hyperthermophilic archaeum Pyrococcus furiosus. Appl Microbiol Biotechnol 38:263–267
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
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
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
Theron J, Cloete TE (2000) Molecular techniques for determining microbial diversity and community structure in natural environments. Crit Rev Microbiol 26:37–57
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
Tor JM, Amend JP, Lovley DR (2003) Metabolism of organic compounds in anaerobic, hydrothermal sulphate-reducing marine sediments. Environ Microbiol 5:583–591
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
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
Acknowledgments
The authors want to thank P.M. Sarradin, chief scientist of the ATOS cruise, as well as the captain and crew of the RV/Atalante and the Victor team. This work was supported by Ifremer, the European VENTOX Program and Région Bretagne. We also wish to thank Dr. C. L. Van Dover and Dr. G. Webster for their helpful reading of the manuscript.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by G. Antranikian.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Postec, A., Lesongeur, F., Pignet, P. et al. Continuous enrichment cultures: insights into prokaryotic diversity and metabolic interactions in deep-sea vent chimneys. Extremophiles 11, 747–757 (2007). https://doi.org/10.1007/s00792-007-0092-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00792-007-0092-z