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Design of 16S rRNA-targeted oligonucleotide probes for detecting cultured and uncultured archaeal lineages in high-temperature environments

Authors

  • Olivier Nercessian,

    1. UMR 6539, Centre National de la Recherche Scientifique and Université de Bretagne Occidentale, Institut Universitaire Européen de la Mer, Technopole Brest-Iroise, Place Nicolas Copernic, 29280 Plouzané, France.
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    • Present address: Department of Chemical Engineering, Box 352125, University of Washington, Seattle, WA 98195, USA. E-mail nerceo@u.washington.edu

  • Maria Prokofeva,

    1. Institute of Microbiology, Russian Academy of Sciences, Prospect 60 Let Oktyabrya 7/2, 117811, Moscow, Russia.
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  • Alexander Lebedinski,

    1. Institute of Microbiology, Russian Academy of Sciences, Prospect 60 Let Oktyabrya 7/2, 117811, Moscow, Russia.
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  • Stéphane L’Haridon,

    1. UMR 6539, Centre National de la Recherche Scientifique and Université de Bretagne Occidentale, Institut Universitaire Européen de la Mer, Technopole Brest-Iroise, Place Nicolas Copernic, 29280 Plouzané, France.
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  • Craig Cary,

    1. University of Delaware, College of Marine Studies, 700 Pilottown Road, Lewes, DE 19958, USA.
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  • Daniel Prieur,

    1. UMR 6539, Centre National de la Recherche Scientifique and Université de Bretagne Occidentale, Institut Universitaire Européen de la Mer, Technopole Brest-Iroise, Place Nicolas Copernic, 29280 Plouzané, France.
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  • Christian Jeanthon

    Corresponding author
    1. UMR 6539, Centre National de la Recherche Scientifique and Université de Bretagne Occidentale, Institut Universitaire Européen de la Mer, Technopole Brest-Iroise, Place Nicolas Copernic, 29280 Plouzané, France.
      E-mail jeanthon@univ-brest.fr; Tel. (+33) 298 498 751; Fax (+33) 298 498 705.
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E-mail jeanthon@univ-brest.fr; Tel. (+33) 298 498 751; Fax (+33) 298 498 705.

Summary

In order to facilitate the evaluation of archaeal community diversity and distribution in high-temperature environments, 14 16S rRNA oligonucleotide probes were designed. Adequate hybridization and wash conditions of the probes encompassing most known hyperthermophilic Archaea, members of the orders Thermococcales, Desulfurococcales and Sulfolobales, of the families Methanocaldococcaceae, Pyrodictiaceae and Thermoproteaceae, of the genera Archaeoglobus, Methanopyrus and Ignicoccus, and of the as yet uncultured lineages Korarchaeota, Crenarchaeota marine group I, deep-sea hydrothermal vent euryarchaeotic group 2 (DHVE 2), and deep-sea hydrothermal vent euryarchaeotic group 8 (DHVE 8) were determined by dot-blot hybridization from target and non-target reference organisms and environmental clones. The oligonucleotide probes were also used to evaluate the archaeal community composition in nine deep-sea hydrothermal vent samples. All probes, except those targeting members of Sulfolobales, Thermoproteaceae, Pyrodictiaceae and Korarchaeota, gave positive hybridization signals when hybridized against 16S rDNA amplification products obtained from hydrothermal DNA extracts. The results confirmed the widespread occurrence of Thermococcales, Desulfurococcales, Methanocaldococcaceae and Archaeoglobus in deep-sea hydrothermal vents, and extended the known ecological habitats of uncultured lineages. Despite their wide coverage, the probes were unable to resolve the archaeal communities associated with hydrothermally influenced sediments, suggesting that these samples may contain novel lineages. This suite of oligonucleotide probes may represent an efficient tool for rapid qualitative and quantitative characterization of archaeal communities. Their application would help to provide new insights in the future into the composition, distribution and abundance of Archaea in high-temperature environments.

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