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Microbial Community Structure in Three Deep-Sea Carbonate Crusts

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Abstract

Carbonate crusts in marine environments can act as sinks for carbon dioxide. Therefore, understanding carbonate crust formation could be important for understanding global warming. In the present study, the microbial communities of three carbonate crust samples from deep-sea mud volcanoes in the eastern Mediterranean were characterized by sequencing 16S ribosomal RNA (rRNA) genes amplified from DNA directly retrieved from the samples. In combination with the mineralogical composition of the crusts and lipid analyses, sequence data were used to assess the possible role of prokaryotes in crust formation. Collectively, the obtained data showed the presence of highly diverse communities, which were distinct in each of the carbonate crusts studied. Bacterial 16S rRNA gene sequences were found in all crusts and the majority was classified as α-, γ-, and δ- Proteobacteria. Interestingly, sequences of Proteobacteria related to Halomonas and Halovibrio sp., which can play an active role in carbonate mineral formation, were present in all crusts. Archaeal 16S rRNA gene sequences were retrieved from two of the crusts studied. Several of those were closely related to archaeal sequences of organisms that have previously been linked to the anaerobic oxidation of methane (AOM). However, the majority of archaeal sequences were not related to sequences of organisms known to be involved in AOM. In combination with the strongly negative δ 13C values of archaeal lipids, these results open the possibility that organisms with a role in AOM may be more diverse within the Archaea than previously suggested. Different communities found in the crusts could carry out similar processes that might play a role in carbonate crust formation.

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Acknowledgments

Samples of carbonate crusts were obtained during the French–Dutch Medinaut expedition, an integrated geological, geochemical, and biological study of mud volcanism and fluid seepage in the eastern Mediterranean Sea. We thank the officers and crew of the R/V Nadir and the Nautile submersible for their helpful cooperation during seagoing activities. We thank Stephen Bent (University of Idaho, Moscow, ID, USA) for help with the Morisita–Horn similarity calculations. We thank two anonymous reviewers for their useful comments. Financial support for this study was provided by the French and Dutch funding organizations, IFREMER and NWO-ALW (project grant 809.63.013), respectively.

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Author notes

  1. G. Aloisi

    Present address: UMR 5125–PEPS–CNRS–UCBL, Domaine Scientifique de la Doua, Bâtiment GEODE, 2 Rue Dubois, F-69622, Villeurbanne Cedex, France

  2. R. D. Pancost

    Present address: Organic Geochemistry Unit, Bristol Biogeochemistry Research Centre, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK

  3. L. J. Forney

    Present address: Department of Biological Sciences, University of Idaho, Moscow, ID, 83844-3051, USA

Authors and Affiliations

  1. Department of Microbiology, Center of Ecological and Evolutionary Studies, University of Groningen, P.O. Box 14, 9750 AA, Haren, The Netherlands

    S. K. Heijs, J. C. Gottschal, J. D. van Elsas & L. J. Forney

  2. Laboratoire d'Océanographie Dynamique et de Climatologie, Université Pierre et Marie Curie, 4, place Jussieu, 75252, Paris, France

    G. Aloisi & C. Pierre

  3. Laboratoire de Physique et Chimie Marines, Université Pierre et Marie Curie, 4, Place Jussieu, 75252, Paris, France

    I. Bouloubassi

  4. Department of Marine Biogeochemistry and Toxicology, Netherlands Institute for Sea Research, P.O. Box 59, 1790AB, Den Burg (Texel), The Netherlands

    R. D. Pancost & J. S. Sinninghe Damsté

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  1. S. K. Heijs
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Heijs, S.K., Aloisi, G., Bouloubassi, I. et al. Microbial Community Structure in Three Deep-Sea Carbonate Crusts. Microb Ecol 52, 451–462 (2006). https://doi.org/10.1007/s00248-006-9099-8

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