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Metagenomic approach studying the taxonomic and functional diversity of the bacterial community in a mesotrophic lake (Lac du Bourget – France)

Authors

  • Didier Debroas,

    Corresponding author
    1. Université Blaise Pascal – Laboratoire «Microorganismes: génome et environnement»– UMR CNRS 6023 63177 Aubiere cedex, France.
      *E-mail didier.debroas@univ-bpclermont.fr; Tel. (+33) 473 407 83771; Fax (+33) 473 407 87670.
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  • Jean-François Humbert,

    1. INRA, UMR CARRTEL, BP 511, 74203 Thonon Cedex, France.
    2. Institut Pasteur-URA CNRS 2172, Unité des Cyanobactéries, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.
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  • François Enault,

    1. Université Blaise Pascal – Laboratoire «Microorganismes: génome et environnement»– UMR CNRS 6023 63177 Aubiere cedex, France.
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  • Gisèle Bronner,

    1. Université Blaise Pascal – Laboratoire «Microorganismes: génome et environnement»– UMR CNRS 6023 63177 Aubiere cedex, France.
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  • Michael Faubladier,

    1. Université Blaise Pascal – Laboratoire «Microorganismes: génome et environnement»– UMR CNRS 6023 63177 Aubiere cedex, France.
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  • Emmanuel Cornillot

    1. Université Blaise Pascal – Laboratoire «Microorganismes: génome et environnement»– UMR CNRS 6023 63177 Aubiere cedex, France.
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    • Present address: Laboratoire de Biologie Cellulaire et Moléculaire UMR CNRS 5235 DIMNP/ERT 1038 ‘Vaccination antiparasitaire’ Université Montpellier I, 34093 Montpellier.


*E-mail didier.debroas@univ-bpclermont.fr; Tel. (+33) 473 407 83771; Fax (+33) 473 407 87670.

Summary

The main goals of this work were to identify the metabolic pathways of the bacterial community in a lacustrine ecosystem and to establish links between taxonomic composition and the relative abundances of these metabolic pathways. For this purpose, we analysed a 16S rRNA gene library obtained by gene amplification together with a sequence library of both insert ends on c. 7700 fosmids. Whatever the library used, Actinobacteria was the most abundant bacterial group, followed by Proteobacteria and Bacteroidetes. Specific aquatic clades such as acI and acIV (Actinobacteria) or LD12 and GOBB-C201 (Alphaproteobacteria) were found in both libraries. From comparative analysis of metagenomic libraries, the metagenome of this lake was characterized by overrepresentation of genes involved in the degradation of xenobiotics mainly associated with Alphaproteobacteria. Actinobacteria were mainly related to metabolic pathways involved in nucleotide metabolism, cofactors, vitamins, energy, replication and repair. Betaproteobacteria appeared to be characterized by the presence of numerous genes implicated in environmental information processing (membrane transport and signal transduction) whereas glycan and carbohydrate metabolism pathways were overrepresented in Bacteroidetes. These results prompted us to propose hypotheses on the ecological role of these bacterial classes in lacustrine ecosystems.

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