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Lake Pavin pp 245–254Cite as

Study of Prokaryotes and Viruses in Aquatic Ecosystems by Metagenetic and Metagenomic Approaches

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Abstract

High-throughput sequencing methods have revolutionized the study of microbial communities in ecosytems. In this chapter, we present the use of metagenetics, targeted metagenomics and viral metagenomics to depict the diversity and the role of Bacteria, Archaea and viruses in the mixolimnion of the lake Pavin. Actinobacteria dominated the bacterial community and was represented by two typical clades: acI and acIV. Focusing on this phylum, we describe its genomic properties characterized by a low GC content (42–52 %) and high substitution rates. Phylogeny based on both SSU rRNA gene and concatenated proteins showed that these clades represented different ecotypes. Archaea was a minor but active component among prokaryotes. The Thaumarchaeota Marine Group I, already known to play an important role in ammonia oxidation dominated the archaeal assemblage in surface waters but surprisingly the Miscellaneous Euryarchaeotic Group (MEG) was the most active in particular zones such as the oxycline. Finally, the analysis of viral particles by a metagenomic approach in the lake Pavin was the first study published about freshwater temperate lakes. Among aquatic datasets, genetic richness of marine viromes was higher in average than that of freshwater ones. The viral community was composed of viruses from families of double-stranded (Caudovirales) and single-stranded (Microviridae, Circoviridae, Nanoviridae) DNA viruses. The phylogeny of the complete Microviridae genomes from the Lake Pavin virome led to the description of a new group, the Pichovirinae, and new “chimeric” genomes could be assembled, challenging the established view of ancient viral evolutionary history.

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Acknowledgement

We are indebted to Dr Steven M. SHORT, University of Toronto (Canada), for a critical review of the manuscript.

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Authors and Affiliations

  1. LMGE, Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, Université Blaise Pascal, BP 80026, 63177, Aubière Cedex, France

    Gisèle Bronner, Didier Debroas, François Enault, Mylène Hugoni, Isabelle Jouan-Dufournel, Isabelle Mary, Viviane Ravet, Simon Roux & Najwa Taïb

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  1. Gisèle Bronner
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  2. Didier Debroas
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  3. François Enault
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  4. Mylène Hugoni
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  5. Isabelle Jouan-Dufournel
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  6. Isabelle Mary
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  7. Viviane Ravet
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  8. Simon Roux
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  9. Najwa Taïb
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Corresponding author

Correspondence to Didier Debroas .

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Editors and Affiliations

  1. LMGE, Laboratoire Microorganismes: Génome et Environnement, UMR CNRS 6023, Université Clermont-Auvergne, Université Blaise Pascal, Aubière, France

    Télesphore Sime-Ngando

  2. LMV, Université Clermont-Auvergne - CNRS - IRD - OPGC, Aubière, France

    Pierre Boivin

  3. ISTO Institut des Sciences de la Terre d’Orléans, Observatoire des Sciences de l’Univers en région Centre, UMR 7327 (CNRS-Université d’Orléans-BRGM), Orléans Cedex, France

    Emmanuel Chapron

  4. IPGP (Institut de Physique du Globe de Paris) Sorbonne Paris Cité, Univ. Paris Diderot, Paris, France

    Didier Jezequel

  5. METIS UMR CNRS 7619, Université Pierre et Marie Curie, Paris, France

    Michel Meybeck

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Bronner, G. et al. (2016). Study of Prokaryotes and Viruses in Aquatic Ecosystems by Metagenetic and Metagenomic Approaches. In: Sime-Ngando, T., Boivin, P., Chapron, E., Jezequel, D., Meybeck, M. (eds) Lake Pavin. Springer, Cham. https://doi.org/10.1007/978-3-319-39961-4_15

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