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Diversity of virus–host systems in hypersaline Lake Retba, Senegal

Authors

  • Télesphore Sime-Ngando,

    1. Laboratoire Microorganismes: Génome et Environnement, Université Blaise Pascal (Clermont-Ferrand II), UMR CNRS 6023, F-63177, Aubière Cedex, France.
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  • Soizick Lucas,

    1. Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, rue du Dr. Roux 25, 75724 Paris Cedex 15, France.
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  • Agnès Robin,

    1. Laboratoire Microorganismes: Génome et Environnement, Université Blaise Pascal (Clermont-Ferrand II), UMR CNRS 6023, F-63177, Aubière Cedex, France.
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  • Kimberly Pause Tucker,

    1. College of Marine Science, University of South Florida, 140 7th Avenue South, Saint Petersburg, FL 33701, USA.
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    • Present address: Department of Natural Sciences, College of Coastal Georgia, 3700 Altama Avenue, Brunswick, GA 31520, USA.

  • Jonathan Colombet,

    1. Laboratoire Microorganismes: Génome et Environnement, Université Blaise Pascal (Clermont-Ferrand II), UMR CNRS 6023, F-63177, Aubière Cedex, France.
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  • Yvan Bettarel,

    1. IRD, UMR 5119 Ecosystèmes lagunaires, Montpellier, France.
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  • Elie Desmond,

    1. Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, rue du Dr. Roux 25, 75724 Paris Cedex 15, France.
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  • Simonetta Gribaldo,

    1. Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, rue du Dr. Roux 25, 75724 Paris Cedex 15, France.
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  • Patrick Forterre,

    1. Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, rue du Dr. Roux 25, 75724 Paris Cedex 15, France.
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  • Mya Breitbart,

    1. College of Marine Science, University of South Florida, 140 7th Avenue South, Saint Petersburg, FL 33701, USA.
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  • David Prangishvili

    Corresponding author
    1. Laboratoire Microorganismes: Génome et Environnement, Université Blaise Pascal (Clermont-Ferrand II), UMR CNRS 6023, F-63177, Aubière Cedex, France.
    2. Institut Pasteur, Molecular Biology of the Gene in Extremophiles Unit, rue du Dr. Roux 25, 75724 Paris Cedex 15, France.
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E-mail david.prangishvili@pasteur.fr; Tel. (+33) 144 38 9119; Fax (+33) 145 68 8834.

Summary

Remarkable morphological diversity of virus-like particles was observed by transmission electron microscopy in a hypersaline water sample from Lake Retba, Senegal. The majority of particles morphologically resembled hyperthermophilic archaeal DNA viruses isolated from extreme geothermal environments. Some hypersaline viral morphotypes have not been previously observed in nature, and less than 1% of observed particles had a head-and-tail morphology, which is typical for bacterial DNA viruses. Culture-independent analysis of the microbial diversity in the sample suggested the dominance of extremely halophilic archaea. Few of the 16S sequences corresponded to known archeal genera (Haloquadratum, Halorubrum and Natronomonas), whereas the majority represented novel archaeal clades. Three sequences corresponded to a new basal lineage of the haloarchaea. Bacteria belonged to four major phyla, consistent with the known diversity in saline environments. Metagenomic sequencing of DNA from the purified virus-like particles revealed very few similarities to the NCBI non-redundant database at either the nucleotide or amino acid level. Some of the identifiable virus sequences were most similar to previously described haloarchaeal viruses, but no sequence similarities were found to archaeal viruses from extreme geothermal environments. A large proportion of the sequences had similarity to previously sequenced viral metagenomes from solar salterns.

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