title: Linking environmental prokaryotic viruses and their host through CRISPRs.
abstract: The ecological pressure that viruses place on microbial communities is not only based on predation, but also on gene transfer. In order to determine the potential impact of viruses and transduction, we need a better understanding of the dynamics of interactions between viruses and their hosts in the environment. Data on environmental viruses are scarce, and methods for tracking their interactions with prokaryotes are needed. Clustered regularly interspaced short palindromic repeats (CRISPRs), which contain viral sequences in bacterial genomes, might help document the history of virus-host interactions in the environment. In this study, a bioinformatics network linking viruses and their hosts using CRISPR sequences obtained from metagenomic data was developed and applied to metagenomes from Arctic glacial ice and soil. The application of our network approach showed that putative interactions were more commonly detected in the ice samples than the soil which would be consistent with the ice viral-bacterial interactions being more dynamic than those in soil. Further analysis of the viral sequences in the CRISPRs indicated that Ralstonia phages might be agents of transduction in the Arctic glacial ice.
authors.affiliation: Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
authors.forename: Laura
authors.initials: L
authors.lastname: Sanguino
authors.affiliation: Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
authors.forename: Laure
authors.initials: L
authors.lastname: Franqueville
authors.affiliation: Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
authors.forename: Timothy M
authors.initials: TM
authors.lastname: Vogel
authors.affiliation: Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Ecole Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France catherine.larose@ec-lyon.fr.
authors.forename: Catherine
authors.initials: C
authors.lastname: Larose
mesh_terms: D001110:Arctic Regions; D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification / Q000821:virology*; D001435:Bacteriophages / Q000235:genetics*; D001483:Base Sequence; D064112:Clustered Regularly Interspaced Short Palindromic Repeats / Q000235:genetics; D019295:Computational Biology; D017753:Ecosystem; D004777:Environment; D016680:Genome, Bacterial / Q000235:genetics*; D046448:Ice Cover / Q000382:microbiology / Q000821:virology; D054892:Metagenome; D056186:Metagenomics; D009664:Norway; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012988:Soil Microbiology; D018406:Virus Physiological Phenomena / Q000235:genetics*
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: CRISPRs; glacial ice; transduction; virus-host interactions