Linking environmental prokaryotic viruses and their host through CRISPRs
International audience 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...
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Online Access: | https://hal.science/hal-01589168 https://doi.org/10.1093/femsec/fiv046 |
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ftunivlyon1:oai:HAL:hal-01589168v1 2023-05-15T14:57:08+02:00 Linking environmental prokaryotic viruses and their host through CRISPRs Sanguino Casado, Laura Franqueville, Laure Vogel, Timothy M. Larose, Catherine Ampère, Département Bioingénierie (BioIng) Ampère (AMPERE) École Centrale de Lyon (ECL) Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL) Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon) Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École Centrale de Lyon (ECL) Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) 2015-04 https://hal.science/hal-01589168 https://doi.org/10.1093/femsec/fiv046 en eng HAL CCSD Wiley-Blackwell info:eu-repo/semantics/altIdentifier/doi/10.1093/femsec/fiv046 hal-01589168 https://hal.science/hal-01589168 doi:10.1093/femsec/fiv046 ISSN: 0168-6496 EISSN: 1574-6941 FEMS Microbiology Ecology https://hal.science/hal-01589168 FEMS Microbiology Ecology, 2015, 91 (5), ⟨10.1093/femsec/fiv046⟩ CRISPRs glacial ice transduction virus-host interactions [SPI.NRJ]Engineering Sciences [physics]/Electric power info:eu-repo/semantics/article Journal articles 2015 ftunivlyon1 https://doi.org/10.1093/femsec/fiv046 2023-04-07T13:18:46Z International audience 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. Article in Journal/Newspaper Arctic HAL Lyon 1 (University Claude Bernard Lyon 1) Arctic FEMS Microbiology Ecology 91 5 |
institution |
Open Polar |
collection |
HAL Lyon 1 (University Claude Bernard Lyon 1) |
op_collection_id |
ftunivlyon1 |
language |
English |
topic |
CRISPRs glacial ice transduction virus-host interactions [SPI.NRJ]Engineering Sciences [physics]/Electric power |
spellingShingle |
CRISPRs glacial ice transduction virus-host interactions [SPI.NRJ]Engineering Sciences [physics]/Electric power Sanguino Casado, Laura Franqueville, Laure Vogel, Timothy M. Larose, Catherine Linking environmental prokaryotic viruses and their host through CRISPRs |
topic_facet |
CRISPRs glacial ice transduction virus-host interactions [SPI.NRJ]Engineering Sciences [physics]/Electric power |
description |
International audience 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. |
author2 |
Ampère, Département Bioingénierie (BioIng) Ampère (AMPERE) École Centrale de Lyon (ECL) Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL) Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon) Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-École Centrale de Lyon (ECL) Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) |
format |
Article in Journal/Newspaper |
author |
Sanguino Casado, Laura Franqueville, Laure Vogel, Timothy M. Larose, Catherine |
author_facet |
Sanguino Casado, Laura Franqueville, Laure Vogel, Timothy M. Larose, Catherine |
author_sort |
Sanguino Casado, Laura |
title |
Linking environmental prokaryotic viruses and their host through CRISPRs |
title_short |
Linking environmental prokaryotic viruses and their host through CRISPRs |
title_full |
Linking environmental prokaryotic viruses and their host through CRISPRs |
title_fullStr |
Linking environmental prokaryotic viruses and their host through CRISPRs |
title_full_unstemmed |
Linking environmental prokaryotic viruses and their host through CRISPRs |
title_sort |
linking environmental prokaryotic viruses and their host through crisprs |
publisher |
HAL CCSD |
publishDate |
2015 |
url |
https://hal.science/hal-01589168 https://doi.org/10.1093/femsec/fiv046 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
ISSN: 0168-6496 EISSN: 1574-6941 FEMS Microbiology Ecology https://hal.science/hal-01589168 FEMS Microbiology Ecology, 2015, 91 (5), ⟨10.1093/femsec/fiv046⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1093/femsec/fiv046 hal-01589168 https://hal.science/hal-01589168 doi:10.1093/femsec/fiv046 |
op_doi |
https://doi.org/10.1093/femsec/fiv046 |
container_title |
FEMS Microbiology Ecology |
container_volume |
91 |
container_issue |
5 |
_version_ |
1766329232648044544 |