Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes
Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of mari...
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| Format: | Online |
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Nature Publishing Group
2013
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3749498/ |
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pubmed-37494982013-09-01 Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes Hingamp, Pascal Grimsley, Nigel Acinas, Silvia G Clerissi, Camille Subirana, Lucie Poulain, Julie Ferrera, Isabel Sarmento, Hugo Villar, Emilie Lima-Mendez, Gipsi Faust, Karoline Sunagawa, Shinichi Claverie, Jean-Michel Moreau, Hervé Desdevises, Yves Bork, Peer Raes, Jeroen de Vargas, Colomban Karsenti, Eric Kandels-Lewis, Stefanie Jaillon, Olivier Not, Fabrice Pesant, Stéphane Wincker, Patrick Ogata, Hiroyuki Original Article Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2–1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 104–105 genomes ml−1 for the samples from the photic zone and 102–103 genomes ml−1 for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts. Nature Publishing Group 2013-09 2013-04-11 /pmc/articles/PMC3749498/ /pubmed/23575371 http://dx.doi.org/10.1038/ismej.2013.59 Text en Copyright © 2013 International Society for Microbial Ecology http://creativecommons.org/licenses/by/3.0/ This work is licensed under a Creative Commons Attribution 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/ |
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Open Access Journal |
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Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Hingamp, Pascal Grimsley, Nigel Acinas, Silvia G Clerissi, Camille Subirana, Lucie Poulain, Julie Ferrera, Isabel Sarmento, Hugo Villar, Emilie Lima-Mendez, Gipsi Faust, Karoline Sunagawa, Shinichi Claverie, Jean-Michel Moreau, Hervé Desdevises, Yves Bork, Peer Raes, Jeroen de Vargas, Colomban Karsenti, Eric Kandels-Lewis, Stefanie Jaillon, Olivier Not, Fabrice Pesant, Stéphane Wincker, Patrick Ogata, Hiroyuki |
| spellingShingle |
Hingamp, Pascal Grimsley, Nigel Acinas, Silvia G Clerissi, Camille Subirana, Lucie Poulain, Julie Ferrera, Isabel Sarmento, Hugo Villar, Emilie Lima-Mendez, Gipsi Faust, Karoline Sunagawa, Shinichi Claverie, Jean-Michel Moreau, Hervé Desdevises, Yves Bork, Peer Raes, Jeroen de Vargas, Colomban Karsenti, Eric Kandels-Lewis, Stefanie Jaillon, Olivier Not, Fabrice Pesant, Stéphane Wincker, Patrick Ogata, Hiroyuki Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes |
| author_facet |
Hingamp, Pascal Grimsley, Nigel Acinas, Silvia G Clerissi, Camille Subirana, Lucie Poulain, Julie Ferrera, Isabel Sarmento, Hugo Villar, Emilie Lima-Mendez, Gipsi Faust, Karoline Sunagawa, Shinichi Claverie, Jean-Michel Moreau, Hervé Desdevises, Yves Bork, Peer Raes, Jeroen de Vargas, Colomban Karsenti, Eric Kandels-Lewis, Stefanie Jaillon, Olivier Not, Fabrice Pesant, Stéphane Wincker, Patrick Ogata, Hiroyuki |
| author_sort |
Hingamp, Pascal |
| title |
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes |
| title_short |
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes |
| title_full |
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes |
| title_fullStr |
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes |
| title_full_unstemmed |
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes |
| title_sort |
exploring nucleo-cytoplasmic large dna viruses in tara oceans microbial metagenomes |
| description |
Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2–1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 104–105 genomes ml−1 for the samples from the photic zone and 102–103 genomes ml−1 for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts. |
| publisher |
Nature Publishing Group |
| publishDate |
2013 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3749498/ |
| _version_ |
1612004809431318528 |