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Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.

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Title: Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.
Authors: Hingamp, Pascal1, Grimsley, Nigel2, Acinas, Silvia G3, Clerissi, Camille2, Subirana, Lucie2, Poulain, Julie4, Ferrera, Isabel3, Sarmento, Hugo3, Villar, Emilie1, Lima-Mendez, Gipsi5, Faust, Karoline5, Sunagawa, Shinichi6, Claverie, Jean-Michel1, Moreau, Hervé2, Desdevises, Yves2, Bork, Peer6, Raes, Jeroen5, de Vargas, Colomban7, Karsenti, Eric6, Kandels-Lewis, Stefanie6
Source: ISME Journal: Multidisciplinary Journal of Microbial Ecology. Sep2013, Vol. 7 Issue 9, p1678-1695. 18p.
Subjects: DNA viruses, Metagenomics, Viral ecology, Geographical distribution of viruses, Viral genomes, Oomycetes
Geographic Terms: Tara (Ireland)
Abstract: 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. [ABSTRACT FROM AUTHOR]
Copyright of ISME Journal: Multidisciplinary Journal of Microbial Ecology is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
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DbLabel: Engineering Source
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PubType: Academic Journal
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  Data: Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.
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  Data: <searchLink fieldCode="JN" term="%22ISME+Journal%3A+Multidisciplinary+Journal+of+Microbial+Ecology%22">ISME Journal: Multidisciplinary Journal of Microbial Ecology</searchLink>. Sep2013, Vol. 7 Issue 9, p1678-1695. 18p.
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  Data: <searchLink fieldCode="DE" term="%22DNA+viruses%22">DNA viruses</searchLink><br /><searchLink fieldCode="DE" term="%22Metagenomics%22">Metagenomics</searchLink><br /><searchLink fieldCode="DE" term="%22Viral+ecology%22">Viral ecology</searchLink><br /><searchLink fieldCode="DE" term="%22Geographical+distribution+of+viruses%22">Geographical distribution of viruses</searchLink><br /><searchLink fieldCode="DE" term="%22Viral+genomes%22">Viral genomes</searchLink><br /><searchLink fieldCode="DE" term="%22Oomycetes%22">Oomycetes</searchLink>
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  Data: <searchLink fieldCode="DE" term="%22Tara+%28Ireland%29%22">Tara (Ireland)</searchLink>
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  Label: Abstract
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  Data: 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. [ABSTRACT FROM AUTHOR]
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  Label:
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  Data: <i>Copyright of ISME Journal: Multidisciplinary Journal of Microbial Ecology is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1038/ismej.2013.59
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        Text: English
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