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Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.
ISME J. 2013 Sep; 7(9):1678-95.IJ

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 10(4)-10(5) genomes ml(-1) for the samples from the photic zone and 10(2)-10(3) 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.

Authors+Show Affiliations

CNRS, Aix-Marseille Université, Laboratoire Information Génomique et Structurale (UMR 7256), Mediterranean Institute of Microbiology (FR 3479), Marseille, France.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

23575371

Citation

Hingamp, Pascal, et al. "Exploring Nucleo-cytoplasmic Large DNA Viruses in Tara Oceans Microbial Metagenomes." The ISME Journal, vol. 7, no. 9, 2013, pp. 1678-95.
Hingamp P, Grimsley N, Acinas SG, et al. Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. ISME J. 2013;7(9):1678-95.
Hingamp, P., Grimsley, N., Acinas, S. G., Clerissi, C., Subirana, L., Poulain, J., Ferrera, I., Sarmento, H., Villar, E., Lima-Mendez, G., Faust, K., Sunagawa, S., Claverie, J. M., Moreau, H., Desdevises, Y., Bork, P., Raes, J., de Vargas, C., Karsenti, E., ... Ogata, H. (2013). Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. The ISME Journal, 7(9), 1678-95. https://doi.org/10.1038/ismej.2013.59
Hingamp P, et al. Exploring Nucleo-cytoplasmic Large DNA Viruses in Tara Oceans Microbial Metagenomes. ISME J. 2013;7(9):1678-95. PubMed PMID: 23575371.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. AU - Hingamp,Pascal, AU - Grimsley,Nigel, AU - Acinas,Silvia G, AU - Clerissi,Camille, AU - Subirana,Lucie, AU - Poulain,Julie, AU - Ferrera,Isabel, AU - Sarmento,Hugo, AU - Villar,Emilie, AU - Lima-Mendez,Gipsi, AU - Faust,Karoline, AU - Sunagawa,Shinichi, AU - Claverie,Jean-Michel, AU - Moreau,Hervé, AU - Desdevises,Yves, AU - Bork,Peer, AU - Raes,Jeroen, AU - de Vargas,Colomban, AU - Karsenti,Eric, AU - Kandels-Lewis,Stefanie, AU - Jaillon,Olivier, AU - Not,Fabrice, AU - Pesant,Stéphane, AU - Wincker,Patrick, AU - Ogata,Hiroyuki, Y1 - 2013/04/11/ PY - 2012/11/06/received PY - 2013/02/28/revised PY - 2013/03/06/accepted PY - 2013/4/12/entrez PY - 2013/4/12/pubmed PY - 2014/2/7/medline SP - 1678 EP - 95 JF - The ISME journal JO - ISME J VL - 7 IS - 9 N2 - 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 10(4)-10(5) genomes ml(-1) for the samples from the photic zone and 10(2)-10(3) 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. SN - 1751-7370 UR - https://www.unboundmedicine.com/medline/citation/23575371/Exploring_nucleo_cytoplasmic_large_DNA_viruses_in_Tara_Oceans_microbial_metagenomes_ L2 - https://doi.org/10.1038/ismej.2013.59 DB - PRIME DP - Unbound Medicine ER -