title: Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.
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.affiliation: CNRS, Aix-Marseille Université, Laboratoire Information Génomique et Structurale (UMR 7256), Mediterranean Institute of Microbiology (FR 3479), Marseille, France.
authors.forename: Pascal
authors.initials: P
authors.lastname: Hingamp
authors.forename: Nigel
authors.initials: N
authors.lastname: Grimsley
authors.forename: Silvia G
authors.initials: SG
authors.lastname: Acinas
authors.forename: Camille
authors.initials: C
authors.lastname: Clerissi
authors.forename: Lucie
authors.initials: L
authors.lastname: Subirana
authors.forename: Julie
authors.initials: J
authors.lastname: Poulain
authors.forename: Isabel
authors.initials: I
authors.lastname: Ferrera
authors.forename: Hugo
authors.initials: H
authors.lastname: Sarmento
authors.forename: Emilie
authors.initials: E
authors.lastname: Villar
authors.forename: Gipsi
authors.initials: G
authors.lastname: Lima-Mendez
authors.forename: Karoline
authors.initials: K
authors.lastname: Faust
authors.forename: Shinichi
authors.initials: S
authors.lastname: Sunagawa
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Claverie
authors.forename: Hervé
authors.initials: H
authors.lastname: Moreau
authors.forename: Yves
authors.initials: Y
authors.lastname: Desdevises
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.forename: Jeroen
authors.initials: J
authors.lastname: Raes
authors.forename: Colomban
authors.initials: C
authors.lastname: de Vargas
authors.forename: Eric
authors.initials: E
authors.lastname: Karsenti
authors.forename: Stefanie
authors.initials: S
authors.lastname: Kandels-Lewis
authors.forename: Olivier
authors.initials: O
authors.lastname: Jaillon
authors.forename: Fabrice
authors.initials: F
authors.lastname: Not
authors.forename: Stéphane
authors.initials: S
authors.lastname: Pesant
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Ogata
mesh_terms: D000818:Animals; D044822:Biodiversity; D002467:Cell Nucleus / Q000821:virology; D003593:Cytoplasm / Q000821:virology; D004267:DNA Viruses / Q000145:classification* / Q000235:genetics / Q000502:physiology*; D056890:Eukaryota / Q000821:virology; D022761:Gene Transfer, Horizontal; D005814:Genes, Viral / Q000235:genetics; D016679:Genome, Viral / Q000235:genetics; D019156:Indian Ocean; D054892:Metagenome; D009792:Oceans and Seas; D009868:Oomycetes / Q000821:virology; D017862:Phycodnaviridae / Q000145:classification / Q000235:genetics / Q000502:physiology; D010802:Phylogeny; D011156:Population Density; D011387:Prokaryotic Cells / Q000502:physiology