Into the dark: exploring the deep ocean with single-virus genomics

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• dc.contributor.author Martínez Hernández, Francisco
• dc.contributor.author Fornas Carreño, Oscar
• dc.contributor.author Martínez García, Manuel
• dc.date.accessioned 2022-11-10T06:49:48Z
• dc.date.available 2022-11-10T06:49:48Z
• dc.date.issued 2022
• dc.description.abstract Single-virus genomics (SVGs) has been successfully applied to ocean surface samples allowing the discovery of widespread dominant viruses overlooked for years by metagenomics, such as the uncultured virus vSAG 37-F6 infecting the ubiquitous Pelagibacter spp. In SVGs, one uncultured virus at a time is sorted from the environmental sample, whole-genome amplified, and sequenced. Here, we have applied SVGs to deep-ocean samples (200-4000 m depth) from global Malaspina and MEDIMAX expeditions, demonstrating the feasibility of this method in deep-ocean samples. A total of 1328 virus-like particles were sorted from the North Atlantic Ocean, the deep Mediterranean Sea, and the Pacific Ocean oxygen minimum zone (OMZ). For this proof of concept, sixty single viruses were selected at random for sequencing. Genome annotation identified 27 of these genomes as bona fide viruses, and detected three auxiliary metabolic genes involved in nucleotide biosynthesis and sugar metabolism. Massive protein profile analysis confirmed that these viruses represented novel viral groups not present in databases. Although they were not previously assembled by viromics, global fragment recruitment analysis showed a conserved profile of relative abundance of these viruses in all analyzed samples spanning different oceans. Altogether, these results reveal the feasibility in using SVGs in this vast environment to unveil the genomes of relevant viruses.
• dc.description.sponsorship This research was funded by the Spanish Ministry of Science and Innovation (RTI2018-094248-B-I00), and Generalitat Valenciana (ACIF/2015/332 and APOSTD/2020/237).
• dc.format.mimetype application/pdf
• dc.identifier.citation Martinez-Hernandez F, Fornas O, Martinez-Garcia M. Into the dark: exploring the deep ocean with single-virus genomics. Viruses. 2022 Jul 21;14(7):1589. DOI: 10.3390/v14071589
• dc.identifier.doi http://dx.doi.org/10.3390/v14071589
• dc.identifier.issn 1999-4915
• dc.identifier.uri http://hdl.handle.net/10230/54777
• dc.language.iso eng
• dc.publisher MDPI
• dc.relation.ispartof Viruses. 2022 Jul 21;14(7):1589
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/RTI2018-094248-B-I00
• dc.rights © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri https://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Deep ocean
• dc.subject.keyword Marine viruses
• dc.subject.keyword Single-virus genomics
• dc.title Into the dark: exploring the deep ocean with single-virus genomics
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion