Into the Dark: Exploring the Deep Ocean with Single-Virus Genomics
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 i...
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Online Access: | http://hdl.handle.net/10045/125570 https://doi.org/10.3390/v14071589 |
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ftunivalicante:oai:rua.ua.es:10045/125570 2023-05-15T17:34:21+02:00 Into the Dark: Exploring the Deep Ocean with Single-Virus Genomics Martinez-Hernandez, Francisco Fornas, Oscar Martinez-Garcia, Manuel Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología Ecología Microbiana Molecular 2022-07-21 http://hdl.handle.net/10045/125570 https://doi.org/10.3390/v14071589 eng eng MDPI https://doi.org/10.3390/v14071589 info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-094248-B-I00 Martinez-Hernandez F, Fornas O, Martinez-Garcia M. Into the Dark: Exploring the Deep Ocean with Single-Virus Genomics. Viruses. 2022; 14(7):1589. https://doi.org/10.3390/v14071589 1999-4915 http://hdl.handle.net/10045/125570 doi:10.3390/v14071589 © 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/). info:eu-repo/semantics/openAccess CC-BY Single-virus genomics Deep ocean Marine viruses info:eu-repo/semantics/article 2022 ftunivalicante https://doi.org/10.3390/v14071589 2022-08-02T23:20:04Z 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. 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). Article in Journal/Newspaper North Atlantic RUA - Repositorio Institucional de la Universidad de Alicante Pacific Viruses 14 7 1589 |
institution |
Open Polar |
collection |
RUA - Repositorio Institucional de la Universidad de Alicante |
op_collection_id |
ftunivalicante |
language |
English |
topic |
Single-virus genomics Deep ocean Marine viruses |
spellingShingle |
Single-virus genomics Deep ocean Marine viruses Martinez-Hernandez, Francisco Fornas, Oscar Martinez-Garcia, Manuel Into the Dark: Exploring the Deep Ocean with Single-Virus Genomics |
topic_facet |
Single-virus genomics Deep ocean Marine viruses |
description |
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. 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). |
author2 |
Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología Ecología Microbiana Molecular |
format |
Article in Journal/Newspaper |
author |
Martinez-Hernandez, Francisco Fornas, Oscar Martinez-Garcia, Manuel |
author_facet |
Martinez-Hernandez, Francisco Fornas, Oscar Martinez-Garcia, Manuel |
author_sort |
Martinez-Hernandez, Francisco |
title |
Into the Dark: Exploring the Deep Ocean with Single-Virus Genomics |
title_short |
Into the Dark: Exploring the Deep Ocean with Single-Virus Genomics |
title_full |
Into the Dark: Exploring the Deep Ocean with Single-Virus Genomics |
title_fullStr |
Into the Dark: Exploring the Deep Ocean with Single-Virus Genomics |
title_full_unstemmed |
Into the Dark: Exploring the Deep Ocean with Single-Virus Genomics |
title_sort |
into the dark: exploring the deep ocean with single-virus genomics |
publisher |
MDPI |
publishDate |
2022 |
url |
http://hdl.handle.net/10045/125570 https://doi.org/10.3390/v14071589 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
North Atlantic |
genre_facet |
North Atlantic |
op_relation |
https://doi.org/10.3390/v14071589 info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-094248-B-I00 Martinez-Hernandez F, Fornas O, Martinez-Garcia M. Into the Dark: Exploring the Deep Ocean with Single-Virus Genomics. Viruses. 2022; 14(7):1589. https://doi.org/10.3390/v14071589 1999-4915 http://hdl.handle.net/10045/125570 doi:10.3390/v14071589 |
op_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/). info:eu-repo/semantics/openAccess |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3390/v14071589 |
container_title |
Viruses |
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14 |
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7 |
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1589 |
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1766133158717161472 |