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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ftupompeufabra:oai:repositori.upf.edu:10230/54777 2023-05-15T17:34:30+02:00 Into the dark: exploring the deep ocean with single-virus genomics Martínez Hernández, Francisco Fornas Carreño, Oscar Martínez García, Manuel application/pdf http://hdl.handle.net/10230/54777 https://doi.org/10.3390/v14071589 eng eng MDPI Viruses. 2022 Jul 21;14(7):1589 info:eu-repo/grantAgreement/ES/2PE/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 Jul 21;14(7):1589. DOI:10.3390/v14071589 1999-4915 http://hdl.handle.net/10230/54777 http://dx.doi.org/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/). https://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess CC-BY Deep ocean Marine viruses Single-virus genomics info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion ftupompeufabra https://doi.org/10.3390/v14071589 2022-11-16T00:19:41Z 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 UPF Digital Repository (Universitat Pompeu Fabra, Barcelona) Pacific Viruses 14 7 1589 |
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Open Polar |
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UPF Digital Repository (Universitat Pompeu Fabra, Barcelona) |
op_collection_id |
ftupompeufabra |
language |
English |
topic |
Deep ocean Marine viruses Single-virus genomics |
spellingShingle |
Deep ocean Marine viruses Single-virus genomics Martínez Hernández, Francisco Fornas Carreño, Oscar Martínez García, Manuel Into the dark: exploring the deep ocean with single-virus genomics |
topic_facet |
Deep ocean Marine viruses Single-virus genomics |
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). |
format |
Article in Journal/Newspaper |
author |
Martínez Hernández, Francisco Fornas Carreño, Oscar Martínez García, Manuel |
author_facet |
Martínez Hernández, Francisco Fornas Carreño, Oscar Martínez García, Manuel |
author_sort |
Martínez Hernández, 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 |
url |
http://hdl.handle.net/10230/54777 https://doi.org/10.3390/v14071589 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
North Atlantic |
genre_facet |
North Atlantic |
op_relation |
Viruses. 2022 Jul 21;14(7):1589 info:eu-repo/grantAgreement/ES/2PE/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 Jul 21;14(7):1589. DOI:10.3390/v14071589 1999-4915 http://hdl.handle.net/10230/54777 http://dx.doi.org/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/). https://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3390/v14071589 |
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Viruses |
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14 |
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1589 |
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