Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic bacteroidetes

Hypersaline environments close to saturation harbor the highest density of virus-like particles reported for aquatic systems as well as low microbial diversity. Thus, they offer unique settings for studying virus-host interactions in nature. However, no viruses have been isolated so far infecting th...

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Autores: Villamor, Judith, Ramos-Barbero, María Dolores, González-Torres, Pedro, Gabaldón Estevan, Juan Antonio, 1973-, Rosselló-Mora, Ramón, Meseguer, Inmaculada, Martínez García, Manuel, Santos, Fernando, Antón, Josefa
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2018
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/42571
Acceso en línea:http://hdl.handle.net/10230/42571
http://dx.doi.org/10.1038/ismej.2017.175
Access Level:acceso abierto
Palabra clave:Biodiversity
Metagenomics
Virus–host interactions
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spelling Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic bacteroidetesVillamor, JudithRamos-Barbero, María DoloresGonzález-Torres, PedroGabaldón Estevan, Juan Antonio, 1973-Rosselló-Mora, RamónMeseguer, InmaculadaMartínez García, ManuelSantos, FernandoAntón, JosefaBiodiversityMetagenomicsVirus–host interactionsHypersaline environments close to saturation harbor the highest density of virus-like particles reported for aquatic systems as well as low microbial diversity. Thus, they offer unique settings for studying virus-host interactions in nature. However, no viruses have been isolated so far infecting the two most abundant inhabitants of these systems (that is, the euryarchaeon Haloquadratum walsbyi and the bacteroidetes Salinibacter ruber). Here, using three different co-occurring strains, we have isolated eight viruses infecting the ubiquitous S. ruber that constitute three new different genera (named as 'Holosalinivirus', 'Kryptosalinivirus' and 'Kairosalinivirus') according to their genomic traits, different host range, virus-host interaction capabilities and abundances in natural systems worldwide. Furthermore, to get a more complete and comprehensive view of S. ruber virus assemblages in nature, a microcosm experiment was set with a mixture of S. ruber strains challenged with a brine virus concentrate, and changes of viral populations were monitored by viral metagenomics. Only viruses closely related to kairosalinivirus (strictly lytic and wide host range) were enriched, despite their low initial abundance in the natural sample. Metagenomic analyses of the mesocosms allowed the complete recovery of kairosalinivirus genomes using an ad hoc assembly strategy as common viral metagenomic assembly tools failed despite their abundance, which underlines the limitations of current approaches. The increase of this type of viruses was accompanied by an increase in the diversity of the group, as shown by contig recruitment. These results are consistent with a scenario in which host range, not only virus and host abundances, is a key factor in determining virus fate in nature.This research was supported by the Spanish Ministry of Economy projects CLG2015_66686-C3-1 (to JA) and CLG2015_66686-C3-3 (to RRM), which were also supported with European Regional Development Fund (FEDER) funds.Nature Research201920192018info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/42571http://dx.doi.org/10.1038/ismej.2017.175reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésISME J. 2018; 12(2): 424-437info:eu-repo/grantAgreement/ES/1PE/CLG2015_66686-C3-1info:eu-repo/grantAgreement/ES/1PE/CLG2015_66686-C3-3© The Author(s) 2018. This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/http://creativecommons.org/licenses/by-nc-sa/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/425712026-06-12T07:21:37Z
dc.title.none.fl_str_mv Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic bacteroidetes
title Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic bacteroidetes
spellingShingle Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic bacteroidetes
Villamor, Judith
Biodiversity
Metagenomics
Virus–host interactions
title_short Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic bacteroidetes
title_full Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic bacteroidetes
title_fullStr Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic bacteroidetes
title_full_unstemmed Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic bacteroidetes
title_sort Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic bacteroidetes
dc.creator.none.fl_str_mv Villamor, Judith
Ramos-Barbero, María Dolores
González-Torres, Pedro
Gabaldón Estevan, Juan Antonio, 1973-
Rosselló-Mora, Ramón
Meseguer, Inmaculada
Martínez García, Manuel
Santos, Fernando
Antón, Josefa
author Villamor, Judith
author_facet Villamor, Judith
Ramos-Barbero, María Dolores
González-Torres, Pedro
Gabaldón Estevan, Juan Antonio, 1973-
Rosselló-Mora, Ramón
Meseguer, Inmaculada
Martínez García, Manuel
Santos, Fernando
Antón, Josefa
author_role author
author2 Ramos-Barbero, María Dolores
González-Torres, Pedro
Gabaldón Estevan, Juan Antonio, 1973-
Rosselló-Mora, Ramón
Meseguer, Inmaculada
Martínez García, Manuel
Santos, Fernando
Antón, Josefa
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Biodiversity
Metagenomics
Virus–host interactions
topic Biodiversity
Metagenomics
Virus–host interactions
description Hypersaline environments close to saturation harbor the highest density of virus-like particles reported for aquatic systems as well as low microbial diversity. Thus, they offer unique settings for studying virus-host interactions in nature. However, no viruses have been isolated so far infecting the two most abundant inhabitants of these systems (that is, the euryarchaeon Haloquadratum walsbyi and the bacteroidetes Salinibacter ruber). Here, using three different co-occurring strains, we have isolated eight viruses infecting the ubiquitous S. ruber that constitute three new different genera (named as 'Holosalinivirus', 'Kryptosalinivirus' and 'Kairosalinivirus') according to their genomic traits, different host range, virus-host interaction capabilities and abundances in natural systems worldwide. Furthermore, to get a more complete and comprehensive view of S. ruber virus assemblages in nature, a microcosm experiment was set with a mixture of S. ruber strains challenged with a brine virus concentrate, and changes of viral populations were monitored by viral metagenomics. Only viruses closely related to kairosalinivirus (strictly lytic and wide host range) were enriched, despite their low initial abundance in the natural sample. Metagenomic analyses of the mesocosms allowed the complete recovery of kairosalinivirus genomes using an ad hoc assembly strategy as common viral metagenomic assembly tools failed despite their abundance, which underlines the limitations of current approaches. The increase of this type of viruses was accompanied by an increase in the diversity of the group, as shown by contig recruitment. These results are consistent with a scenario in which host range, not only virus and host abundances, is a key factor in determining virus fate in nature.
publishDate 2018
dc.date.none.fl_str_mv 2018
2019
2019
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/42571
http://dx.doi.org/10.1038/ismej.2017.175
url http://hdl.handle.net/10230/42571
http://dx.doi.org/10.1038/ismej.2017.175
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv ISME J. 2018; 12(2): 424-437
info:eu-repo/grantAgreement/ES/1PE/CLG2015_66686-C3-1
info:eu-repo/grantAgreement/ES/1PE/CLG2015_66686-C3-3
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Nature Research
publisher.none.fl_str_mv Nature Research
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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