Assessing the diversity and specificity of two freshwater viral communities through metagenomics.

Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades. Yet, little is known about the composition and diversity of th...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Simon Roux, Francois Enault, Agnès Robin, Viviane Ravet, Sébastien Personnic, Sébastien Theil, Jonathan Colombet, Télesphore Sime-Ngando, Didier Debroas
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c6931095d673469f9d944f5fe272fc07
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:c6931095d673469f9d944f5fe272fc07
record_format	dspace
spelling	oai:doaj.org-article:c6931095d673469f9d944f5fe272fc072021-11-18T07:25:08ZAssessing the diversity and specificity of two freshwater viral communities through metagenomics.1932-620310.1371/journal.pone.0033641https://doaj.org/article/c6931095d673469f9d944f5fe272fc072012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22432038/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades. Yet, little is known about the composition and diversity of the temperate freshwater viral communities, and even if freshwater lakes and marine waters harbor distinct clades for particular viral sub-families, this distinction remains to be demonstrated on a community scale.To help identify the characteristics and potential specificities of freshwater viral communities, such communities from two lakes differing by their ecological parameters were studied through metagenomics. Both the cluster richness and the species richness of the Lake Bourget virome were significantly higher that those of the Lake Pavin, highlighting a trend similar to the one observed for microorganisms (i.e. the specie richness observed in mesotrophic lakes is greater than the one observed in oligotrophic lakes). Using 29 previously published viromes, the cluster richness was shown to vary between different environment types and appeared significantly higher in marine ecosystems than in other biomes. Furthermore, significant genetic similarity between viral communities of related environments was highlighted as freshwater, marine and hypersaline environments were separated from each other despite the vast geographical distances between sample locations within each of these biomes. An automated phylogeny procedure was then applied to marker genes of the major families of single-stranded (Microviridae, Circoviridae, Nanoviridae) and double-stranded (Caudovirales) DNA viruses. These phylogenetic analyses all spotlighted a very broad diversity and previously unknown clades undetectable by PCR analysis, clades that gathered sequences from the two lakes. Thus, the two freshwater viromes appear closely related, despite the significant ecological differences between the two lakes. Furthermore, freshwater viral communities appear genetically distinct from other aquatic ecosystems, demonstrating the specificity of freshwater viruses at a community scale for the first time.Simon RouxFrancois EnaultAgnès RobinViviane RavetSébastien PersonnicSébastien TheilJonathan ColombetTélesphore Sime-NgandoDidier DebroasPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 3, p e33641 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Simon Roux Francois Enault Agnès Robin Viviane Ravet Sébastien Personnic Sébastien Theil Jonathan Colombet Télesphore Sime-Ngando Didier Debroas Assessing the diversity and specificity of two freshwater viral communities through metagenomics.
description	Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests the existence of freshwater-specific viral clades. Yet, little is known about the composition and diversity of the temperate freshwater viral communities, and even if freshwater lakes and marine waters harbor distinct clades for particular viral sub-families, this distinction remains to be demonstrated on a community scale.To help identify the characteristics and potential specificities of freshwater viral communities, such communities from two lakes differing by their ecological parameters were studied through metagenomics. Both the cluster richness and the species richness of the Lake Bourget virome were significantly higher that those of the Lake Pavin, highlighting a trend similar to the one observed for microorganisms (i.e. the specie richness observed in mesotrophic lakes is greater than the one observed in oligotrophic lakes). Using 29 previously published viromes, the cluster richness was shown to vary between different environment types and appeared significantly higher in marine ecosystems than in other biomes. Furthermore, significant genetic similarity between viral communities of related environments was highlighted as freshwater, marine and hypersaline environments were separated from each other despite the vast geographical distances between sample locations within each of these biomes. An automated phylogeny procedure was then applied to marker genes of the major families of single-stranded (Microviridae, Circoviridae, Nanoviridae) and double-stranded (Caudovirales) DNA viruses. These phylogenetic analyses all spotlighted a very broad diversity and previously unknown clades undetectable by PCR analysis, clades that gathered sequences from the two lakes. Thus, the two freshwater viromes appear closely related, despite the significant ecological differences between the two lakes. Furthermore, freshwater viral communities appear genetically distinct from other aquatic ecosystems, demonstrating the specificity of freshwater viruses at a community scale for the first time.
format	article
author	Simon Roux Francois Enault Agnès Robin Viviane Ravet Sébastien Personnic Sébastien Theil Jonathan Colombet Télesphore Sime-Ngando Didier Debroas
author_facet	Simon Roux Francois Enault Agnès Robin Viviane Ravet Sébastien Personnic Sébastien Theil Jonathan Colombet Télesphore Sime-Ngando Didier Debroas
author_sort	Simon Roux
title	Assessing the diversity and specificity of two freshwater viral communities through metagenomics.
title_short	Assessing the diversity and specificity of two freshwater viral communities through metagenomics.
title_full	Assessing the diversity and specificity of two freshwater viral communities through metagenomics.
title_fullStr	Assessing the diversity and specificity of two freshwater viral communities through metagenomics.
title_full_unstemmed	Assessing the diversity and specificity of two freshwater viral communities through metagenomics.
title_sort	assessing the diversity and specificity of two freshwater viral communities through metagenomics.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/c6931095d673469f9d944f5fe272fc07
work_keys_str_mv	AT simonroux assessingthediversityandspecificityoftwofreshwaterviralcommunitiesthroughmetagenomics AT francoisenault assessingthediversityandspecificityoftwofreshwaterviralcommunitiesthroughmetagenomics AT agnesrobin assessingthediversityandspecificityoftwofreshwaterviralcommunitiesthroughmetagenomics AT vivianeravet assessingthediversityandspecificityoftwofreshwaterviralcommunitiesthroughmetagenomics AT sebastienpersonnic assessingthediversityandspecificityoftwofreshwaterviralcommunitiesthroughmetagenomics AT sebastientheil assessingthediversityandspecificityoftwofreshwaterviralcommunitiesthroughmetagenomics AT jonathancolombet assessingthediversityandspecificityoftwofreshwaterviralcommunitiesthroughmetagenomics AT telesphoresimengando assessingthediversityandspecificityoftwofreshwaterviralcommunitiesthroughmetagenomics AT didierdebroas assessingthediversityandspecificityoftwofreshwaterviralcommunitiesthroughmetagenomics
_version_	1718423499594268672

Assessing the diversity and specificity of two freshwater viral communities through metagenomics.

Ejemplares similares