The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics

ABSTRACT Viruses have a profound influence on the ecology and evolution of plankton, but our understanding of the composition of the aquatic viral communities is still rudimentary. This is especially true of those viruses having RNA genomes. The limited data that have been published suggest that the...

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Autores principales:	Alexander I. Culley, Jaclyn A. Mueller, Madhi Belcaid, Elisha M. Wood-Charlson, Guylaine Poisson, Grieg F. Steward
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2014
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/a2b6565974f946679fc303ec726e8da9
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spelling	oai:doaj.org-article:a2b6565974f946679fc303ec726e8da92021-11-15T15:47:38ZThe Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics10.1128/mBio.01210-142150-7511https://doaj.org/article/a2b6565974f946679fc303ec726e8da92014-07-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01210-14https://doaj.org/toc/2150-7511ABSTRACT Viruses have a profound influence on the ecology and evolution of plankton, but our understanding of the composition of the aquatic viral communities is still rudimentary. This is especially true of those viruses having RNA genomes. The limited data that have been published suggest that the RNA virioplankton is dominated by viruses with positive-sense, single-stranded (+ss) genomes that have features in common with those of eukaryote-infecting viruses in the order Picornavirales (picornavirads). In this study, we investigated the diversity of the RNA virus assemblages in tropical coastal seawater samples using targeted PCR and metagenomics. Amplification of RNA-dependent RNA polymerase (RdRp) genes from fractions of a buoyant density gradient suggested that the distribution of two major subclades of the marine picornavirads was largely congruent with the distribution of total virus-like RNA, a finding consistent with their proposed dominance. Analyses of the RdRp sequences in the library revealed the presence of many diverse phylotypes, most of which were related only distantly to those of cultivated viruses. Phylogenetic analysis suggests that there were hundreds of unique picornavirad-like phylotypes in one 35-liter sample that differed from one another by at least as much as the differences among currently recognized species. Assembly of the sequences in the metagenome resulted in the reconstruction of six essentially complete viral genomes that had features similar to viruses in the families Bacillarna-, Dicistro-, and Marnaviridae. Comparison of the tropical seawater metagenomes with those from other habitats suggests that +ssRNA viruses are generally the most common types of RNA viruses in aquatic environments, but biases in library preparation remain a possible explanation for this observation. IMPORTANCE Marine plankton account for much of the photosynthesis and respiration on our planet, and they influence the cycling of carbon and the distribution of nutrients on a global scale. Despite the fundamental importance of viruses to plankton ecology and evolution, most of the viruses in the sea, and the identities of their hosts, are unknown. This report is one of very few that delves into the genetic diversity within RNA-containing viruses in the ocean. The data expand the known range of viral diversity and shed new light on the physical properties and genetic composition of RNA viruses in the ocean.Alexander I. CulleyJaclyn A. MuellerMadhi BelcaidElisha M. Wood-CharlsonGuylaine PoissonGrieg F. StewardAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 5, Iss 3 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Alexander I. Culley Jaclyn A. Mueller Madhi Belcaid Elisha M. Wood-Charlson Guylaine Poisson Grieg F. Steward The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics
description	ABSTRACT Viruses have a profound influence on the ecology and evolution of plankton, but our understanding of the composition of the aquatic viral communities is still rudimentary. This is especially true of those viruses having RNA genomes. The limited data that have been published suggest that the RNA virioplankton is dominated by viruses with positive-sense, single-stranded (+ss) genomes that have features in common with those of eukaryote-infecting viruses in the order Picornavirales (picornavirads). In this study, we investigated the diversity of the RNA virus assemblages in tropical coastal seawater samples using targeted PCR and metagenomics. Amplification of RNA-dependent RNA polymerase (RdRp) genes from fractions of a buoyant density gradient suggested that the distribution of two major subclades of the marine picornavirads was largely congruent with the distribution of total virus-like RNA, a finding consistent with their proposed dominance. Analyses of the RdRp sequences in the library revealed the presence of many diverse phylotypes, most of which were related only distantly to those of cultivated viruses. Phylogenetic analysis suggests that there were hundreds of unique picornavirad-like phylotypes in one 35-liter sample that differed from one another by at least as much as the differences among currently recognized species. Assembly of the sequences in the metagenome resulted in the reconstruction of six essentially complete viral genomes that had features similar to viruses in the families Bacillarna-, Dicistro-, and Marnaviridae. Comparison of the tropical seawater metagenomes with those from other habitats suggests that +ssRNA viruses are generally the most common types of RNA viruses in aquatic environments, but biases in library preparation remain a possible explanation for this observation. IMPORTANCE Marine plankton account for much of the photosynthesis and respiration on our planet, and they influence the cycling of carbon and the distribution of nutrients on a global scale. Despite the fundamental importance of viruses to plankton ecology and evolution, most of the viruses in the sea, and the identities of their hosts, are unknown. This report is one of very few that delves into the genetic diversity within RNA-containing viruses in the ocean. The data expand the known range of viral diversity and shed new light on the physical properties and genetic composition of RNA viruses in the ocean.
format	article
author	Alexander I. Culley Jaclyn A. Mueller Madhi Belcaid Elisha M. Wood-Charlson Guylaine Poisson Grieg F. Steward
author_facet	Alexander I. Culley Jaclyn A. Mueller Madhi Belcaid Elisha M. Wood-Charlson Guylaine Poisson Grieg F. Steward
author_sort	Alexander I. Culley
title	The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics
title_short	The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics
title_full	The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics
title_fullStr	The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics
title_full_unstemmed	The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics
title_sort	characterization of rna viruses in tropical seawater using targeted pcr and metagenomics
publisher	American Society for Microbiology
publishDate	2014
url	https://doaj.org/article/a2b6565974f946679fc303ec726e8da9
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The Characterization of RNA Viruses in Tropical Seawater Using Targeted PCR and Metagenomics

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