The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses

ABSTRACT Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Torneträsk in order to investigate the diversity, distribution, and transcriptional activity of virioplankton....

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Autores principales:	Lisa Zeigler Allen, John P. McCrow, Karolina Ininbergs, Christopher L. Dupont, Jonathan H. Badger, Jeffery M. Hoffman, Martin Ekman, Andrew E. Allen, Birgitta Bergman, J. Craig Venter
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	marine microbiology viral ecology viral metagenomics viral metatranscriptomics viral/host inference Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/b53b0fd5c4034139b1c60ce6ef31e171
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spelling	oai:doaj.org-article:b53b0fd5c4034139b1c60ce6ef31e1712021-12-02T18:15:43ZThe Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses10.1128/mSystems.00125-162379-5077https://doaj.org/article/b53b0fd5c4034139b1c60ce6ef31e1712017-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00125-16https://doaj.org/toc/2379-5077ABSTRACT Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Torneträsk in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae. The distribution of phage reported to infect diverse and ubiquitous heterotrophic bacteria (SAR11 clades) and cyanobacteria (Synechococcus sp.) displayed population-level shifts in diversity. Samples from higher-salinity conditions (>14 practical salinity units [PSU]) had increased abundances of viruses for picoeukaryotes, i.e., Ostreococcus. These data, combined with host diversity estimates, suggest viral modulation of diversity on the whole-community scale, as well as in specific prokaryotic and eukaryotic lineages. RNA libraries revealed single-stranded DNA (ssDNA) and RNA viral populations throughout the Baltic Sea, with ssDNA phage highly represented in Lake Torneträsk. Further, our data suggest relatively high transcriptional activity of fish viruses within diverse families known to have broad host ranges, such as Nodoviridae (RNA), Iridoviridae (DNA), and predicted zoonotic viruses that can cause ecological and economic damage as well as impact human health. IMPORTANCE Inferred virus-host relationships, community structures of ubiquitous ecologically relevant groups, and identification of transcriptionally active populations have been achieved with our Baltic Sea study. Further, these data, highlighting the transcriptional activity of viruses, represent one of the more powerful uses of omics concerning ecosystem health. The use of omics-related data to assess ecosystem health holds great promise for rapid and relatively inexpensive determination of perturbations and risk, explicitly with regard to viral assemblages, as no single marker gene is suitable for widespread taxonomic coverage.Lisa Zeigler AllenJohn P. McCrowKarolina IninbergsChristopher L. DupontJonathan H. BadgerJeffery M. HoffmanMartin EkmanAndrew E. AllenBirgitta BergmanJ. Craig VenterAmerican Society for Microbiologyarticlemarine microbiologyviral ecologyviral metagenomicsviral metatranscriptomicsviral/host inferenceMicrobiologyQR1-502ENmSystems, Vol 2, Iss 1 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	marine microbiology viral ecology viral metagenomics viral metatranscriptomics viral/host inference Microbiology QR1-502
spellingShingle	marine microbiology viral ecology viral metagenomics viral metatranscriptomics viral/host inference Microbiology QR1-502 Lisa Zeigler Allen John P. McCrow Karolina Ininbergs Christopher L. Dupont Jonathan H. Badger Jeffery M. Hoffman Martin Ekman Andrew E. Allen Birgitta Bergman J. Craig Venter The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses
description	ABSTRACT Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Torneträsk in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae. The distribution of phage reported to infect diverse and ubiquitous heterotrophic bacteria (SAR11 clades) and cyanobacteria (Synechococcus sp.) displayed population-level shifts in diversity. Samples from higher-salinity conditions (>14 practical salinity units [PSU]) had increased abundances of viruses for picoeukaryotes, i.e., Ostreococcus. These data, combined with host diversity estimates, suggest viral modulation of diversity on the whole-community scale, as well as in specific prokaryotic and eukaryotic lineages. RNA libraries revealed single-stranded DNA (ssDNA) and RNA viral populations throughout the Baltic Sea, with ssDNA phage highly represented in Lake Torneträsk. Further, our data suggest relatively high transcriptional activity of fish viruses within diverse families known to have broad host ranges, such as Nodoviridae (RNA), Iridoviridae (DNA), and predicted zoonotic viruses that can cause ecological and economic damage as well as impact human health. IMPORTANCE Inferred virus-host relationships, community structures of ubiquitous ecologically relevant groups, and identification of transcriptionally active populations have been achieved with our Baltic Sea study. Further, these data, highlighting the transcriptional activity of viruses, represent one of the more powerful uses of omics concerning ecosystem health. The use of omics-related data to assess ecosystem health holds great promise for rapid and relatively inexpensive determination of perturbations and risk, explicitly with regard to viral assemblages, as no single marker gene is suitable for widespread taxonomic coverage.
format	article
author	Lisa Zeigler Allen John P. McCrow Karolina Ininbergs Christopher L. Dupont Jonathan H. Badger Jeffery M. Hoffman Martin Ekman Andrew E. Allen Birgitta Bergman J. Craig Venter
author_facet	Lisa Zeigler Allen John P. McCrow Karolina Ininbergs Christopher L. Dupont Jonathan H. Badger Jeffery M. Hoffman Martin Ekman Andrew E. Allen Birgitta Bergman J. Craig Venter
author_sort	Lisa Zeigler Allen
title	The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses
title_short	The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses
title_full	The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses
title_fullStr	The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses
title_full_unstemmed	The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses
title_sort	baltic sea virome: diversity and transcriptional activity of dna and rna viruses
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/b53b0fd5c4034139b1c60ce6ef31e171
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The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses

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