title: 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. 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 orderCaudoviraleswere identified with enrichments in lesser-known families such asPodoviridaeandSiphoviridae. The distribution of phage reported to infect diverse and ubiquitous heterotrophic bacteria (SAR11 clades) and cyanobacteria (Synechococcussp.) 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 asNodoviridae(RNA),Iridoviridae(DNA), and predicted zoonotic viruses that can cause ecological and economic damage as well as impact human health.IMPORTANCEInferred 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.
authors.affiliation: Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, USA.
authors.forename: Lisa
authors.initials: L
authors.lastname: Zeigler Allen
authors.affiliation: Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, USA.
authors.forename: John P
authors.initials: JP
authors.lastname: McCrow
authors.affiliation: Department of Ecology, Environment and Plant Sciences, Stockholm University/Science for Life Laboratory, Solna, Sweden.
authors.forename: Karolina
authors.initials: K
authors.lastname: Ininbergs
authors.affiliation: Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, USA.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Dupont
authors.affiliation: Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, USA.
authors.forename: Jonathan H
authors.initials: JH
authors.lastname: Badger
authors.affiliation: Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, USA.
authors.forename: Jeffery M
authors.initials: JM
authors.lastname: Hoffman
authors.affiliation: Department of Ecology, Environment and Plant Sciences, Stockholm University/Science for Life Laboratory, Solna, Sweden.
authors.forename: Martin
authors.initials: M
authors.lastname: Ekman
authors.affiliation: Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, USA; Scripps Institution of Oceanography, La Jolla, California, USA.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Allen
authors.affiliation: Department of Ecology, Environment and Plant Sciences, Stockholm University/Science for Life Laboratory, Solna, Sweden.
authors.forename: Birgitta
authors.initials: B
authors.lastname: Bergman
authors.affiliation: Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, California, USA.
authors.forename: J Craig
authors.initials: JC
authors.lastname: Venter
keywords: marine microbiology; viral ecology; viral metagenomics; viral metatranscriptomics; viral/host inference