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

被引:56
作者
Allen, Lisa Zeigler [1 ]
McCrow, John P. [1 ]
Ininbergs, Karolina [3 ]
Dupont, Christopher L. [1 ]
Badger, Jonathan H. [1 ,4 ]
Hoffman, Jeffery M. [1 ]
Ekman, Martin [3 ]
Allen, Andrew E. [1 ,2 ]
Bergman, Birgitta [3 ]
Venter, J. Craig [1 ]
机构
[1] J Craig Venter Inst, Microbial & Environm Genom, San Diego, CA 92037 USA
[2] Scripps Inst Oceanog, La Jolla, CA USA
[3] Stockholm Univ, Sci Life Lab, Dept Ecol Environm & Plant Sci, Solna, Sweden
[4] NCI, Natl Canc Inst, Bethesda, MD 20892 USA
基金
瑞典研究理事会; 美国国家科学基金会;
关键词
marine microbiology; viral ecology; viral metagenomics; viral metatranscriptomics; viral/host inference; KM SALINITY GRADIENT; MARINE VIRUSES; VIRAL LYSIS; BACTERIOPLANKTON; BIODIVERSITY; CYANOBACTERIA; ABUNDANCE; GENOME; AMPLIFICATION; COMMUNITIES;
D O I
10.1128/mSystems.00125-16
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
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 Tornetrask 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 Tornetrask. 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.
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页数:16
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