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The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology.

Hurwitz BL, Sullivan MB - PLoS ONE (2013)

Bottom Line: These protein clusters more than double currently available viral protein clusters, including those from environmental datasets.Further, a protein cluster guided analysis of functional diversity revealed that richness decreased (i) from deep to surface waters, (ii) from winter to summer, (iii) and with distance from shore in surface waters only.These data provide a framework from which to draw on for future metadata-enabled functional inquiries of the vast viral unknown.

View Article: PubMed Central - PubMed

Affiliation: Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.

ABSTRACT
Bacteria and their viruses (phage) are fundamental drivers of many ecosystem processes including global biogeochemistry and horizontal gene transfer. While databases and resources for studying function in uncultured bacterial communities are relatively advanced, many fewer exist for their viral counterparts. The issue is largely technical in that the majority (often 90%) of viral sequences are functionally 'unknown' making viruses a virtually untapped resource of functional and physiological information. Here, we provide a community resource that organizes this unknown sequence space into 27 K high confidence protein clusters using 32 viral metagenomes from four biogeographic regions in the Pacific Ocean that vary by season, depth, and proximity to land, and include some of the first deep pelagic ocean viral metagenomes. These protein clusters more than double currently available viral protein clusters, including those from environmental datasets. Further, a protein cluster guided analysis of functional diversity revealed that richness decreased (i) from deep to surface waters, (ii) from winter to summer, (iii) and with distance from shore in surface waters only. These data provide a framework from which to draw on for future metadata-enabled functional inquiries of the vast viral unknown.

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Sampling site map for the POV dataset.Thirty-two viral metagenomes represent discretely sampled and processed datasets that vary over time and space in the pelagic Pacific Ocean. (A) Overview of sampling sites, (B) GBR – Great Barrier Reef, Australia, near Dunk and Fitzroy Islands. (C) LineP- oceanographic transect off Vancouver Island, British Columbia (D) MBARI- Line67 oceanographic transect off of Monterey Bay, California (E) SIO- Scripps Pier, San Diego, CA. Images were created using Ocean Data View.
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pone-0057355-g001: Sampling site map for the POV dataset.Thirty-two viral metagenomes represent discretely sampled and processed datasets that vary over time and space in the pelagic Pacific Ocean. (A) Overview of sampling sites, (B) GBR – Great Barrier Reef, Australia, near Dunk and Fitzroy Islands. (C) LineP- oceanographic transect off Vancouver Island, British Columbia (D) MBARI- Line67 oceanographic transect off of Monterey Bay, California (E) SIO- Scripps Pier, San Diego, CA. Images were created using Ocean Data View.

Mentions: The 32 POV source waters varied by depth, proximity to land, and season and were derived from four regions in the Pacific Ocean (Figure 1): Scripps Pier in San Diego, California (SIO), Monterey Bay, California (MBARI), near Vancouver Island in British Columbia (LineP), and the Great Barrier Reef in Australia (GBR). Samples, metadata, and metagenomic descriptive statistics are summarized in Table 2.


The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology.

Hurwitz BL, Sullivan MB - PLoS ONE (2013)

Sampling site map for the POV dataset.Thirty-two viral metagenomes represent discretely sampled and processed datasets that vary over time and space in the pelagic Pacific Ocean. (A) Overview of sampling sites, (B) GBR – Great Barrier Reef, Australia, near Dunk and Fitzroy Islands. (C) LineP- oceanographic transect off Vancouver Island, British Columbia (D) MBARI- Line67 oceanographic transect off of Monterey Bay, California (E) SIO- Scripps Pier, San Diego, CA. Images were created using Ocean Data View.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3585363&req=5

pone-0057355-g001: Sampling site map for the POV dataset.Thirty-two viral metagenomes represent discretely sampled and processed datasets that vary over time and space in the pelagic Pacific Ocean. (A) Overview of sampling sites, (B) GBR – Great Barrier Reef, Australia, near Dunk and Fitzroy Islands. (C) LineP- oceanographic transect off Vancouver Island, British Columbia (D) MBARI- Line67 oceanographic transect off of Monterey Bay, California (E) SIO- Scripps Pier, San Diego, CA. Images were created using Ocean Data View.
Mentions: The 32 POV source waters varied by depth, proximity to land, and season and were derived from four regions in the Pacific Ocean (Figure 1): Scripps Pier in San Diego, California (SIO), Monterey Bay, California (MBARI), near Vancouver Island in British Columbia (LineP), and the Great Barrier Reef in Australia (GBR). Samples, metadata, and metagenomic descriptive statistics are summarized in Table 2.

Bottom Line: These protein clusters more than double currently available viral protein clusters, including those from environmental datasets.Further, a protein cluster guided analysis of functional diversity revealed that richness decreased (i) from deep to surface waters, (ii) from winter to summer, (iii) and with distance from shore in surface waters only.These data provide a framework from which to draw on for future metadata-enabled functional inquiries of the vast viral unknown.

View Article: PubMed Central - PubMed

Affiliation: Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.

ABSTRACT
Bacteria and their viruses (phage) are fundamental drivers of many ecosystem processes including global biogeochemistry and horizontal gene transfer. While databases and resources for studying function in uncultured bacterial communities are relatively advanced, many fewer exist for their viral counterparts. The issue is largely technical in that the majority (often 90%) of viral sequences are functionally 'unknown' making viruses a virtually untapped resource of functional and physiological information. Here, we provide a community resource that organizes this unknown sequence space into 27 K high confidence protein clusters using 32 viral metagenomes from four biogeographic regions in the Pacific Ocean that vary by season, depth, and proximity to land, and include some of the first deep pelagic ocean viral metagenomes. These protein clusters more than double currently available viral protein clusters, including those from environmental datasets. Further, a protein cluster guided analysis of functional diversity revealed that richness decreased (i) from deep to surface waters, (ii) from winter to summer, (iii) and with distance from shore in surface waters only. These data provide a framework from which to draw on for future metadata-enabled functional inquiries of the vast viral unknown.

Show MeSH
Related in: MedlinePlus