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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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Viral community functional richness based on season and proximity to shore.Rarefaction analysis of hits to protein clusters from: (A) 11 POV metagenomes from a single LineP open ocean site (station P26) (B) 11 POV metagenomes from LineP stations P4, P12, and P26 from a single research cruise (June 2009). To be conservative, only protein clusters with >20 members were used in these analyses.
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pone-0057355-g003: Viral community functional richness based on season and proximity to shore.Rarefaction analysis of hits to protein clusters from: (A) 11 POV metagenomes from a single LineP open ocean site (station P26) (B) 11 POV metagenomes from LineP stations P4, P12, and P26 from a single research cruise (June 2009). To be conservative, only protein clusters with >20 members were used in these analyses.

Mentions: To examine ocean viral functional richness across the depth continuum (10 m to 2000 m) and season (spring, summer, and winter), 11 metagenomes from a single LineP open ocean site (station P26) were analyzed by protein cluster/rarefaction analysis [33], [47]. Rarefaction analysis showed that photic samples were less functionally rich than aphotic samples from the same season (Figure 3A). When comparing samples from different seasons in the same photic zone rarefaction analysis showed that winter was the most functionally rich, followed by spring, and summer (Figure 3A). All aphotic samples clearly separated by season, whereas photic samples showed similar levels of functional richness in spring and summer but increased richness in winter. Overall, rarefaction patterns indicate that season and photic zone are important drivers of viral community functional richness at LineP.


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)

Viral community functional richness based on season and proximity to shore.Rarefaction analysis of hits to protein clusters from: (A) 11 POV metagenomes from a single LineP open ocean site (station P26) (B) 11 POV metagenomes from LineP stations P4, P12, and P26 from a single research cruise (June 2009). To be conservative, only protein clusters with >20 members were used in these analyses.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3585363&req=5

pone-0057355-g003: Viral community functional richness based on season and proximity to shore.Rarefaction analysis of hits to protein clusters from: (A) 11 POV metagenomes from a single LineP open ocean site (station P26) (B) 11 POV metagenomes from LineP stations P4, P12, and P26 from a single research cruise (June 2009). To be conservative, only protein clusters with >20 members were used in these analyses.
Mentions: To examine ocean viral functional richness across the depth continuum (10 m to 2000 m) and season (spring, summer, and winter), 11 metagenomes from a single LineP open ocean site (station P26) were analyzed by protein cluster/rarefaction analysis [33], [47]. Rarefaction analysis showed that photic samples were less functionally rich than aphotic samples from the same season (Figure 3A). When comparing samples from different seasons in the same photic zone rarefaction analysis showed that winter was the most functionally rich, followed by spring, and summer (Figure 3A). All aphotic samples clearly separated by season, whereas photic samples showed similar levels of functional richness in spring and summer but increased richness in winter. Overall, rarefaction patterns indicate that season and photic zone are important drivers of viral community functional richness at LineP.

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