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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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The POV dataset and its place in the viral protein universe.(A) Summary superkingdom taxonomy statistics for quantitative Pacific Ocean viral metagenomes from 16 photic and 16 aphotic zone samples. Reads were taxonomically assigned based on matches to proteins in SIMAP and curated as described in the methods. (B) Venn diagram representing medium- to large membership PCs documents the relative contributions of the POV, GOS microbial, and SIMAP datasets to the ‘viral protein universe’.
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pone-0057355-g002: The POV dataset and its place in the viral protein universe.(A) Summary superkingdom taxonomy statistics for quantitative Pacific Ocean viral metagenomes from 16 photic and 16 aphotic zone samples. Reads were taxonomically assigned based on matches to proteins in SIMAP and curated as described in the methods. (B) Venn diagram representing medium- to large membership PCs documents the relative contributions of the POV, GOS microbial, and SIMAP datasets to the ‘viral protein universe’.

Mentions: Long-standing questions in marine viral ecology are centered on understanding the extent to which viral assemblages change spatially, temporally and under different environmental conditions in the ocean [2]. Yet, given the paucity of known viruses in biological databases comparatively examining viral assemblages from diverse environments in the sea is stymied. As commonly observed in marine viral metagenomic studies [20], [25], [41]–[43], the majority (87% photic zone, 91% aphotic zone) of the reads could not be classified based on sequence similarity to known taxa (see Materials and Methods, Figure 2A). Moreover, we found a smaller fraction of reads that matched known viruses in the aphotic zone (3.3%) than the photic zone (8.3%) likely due to more sampling in the surface oceans (Figure 2A and Table 1).


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)

The POV dataset and its place in the viral protein universe.(A) Summary superkingdom taxonomy statistics for quantitative Pacific Ocean viral metagenomes from 16 photic and 16 aphotic zone samples. Reads were taxonomically assigned based on matches to proteins in SIMAP and curated as described in the methods. (B) Venn diagram representing medium- to large membership PCs documents the relative contributions of the POV, GOS microbial, and SIMAP datasets to the ‘viral protein universe’.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0057355-g002: The POV dataset and its place in the viral protein universe.(A) Summary superkingdom taxonomy statistics for quantitative Pacific Ocean viral metagenomes from 16 photic and 16 aphotic zone samples. Reads were taxonomically assigned based on matches to proteins in SIMAP and curated as described in the methods. (B) Venn diagram representing medium- to large membership PCs documents the relative contributions of the POV, GOS microbial, and SIMAP datasets to the ‘viral protein universe’.
Mentions: Long-standing questions in marine viral ecology are centered on understanding the extent to which viral assemblages change spatially, temporally and under different environmental conditions in the ocean [2]. Yet, given the paucity of known viruses in biological databases comparatively examining viral assemblages from diverse environments in the sea is stymied. As commonly observed in marine viral metagenomic studies [20], [25], [41]–[43], the majority (87% photic zone, 91% aphotic zone) of the reads could not be classified based on sequence similarity to known taxa (see Materials and Methods, Figure 2A). Moreover, we found a smaller fraction of reads that matched known viruses in the aphotic zone (3.3%) than the photic zone (8.3%) likely due to more sampling in the surface oceans (Figure 2A and Table 1).

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