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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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Related in: MedlinePlus

Viral community functional richness in the Pacific Ocean.Rarefaction analysis of hits to protein clusters from all POV metagenomes in (A) photic zone samples and (B) aphotic zone samples. To be conservative, only protein clusters with >20 members were used in these analyses.
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pone-0057355-g004: Viral community functional richness in the Pacific Ocean.Rarefaction analysis of hits to protein clusters from all POV metagenomes in (A) photic zone samples and (B) aphotic zone samples. To be conservative, only protein clusters with >20 members were used in these analyses.

Mentions: Given that functional richness differed by photic zone in the smaller subset of LineP samples examined above, we analyzed the complete POV dataset by photic zone using a protein cluster/rarefaction analysis (Figure 4A and B). In the photic rarefaction analysis (Figure 4A), we found that deeply sequenced SIO samples were the most functionally rich. Though the rarefaction analysis should normalize the samples in terms of sequencing effort, the limitation we placed on our analysis to include only 20+ member clusters may have included rare SIO clusters that are highly represented due to the exceptional sequencing effort for this single sample. The samples with the next highest functional richness came from MBARI samples in the same current system as a local upwelling, followed by samples from fall/winter and spring/summer. We noted several exceptions to these general trends. First, the LineP spring coastal sample, L.Spr.C.10 m, grouped more closely to fall/winter samples, likely due to the higher functional richness noted previously in photic coastal samples. Secondly, the MBARI fall open ocean sample taken from waters in a deep chlorophyll maximum (DCM), M.Fall.O.105 m, grouped more closely to fall/winter samples, which could be due to increased functional richness in the DCM. Yet, we could not confirm this given the low sequencing effort and limited trend information in the rarefaction curve from other DCM sample, M.Fall.I.42 m. In the aphotic rarefaction analysis (Figure 4B), winter/fall/spring samples were the most functionally rich followed by summer.


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 in the Pacific Ocean.Rarefaction analysis of hits to protein clusters from all POV metagenomes in (A) photic zone samples and (B) aphotic zone samples. To be conservative, only protein clusters with >20 members were used in these analyses.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0057355-g004: Viral community functional richness in the Pacific Ocean.Rarefaction analysis of hits to protein clusters from all POV metagenomes in (A) photic zone samples and (B) aphotic zone samples. To be conservative, only protein clusters with >20 members were used in these analyses.
Mentions: Given that functional richness differed by photic zone in the smaller subset of LineP samples examined above, we analyzed the complete POV dataset by photic zone using a protein cluster/rarefaction analysis (Figure 4A and B). In the photic rarefaction analysis (Figure 4A), we found that deeply sequenced SIO samples were the most functionally rich. Though the rarefaction analysis should normalize the samples in terms of sequencing effort, the limitation we placed on our analysis to include only 20+ member clusters may have included rare SIO clusters that are highly represented due to the exceptional sequencing effort for this single sample. The samples with the next highest functional richness came from MBARI samples in the same current system as a local upwelling, followed by samples from fall/winter and spring/summer. We noted several exceptions to these general trends. First, the LineP spring coastal sample, L.Spr.C.10 m, grouped more closely to fall/winter samples, likely due to the higher functional richness noted previously in photic coastal samples. Secondly, the MBARI fall open ocean sample taken from waters in a deep chlorophyll maximum (DCM), M.Fall.O.105 m, grouped more closely to fall/winter samples, which could be due to increased functional richness in the DCM. Yet, we could not confirm this given the low sequencing effort and limited trend information in the rarefaction curve from other DCM sample, M.Fall.I.42 m. In the aphotic rarefaction analysis (Figure 4B), winter/fall/spring samples were the most functionally rich followed by summer.

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