The Pacific Ocean Virome (POV): A Marine Viral Metagenomic Dataset and Associated Protein Clusters for Quantitative Viral Ecology

By Bonnie L. Hurwitz, Matthew B. Sullivan. 2013

327 citations recorded by the source corpus.

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.

Subfields: Ecology, Epidemiology

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Citations in the corpus

MMseqs2: sensitive protein sequence searching for the analysis of massive data sets (2017, background): “Because many species found in metagenomics and metatranscriptomics studies are not closely related to any organism with a well-annotated genome, the fraction of unannotatable sequences is often as high as 65% to 90% [1, 14], and the widen45”
Marine DNA viral macro- and micro-diversity from pole to pole (2019, background): “Based on our previous observation from a time-series data in a sub-arctic system (Hurwitz and Sullivan, 2013), our viralmacrodiversity is expected to be lowest during the spring and summer and increase toward the winter season.”
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data (2017, background): “It is estimated that only about 15% of viruses in human gut microbiome and 10% in the ocean have similarity to the known viruses [3, 20].”
New perspectives in benthic deep-sea microbial ecology (2015, background): “, 2006 ; Duhaime and Sullivan , 2012 ; Hurwitz and Sullivan , 2013 ) , its exploration in benthic ecosystems is still very scarce .”