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

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.

Bridging the Gap between Knowing and Modeling Viruses in Marine Systems—An Upcoming Frontier

“…Viral metagenomics has not only confirmed what was previously known about viruses, but it also shed new light on topics such as geographical patterns (Angly et al, 2006;De Corte et al, 2016), and the relationship between their diversity and abundance with biotic and abiotic variables (Breitbart et al, 2004;Dunigan et al, 2006). Recent works have definitely confirmed the early views on viruses as fundamental drivers of many ecosystem processes (Hurwitz and Sullivan, 2013;Malits et al, 2014), and even manipulators of the marine environments (Rohwer and Thurber, 2009).…”

Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages

“…In addition, we constructed a database containing protein sequence from S-EIV1 and the NCBI viral database (n ¼ 181 331 proteins). Each read from the Pacific Ocean virome (Hurwitz and Sullivan, 2013) was used as a query in a BLASTx analysis against the protein database (cutoff e-value ¼ 10 À 3 ). Each read was assigned to a single best matching reference viral protein based on the e-value.…”

“…Lake Bourget is an oligo-mesotrophic lake dominated by cyanobacteria (Zhong et al, 2013), whereas Lake Pavin is believed to be dominated by picoeukaryotes (Lefèvre et al, 2008). In addition, a BLASTx analysis of a database containing S-EIV1 and the NCBI viral proteins with the Pacific Ocean Virome (POV) metagenomes (Hurwitz and Sullivan, 2013) indicates that S-EIV1-like phages are prevalent in these samples (Figure 6c). Only sequences with higher similarity to the cyanophages S-SSM4, S-SM2 and S-TIM5 occurred more frequently in the POV metagenomes.…”

Assessment of a metaviromic dataset generated from nearshore Lake Michigan

“…Although they have inherent limitations (as with all experimental techniques), and should be used to draw conclusions with regard to microbial communities within the scope of strong experimental design, they have allowed for a glimpse into phage diversity and relative abundances for a range of niches, e.g. human microbiota (Reyes et al 2012;Minot et al 2011), soil (Fierer et al 2007), marine environments (Angly et al 2006;Hurwitz and Sullivan 2013) and freshwater environments (Djikeng et al 2009;Roux et al 2012).…”