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.

Figure 1. Sampling site map for the POV dataset.

Thirty-two viral metagenomes represent discretely sampled and processed datasets that vary over time and space in the pelagic Pacific Ocean. (A) Overview of sampling sites, (B) GBR – Great Barrier Reef, Australia, near Dunk and Fitzroy Islands. (C) LineP- oceanographic transect off Vancouver Island, British Columbia (D) MBARI- Line67 oceanographic transect off of Monterey Bay, California (E) SIO- Scripps Pier, San Diego, CA. Images were created using Ocean Data View.

Figure 2. 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’.

Figure 3. 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.

Figure 4. 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.