SAR11 and Pelagiphage Distribution and Viral Host Gene Analysis Through Metagenomic Depth Profiles in Oligotrophic Ocean Environments

The SAR11 bacterial clade (pelagibacterales) is the most abundant heterotrophic marine bacterial group thought to account for ~25 percent of ocean bacteria. The environmental distribution of pelagiphage, viruses that infect SAR11, is an important control on ocean heterotrophy but is not well characterized. We investigated the SAR11 and pelagiphage community distributions across the Northern Atlantic Ocean using 11 publicly available cellular metagenomic depth profiles taken on the GA03 cruise of the GEOTRACES program and one metagenomic depth profile taken in the oligotrophic Eastern Tropical North Pacific (ETNP) oxygen deficient zone. SAR11 phylotype distributions were determined using the core bacterial DNA polymerase β subunit gene (rpoB) and pelagiphage phylotype distributions were determined using the gene coding for the large terminase subunit (terL), a known single copy core gene for phages of the order Caudovirales. We found several novel viral host genes in environmental contigs phylogenetically identified as pelagiphage and investigated their distributions throughout the water column using normalized ratios with terL. Distributions of SAR11 ecotypes in both systems indicate that different ecotypes peak at different locations in the water column though dominant ecotypes differed in oxic and anoxic regimes. Depth trends are visible within many of the phylotypes of pelagiphage but the community was nearly always dominated by a single pelagiphage of the myoviridae family. Two of the viral host genes examined were tagD, a recombinant protein, and queE, a tRNA modification gene, which were seen in myopelagiphage but not podopelagiphage. The proportion of myopelagiphage containing these genes decreased with depth in both systems with tagD decreasing consistently from ~0.7 to ~0.2 and queE decreasing typically from ~0.4 to nearly 0. The proportion of pelagiphage containing a gene is representative of its benefit to a virus at a location within the water column. The proportional decrease we observed indicates that the benefit of these genes is less at depth. Understanding the dynamics between SAR11 and the viruses that infect them is important in further understanding global marine biogeochemical cycling especially in oligotrophic environments that constitute so much of the globe.