Deep sequencing of the viral phoH gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral phoH genes in the Sargasso Sea

Dawn B Goldsmith; Rachel J Parsons; Damitu Beyene; Peter Salamon; Mya Breitbart

doi:10.7717/peerj.997

Deep sequencing of the viral phoH gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral phoH genes in the Sargasso Sea

PeerJ. 2015 Jun 16:3:e997. doi: 10.7717/peerj.997. eCollection 2015.

Authors

Dawn B Goldsmith¹, Rachel J Parsons², Damitu Beyene³, Peter Salamon³, Mya Breitbart¹

Affiliations

¹ College of Marine Science, University of South Florida , St. Petersburg, FL , USA.
² Bermuda Institute of Ocean Sciences , St. George's , Bermuda.
³ Department of Mathematics and Statistics, San Diego State University , San Diego, CA , USA.

Abstract

Deep sequencing of the viral phoH gene, a host-derived auxiliary metabolic gene, was used to track viral diversity throughout the water column at the Bermuda Atlantic Time-series Study (BATS) site in the summer (September) and winter (March) of three years. Viral phoH sequences reveal differences in the viral communities throughout a depth profile and between seasons in the same year. Variation was also detected between the same seasons in subsequent years, though these differences were not as great as the summer/winter distinctions. Over 3,600 phoH operational taxonomic units (OTUs; 97% sequence identity) were identified. Despite high richness, most phoH sequences belong to a few large, common OTUs whereas the majority of the OTUs are small and rare. While many OTUs make sporadic appearances at just a few times or depths, a small number of OTUs dominate the community throughout the seasons, depths, and years.

Keywords: Bermuda Atlantic Time-series Study; Sargasso Sea; Viral diversity; phoH.

Grants and funding

This research was funded by grants MCB-0701984 and DBI-0850206 from the National Science Foundation to MB. DBG was supported by a Presidential Doctoral Fellowship from the University of South Florida and the Von Rosenstiel Endowed Fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.