Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean

• Published in: The ISME Journal 2011-05, Vol.5 (5), p.822-830
• Main Authors: Tucker, Kimberly P, Parsons, Rachel, Symonds, Erin M, Breitbart, Mya
• Format: Article
• Language: English
• Subjects: 631/158/852; 631/326/1321; 631/326/596/2142; 631/326/596/2554; Amino acid sequence; Atlantic Ocean; Base Composition; Biodiversity; Biomedical and Life Sciences; Data processing; Deoxyribonucleic acid; DNA; DNA Helicases - genetics; DNA, Single-Stranded - genetics; DNA, Viral - genetics; Ecology; Evolution; Evolutionary Biology; Genes, Viral; Genetic distance; Genome, Viral; Genomes; Geography; Guanylate cyclase; Host range; Life Sciences; Marine ecosystems; Metagenome; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Microviridae; Microviridae - classification; Microviridae - genetics; Oceans; Original; original-article; Phages; Polymerase chain reaction; rep gene; Replication initiation; Sampling; Seawater - virology; Sequence Analysis, DNA; Time Factors; Time series; Trans-Activators - genetics; Virions; Water column; Water Microbiology
• ISSN: 1751-7362; 1751-7370
• DOI: 10.1038/ismej.2010.188

Knowledge of marine phages is highly biased toward double-stranded DNA (dsDNA) phages; however, recent metagenomic surveys have also identified single-stranded DNA (ssDNA) phages in the oceans. Here, we describe two complete ssDNA phage genomes that were reconstructed from a viral metagenome from 80 m depth at the Bermuda Atlantic Time-series Study (BATS) site in the northwestern Sargasso Sea and examine their spatial and temporal distributions. Both genomes (SARssφ1 and SARssφ2) exhibited similarity to known phages of the Microviridae family in terms of size, GC content, genome organization and protein sequence. PCR amplification of the replication initiation protein ( Rep ) gene revealed narrow and distinct depth distributions for the newly described ssDNA phages within the upper 200 m of the water column at the BATS site. Comparison of Rep gene sequences obtained from the BATS site over time revealed changes in the diversity of ssDNA phages over monthly time scales, although some nearly identical sequences were recovered from samples collected 4 years apart. Examination of ssDNA phage diversity along transects through the North Atlantic Ocean revealed a positive correlation between genetic distance and geographic distance between sampling sites. Together, the data suggest fundamental differences between the distribution of these ssDNA phages and the distribution of known marine dsDNA phages, possibly because of differences in host range, host distribution, virion stability, or viral evolution mechanisms and rates. Future work needs to elucidate the host ranges for oceanic ssDNA phages and determine their ecological roles in the marine ecosystem.