Genomic diversification of marine cyanophages into stable ecotypes

Understanding the structure and origin of natural bacteriophage genomic diversity is important in elucidating how bacteriophages influence the mortality rates and composition of their host communities. Here, we examine the genetic structure and genomic diversification of naturally occurring bacteriophages by analyzing the full genomic sequences of over 100 isolates of Synechococcus-infecting cyanophages collected over 15 years from coastal waters of Southern New England, USA. Our analysis revealed well-supported cyanophage genomic clusters (genome-wide average nucleotide identity (ANI) >93%) and subclusters (genome-wide ANI >98%) that remained consistent for a decade or longer. Furthermore, by combining the genomic data with genetic analysis of an additional 800 isolates and environmental amplicon sequence data both genomic clusters and subclusters were found to exhibit clear temporal and/or spatial patterns of abundance, suggesting that these units represent distinct viral ecotypes. The processes responsible for diversification of cyanophages into genomic clusters and subclusters were similar across genetic scales and included allelic exchange as well as gene gain and loss. Isolates belonging to different subclusters were found to differ in genes that encoded auxiliary metabolic functions, restriction modification enzymes, and virion structural proteins, although the specific traits and selection pressures responsible for the maintenance of distinct ecotypes remain unknown.