Ecology, Diversity and Comparative Genomics of Oceanic Cyanobacterial Viruses

Matthew Sullivan, Ph.D., 2004
Sallie Chisholm and John Waterbury, Advisors

This thesis describes the isolation and subsequent characterization of viruses (cyanophages) that infect the numerically dominant primary producers in the oceans, Prochlorococcus and Synechococcus. These cyanophage isolates belong to one of three morphological families, Myoviridae, Podoviridae and Siphoviridae, with host strains of similar ecotypes often yielding cyanophages of the same family. Host-range analyses demonstrated varying levels of specificity, ranging from infection of a single strain to infection across ecotypes and even across both cyanobacterial genera. Strain-specific cyanophage titers were low in open ocean waters where total cyanobacterial abundances were high, suggesting low phage titers might be a feature of open oceans. The diversity of Myoviridae isolates, examined using the portal protein gene, suggested that cultured isolates were not representative of naturally occurring portal protein gene diversity. Finally, three Prochlorococcus cyanophage genome sequences revealed these genomes were similar to well-studied T7- and T4-like phages, but additionally suggested modification for infection of photosynthetic hosts, that live in nutrient-limited environments. Many 'non-phage' genes were found to be full-length and conserved in sequence suggesting they are functional during infection. Phylogenetic inference suggests that some of these genes were horizontally transferred between host and phage influencing the evolution and ecology of both host and phage.