Marine viruses (principally bacteriophages) are perhaps the most abundant form of life on the planet. Active (lytic) viral infections cause cell to lyse and thus control carbon flow through marine microbial food webs, in some cases initiating the collapse of algal blooms. In contrast, inactive (lysogenic) infections confer immunity to superinfection and cause conversion to a diverse array of phenotypes. The majority of marine bacteria in culture produce some type of virus-like particles (VLP.s), indicating that the occurrence of lysogeny is widespread. Marine viral genomes are economical to study because of their small size (usually 50-100 kb).
The biocomplexity of viromics arises from the interaction and response of viral genomes to environmental cues. This project will focus on lysogeny, whereby a viral genome establishes a stable interaction with its host. The occurrence of lysogeny in the marine environment is complex, as indicated by the seasonal distribution of lysogens observed in estuarine environments. The lytic-lsyogenic shift is hypothesized to occur when viral genes respond to environmental cues, and preliminary evidence suggests that phosphate levels and the pho genes may play a role in this interaction. Specific research objectives are to: 1) determine what physiological and environmental cues catalyze the shift from lysogenic to lytic lifestyles in cultures and natural microbial populations, 2) sequence the genomes of several temperate phages, 3) determine how phage genes work together to confer lytic or lysogenic existence in marine bacteria, and 4) incorporate the effects of temperate phage into models of the marine microbial food web.
The first objective will be addressed by employing cultures (cyanobacteria and heterotrophic bacteria) and natural populations to investigate cues that might control the "lysogenic decision". Cultures and natural populations will be exposed to shifts in temperature, nutrients, sunlight, salinity, and exposure to xenobiotics to elicit shift from lytic to lysogeny and vice versa. For the second objective, five of these phage-host systems will be sequenced. Comparative genomics will be used to identify common genes and modules. For the third objective, prophage gene expression will be quantified by northern analysis. Differences in patterns of expression will yield information on genome response to shifting environmental conditions. If conserved lysogeny genes are found in cyanophage, their expression in natural bacterial populations of Tampa Bay will be measured. Finally, a computational model will be developed to describe the interaction of temperate phage with marine microbial food webs, based upon a 13 month seasonal study of lysogeny in Tampa Bay. The broader impacts of this research include educational outreach in the form of undergraduate workshops at San Diego State University, and participation in Oceanography Camp for Girls and Project Oceanography at the University of South Florida.