Award: OCE-1029684

Microbial communities are an abundant and essential component of the world’s oceans. These communities consist of many different types of bacteria, archaea and small eukaryotes that are responsible for creating food for larger marine organisms, decomposing organic matter, and converting nutrients into usable forms. In other words, these single-celled organisms help drive the global cycling of carbon and nutrients in the oceans. One important microbial group is the marine cyanobacteria. Cyanobacteria are photosynthetic and, like land plants, use light to convert carbon dioxide from the atmosphere into carbohydrates that can be used by other organisms. Cyanobacteria thus are at the base of the marine food web and are responsible for up to 30% of the oceans’ primary productivity. Viruses that can infect cyanobacteria (called cyanophages) are also extremely abundant in the oceans. These viruses influence the marine food web by infecting and killing cyanobacteria, making these cells unavailable to organisms higher up on the food chain. The interactions between cyanobacteria and viruses are dynamic and complex and while the outcomes of these interactions directly affect marine biogeochemical cycles, it has been difficult to predict exactly how viruses at any particular time or place will influence cyanobacteria mortality.  This is in part due to the fact that cyanobacteria can develop resistance to co-occurring viruses. Viruses, in response, can evolve to overcome resistance and also frequently carry in their genomes cyanobacteria-derived genes that may help them better infect specific hosts in particular environments.

Despite their importance, we know very little about the diversity of cyanophages except that their diversity is very high. We do not know much about what that genetic diversity means; for instance, what genes control whether a virus can infect a particular type of cyanobacterium or how fast the virus kills its host. However, this detailed information is essential to predict how viruses affect other marine organisms and ocean nutrient cycling.

This project used cyanobacteria and cyanophages to ask how and why the diversity of marine viruses varies over time and space. During the project, we completed a five-year time-series where we sampled cyanophages from both the Pacific and Atlantic coasts of North America. We sampled in such a way to facilitate comparisons between the locations and ask how other environmental and biological measurements correlated with cyanophage diversity in a sample. We then sequenced the genomes of a variety of the viral isolates to investigate which particular genes varied over space and time. We also used the viral genomes to search for particular genes that might act as “markers” of which bacterial hosts a virus could infect. Finally, we compared the genetic information with measured “traits” of the cyanophages – like which bacteria they infect and how fast they infect them.

We found that like other organisms, cyanophages are highly seasonal. Some cyanophage types dominate in the summer months and others dominate in the winter months. We also found that there was very little overlap in the diversity of viruses in southern California and Rhode Island. We investigated these trends further and saw that the strength of UV at the time was highly correlated with changes in the virus community over time and space. This suggests that some viruses may be more or less susceptible to UV damage, but this hypothesis needs to be tested further. Finally, we saw that the genetic variation within a cyanophage “type” is highly restricted to particular genes and regions of the genome. The identification of these genes and regions can now be compared to measured traits of the cyanophages and will help us understand the effect these viruses have on their host ...