UC San Diego

Marine viruses impact their communities in a variety of ways, modulating community composition, driving diversity, and influencing biogeochemical cycling through lytic infection and the expression of auxiliary metabolic genes. However, there are still many unknowns regarding the effects of viral diversity and infection on microbial communities across ecosystems. As an eastern boundary current, the California Current Ecosystem (CCE) ranges from nutrient-rich, coastal upwelled zones to oligotrophic offshore waters, spanning a range of physical and chemical gradients that structure distinct microbial communities. In this dissertation, I explore how viral infection and grazing predation rates change along a transect associated with upwelling filaments in Chapters 1 and 2, while in Chapter 3, I explore how viral communities are structured by changes in space and time, leveraging metatranscriptomes that were collected on quarterly California Cooperative Oceanic Fisheries Investigation (CalCOFI) surveys from 2014-2020 as part of the NOAA CalCOFI Ocean Genomics (NCOG) program. Across two separate modified dilution experiment cruises, I found that direct viral infection of phytoplankton was more likely to occur within the nutrient-rich waters of the filament, though infection was often difficult to identify by standard dilution experiment measurements alone. In comparison, virus infection seemed to stimulate phytoplankton growth in transitionary waters between upwelled and offshore waters, where smaller phytoplankton such as Ostreococcus and some bacteria such as those in the SAR11 clade were positively impacted by increased viral presence. Finally, we identified consistent declines in viral diversity with increased distance from shore that was unmatched in the cellular community, as well as a reduced impact of depth and time on viral community composition. However, viral activity in the CCE was driven primarily by depth and region, where each depth regime sampled had a unique associated viral module, as did the upwelling region. Overall, this dissertation highlights that viruses in the CCE differentially impact their associated community depending on environmental conditions, but also recognizes the need for future research to further investigate the variety of indirect interactions within the microbial community.