Challenges of Viral Ecology in OIigotrophic Systems

Marine viruses are fundamental key players of the global biogeochemical cycles. Through host lysis and genetic manipulation, viruses impact nutrient dynamics and shape microbial community structure. This thesis aimed to unravel the complex interactions between viruses and their hosts in the Sargasso Sea, focusing on the globally abundant SAR11 bacterioplankton and their viral predators, pelagiphages. Results revealed that SAR11 undergo minimal metabolic reprogramming during pelagiphage infections, suggesting that pelagiphage predation may not contribute significantly to models of marine carbon biogeochemical cycling despite being the most abundant biological entity. Only intracellular thiamine increased significantly during infection, potentially linking pelagiphage replication into diel cycles of phototrophs in the Sargasso Sea. Leveraging several campaigns of viral metagenomics in the Sargasso Sea, work in this thesis: (i) identified potential novel auxiliary metabolic genes aiding viruses in the deep with the degradation of refractory carbon; (ii) identified a putative mesopelagic pelagiphage with high abundance globally that followed patterns associated with the ocean conveyor belt, providing more evidence towards the Seed Bank Hypothesis; and (iii) a diel cycle of pelagiphage production in surface waters. Additionally, this thesis highlighted several limitations in current culture-independent methodology. Viral-like particle counting using epifluorescence microscopy was found to be susceptible to high false-positive rates; and read recruitment using standard, stringent bioinformatic cut-offs may underestimate pelagiphage diversity and abundance in the Sargasso Sea. Collectively, the findings throughout this thesis contribute to identifying the challenges within viral ecology in oligotrophic systems and broadening the evidence that pelagiphages may not be important drivers of biogeochemical cycles. As oligotrophic stratified systems similar to conditions found in the Sargasso Sea expand due to climate change, understanding the ecological impacts of viral predation will improve our ability to predict associated changes in carbon flux.