Diversity and dynamics of RNA viruses in equatorial coastal waters

Abstract

Studies on the ecological effects of marine RNA viruses are critically lacking, despite the fact that viral infections impact health and evolution of individual species, the community structure of populations, and the biogeochemistry of the entire marine ecosystem. In this thesis, using a high-resolution time-series, I uncover a remarkable difference between life-cycles of lytic DNA and RNA phytoplankton viruses with a combination of metagenomics, metatranscriptomics and bioinformatics. The giant DNA viruses, known for lower burst sizes, exhibited low and continuous transcriptional activity, suggesting coexistence with their potential hosts. In contrast, fast-replication RNA viruses, known for high burst sizes, experienced short “bloom and bust” cycles of transcriptional activity which, along with the nutrient limitation, stopped potential bloom formation on two separate instances. Persistent, asymptomatic infections with RNA viruses without an extracellular stage were widely present in the Johor Strait marine ecosystem. Fifty nearly full-length RNA viral genomes and 319 verified RNA viral fragments were discovered using and optimized wet lab protocol and integrated bioinformatic pipeline OrVIT, which through extraction of conserved RdRp domains, produces high-quality phylogenetic trees of RNA viruses. Most recovered sequences clustered within the Sogarnavirus genus, which infects diatoms. Both datasets contained a pool of sequences from dsRNA and ssRNA viruses that infect marine animals, suggesting a possible hazard to aquaculture. This thesis underscores the potential of using an integrated multi-omic approach to capture the complex interplay between viruses and their hosts in marine ecosystems and emphasises the critical importance of phytoplankton RNA viruses in top-down control of blooming, fast-growing phytoplankton populations, especially in eutrophic ecosystems.