UBC Theses and Dissertations
Distribution and diversity of aquatic RNA virus assemblages in an environmental context Vlok, Marli
RNA viruses are ubiquitous and abundant in aquatic environments, but not well studied; of these, picorna-like viruses are dominant in coastal waters. They are genetically diverse, and primarily infect microbial eukaryotes; thereby, influencing microbial community composition and nutrient cycling. Few studies have elucidated the diversity of marine and freshwater RNA virus assemblages. In this dissertation, metagenomic data were used to address the hypothesis that aquatic RNA viruses are diverse and broadly distributed, as well as the abiotic factors and evolutionary pressures shaping these assemblages. Mapping reads from geographically separate sites to six reference genomes showed that these viruses were subject to purifying selection, with synonymous single-nucleotide variations dominating the mutations. These marine RNA viruses exhibited distinct biogeographic patterns with different quasispecies detectable in different areas. Marine RNA virus assemblages from polar to tropical environments were taxonomically complex. Viruses in the order Picornavirales were consistently in high relative abundance, and dominated marine RNA virus assemblages. Virus families that are thought to only occur in terrestrial systems were detected in oceanic samples, implying that these viruses infect marine organisms and, therefore, likely originated in the ocean. Freshwater RNA virus assemblages are equally diverse throughout six sites characterized by different associated land use. A complex suite of abiotic factors is associated with seasonal changes in viral diversity across all sites over 14 months, with high variability in site-specific RNA virus diversity. Certain viruses were associated with specific abiotic factors and sites, suggesting that some RNA viral taxa may be useful as indicator species. Lastly, a sequence-dependent taxonomic framework was developed to incorporate genomes assembled from metagenomic data into the current taxonomic classification system. This led to a proposed expansion of the Marnaviridae from a single isolate to 20 viruses classified into seven genera. The data presented here revealed unprecedented diversity in RNA aquatic viruses, and greatly expanded our knowledge of the distribution and dynamics of aquatic RNA viruses with consequent implications for understanding their role in aquatic ecosystems.
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