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.Science, Faculty ofBotany, Department ofGraduat