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UBC Theses and Dissertations

The use of high-throughput amplicon deep sequencing to explore aquatic virus communities Tian, Xi


Viruses are the most abundant biological entity in aquatic ecosystems. In each milliliter of marine or fresh water, there are typically between one to ten million viruses. Aquatic viruses influence microbial diversity, mortality and evolution, which in turn affect biogeochemical cycles and energy fluxes in marine ecosystems. As most aquatic microbes have not been cultured, the viruses which infect them cannot be cultured; hence, non-culture based approaches are needed to ascertain changes in the composition and diversity of virus communities. This research involves using PCR amplicons and high-throughput sequencing to uncover unknown diversity in marine and freshwater viruses and determine its temporal and spatial variation. Differences in the taxonomic profiles of viruses in the families Phycodnaviridae, Myoviridae, and Podoviridae across marine locations were assessed using 454 pyrosequencing. Temporal and spatial changes in the taxonomic profiles of viruses in the family Myoviridae were assessed in a stream using Illumina sequencing. Results show that high-throughput sequencing of marker genes is a robust method to explore viral diversity, and revealed many previously unknown Operational Taxonomic Units (OTUs). Furthermore, distributions of OTUs within virus families differed markedly among samples, indicating that the virus distributions were spatially dynamic. Moreover, the variation of OTUs within the freshwater Myoviridae communities suggested that some OTUs could be used as indicators of agricultural runoff.

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