| Summary: | Understanding microbial diversity and evolution in under- and unexplored biological systems has the capacity to shed important new light on evolutionary history and disease emergence. By sequencing viral and microbial communities within unexplored species and ecosystems, my thesis aims to uncover transformational biodiversity. I deployed metagenomic sequencing to reveal novel microbial and viral biodiversity in vertebrates, invertebrates, and bacteria. I also performed a detailed metatranscriptomic search for RNA viruses in archaea from extreme environments. I obtained full genomes of pathogenic Bartonella bacteria, cultured from rodents collected in the biodiversity hotspot of the Yunnan province, China. These genomes depict high bacterial diversity at the village scale and were the first metagenomically acquired genomes for Bartonella from China, providing data on how these bacteria emerge in new hosts. I identified 67 novel RNA virus species within termites, some infecting the termite itself and others infecting microbial symbionts. This study was the first investigation of the termite RNA virome and considered how aspects of termite social structure impact virome composition. Similarly, I discovered 23 viruses within the geothermal pools of Kuirau Park, located in the North Island of New Zealand. Of most note in this study was the discovery of divergent species of the expanding viral phylum Lenarviricota, that have important implications for the origins and early evolution of RNA viruses as a whole, as well as the discovery of multiple DNA viruses. This study was only the second to investigate RNA viruses from geothermal pools. Finally, I performed a metagenomic investigation of RNA viruses from hypersaline lakes in Australia and Antarctica. This study, the first of its kind, identified highly divergent RNA virus sequences that could not be placed within the global RNA virus phylogeny, but which could plausibly have bacterial or archaeal hosts.
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