A Metagenomic Examination of Virus Diversity, Host Interactions, and Genetic Potential Across Municipal Waste Sites
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Date
2023-09-18
Authors
George, Nikhil Anil
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Publisher
University of Waterloo
Abstract
Viruses are the most abundant microbial guild on the planet, impacting microbial community structure and ecosystem services. Despite this, they have been underrepresented in reference databases compared to Bacteria and Archaea, which viruses are predicted to outnumber by at least an order of magnitude. The advent of metagenomics allowed the discovery of a multitude of viruses from a variety of environments. These metagenomic examinations illustrated that prokaryotic viruses are specifically understudied in engineered environments. In this thesis, I employ metagenomic and computational biology methods to examine the diversity, host interactions, and genetic systems of prokaryotic viruses that were predicted from 27 in-house metagenomes from samples taken at three municipal landfills across North America. I identified numerous viruses that are not represented in reference databases, including the third largest bacteriophage genome identified to date (~678 kbp), and note a cosmopolitan diversity of viruses in landfills that are distinct from viromes in other systems. Host-virus interactions were examined via host CRISPR spacer to viral protospacer mapping which captured hyper-targeted viral populations and 11 viruses predicted to infect across multiple phyla, suggesting that some viruses are far less host- specific than is typically expected. Viruses in my study encode Auxiliary Metabolic Genes (AMGs) with the potential to augment their hosts’ methane, sulfur, and contaminant degradation metabolisms, including AMGs not previously reported in literature. CRISPR arrays and CRISPR-Cas systems were identified from predicted viral genomes, including the two largest bacteriophage genomes reported to contain these genetic features. Some virally encoded Cas effector proteins appear distinct relative to previously reported Cas systems, and are interesting targets for potential biotechnological tools. Virally encoded CRISPR arrays were predicted to target other viral elements, causing interviral conflicts; and CRISPR- encoding proviruses integrated into host chromosomes were latent examples of CRISPR- immunity-based superinfection exclusion. My observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for diverse viruses and atypical virus-host dynamics, meriting further study of these ecosystems.
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Keywords
metagenomics, viruses