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This work presents evidence that temperate and virulent viruses impact the ecology, evolution, and health state of their bacterial and eukaryotic hosts across ecosystems including the ocean, human gut, and urban environment.

Temperate viruses can switch between a lysogenic and a lytic lifestyle. In the lytic cycle, phage lyse the host cell shortly after infection to release the progeny into the environment. In the lysogenic cycle, phage integrate into the bacterial genome to replicate with it during cell division. Here, it is shown how bacteriophage, viruses that infect bacteria, are key drivers of evolution in the marine environment and presents ongoing work on a mechanism that regulates prophage lysogenic-to-lytic the switch in the human gut.

Part of this research was conducted amidst a global pandemic caused by a virulent virus; this inspired the assembly of a workflow that combines community building with molecular biology to identify environmental reservoirs of SARS-CoV-2 and other eukaryotic RNA viruses. Using these methods, SARS-CoV-2 RNA was detected on surfaces of the urban environment and the risk of infection by contact with contaminated fomites in San Diego County was predicted. The viral RNA community present on these surfaces was also characterized.

Lastly, with the aim to uncover novel virus-derived systems where bacteria interact with their eukaryotic host, this thesis presents the identification of a new phage tail-like contractile injection system in Bacteroides, that was found prevalent in the gut of healthy adults.

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