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Genomics-Based Investigations of Algae-Bacteria Interactions


Interactions between eukaryotic algae and bacteria play an important role in natural ecosystems. Defining the details of these interactions enables a better understanding of organismal distribution and evolution, and also presents an opportunity to further human well-being via biotechnology and protect human health. In this thesis I utilize genomic techniques to elucidate interactions between bacteria and algae in the laboratory and the field. I demonstrate dynamic carbon and nitrogen-dependent interactions between model marine algae and bacteria in a newly developed genetically tractable model laboratory system. I then describe how horizontal gene transfer (HGT) from bacteria to diatoms can be used as a molecular tool for diatom genetic manipulation. The low-GC content of transferred DNA sequences enables autonomous replication as a diatom episome, effectively expanding the diatom’s gene repertoire and providing opportunities for nuclear genome integration. Lastly, I discuss associations between pathogenic species of Vibrio bacteria along the San Diego coast and their abundant algal counterparts. I report the first quantitative survey of pathogenic Vibrio species in San Diego coastal waters, which are abundant during summer months and possess genes associated with human virulence. When examining the ecological interactions of these species, traditional grouping of diatoms at a high taxonomic level has led to conflicting reports of associations with pathogenic Vibrio species. I show that high-resolution taxonomic grouping at the genus level or lower, based on 18S amplicon sequencing, reveals specific interactions that may have important consequences for Vibrio ecology and human health, yet would be overlooked in previous studies. Together, these chapters demonstrate how new molecular tools, including next-generation sequencing, can be used to gain a deeper understand of microbial interactions that are ecologically important on a global scale and also important to human health and well-being.

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