UC San Diego

This dissertation work contains the following chapters: Chapter 1 revealed that bacterial pathogens of marine animals contain a higher abundance of prophages in their genomes than non-disease-causing host-associated bacteria. The work highlights the importance of horizontal gene transfer between bacteria and phages in the context of marine fauna, and reviews what is known about prophages in the context of marine diseases. Additionally, a comparison of the prophage-encoding genes between pathogens and non-pathogens, found that predicted prophage-encoded genes in disease-causing bacteria are enriched for carbohydrate and nitrogen metabolism, virulence factors, and membrane transport. Chapter 2 consisted of utilizing multi-omics and microscopy to characterize coral-turf algal interactions in situ that led to a working model of the ecology of these benthic holobiont interactions. I applied metagenomic sequencing in parallel with metabolomics to uncover the underlying bacterial, viral, and biochemical processes associated with coral-turf algal competition and reef decline. This work emphasizes the important role of host-associated bacteria and viruses in the ecological outcome of competing coral-algal interactions. In this context, the study fits into what was coined the “Algal Feeding Hypothesis”, which posits that changes in coral-algal interface communities are driven by bacteria that feed on algal-derived compounds. Chapter 3 focused on the molecular and microbial cartography of massive coral colonies using a multi-omics approach to understand the natural history of endangered massive coral colonies competing with benthic algae. In this work I combined 3D photography with metatranscriptomics, metabolomics, and metabarcoding to investigate all portions of the massive coral Orbicella faveolata visually and spatially in situ.