UC San Diego

Viruses and microbes are foundational to the healthy functioning of coral reef ecosystems. However, dysregulation among viral and microbial communities owing to global and local pressures is driving widespread coral reef collapse. The objective of this dissertation was to investigate the drivers of this ecosystem degradation process, termed microbialization, on coral reefs and to identify mechanisms associated with ecosystem recovery from microbialized states.

To begin the dissertation, I review the biochemistry underlying coral reef function and describe how ecosystem energy is differentially stored in predominantly the macroorganisms on healthy coral reefs versus the microbes on degraded coral reefs as a result of positive feedback loops. In this review, I develop hypotheses concerning how microbes, organic matter, and oxygen interact to drive shifts to microbialized states and propose a tool to manipulate reef biochemistry to counter microbialization. To begin testing these hypotheses, I build midwater mesocosm tools called Coral Arks, develop protocols for designing, deploying, and monitoring them in situ, and demonstrate their structural integrity in the marine environment. Next, I use Coral Arks in a long-term field experiment, demonstrating that microbial ecology, water quality, and biogeochemistry are improved on Arks relative to seafloor sites at the same depth. Lower microbialization on the Arks enhanced survival and growth of transplanted corals and recruited diverse assemblages of reef organisms, including fish and benthic invertebrates. These findings highlight the role of microbes in shaping the coral reef abiotic environment and suggest microbialization can be countered by reducing organic matter inputs, enhancing dissolved oxygen, and reinstating viral predatory control over microbes. Lastly, I discuss the future of coral reef restoration, identify explicit goals for reinstating reef ecosystem services, and through a literature review, summarize potential interventions for manipulating coral reefs. Using this information, I propose a restoration framework based in control theory that uses Coral Arks as experimental platforms for identifying effective restoration interventions and scaling these interventions to a natural reef.