Examining coral reef ecosystem dynamics using microorganisms and metabolites

Abstract

Microorganisms and metabolites are foundational to the success and productivity of biodiverse and economically important coral reef ecosystems and are also tightly connected. Metabolites are small organic compounds produced by reef organisms and are the chemical currencies exchanged by unicellular microorganisms (bacteria and archaea) within the seawater. Although central to reef biogeochemical cycling, we still lack fundamental information on the dynamics of these components of reefs. In this dissertation, I analyzed microorganisms in Caribbean coral reef habitats over temporal, spatial and reef health gradients as well as metabolites in a spatial reef study. In Chapter 2, I applied a rapid sequencing methodology to corals afflicted with the lethal stony coral tissue loss disease and identified specific microorganisms which were biological indicators of the disease. In Chapter 3, I investigated the dynamics of microorganisms over short temporal tidal and diurnal cycles, as well as spatially across US Virgin Island (USVI) coastal habitats. In these habitats, I found tidal cycles were driving changes in microbial communities within mangroves, but diurnal patterns were more important in reef habitats. In Chapter 4, I examined reefs over a longer temporal scale by contributing to the building of a 7-year time-series of USVI reef ecology and found that reef water microorganisms were predictive of hurricane and stony coral tissue loss disease impacts. Finally, in Chapter 5, I combined analyses of untargeted and targeted metabolomics, microbial taxa, and functional genes from metagenomics across 300 km of reefs in Florida, in addition to microorganisms in healthy and diseased corals. With this unprecedented combination of ‘omics datasets, I found that biogeographic zones, environmental features, and underlying habitat characteristics were related to microbial and metabolite features in the reef ecosystem. Further, I identified microorganisms and metabolites which were characteristic of specific reef biogeographic zones. Collectively, my work advances our understanding into the dynamics of microorganisms and metabolites in biodiverse coral reef habitats across natural temporal and spatial gradients and in the face of unprecedented stress and disturbance.