- Seagrasses and coral reefs play important roles in nutrient cycling, coastal protection, and maintaining marine biodiversity. However, these coastal marine organisms are declining globally due to anthropogenic stressors, such as rising ocean temperatures, ocean acidification, and eutrophication. These organisms live in close association with their microbiomes, which can be beneficial or detrimental to the host organism, depending upon environmental conditions. This body of work utilized 16S rRNA amplicon and metagenome sequencing to characterize changes in the taxonomic composition and functional potential of seagrass and coral microbiomes under varying environmental stressors. This work was done to gain fuller understanding of seagrass and coral holobiont responses to the changing oceans. Chapter 2 describes the increased prevalence of Dark Spot Syndrome (DSS) in the coral Siderastrea siderea associated with thermal stress, and changes in the microbiome associated with diseased corals, exhibiting characteristics of dysbiosis (increased compositional variation amongst diseased samples). Importantly, we found no microbial taxa associated with DSS, and concluded DSS is a general stress
response and not microbe mediated. Chapter 3 presents the effects of eutrophication on Zostera marina, or eelgrass. Using a mesocosm experiment, we characterized the microbiome and plant host morphology and physiology responses to nutrient enrichment. Fertilization led to increased plant size and enriched nitrogen and sulfur cycling bacteria in root-associated samples. This study contributes both eelgrass physiology and microbiome responses to eutrophication to the breadth of seagrass literature. Chapter 4 examines changes to the leaf microbiome of the seagrass Posidonia oceanica under acidified conditions. Samples were collected from naturally occurring CO2 vents in Ischia, Italy, which simulate future ocean acidification scenarios. In acidified samples, we identified decreases in relative abundance of microbial carbon fixation genes, and enrichment for heterotrophic bacteria and genes involved in biofilm production. Seagrass transplantation is a major component of restoration efforts after population declines, and Chapter 5 examines the eelgrass rhizobiome response to transplantation. We transplanted eelgrass individuals with and without intact rhizosphere sediment and characterized plant morphology and belowground microbiome succession over 4 weeks. Eelgrass transplanted without intact rhizospheres exhibited declines in root biomass and dysbiosis at the start of the experiment, but after one week, eelgrass plants and their belowground microbiomes demonstrated resilience to transplantation in our mesocosm environment.
As a whole, these studies described demonstrable changes to host-associated microbiomes under future ocean conditions. In particular, this work presents a significant contribution to the nascent field of seagrass microbiome research. These
studies have identified key members of healthy and disturbed seagrass microbiomes; this knowledge can be used to generate hypotheses and future experiments targeting specific host-microbe interactions. This work shows the importance of interdisciplinary collaboration and integration of microbiome data with plant and environmental metrics to gain a full appreciation of the system. Lastly, though these valuable coastal organisms are currently on the decline, the integration of microbiome data may lead to successful management and restoration efforts.