Variations in Marine Microbiomes: From Habitat to Host

Lei Ma, Ph.D., 2022
Amy Apprill, Advisor

Microorganisms are the dominant life form on Earth and inextricably tied to the ecology and evolution of all multicellular life, including marine animals. As the importance of microorganisms to our conception of life gains prominence, animals (and other macroorganisms) are increasingly viewed as “holobionts”, an assemblage of the host plus all its symbiotic microbes. This dissertation examines holobiont biology from the perspective of the microbial communities that live in and around marine hosts. Using both amplicon and metagenomic sequencing, I study the microbiomes of reef-associated seawater and Atlantic killifish to better understand habitat and host effects on microbiome structure. In two Caribbean reef systems, I used examined the biogeography of reef water microbes. I found that the microbiome of reef seawater varies with reef system and individual reefs but that microbiomes within individual reefs were similar to each other and did not vary with benthic composition. The regionalism of reef seawater microbiomes was further assessed upon incorporation of global scale data from five additional studies, which revealed that microbial communities were more distinct with increasing geographic distance. These results contribute to our understanding of the coral holobiont’s microbial environment and can inform monitoring efforts for reef health. Atlantic killifish populations can be categorized as sensitive or tolerant to industrial pollutants based on history of pollutant exposure. Thus, they are an excellent “natural laboratory” for understanding the combined effect of environment and host on microbiome composition. I examined the gut microbiomes of two populations of wild fish as well as captive fish originating from each of these wild populations. I found that living in and adapting to polluted waters can impact microbiome composition and structure, resulting in a microbiome that appears more disordered. Additionally, captivity resulted in a complete turnover of dominant microbial taxa, indicating the environment plays a large role in shaping killifish gut microbiomes. This dissertation demonstrates that diverse systems, from coral reefs to killifish, can benefit from a better understanding of its associated microorganisms. For holobiont studies, these results highlight the importance of considering the context of microbial communities, from environment to host population.