COMMUNITY ASSEMBLY IN HOST-ASSOCIATED AND ENVIRONMENTAL MICROBIOMES
Clavere Graciette, Ana Gabriel
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Microbes play ecological and biogeochemical roles in all environments, including in host-associated systems. They are central providers of ecosystem services, notably by transforming matter and energy. They also engage in social interactions that directly affect the health, development, and behavior of animals and plants. Identifying the factors that influence community taxonomic assembly in microbiomes - i.e., which microbes are present and in what abundance - is necessary to predict how microbiomes might influence an ecosystem’s diversity, functional services, and overall health. Many studies have investigated the factors shaping microbial distributions and community diversity. Despite a wealth of data on the topic, it has been challenging to identify universal principles of microbiome assembly across diverse systems. For host-associated microbiomes, for instance, it is often hard to quantify the relative contributions of host physiology versus environmental conditions in shaping microbiomes. This dissertation explores these challenges in both host-associated and free-living microbiomes that are subjected to distinct organizing factors. In Chapter 2, I sample across a diverse set of host-associated niches to understand how the microbiome of wild spotted eagle rays (Aetobatus narinari) differs from that of individuals housed at Georgia Aquarium. In Chapter 3, I provide the first assessment of the microbiomes of African penguins (Spheniscus demersus), focusing the analysis on the variation among body site niches and one of the first characterizations of the oral microbiome of birds. Finally, in a collaborative study that couples electrochemical measurements of redox substrates with analysis of both bacterial and archaeal microbiomes, I explore the role of environmental substrate availability in shaping community assembly.