UC San Diego

Ecological communities have been shown to vary in some predictable ways through space, time, and along environmental gradients, suggesting there may be underlying “rules” in ecology which govern these patterns and processes. However, nearly all our knowledge of these trends comes from studies of large eukaryotes such as plants and animals, and we know very little about how these eukaryotic patterns compare to those of bacteria and archaea, the most dominant life forms on the planet. The goal of this dissertation is to determine whether ecological patterns that are evident in plants and animals are also applicable to host-associated microbes. First, I investigated whether these microbes exhibit large-scale spatial trends in diversity and community composition that are concordant with those of their eukaryotic hosts. Specifically, I investigated changes in community composition across a marine biogeographic boundary and changes in diversity along a latitudinal transect. Results showed that microbiome compositions varied significantly between geographic sites, but that the identity of the host species played a greater role than geography in determining community composition. Further, microbes associated with the California mussel, Mytilus californianus, did not show a traditional latitudinal diversity gradient, and latitudinal diversity patterns varied based on microbial group and host body site. Next, I investigated whether host-associated microbial communities vary over time and in response to environmental change in similar ways to their eukaryotic hosts. I found that over an 11-year period, and in response to environmental change, microbial communities of the bean clam, Donax gouldii, significantly differed in composition, but not in richness. Further, I found that microbes did not regularly diverge in concordance with their intertidal gastropod hosts in the ~3.5 million years since the closure of the Isthmus of Panama, though this was dependent on the host taxa and the body site from which the microbes were collected. Finally, I investigated whether current methodologies for determining the core microbiome are guided by ecological and evolutionary principles and identify critical areas for future research. Overall, this dissertation shows that large-scale patterns in host-associated microbial taxa are often context-dependent and distinct from those of their hosts.