UC Santa Cruz

Animals can be viewed as complex, co-evolving networks of microbes and host cells. Understanding the diversity, form, and function of microbes associated with different animals is therefore essential to understanding the patterns and processes underlying evolution across all domains of life. Extant marine mammals present an interesting opportunity to study the microbiota of animals with an unusual lifestyle that has arisen independently six times since the time of their last common ancestor. The manner in which the marine mammal-associated microbiota has evolved in response to the host's marine lifestyle remains unclear. In this thesis, I describe three studies of the microbiota of marine mammals. In the first, I characterize bacterial community composition associated with sea otters, which are a keystone species that is listed as endangered by the IUCN. They are also the sole representatives of an entire lineage of marine mammal. The findings suggest that environment plays a major role in structuring sea otter-associated bacterial community composition and raises the question of whether sea otters may have a reduced bacterial biomass in their guts compared to other mammals. As seen in other marine mammal species, results show that sea otters host a diversity of ‘microbial dark matter'. In chapter two of this thesis, I study such ‘microbial dark matter' present in the dolphin mouth and propose two new bacterial phyla (Candidatus Delphibacteria and Candidatus Fertabacteria), the former of which our metabolic reconstruction suggests may have a direct effect on dolphin physiology and health. In the third chapter of my thesis, I operate under the assumption that novel phylogenetic diversity is correlated with novel functional diversity, and thereby discover a previously uncharacterized rectangular microbe in dolphin oral samples with several unusual morphological features, such as pili-like appendages whose architecture differs substantially from known surface structures seen in bacteria and archaea. A single-cell genomics experiment suggested that this microbe was a type of bacteria from one of the following three groups: Bacteroidetes, TM7, or Epsilonproteobacteria. Collectively, these studies provide insight into diversity, form, and function within the marine mammal microbiota, and contribute towards our understanding of the microbial diversity, both phylogenetic and functional, which has evolved on Earth.