Coyotes in cities and sponges in streams: Microbiomes in the face of environmental change

• Author / Creator

  Sugden, Scott A

• Animals live in close association with communities of microbes that play important roles modulating host nutrition, immunity, health, and behavior. Many of these microbes live on or in their animal host, most notably in the vertebrate gut, but microbiome studies now encompass disparate taxa from diverse environments. With the increasing awareness that no animal is devoid of commensal microbes comes a new appreciation of the role these microbes may play as animals adapt to ongoing and future environmental changes, which already have well-described ecological consequences. In this thesis, I complemented 16S rRNA gene sequencing with information about diet, health, and environmental conditions to preliminarily explore how different environments may affect the microbiome of two phylogenetically diverse organisms, coyotes (Canis latrans) and freshwater sponges (Ephydatia muelleri). Coyotes are adapting to life in urban environments and now inhabit cities across North America. I profiled microbiome composition along the length of the gastrointestinal tract in 10 coyotes that were trapped for other reasons and confirmed that coyotes largely resembled other mammals, and additionally noted that fecal samples were not reliable indicators of the microbiome in upper intestinal environments. I then used a larger sample of 76 trapped or road-killed coyotes to evaluate which components of the microbiome are most strongly linked to diet, measured as both stomach contents and stable isotope signatures (δ13C and δ15N), and to health, measured as both body condition and infection by the zoonotic parasite Echinoccocus multilocularis. Healthy coyotes harbored Fusobacteria-rich gut microbiomes which correlated with protein-rich diets; despite the emphasis on diversity in microbiome studies, microbiome diversity did not correlate with body condition. I lastly compared the duodenal and fecal microbiomes, in relation to diet and body condition, between urban and peri-urban coyotes. Urban coyotes consumed broader diets containing more anthropogenic food, resulting in greater divergence in the duodenal microbiome among individuals and a slightly altered fecal microbiome characteristic of carbohydrate-rich diets. These changes were associated with poorer average body condition and double the prevalence of E. multilocularis. Freshwater sponges have received little attention in microbiome research, despite the ecosystem services they provide in aquatic environments and the considerable work that has been done on their marine counterparts. I sampled sponges from three streams on Vancouver Island, BC, and showed that sponges harbor microbial communities distinct from ambient water and adjacent biofilms. These communities were dominated by the families Chitinophagaceae and Comamonadaceae, which may play ecological roles degrading sponge-derived chitin and steroids. Several aspects of these communities appeared to be stream-specific, suggesting that sponge-microbe associations may be driven by ecological factors unique to each stream. Collectively, my results provide a foundational understanding of how the host-associated microbiome relates to environmental conditions in two organisms living in vastly different habitats. They suggest the potential for the microbiome to figure importantly in the ongoing process of urban adaptation in coyotes and in possible future changes in limnological conditions for sponges, with implications for host physiology and behavior.

• Subjects / Keywords

  • diet
  • coyote
  • Echinococcus multilocularis
  • freshwater sponge
  • Fusobacteria
  • environmental change
  • microbiome
  • intestine

• Graduation date

  Spring 2020

• Type of Item

  Thesis

• Degree

  Master of Science

• DOI

  https://doi.org/10.7939/r3-p1g3-qm68

• License

  Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.