Profiling Bacterial Community Dynamics For Wildlife Ecology and Geological Mineral Exploration

Suchan, Danae Marie
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Faculty of Graduate Studies and Research, University of Regina

Bacterial communities are dynamic biological systems with complex metabolic interactions that influence ecological functions across a broad range of microbiome environments. Bacterial community 16S rRNA gene amplicon sequencing is an approach to microbiome exploration that profiles community composition, structure, and dynamics across environmental conditions. In this thesis, 16S rRNA gene amplicon sequencing is used to investigate the bacterial communities of two distinct microbial environments. In the first study I explore how hyperthermia in a mammalian host may affect bacterial communities to understand the impacts of thermal stress in warming climates. Small endotherms such as birds and bats have evolved diverse physiological adaptations and behavioural strategies to tolerate or avoid extreme high temperatures. Less understood is how animal-associated microbiomes respond to heat challenges, raising the concern that declines in resident microflora during hyperthermia could compromise whole organism health by decreasing microbiome complexity and functions. To investigate this, amplicon-based 16S rRNA gene community sequencing was used to assess whether heat exposure alters cultured intestinal bacterial community structure in Cape Horseshoe bats, Rhinolophus capensis. Bacterial cultures demonstrated a decrease in community size as temperatures increased between 37 ºC and 50 ºC, with temperatures above 40 ºC causing a decrease in average growth yields. Shifts in bacterial community structure were evaluated for transient (44 ºC for 5 hours) and sustained (45 ºC for 18 hours) heat challenges. A decrease in bacterial species richness was observed in both conditions. Enterococcus was the most abundant and diverse genus detected before and after heat exposure. Klebsiella were the next most abundant taxon, but this genus was more sensitive to heat challenge. These results suggest that as global climates get hotter, it will be important to consider microbiome health as a contributing factor to the survival of wildlife populations. In the second study I explore how microbial genetic-based methods have the potential to complement current geophysical and geochemical approaches to mineral exploration. Mineral-associated metals are hypothesized to dissociate into surrounding soils and thus promote the growth of heavy metal resistant bacteria while inhibiting sensitive taxa. In this study, amplicon-based bacterial 16S rRNA gene community sequencing was used to profile the bacterial communities inhabiting soils above a known metal-rich kimberlite formation in the subarctic Canadian tundra. It was found that surface soils (5-15 cm depth) above the kimberlite had higher alpha-diversity estimates relative to background soils, with no differences in diversity observed across deep samples (15-30 cm depth). Overall bacterial community composition and structure did not vary between kimberlitic and background soils; however, differential abundance analysis identified eight amplicon sequence variants (ASVs) with kimberlitic bioindicator potential. Two unclassified ASVs from the Bacteroidota family env.OPS 17 were highly specific to kimberlitic soils, and conversely three ASVs from the uncultured acidobacteria genus RB41 exhibited specificity to background soils. The identification of two candidate bioindicator taxonomic groups highlights potential applications of microbial ecology to kimberlite mineral exploration. Altogether, this thesis presents the application of amplicon-based bacterial community profiling and statistical analysis to two distinct microbial environments.

A Thesis Submitted to the Faculty of Graduate Studies and Research In Partial Fulfillment of the Requirements for the Degree of Master of Science in Biology, University of Regina. x, 87 p.