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Characterization of the impacts of polycyclic aromatic hydrocarbons on the fish gut microbiome



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The microbiome has been described as an additional host “organ” with well-established beneficial roles. In addition to aiding in digestion of food and uptake of nutrients, microbiota in guts of vertebrates are responsible for regulating several beneficial functions, including stimulating immune responses and maintaining homeostasis. However, effects of exposures to chemicals on both structure and function of the gut microbiome of fishes are understudied. The overall purpose of research reported in this thesis was to characterize the effects of polycyclic aromatic hydrocarbons (PAHs) on the gut microbiomes of freshwater fishes, using both laboratory- and field-based assessments. PAHs have a number of well-characterized deleterious impacts in fish and are known modulators of the aryl hydrocarbon receptor, a receptor that has a bidirectional relationship with the microbiome. As such, this chemical class was selected to investigate targeted effects on the microbiome. The objectives of this thesis were to: (1) Determine if aqueous exposures to BaP modulate the gut microbiome in fathead minnows (Pimephales promelas) and to discern whether these community shifts were sex-dependent; (2) Assess whether a dietary exposure to BaP also affects genomic and active microbiomes in juvenile fathead minnows; and (3) Evaluate the gut microbiomes in native fishes following exposure to an oil spill of heavy crude on the North Saskatchewan River. To accomplish this, adult male and female fathead minnows were aqueously exposed to a short-term environmentally-relevant low concentrations of benzo[a]pyrene (BaP) and composition of the gut microbiome were assessed with 16S rRNA metagenetics. Following this, juvenile fathead minnows were exposed via the diet to environmentally-relevant higher concentrations of BaP for two weeks, and composition of both the genomic and active gut microbiome were assessed with DNA- and RNA-based 16S rRNA metagenetics, respectively. Lastly, fishes from the North Saskatchewan River were collected a year after an oil spill, and differences in the microbiome based on fish species and measured PAH muscle concentrations were assessed with 16S rRNA metagenetics. Studies presented in this thesis revealed a clear influence of PAHs on the microbiome, even with relatively small exposures, while exposures to higher concentrations of PAHs resulted in microbial communities of the gut that were distinctly altered, with lost community structure as determined by co-occurrence networks. Notably, microbiomes in guts of male and female fish were affected differently by exposure to BaP, suggesting sex specific responses to the chemical. Moreover, certain bacterial taxa were correlated with exposure to BaP, many of which were associated with hydrocarbon degradation and disease. Predicted functional analyses revealed several pathways that were correlated with BaP exposure, including increases in aromatic degradation pathways. Many of the conclusions were similar when analyzing the genomic and active microbiomes, but the active and DNA-normalized (the RNA/DNA ratio of bacterial abundances) active microbiomes provided greater resolution of the effects of BaP exposure. Finally, with the field study, it was determined that among goldeye (Hiodon alosoides), walleye (Sander vitreus), northern pike (Esox lucius), and shorthead redhorse (Moxostoma macrolepidotum), host species drive the assemblages of gut microbiomes. Additionally, several taxa associated with hydrocarbon degradation, inflammation, and disease were correlated with PAH concentrations in muscle tissue across the field-collected fishes, and walleye community composition was correlated with concentrations of PAHs in muscle tissue. Across all studies, PAH exposure can be a driver of bacterial community composition, and Desulfovibrionaceae, Shewanellaceae and Chitinophagaceae were positively correlated with PAH exposure in both laboratory-exposed fathead minnows and wild-caught fishes. Overall, this thesis provides novel data and new understanding into the effects of PAHs on the gut microbiomes of freshwater fish that can ultimately be used to better understand the connection between a toxicant and an adverse outcome via the microbiome.



microbiome, toxicology



Doctor of Philosophy (Ph.D.)


Toxicology Centre




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