Abstract:

Environmental contaminants threaten wildlife and human health. Despite the suitability of wild birds for monitoring ecosystem changes resulting from pollution and their microbiomes being good indicators of stressors in the environment and of host health, research on their microbiomes is limited. This study focuses on tree swallows (Tachicyneta bicolor) as a model species to investigate the impact of contaminants on the gut microbiome. Objectives include 1) Developing an optimized protocol for extracting DNA from tree swallow fecal samples; 2) Comparing the composition of fecal microbiomes collected from a polluted site versus a less polluted site; and 3) Characterizing the fecal microbiome as an indicator of host health. Gut microbiomes were characterized by 16S rRNA sequencing of fecal samples collected from nestlings at a historically contaminated site near a Wastewater Treatment Plant outfall in Hamilton, ON and at another site further from the outfall. It was expected that the gut microbiome composition would change in response to pollution and that fecal samples containing a lower microbial diversity would correlate with a less healthy host. In this study, we provide an optimized DNA extraction protocol using the HiPure Soil DNA Kit with a modified temperature of 50°C, which performed best when considering both dsDNA concentration and purity. While no significant differences were found in alpha or beta diversity, or in pathogenic or commensal microbial abundance between sites, there were correlations between alpha diversity and several chick morphometrics, suggesting connections between host health and microbiome diversity. The use of fecal sampling, a novel and non-invasive microbiome sampling technique, allows repeated sampling of individuals, which is especially important for monitoring endangered wild species. Understanding the impact of contaminants on microbiomes may aid in conservation efforts to mitigate contamination to protect vulnerable species.