Abstract
Environmental conditions, host genetic background, and temperature jointly influence the microbiomes of cold-water fishes, yet their relative contributions are not well understood. To address this knowledge gap, this dissertation employed several experiments across field surveys and controlled common garden setups. We integrated 16S rRNA gene sequencing, shotgun metagenomics, and GTseq SNP genotyping to evaluate how habitat features and host genotype structure microbiomes from environmental reservoirs to mucosal surfaces in redband trout (Oncorhynchus mykiss gairdneri). In the first study, river water and sediment from six thermally distinct Idaho streams, along with water from unique temperature regimen in Recirculating Aquaculture Systems (RAS) harboring trout were assessed. RAS waters supported a metabolically efficient but constrained microbiome optimized for waste recycling, as opposed to the natural rivers which hosted seasonally dynamic microbial communities with greater functional versatility. Additionally, seasonality and population source, shaped the microbial communities and function in the rivers, while temperature regimen and variability influenced the microbiome taxonomy and function of RAS waters. The second study examined environmental and genotypic influences on redband trout mucosal microbiomes. Significant differences in alpha and beta diversity were observed in mucosal microbiomes (𝑝 < 0.05), with gill and skin showing more microbiome divergence between populations than digesta. Host genetic distance was significantly correlated with skin and gill microbiome dissimilarity in both seasons, and MRM models explained ~20-25% of gill and ~20% of skin (in the summer) microbiome variance using neutral and adaptive genetic distances, whereas digesta microbiomes showed little genetic signal. The third study utilized a common garden approach in which fish from disparate populations were reared under homogenous experimental conditions across stressful and optimal temperature regimens. Differences in microbiome profiles between populations observed in the field studies largely disappeared in this study, except for 19–23 °C where the desert fish had significantly (𝑝 < 0.05) higher alpha diversity than other populations. Despite the homogenizing effect of the common garden experiment, fish from each population still maintained significantly (𝑞 < 0.05) differentially abundant genera in the skin and gill, but not in gut. Collectively, these results demonstrate that environmental exposure is the primary driver of mucosal microbiome structure in redband trout, while host genetic background could modulate microbiome stability and composition under thermal stress at environmentally exposed tissues. These findings have important implications for understanding local adaptation, predicting trout responses to climate change, and integrating microbiome dynamics into conservation and aquaculture management.