Climate change poses a significant survival challenge for cold water fish species such as the redband trout (Oncorhynchus mykiss gairdneri), a subspecies of rainbow trout native to freshwater habitats in the Pacific Northwest of North America. While previous studies have focused on the genetic factors influencing their adaptability to warmer temperatures, our research involves understanding host-microbiome interactions as potential mechanisms contributing to phenotypic variation in response to temperature increases.
This study included two seasonal field samplings (summer and winter) and a common garden experiment where trout from different thermal habitats were acclimated to standardized temperature regimes: constant temperatures at 15 °C, 18 °C, and 21 °C; and diel fluctuations of 13 to 17 °C, 16 to 20 °C, and 19 to 23 °C. We collected mucosal samples from the gills, skin, and digestive tracts of trout, along with sediment and water samples from desert and cold montane creeks, and from the common garden system. To investigate bacterial and archaeal community composition—including assessments of alpha and beta diversity and differential abundance—we employed 16S rRNA gene sequencing and analyzed the data using the DADA2, vegan, ANCOM-BC, and phyloseq packages in R. Nanopore sequencing was used to identify microbial functions and determine the relative abundances of bacterial and nonbacterial sequences. Genotyping by sequencing (GTseq) was utilized to genotype single nucleotide polymorphisms (SNPs) in individual fish, enabling analysis of neutral and adaptive genetic markers relative to their habitats.
Results showed statistically significant differences (p < 0.05) in both alpha and beta diversity of gill and skin microbiomes among field samples from different populations. In contrast, common garden samples exhibited no significant differences (p > 0.05), suggesting that environment (season and temperature) influences mucosal microbiome compositions.
Future analyses will focus on integrating microbiome and genetic data from both field and common garden samples to elucidate gene-by-environment interactions contributing to the adaptability of redband trout to warmer temperatures.