Intestinal microbial communities are influenced by a confluence of ecological forces. Understanding the dynamics between environment, microbiota and host is essential to gain insights into microbial community assembly processes. However, few studies systematically assess the contribution of different environmental sources to gut microbial community composition. We used a common garden experiment to determine the roles of biotic, abiotic and stochastic processes shaping gut microbial communities in Atlantic salmon (Salmo salar) in a natural river during a simulated 10-month farm escape scenario. Most of the taxa found in the salmon intestine originated from macroinvertebrates (the potential food source) rather than the water column, indicating that diet is an important factor in community assembly. The contribution of food sources to the fish gut community was lowest in winter and increased over March and May, reflecting seasonality in fish appetite. Previous work in salmon has hinted at a role for maternal effects in driving inter-generational sharing of microbial taxa. Our results suggest a possible host and/or maternal genetic effect affecting inter-individual differences in gut microbial community composition, whereby distinct assemblages were noted between farmed, wild and hybrid fish. Neutral modelling estimated that the majority (86%) of taxa present in the gut are transient. Overall, our data highlight the significance of both deterministic and stochastic drivers influencing the seasonal fluctuations of gut microbial communities in young Atlantic Salmon and hint at potential genetic or maternal effects on fish microbiota. These findings greatly enhance our understanding of the complex interactions between hosts, their living environment and associated microbiota.

Natural host populations differ in their susceptibility to infection by parasites, and these intra-population differences are still an incompletely understood component of host-parasite dynamics. In this study, we used controlled infection experiments with wild-caught guppies (Poecilia reticulata) and their ectoparasite Gyrodactylus turnbulli to investigate the roles of local adaptation and host genetic composition (immunogenetic and neutral) in explaining differences in susceptibility to infection. We found differences between our four study host populations that were consistent between two parasite source populations, with no indication of local adaptation by either host or parasite at two tested spatial scales. Greater host population genetic variability metrics broadly aligned with lower population mean infection intensity, with the best alignments associated with Major Histocompatibility Complex (MHC) ‘supertypes’. Controlling for intra-population differences and potential inbreeding variance, we found a significant negative relationship between individual-level functional MHC variability and infection: fish carrying more MHC supertypes experienced infections of lower severity, with limited evidence for supertype-specific effects. We conclude that population-level differences in host infection susceptibility likely reflect variation in parasite selective pressure and/or host evolutionary potential, underpinned by functional immunogenetic variation.