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.

The occurrence of alternative morphs within populations is common but the underlying molecular mechanisms remain poorly understood. Many animals, for example, exhibit facultative migration, where two or more alternative migratory tactics (AMTs) coexist within populations. In certain salmonid species, some individuals remain in natal rivers all their lives, whilst others (in particular, females) migrate to sea for a period of marine growth. Here we performed transcriptional profiling (“RNA-seq”) of the brain and liver of male and female brown trout to understand the genes and processes that differentiate migratory and residency morphs (AMT-associated genes) and how they may differ in expression between the sexes. We found tissue-specific differences with greater number of genes expressed differentially in the liver (n = 867 genes) compared to the brain (n = 10) between the morphs. Genes with increased expression in resident livers were enriched for Gene Ontology terms associated with metabolic processes, highlighting key molecular-genetic pathways underlying the energetic requirements associated with divergent migratory tactics. In contrast, smolt-biased genes were enriched for biological processes such as response to cytokines, suggestive of possible immune function differences between smolts and residents. Finally, we identified evidence of sex-biased gene expression for AMT-associated genes in the liver (n = 18) but not the brain. Collectively, our results provide insights into tissue-specific gene expression underlying the production of alternative life-histories within and between the sexes, and point towards a key role for metabolic processes in the liver in mediating divergent physiological trajectories of migrants versus residents.