Early life stress causes lasting impacts on the microbiome of Atlantic salmon

Farmed fish are often exposed to stress within intensive aquaculture, leading to immune impairment and increased disease susceptibility. Microbial communities associated with the gut and skin are vital to host immune function, therefore microbiome disruption may represent an important mechanism contributing to the adverse effects of stress on fish health. However, little is known about the effects of stress on the fish microbiome, especially during early life stages which may be particularly sensitive. We compared the effects of two aquaculture-relevant stressors on the gut and skin microbiome of Atlantic salmon fry; an acute cold shock during late embryogenesis, and a chronic environmental stress during the larval stage. We identified a lasting effect of the acute temperature stress on both the gut and the skin microbiome, likely due to disruption of the eggshell microbial communities which seed the initial colonisation of the teleost microbiome upon hatching. Chronic post hatch stress altered the diversity and structure of the gut microbiome, potentially reflecting the impact of host cortisol stress response. Notably, we found that both types of stress promoted similar Gammaproteobacteria OTUs, particularly the genera Acinetobacter and Aeromonas which include several important fish pathogens and, in the gut, reduced the abundance of Lactobacillales. This suggests that there may be common identifiable signatures of stress in the salmon microbiome, which may be useful for screening. Our results highlight how stress during early life can cause long-lasting changes in the salmon microbiome, and may also increase the risk of opportunistic infections in the case of injury or further stress.