Climate change-related stressors in aquaculture: modulation of gill microbiota and transcriptome in Atlantic salmon

Despite aquaculture's innovations to reach sustainability, the sector is not disaster-proof against climate change, which threatens its development. Increasing temperatures are becoming more frequent and have been implicated in the occurrence of jellyfish blooms, which is the case of Aurelia aurita, a common jellyfish in Norwegian waters. These blooms have been linked to high mortality events, likely related to their capability of causing gill and skin damage, compromising mucosal barrier functions. Nowadays, gill disorders in farmed Atlantic salmon (Salmo salar) have become one of the most significant challenges for the salmon industry and are caused by a mix of infections and environmental stressors. The fish gill mucosal microbiome interacts with the environment, being the primary barrier of defense against external agents, making it useful for monitoring mucosal health. In addition, fish microbiota plays a critical role in many host functions such as stress response, immunity, and protection against pathogens. Up to date, few studies have explored the interactions between fish mucosal microbial communities and scyphozoans within a climate change context. Thus, this study aimed to explore how multiple climate change-related environmental stressors, such as increasing temperature and limited oxygen availability, interact with salmon gill mucosal microbiota and gill gene expression after jellyfish (A. aurita) exposure. Gill microbial diversity significantly differed among groups where samples of fish exposed to increased temperatures and limited oxygen, separated from the control groups regardless of the jellyfish mucus exposure. In addition two bacterial biomarkers Streptococcus and Staphylococcus were identified for the groups exposed to increased temperatures. Conversely, at the transcriptomic level, the separation between groups was driven by the increasing temperatures, regardless of the oxygen availability and the exposure to jellyfish mucus. The different experimental conditions significantly impacted pathways related to cellular response to stress, oxidative phosphorylation, response to heat, and cellular response to type I interferon, among others. Moreover, 67 correlations were found between the most abundant bacterial taxa and the differentially expressed transcripts (DETs) of the pathways of interest. These results provide insights for characterizing and identifying potential microbial markers and genes involved in salmon resilience against climate-change-related stressors.