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

Summary

The aquaculture industry is not sufficiently prepared to deal with the impacts of climate change. Increasing temperatures, intensified marine heat waves, and more frequent jellyfish blooms threaten production. Gill disorders in farmed Atlantic salmon ( Salmo salar ) have become one of the most significant challenges for the industry. Few studies have explored the interactions between fish mucosal microbiomes and scyphozoans within a climate change context. This study explored how increased temperature and limited oxygen availability interact with the salmon gill microbiome and gill gene expression after jellyfish ( Aurelia aurita ) exposure. Gill microbiota changes were determined by ONT MinION sequencing of the V1-V3 hypervariable region of the 16S rRNA gene and gill transcriptomic responses were assessed by total RNA sequencing with Illumina. Alpha diversity Shannon index was significantly higher in fish exposed to increased temperature, regardless of exposure to jellyfish. In addition, LEfSe analysis identified a significant increase in the abundance of Streptococcus and Staphylococcus , which were identified as biomarkers in all groups exposed to increased temperatures. At the transcriptomic level, principal component analysis showed that group separation was mainly driven by the increased temperature variable, which was responsible for the largest number of differentially expressed transcripts. Pathway analysis revealed that the different experimental conditions significantly impacted the expression of transcripts related to glycosylation, immune response and tissue development and integrity. Although the jellyfish exposure did not significantly affect the gill transcriptomic response, the combination with the other environmental stressors induced further changes related to haemostasis, protein modification and cell migration. Overall, the results provide important evidence regarding how combined stressors may affect Atlantic salmon's gill mucosal health and highlight key genes and microbial taxa to be explored in more detail to understand the mechanisms behind climate-change effects on aquaculture.

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DOI : doi.org/10.3389/fmars.2026.191...
NVA : hdl.handle.net/11250/5557768