Chile is the second largest worldwide producer of Atlantic salmon ( S. salar ). This industry has to deal with sanitary issues causing significant economic losses, such as sea lice ( C. rogercresseyi , henceforth called caligus ) infestations. Caligus is an ectoparasite that infests the skin of Atlantic salmon. Despite its relevance, few studies have focused on evaluating the health status of the skin of Atlantic salmon reared in sea cage farms. In addition, environmental fluctuations such as water temperature can influence the fish skin’s health status and the resident microbiota. For this reason, we evaluated the Atlantic salmon skin response and resident microbiota in fish infested with caligus in different seasons of the year.
For transcriptomic analysis (RNA-Seq), total RNA was obtained from the epithelial skin tissue. D ifferential gene expression analysis between the infested and non-infested salmon was obtained based on the negative binomial distribution using the DESeq2 package. Pathways enrichment analysis was performed using the Gene Ontology Consortium databas e, STRING, and Reactome. Metatranscriptomics analysis of the metabolically- active microbiome was performed using Kraken2 software and the PlusPFP database.
Enrichment analysis showed the preference of the extracellular matrix process for upregulated DEGs during summer. In autumn, we observed upregulated DEGs associated with cellular response to corticotropin-releasing hormone stimulus, metabolic processes, cell proliferation, and nitric oxide biosynthetic process regulation. In autumn, the downregulated DEGs were associated with processes like riboflavin transport and mitochondrion organization . Conversely, downregulated DEGs during summer showed no enrichment. The composition of the metabolically-active microbiome in summer non-infested samples was found to have a greater bacterial diversity (33%) than in infested samples (22%); in autumn, the bacterial diversity of the non-infested was slightly higher (26%) than in infested fish (24%). The most abundant phylum in the bacteria domain was Pseudomonadota, followed by Actinomycetota and Bacillota. These results suggest that the presence of the Caligus parasite could be associated with a change in the salmon microbiota, whose representation would be modulated in a seasonal-dependent manner.
Our analysis revealed that sea lice infestation does not appear to dominate the differential expression profile in summer. This suggests that infested and non-infested fish are more concerned with seawater environmental adaptation to high temperatures . On the contrary, during autumn, the infested and non-infested fish show a differential expression profile and biological processes more associated with the response to sea lice. Taken together, the presence of Caligus affects the skin health of salmon and can alter their microbiome in a seasonal-dependent fashion, which could influence their growth, well-being, and, ultimately, Atlantic salmon production.
Acknowledgments: Fondecyt (1211841; 11221308), DICYT-USACH (082344RL_Postdoc; 082344RL_Ayudante) grants and Proyecto Regular UDLA (DI-14/23)