Introduction
The ability of fish to respond to environmental challenges is critical for their survival and the maintenance of healthy populations. Therefore, to ensure a sustainable aquaculture while meeting the increasing demand for fish, it is essential to prioritize the welfare of farmed fish by minimizing the stress levels associated with aquaculture practices. The study of the molecular mechanisms of fish stress appraisal is paramount to achieving this goal and avoid negative impacts on fish health and ultimately on the aquaculture productivity. In this study, we performed, an integrated multiomics characterization of the fish liver, a central organ during stress adaptation, to provide a holistic assessment of the molecular stress response at different organizational levels. Widen our understanding into the physiological changes occurring in the fish organism during stress adaptation can leverage the industry with valuable scientific knowledge for developing forthcoming species-specific welfare assessment protocols.
Methods
Sparus aurata adults were exposed to different suboptimal rearing conditions in three separate trials: overcrowding (45 kg/m3), repetitive net handling (4 times/week), and hypoxia (15% DO). A control group was also included, consisting of fish reared under optimal conditions for the species. By the end of the trials, fish were sampled (n = 6) and liver extracts were prepared for further transcriptomics (RNA-seq), proteomics (label-free shotgun) and metabolomics (untargeted LC-MS) analyses. In transcriptomics, after reference-guided transcriptome assembly, differential expression analysis was performed with DESeq2 (adjusted p-value < 0.01, log2|fold-change| >1). In proteomics and metabolomics, pairwise comparisons between identified proteins (protein FDR < 1%; peptide FDR < 0.1%) and metabolites, were achieved by a student’s t-test, p < 0.05; FDR controlled at 0.05. Gene set enrichment analysis (GSEA) and overrepresentation (ORA) analyses based on GO, KEGG and REACTOME databases were performed.
Results and conclusions
A total of 946 genes, 397 proteins and 121 metabolites were differentially regulated between challenged and control fish across the three trials. Integration and functional analysis of these selected features suggested a scenario of challenge-specific responses at the transcriptome, proteome, and metabolome levels. Net handling and hypoxia triggered a more impactful effect on hepatocytes than overcrowding, inducing an overall metabolism reprogramming to shift energy towards stress response processes and cell cycle arrest, mainly driven by ribosomal assembly stress, DNA replication stress, endoplasmic reticulum stress, and downregulation of insulin growth factor signalling. These results support the high phenotypic plasticity of this species and its differential responses to distinct challenging environments at different molecular levels. Additionally, the study provides valuable resources for characterizing and identifying potentially novel features essential for gilthead seabream resilience and aquaculture production efficiency concerning fish welfare.