Transcriptomic and physiological responses of rainbow trout (Oncorhynchus mykiss) gill tissues to hypoxic stress

Hypoxic stress poses a significant challenge to aquaculture productivity. As a hypoxia-intolerant species, rainbow trout (Oncorhynchus mykiss) requires further investigation regarding their molecular and physiological adaptations to prolonged hypoxia. In this study, we investigated the temporal dynamics of the hypoxic response in rainbow trout gill cells through an integrated analysis of transcriptomics, histopathology, and biochemical analysis. Primary gill cells exposed to hypoxic conditions (3 % O₂) for 0, 24, and 48 h exhibited a progressive increase in reactive oxygen species (ROS) levels. A total of 6744 differentially expressed genes (DEGs) were identified through RNA sequencing, with the Glycolysis/Gluconeogenesis and Biosynthesis of amino acids pathways significantly upregulated at both 24 and 48 h, indicating a metabolic shift toward anaerobic energy production and antioxidant defense. In contrast, steroid biosynthesis was enriched at 48 h, potentially supporting membrane repair and cortisol-mediated stress adaptation, whereas apoptosis transitioned from inhibition at 24 h to activation at 48 h, correlating with irreversible cellular damage. Weighted Gene Co-expression Network Analysis (WGCNA) identified the module most associated with 48-h hypoxia, which was also enriched in these four pathways. Histopathological and physiological indicators also proved time-dependent changes in tissues upon hypoxic stress. These findings indicated that during early hypoxia (24 h), metabolic adaptation, including Glycolysis/Gluconeogenesis and Biosynthesis of amino acids, was prioritized in rainbow trout. However, after 48 h of hypoxia, a transition from metabolic adaptation to apoptosis-mediated cell clearance was induced, accompanied by the upregulation of steroid biosynthesis to mitigate sustained oxidative damage.