Integrative Multi-Omics Analysis of Gill Responses to Long-Term Salinity Stress in Grass Carp (Ctenopharyngodon idella)

Salinity is an important environmental factor affecting the physiological homeostasis of freshwater fish, yet the underlying mechanisms in grass carp (Ctenopharyngodon idella) gills remain unclear. Therefore, grass carp were exposed to different salinity levels for 60 days, and gill responses were evaluated using histopathological, ion regulatory, antioxidant, transcriptomic, and metabolomic analyses. Histological observations showed that high salinity (8 g/L) caused marked structural damage to the gill lamellae. Specifically, Na+ and Ca2+ concentrations and Na+/K+-ATPase activity significantly decreased, while K+ concentration and Ca2+-ATPase activity increased, revealing disrupted ion homeostasis. Salinity exposure also led to decreased antioxidant enzyme activities. Integrated omics analysis further demonstrated that a total of 2447 differentially expressed genes and 268 differentially expressed metabolites were identified, with significant enrichment in pathways related to biosynthesis of amino acids, arachidonic acid metabolism, glutathione metabolism, PPAR signaling, and calcium signaling. Notably, the PPAR and calcium signaling pathways showed positive enrichment under salinity stress, suggesting their potential involvement in the regulation of lipid metabolism, energy allocation, and cellular stress responses. Our findings indicated amino acid biosynthesis and arachidonic acid metabolism as key pathways involved in the adaptation of grass carp gills to salinity stress. Overall, chronic salinity exposure caused structural alterations, disrupted ion regulation, altered antioxidant status, and marked transcriptomic and metabolomic changes in grass carp gills, offering new insight into salinity adaptation in freshwater fish.