Multi-omics insights into the response of the tropical copepod Apocyclops royi-TH to salinity stress: implications for immunity and polyunsaturated fatty acid biosynthesis

Salinity is a key environmental factor influencing biological processes in aquatic organisms. Apocyclops royi-TH, a copepod species native to Thailand, is a promising live feed candidate due to its high nutritional value. However, its responses to salinity stress remain poorly understood. This study employed a multi-omics approach, integrating transcriptomics, fatty acid profiling, and microbiome analysis, to assess low-salinity (15 ppt) adaptation versus a control (25 ppt). RNA-seq identified 6371 differentially expressed genes, including 294 immune-related genes enriched in 21 KEGG pathways. Up-regulated genes included pattern recognition receptors (PRRs), serine proteases, peroxidases, and antimicrobial effectors, while genes related to oxidative stress and proteinase inhibition were down-regulated. Additionally, 136 genes related to lipid metabolism were differentially expressed, with selective up-regulation of desaturases and down-regulation of elongases. Fatty acid analysis showed no significant differences in total polyunsaturated fatty acid (PUFA), docosahexaenoic acid (DHA), or eicosapentaenoic acid (EPA) between groups, but levels of n-6 PUFA and arachidonic acid (ARA) were significantly higher under low salinity. Microbiome profiling revealed increased bacterial richness and a shifted community composition in the low salinity group, including elevated abundance of Pseudomonas and Acholeplasma, and reduced levels of Vibrio. These findings demonstrate that salinity stress modulates immune responses, lipid biosynthesis, and microbial composition in A. royi-TH, offering insights into its adaptive metabolic and immune responses, and its potential as a resilient and nutritionally valuable live feed in aquaculture.