Transcriptomics reveals crowding stress inhibit the immune defense of the head kidney of the pearl gentian grouper juvenile through NF-κB signal pathway

Crowding stress is a significant welfare factor affecting aquatic animals in recirculating aquaculture systems. Little is known regarding the influence of prolonged crowding stress on the immunity of juvenile pearl gentian groupers. However, research exploring the potential mechanisms through which crowding stress affects fish immune function is limited. Therefore, this study aims to investigate the effect of crowding stress on the immune stress of the pearl gentian grouper juvenile (♀Epinephelus fuscoguttatus × ♂ Epinephelus lanceolatus) under prolonged conditions. We focused on the pearl gentian grouper juvenile and selected low- and high-density groups as the experimental breeding densities. Research shows that crowding stress increases the activities of alkaline acid plum and acid phosphatase, reduces the activities of lysozyme and immunoglobulin M content. RNA sequencing and comparative transcriptomic analyses were employed to explore changes in the gene expression of juvenile pearl gentian groupers subjected to crowding stress. Differential gene expression analyses between the low- and high-density groups identified 5777 unigenes that were differentially expressed following crowding stress, with 3216 and 2561 upregulated and downregulated, respectively. In the GO and KEGG enrichment analyses, many of the enriched signaling pathways related to genes were associated with immunity and oxidative stress. In addition, the combined analyses of enzyme activity and transcriptomics indicated that crowding stress suppressed the immune function of juvenile pearl gentian groupers, reducing their immune ability. Overall, these findings offer new insights into the molecular mechanisms underlying crowding stress tolerance in juvenile pearl gentian grouper, suggesting that the NF-κB pathway plays a crucial role in the immune response of the head kidney of the pearl gentian grouper to long-term crowding stress.