Transcriptome Analysis of Different Aquaculture Substrates on the Immune Response of Babylonia areolata

To assess the impact of different substrates in a recirculating water system on the immune response and antioxidant capacity of Babylonia areolata, we conducted a comparative analysis of the transcriptomes and antioxidant performance of the digestive glands in three substrate environments (sand-S group, ceramic granules-C group, and PVC breeding nest-P group). Transcriptome results revealed that the S group and P group exhibited the highest number of differentially expressed genes (DEGs), with a total of 2218 DEGs, including 928 upregulated and 1290 downregulated DEGs. The C group and P group had 1055 DEGs in common, with 316 upregulated and 739 downregulated DEGs. The C group and S group had the fewest DEGs, with 521 in total, including 303 upregulated and 218 downregulated DEGs. GO enrichment analysis showed that in the S vs P group, terms such as catalytic activity, membrane part, and cellular process were enriched with 287, 262, and 180 DEGs, respectively. In the C vs P group, binding, cellular process, and cell part were enriched with 146, 135, and 127 DEGs, respectively. In the C vs S group, catalytic activity, membrane part, and metabolic process were enriched with 90, 83, and 59 DEGs, respectively. Kegg enrichment analysis revealed significant changes in immune-related pathways in the S vs P group, including lysosome, phagosome, and leukocyte transendothelial migration, with 30, 13, and 10 enriched DEGs, respectively. In the C vs P group, phagosome, drug metabolism-other enzymes, and N-Glycan biosynthesis showed significant changes in immune-related pathways, with 9, 6, and 4 enriched DEGs, respectively. In the C vs S group, lysosome, PPAR signaling pathway, and fatty acid degradation exhibited significant changes in immune-related pathways, with 8, 4, and 3 enriched DEGs, respectively. Regarding antioxidant capacity, the S group showed significantly higher total T-AOC than the other experimental groups, while CAT, SOD, POD, and AKP were lower than in the C and P groups. The ACP level in the Sand group was not significantly different from the P group but significantly lower than the C group. In conclusion, substrate environments significantly influence the immune-related genes and key antioxidant enzyme activities in B. areolata.