A comparative study on growth performance, physiological responses and transcriptomic regulation of kuruma shrimp (Penaeus japonicus) under sandy and non-sandy bottom conditions

Substrate is a critical environmental factor influencing growth and health of Penaeus japonicus . Traditional sandy substrates readily accumulate organic pollutants, deteriorating sediment conditions and increasing disease risks. In this 56-day trial, a shared-water indoor cage system was adopted to compare growth, physiological metabolism and hepatopancreatic transcriptomic responses between sandy-substrate (SL) and sand-free (SF) groups. On day 28, SF exhibited significantly higher survival (89.52 ± 1.56%, P < 0.05) than SL (77.14 ± 5.72%), while body length, body weight and yield per unit area remained comparable. SF showed elevated hepatopancreatic SOD, AKP, ACP, MDA and gill NKA activity, together with reduced intestinal amylase and protease activities ( P < 0.05). At day 56, SF achieved higher cumulative survival (89.52 ± 3.30%) and yield (408.09 ± 24.19 g·m⁻²) than SL (76.19 ± 4.36%, 345.69 ± 27.58 g·m⁻²; P < 0.05). SF displayed markedly higher gill SOD, hepatopancreatic CAT, haemolymph LZM and PO activities, but lower hepatopancreatic MDA, AKP, ACP, gill NKA and intestinal digestive enzyme activities ( P < 0.01), reflecting long-term physiological adaptation. Transcriptomics revealed a “short-term suppression, long-term activation” pattern of differentially expressed genes; core PPI hub proteins shifted from Hspbp1/Hif1a to Bub1b/plk1. Collectively, sand-free culture improves P. japonicus survival, and shrimp adapt to sand-free surroundings via sequential modulation of antioxidant, immune and metabolic pathways.