Recovery of the hepatopancreas transcriptome of Penaeus vannamei after different ammonia nitrogen stresses

Here we establish a threshold for irreversible injury in Penaeus vannamei by coupling a 7 day gradient of unionized ammonia exposure with a 40 day recovery phase under biofloc technology (BFT). The unionized ammonia concentrations used for the stress treatments were 0.00, 0.05, 0.10, 0.20, 0.40, and 0.80 mg/L.AS4 and AS8 shrimp continued to show severe oxidative and biochemical impairment with limited repair, alongside persistently elevated apoptosis rates and higher expression of apoptosis-related genes relative to AS0; survival and growth performance also remained significantly reduced. Transcriptomic profiling further revealed sustained activation of genes and pathways involved in damage control, detoxification, autophagy lysosome processes, and energy metabolic reprogramming in AS4 and AS8 during recovery, indicating a prolonged reparative burden. Collectively, once unionized ammonia exceeds 0.40 mg/L, it induces irreversible, deep-seated hepatopancreatic injury marked by oxidative stress and mitochondrial damage.