Ammonia nitrogen is one of the main toxic substances in aquatic cultivation environments. Chronic exposure to excessive amounts of ammonia-N creates toxic consequences, retarding the growth of aquatic organisms. This study investigated the growth performance, morphological and physiological alterations, and transcriptome changes in the hepatopancreas and gills of white shrimp Litopenaeus vannamei. The results showed that there was no significant difference in the survival rate (p > 0.05), whereas growth performance was reduced significantly in the treated groups compared to the control groups (p < 0.05). Significant structural damage and vacuolation occurred in hepatopancreas and gill tissues in the treated groups. Superoxide dismutase (SOD) activity and Na⁺/K⁺-ATPase content were significantly increased by chronic ammonia-N exposure in the two tissue groups. In addition, catalase (CAT) activity and malondialdehyde (MDA) levels were significantly altered in the hepatopancreas groups (p < 0.05), whereas no differences were observed in the gill groups (p > 0.05). There were 890 and 1572 differentially expressed genes identified in the hepatopancreas (treated versus control groups) and gills (treated versus control groups), respectively, of L. vannamei under chronic ammonia-N exposure. Functional enrichment analysis revealed associations with oxidative stress, protein synthesis, lipid metabolism, and different serine proteases. The gills maintained cellular homeostasis mainly through high expression of cytoskeleton and transcription genes, whereas the hepatopancreas down-regulated related genes in the ribosome, proteasome, and spliceosome pathways. These genes and pathways are important in the biosynthesis and transformation of living organisms. In addition, both tissues maintained organismal growth primarily through lipid metabolism, which may serve as an effective strategy for ammonia-N resistance in L. vannamei. These results provided a new perspective in understanding the mechanisms of ammonia-N resistance in crustaceans.

Ammonia nitrogen tolerance is an economically important trait of the farmed penaeid shrimp Litopenaeus vannamei. To identify the genes associated with ammonia nitrogen tolerance, we performed an extreme phenotype genome-wide association study method (XP-GWAS) on a population of 200 individuals. The single nucleotide polymorphism (SNP) genotyping array method was used to construct the libraries and 36,048 SNPs were genotyped. Using the MLM, FarmCPU and Blink models, six different SNPs, located on SEQ3, SEQ4, SEQ5, SEQ7 and SEQ8, were determined to be significantly associated with ammonia nitrogen tolerance. By integrating the results of the GWAS and the biological functions of the genes, seven candidate genes (PDI, OZF, UPF2, VPS16, TMEM19, MYCBP2, and HOX7) were found to be associated with ammonia nitrogen tolerance in L. vannamei. These genes are involved in cell transcription, cell division, metabolism, and immunity, providing the basis for further study of the genetic mechanisms of ammonia nitrogen tolerance in L. vannamei. Further candidate gene association analysis in the offspring population revealed that the SNPs in the genes zinc finger protein OZF-like (OZF) and homeobox protein Hox-B7-like (HOX7) were significantly associated with ammonia nitrogen tolerance trait of L. vannamei. Our results provide fundamental genetic information that will be useful for further investigation of the molecular mechanisms of ammonia nitrogen tolerance. These associated SNPs may also be promising candidates for improving ammonia nitrogen tolerance in L. vannamei.

The toxic effects of ammonia exposure on Litopenaeus vannamei have been widely reported, including tissue damage, oxidative stress, and metabolic disorders, but the ability of L. vannamei to recover from ammonia damage is still unclear. To further understand the adaptation mechanism of L. vannamei to ammonia, this study explored the effects of ammonia exposure and recovery on histopathology, physiological indicators, and transcriptomic responses. In the ammonia exposure (NH₄⁺-N 25 mg/L) and recovery experiment, shrimp were sampled at 0 h, 24 h, 48 h of exposure, and 24 h, 48 h of recovery. The results showed that histopathological damage to the hepatopancreas and gills caused by short-term ammonia exposure could be alleviated after recovery. Ammonia exposure inhibited superoxide dismutase (SOD) and catalase (CAT) activities, decreased total antioxidant capacity (T-AOC), and increased malondialdehyde (MDA) in shrimp. Restoration of the antioxidant system after exposure mitigated oxidative damage and reduced MDA levels. The inhibition of acid phosphatase (ACP) and alkaline phosphatase (AKP) activities in shrimp caused by ammonia exposure was reversible. Ammonia excretion and metabolism attenuate ammonia toxicity and promote recovery in L. vannamei. Transcriptome analysis identified 1690, 1568, and 1463 differentially expressed genes (DEGs) in the hepatopancreas at 48 h of stress, 24 h, and 48 h of recovery, respectively. KEGG enrichment analysis revealed that ammonia exposure induced oxidative damage, resulting in apoptosis. Furthermore, activation of antioxidant-related pathways, such as glutathione metabolism and peroxisomes, helped reduce oxidative damage during the post-exposure recovery period. The addition of exogenous spermine and spermidine may contribute to post-exposure recovery and enhance ammonia acclimation in L. vannamei. Differential expression of the inflammatory gene STEAP4 in the ammonia stress and recovery phases, as screened by transcriptome analysis, may play a positive role in post-stress recovery. This study demonstrated the reversibility of the toxic effects of ammonia exposure on L. vannamei, complemented the knowledge of the mechanisms of adaptation of shrimp under ammonia exposure, and provided a basis for subsequent ammonia tolerance studies in crustaceans.