Ammonia can easily accumulate in water during the culture period, and the accumulated concentrations can reach high levels, which is one of the main stress factors with severely negative effects on the growth and health of cultured shrimp. Dietary manipulation, such as feeding Ampithoe sp. meal, has been proven to be an effective method for reducing the mortality of Litopenaeus vannamei under sublethal ammonia stress and thus improving the ammonia tolerance of the shrimp, but the underlying mechanism needs to be further studied. In this study, L. vannamei with increased ammonia tolerance (PV_T) were obtained by feeding Ampithoe sp. meal, shrimp not fed Ampithoe sp. meal were used as a control (PV_C), and a comprehensive transcriptome analysis of the response of L. vannamei exposed to ammonia-N at the 50% lethal concentration for 96 h was performed. A total of 318,815,732 clean reads, including 170,156,604 and 148,659,128 clean reads from the shrimp in the PV_T and PV_C groups, were obtained. The expression of genes involved in carbohydrate and lipid metabolism pathways was upregulated in the PV_T group compared with the PV_C group, which indicated that the shrimp in the PV_T group had a higher energy supply level than those in the PV_C group, and this difference was the main cause of the observed improvement in ammonia tolerance. Additionally, the upregulated expression of genes involved in the AMP-activated protein kinase (AMPK) pathway in the PV_T group was responsible for the observed upregulation of the expression of genes involved in the carbohydrate and lipid metabolism pathways. However, among the GO terms that were significantly enriched in the DEGs identified from the comparison of the PV_T and PV_C groups, only one GO term was related to the immune system process. In conclusion, feeding Ampithoe sp. meal to L. vannamei exposed to sublethal ammonia can enhance the carbohydrate and lipid metabolism pathways to increase the energy supply and thus reduce the mortality of the shrimp.
