Carbonic Anhydrase 2 and Na+/K+-ATPase Mediate Family-Dependent Nitrite Tolerance via Modulating Branchial Ion Transport and Acid–Base Balance in Penaeus vannamei

Nitrite is a key environmental challenge in intensive shrimp aquaculture, adversely affecting physiological regulation and survival. Although tolerant Penaeus vannamei families have been established by selective breeding, the basis of family-level variation in tolerance has yet to be clarified. In this study, nitrite-tolerant and nitrite-sensitive families were compared using survival analysis, transcriptomics, targeted qPCR validation, physiological assays, and RNA interference of representative transport-related genes. Under nitrite exposure, the tolerant family exhibited significantly higher survival and a distinct gill transcriptional response, characterized by stronger induction of acid–base and ion-transport genes, including carbonic anhydrase 2 (CA2), the Na+/K+-ATPase subunits ATP1A and ATP1B, as well as several V-type H+-ATPase-related genes. These transcriptional changes were accompanied by elevated ATP content and Na+/K+-ATPase activity, improved hemolymph pH stability, and reduced nitrite accumulation in both gill and hemolymph. RNAi-mediated knockdown of CA2 or ATP1B attenuated the nitrite-induced transport response, decreased ATP content and NKA activity, exacerbated hemolymph acidification, promoted internal nitrite accumulation, and ultimately reduced shrimp survival under nitrite stress. Family-based validation further showed that the tolerant family displayed higher survival than the sensitive family in the dsEGFP group, whereas this advantage was markedly reduced after CA2 or ATP1B knockdown under nitrite stress. These findings highlight that strengthened branchial ion transport and acid–base regulation represent key physiological mechanisms underlying nitrite tolerance in resistant shrimp families.