Ammonia is a critical pollutant in aquatic environments, posing significant risks to aquaculture by accumulating in culture systems due to fish excretion and organic matter decomposition. This study investigated the effects of ammonia toxicity on juvenile largemouth bass (Micropterus salmoides) under varying salinity conditions (0 and 5 psu), focusing on physiological responses and gut microbiota changes. Results indicated that ammonia exposure led to increased mortality, oxidative stress, liver damage, and significant shifts in gut microbial communities, especially under freshwater conditions. Elevated salinity mitigated these effects by reducing the bioavailability of toxic un-ionized ammonia (UIA) and enhancing the fish's physiological resilience, particularly in the kidney and intestine. Ammonia exposure significantly increased the IBR index values in all three organs, with the gills showing the most pronounced stress response, followed by the kidney and intestine. Salinity had a significant mitigating effect by reducing the oxidative stress response in comparison to freshwater conditions. However, in the gills, the protective effect of salinity was not enough to fully counteract the oxidative stress induced by ammonia. Ammonia exposure in freshwater favored pathogenic gut bacteria genera such as Aeromonas, while higher salinity enriched stress-resistant genera like Ralstonia and Klebsiella. These findings contribute to a better understanding of the interaction between salinity and ammonia toxicity, suggesting that moderate salinity increases within the fish's tolerance range could be an effective strategy in aquaculture to reduce ammonia toxicity and promote fish health.
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