Salinity Effects on Aquatic and Host Intestinal Microbiota Dynamics in Rhinogobio ventralis

The endangered <i>Rhinogobio ventralis</i>, endemic to the upper Yangtze River, is dependent on captive breeding for its conservation. However, this highly stress-sensitive species is exceptionally susceptible to <i>Ichthyophthirius multifiliis</i>, leading to severe pathology and high mortality in culture. Elevated salinity holds potential for managing key aquaculture pathogens, including <i>Ichthyophthirius multifiliis</i> and <i>Saprolegnia</i> spp. However, its potential unintended ecological consequences remain insufficiently understood. This study evaluated the systemic impacts of 5‱ salinity on the culture environment of the endangered species <i>Rhinogobio ventralis</i>, using integrated 16S/18S rRNA gene sequencing and water quality analysis. The results demonstrated that while salinity treatment effectively reduced the environmental molecular signal of harmful eukaryotes such as <i>Ichthyophthirius</i> and <i>Saprolegnia</i>, it also induced significant ecological shifts: (1) aquatic prokaryotic diversity increased, yet the self-purification capacity of the water was compromised, indicated by elevated dissolved oxygen, nitrate nitrogen, and total nitrogen; (2) in the fish intestinal microbiome, a decline in potentially beneficial taxa (e.g., <i>Exiguobacterium</i>) co-occurred with an enrichment of genera containing potentially pathogenic species (e.g., <i>Staphylococcus</i> and <i>Pseudomonas</i>), collectively suggesting a state of dysbiosis; (3) co-occurrence network analysis revealed that the aquatic microbial community developed greater complexity, while the intestinal network became structurally simplified and more antagonistic. These findings reveal that elevating salinity in freshwater aquaculture systems compromises both host microbiome health and aquatic ecosystem functioning. As such, future aquaculture management should integrate supportive measures like probiotic supplementation to maintain overall system stability.