Long-term ecological restoration can restore aquatic ecosystems to a certain extent and alleviate the crisis of freshwater fish biodiversity. In order to explore the fish community distribution patterns and key factors after ecological restoration and the health status of the watershed, fish and environmental data were collected from 39 sampling points in the Hun River Basin in the spring and autumn of 2021. A total of 51 fish species belonging to 11 families and 37 genera were collected during the survey, and the dominant species were Rhynchocypris lagowskii, Zacco platypus, Carassius auratus and Pseudorasbora parva. Compared with the results of past studies, the number of fish species has increased. The study found that the distribution of fish along the longitudinal gradient of the watershed showed obvious spatial differences and was divided into two groups. The results of canonical correspondence analysis (CCA) showed that agricultural land, urban land and grassland were the key factors for the spatial variation in fish communities in the Hun River Basin. The results of the F-IBI evaluation showed that the health status of the Hun River was fair or above fair, among which healthy, good, fair, poor and bad points accounted for 5.13%, 30.77%, 33.33%, 25.64% and 5.13%, respectively. The upper and middle reaches of the Hun River Basin were in better health, while the lower reaches were in poorer health, which was mainly affected by the intensity of human activities in different regions. This study will help watershed managers to make targeted restoration and protection measures for different regions.

Topmouth Gudgeon (Pseudorasbora parva), a typical invasive fish worldwide, has successfully invaded various aquatic ecosystems and colonized saline–alkali waters from freshwater due to its broad environmental tolerances. However, the molecular mechanisms of adaptation to saline–alkali stress for P. parva remain poorly characterized. To explore the potential genetic mechanisms, we conducted differential gene expression analysis using gill transcriptome of wild P. parva populations collected from four waters with different salinity–alkalinity levels. Comparative transcriptomics analysis showed that DEGs involved in osmoregulation, ano6, cftr, aqp1, and aqp3, were down-regulated; DEGs related to ammonia excretion, Rhcg and Rhbg, were up-regulated; DEGs for acid–base accommodation, nhe2, slc4a1, and ca2, were down-regulated while ca4 was up-regulated; and immune-system-related DEGs, il8 and il17, were down- and up-regulated, respectively, in a high saline–alkaline water environment. The DEGs were enriched in multiple KEGG pathways, such as the ribosome, thermogenesis, oxidative phosphorylation, necroptosis, and HIF-1 signaling pathways. In addition, more DEGs were significantly enriched in immune-disease-related pathways in high saline–alkaline water populations. This suggests that P. parva exposed to chronic saline–alkali stress, despite survival, still needed immune system regulation to defend against potential diseases. These results revealed the gill molecular mechanisms underlying P. parva saline–alkaline adaptation and offered valuable insights into the development of saline–alkaline water aquaculture fisheries