This study focused on monitoring the dynamics of bacterial communities and assessment of the influences of physicochemical parameters during a culture cycle in black carp polyculture ponds. Our results showed high variation in microbial diversity and microbial composition in the water column during the culture period. Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla, while the abundances of the phyla Cyanobacteria, Firmicutes, and Bacteroidetes changed in different months. Moreover, 13 abundant genera with significant difference were found between different months. Thus, samples in different months were divided into three groups according to principal coordinate analysis (PCoA) and unweighted pair-group method (UPGMA) clustering results. RDA showed that total nitrogen (TN), total phosphorus (TP), phosphate (PO₄³⁻-P), nitrate (NO₃⁻-N), temperature (T), dissolved oxygen (DO), and pH significantly shaped the microbial community composition in different months. While Pearson correlation coefficient showed that T, SD, and pH were strongly correlated to the dominant genera. Considering some genera are potential pathogenic bacteria, we could manage the black carp pond by quickly monitoring the water temperature and SD in the future.

It is necessary to determine the optimal temperature for Percocypris pingi growth in recirculating aquaculture systems. To describe the effects of temperature, we evaluated the growth, antioxidant enzyme activity, and gut microbiota structure of P. pingi at different temperatures, including 14, 18, 22, and 26 °C. Results showed that increases in body weight of individuals of the groups subjected to 18 and 22 °C temperatures were considerably higher than those in the groups subjected to temperatures of 14 and 26 °C between 20 and 60 d after the experiment started. Acid phosphatase activity in the liver and kidneys of P. pingi did not differ significantly among the various temperature groups (p > 0.05). A gradual restoration of the alkaline phosphatase and superoxide dismutase activities to variations in the surrounding temperature was observed in the liver and kidney of P. pingi. Interestingly, the water temperature did not affect the α-diversity or composition of the gut microbiota of P. pingi. In conclusion, water temperatures between 14 and 26 °C significantly impacted the growth of P. pingi (p < 0.05) but not the liver and kidney antioxidant capacity or the gut microbiota within 60 d.

Rhinogobio ventralis is a rare fish found in the Yangtze River in China and has significant ecological and economic value. In this study, a bacterial strain (RV-JZ01) was isolated from the livers of diseased R. ventralis. This isolate was identified as Aeromonas veronii based on its morphology, biochemical features and 16S rDNA phylogenetic analysis. The artificial infection of healthy R. ventralis (16 ± 2 cm) with RV-JZ01 resulted in the manifestation of clinical symptoms, in accordance with those of naturally infected fish. The 50% lethal dose (LD₅₀) of RV-JZ01 for R. ventralis was 6.3 × 10⁶ CFU/mL. Histopathological examination revealed various pathological changes in the diseased fish, including intestinal villus swelling and rupture, hepatocyte vacuolization, renal tubular cell nuclear enlargement and pyknosis, and myocardial fiber fracture and atrophy. RV-JZ01 infection significantly reduced the gut flora diversity of R. ventralis, with the relative abundances of Firmicutes and Fusobacteria increasing, and those of the Proteobacteria and Bacteroidetes decreasing. The abundance of Lactobacillus and Streptococcus dramatically increased, and the abundance of Clostridium and Escherichia reduced in the intestinal microbiota of R. ventralis infected with RV-JZ01. Antibiotic sensitivity testing revealed that RV-JZ01 was highly susceptible to 12 antimicrobials, including erythromycin, cefalexin, norfloxacin, furazolidone, sulfonamides, enrofloxacin, doxycycline, piperacillin, florfenicol, gentamicin, and lincomycin. These results contribute to the understanding of pathological alterations in R. ventralis following A. veronii infection, offering valuable data to support the implementation of disease treatment.

Coreius guichenoti, an endemic fish of the upper Yangtze River, has experienced severe population decline due to overfishing and habitat fragmentation. To inform its conservation, this study compared life-history traits between artificially bred and historical wild populations, revealing pronounced plasticity in response to environmental conditions. The cultured population, dominated by age 0–4 individuals but retaining a notable proportion of age 5–6 fish, exhibited faster growth and higher fecundity (mean absolute fecundity 32,724 ± 24,132 eggs; relative fecundity 37.5 ± 18.5 eggs/g) than the wild population. In contrast, the wild group consisted of >90% age 0–4 individuals, showed virtually no fish aged 5–7, reproduced seasonally with high total egg output, and tended toward a periodic life-history strategy, whereas the cultured group tended toward an opportunistic strategy that still retained some periodic traits. These results demonstrate that C. guichenoti can adjust its life history on a within-generation scale. Accordingly, we recommend pre-release conditioning with moderate flow and temperature variations to enhance field adaptability. This study provides evidence-based guidance for broodstock selection and preconditioning in restocking programs, aimed at improving post-release survival and reproductive success in the wild.

Rhinogobio ventralis is a typical endemic fish and an important economic species in the upper reaches of the Yangtze River. However, it is highly susceptible to Ichthyophthirius multifiliis (Ich) during artificial breeding, resulting in elevated mortality rates following infection. In this study, we established an infection model using Ich to investigate its effects on the skin of R. ventralis. Pathological changes on the skin were examined through tissue sections and transmission electron microscopy. The results showed a significant increase in mucus cells, club cells and epidermal thickness, the abnormal desmosome junction between epithelial cells, mucous cells pyknosis shrinkage along with morphological and structural abnormalities in their organelles within the skin after infection. We employed transcriptomics and metabolomics to characterize key genes, metabolites, and signaling pathways in the skin following Ich infection. A total of 84,016 unigenes and 1075 metabolites were obtained from skin tissues. Respectively, 388 DEGs and 135 differentially expressed metabolites, 233 DEGs and 72 differentially expressed metabolites were obtained at 7 dpi and 14 dpi, respectively. In response to Ich infection, the host modifies the ribosome pathway, protein processing in endoplasmic reticulum pathway, antigen processing and presentation pathway and glycerophospholipid metabolism, which suggests both disruption and activation of the immune system, alongside disruptions in metabolic processes among infected R. ventralis. Our results shed light on the immune strategies employed by R. ventralis in response to Ich infections, thereby providing a valuable dataset for further investigation into the mechanisms underlying resistance regulation in R. ventralis against such infections.

Schizothorax kozlovi, as an endemic and vulnerable fish of the upper Yangtze River in China, faces many threats. In order to expose the population structure of wild S. kozlovi, the carbon and oxygen isotopic ratios in the otoliths, and the gene sequences of two common mitochondrial markers (Cytb and COI) were investigated in four sampling locations, and then their relationship with ambient temperature was further investigated. In general, it exhibits limited geographic population structuring of S. kozlovi in the upper Yangtze River by both mtDNA and stable isotopes. The values of otolith stable isotope ratios varied from −15.30‰ to −12.37‰ for δ¹⁸O and from −10.10‰ to −6.13‰ for δ¹³C. Significant relationships were revealed between stable isotope ratios and specific mean monthly water temperature variables (from November to March), indicating low temperature effect on otolith stable isotope ratios. Haplotype diversity and nucleotide diversity were 0.928 and 0.00778, both exhibiting high levels. A median-joining haplotype network indicated a mixture of geographical distribution but exhibited two distinct haplotype lineages (Clade I and Clade II). AMOVA detected that the higher percentage of genetic variance was within sampling locations (96.94%) and between two haplotype lineages (72.82%). Most F_ST values between sampling locations showed small levels of genetic differentiation except the differentiation between population SJ (Sanjiangkou) and JP (Jinping). Therefore, two haplotype lineages and population JP of S. kozlovi in the upper Yangtze River are suggested as three management units for conservation due to their moderate-to-great genetic differentiation and isolated habitat.