The assessment of genetic improvement was comprehensively analyzed using the mtDNA Cyt b gene and SSR markers among three farmed grass carp populations caught in May 2024. The results of an mtDNA Cyt b gene analysis in 198 individuals showed that the haplotype diversity index (H_i) and nucleotide diversity index (P_i) were 0.555 and 0.00058, respectively. The results of the analysis of SSR marker data in 196 individuals indicated that the unequal dosage amplification at the same locus was found in the CC population. Moreover, the total number of alleles (A: 338), number of alleles per locus (Na: 15.36), observed heterozygosity (Ho: 0.8391), expected heterozygosity (He: 0.8380), and polymorphic information content (PIC: 0.8191) in the KC population was relatively higher than that in the CC (A: 129; Na: 5.86; Ho: 0.0025; He: 0.6191; PIC: 0.5747) and CY (A: 293; Na: 8.77; Ho: 0.821; He: 0.7483; and PIC: 0.5747) populations. The FST and AMOVA analysis showed the existence of a significant differentiation (p < 0.001), with a high genetic differentiation between the CC and CY populations. In summary, a high genetic variability exists in the KC population, while the father (CY) and mother (CC) populations have relatively low genetic variability. This study reveals evidence of the existence of a “micro-hybrid”. Moreover, the results demonstrated that combining both gynogenesis and backcross breeding technology is vital for the genetic improvement of grass carp. Moreover, continuous research into the genetic health of these populations is required as well as support for the protection of germplasm resources and artificial breeding.

The lotus–fish co-culture (LFC) system leverages plant–fish symbiosis to optimize aqua-culture environments, enhancing both economic and ecological yields. However, the eco-logical mechanisms of microbial communities in LFC systems remain poorly understood, particularly regarding the functional roles of fungi, archaea, and viruses. This study compared microbiota (viruses, archaea, fungi) in water, sediment, and fish (crucian carp) gut of LFC and intensive pond culture (IPC) systems using integrated metagenomic and environmental analyses. Results demonstrated that LFC significantly reduced concentrations of total nitrogen, total phosphorus, and nitrite nitrogen and chemical oxygen demand in water, and organic matter and total nitrogen in sediment compared to IPC. Community diversity analysis, LefSe, and KEGG annotation revealed suppressed viral diversity in LFC, yet increased complexity and stability of intestinal virus communities compared to IPC. Archaeal and functional analyses revealed significantly enhanced ammonia oxidation and OM decomposition in LFC versus IPC, promoting methane metabolism equilibrium and sediment organic matter decomposition. Moreover, crucian carp intestines in LFC harbored abundant Methanobacteria, which contributed to maintaining a low hydrogen partial pressure, suppressing facultative anaerobes and reducing intestinal infection risk. The abundance of fungi in sediment and crucian carp intestine in LFC was significantly higher than that in IPC, showing higher ecological self-purification ability and sustainability potential in LFC. Collectively, LFC's optimized archaeal–fungal networks strengthened host immunity and environmental resilience, while viral community suppression reduced pathogen risks. These findings elucidate microbiome-driven mechanisms underlying LFC’s ecological advantages, providing a framework for designing sustainable aquaculture systems through microbial community modulation.

Aiming to understand the genetic diversity of Culter and Cultrichthys fishes in West Dongting Lake following the implementation of fishing ban, this study analyzed the genetic diversity and phylogeny of five Cultrinae species based on mitochondrial Cytb and COI gene sequences. For Cytb, 50 haplotypes were identified with high overall genetic diversity (H_d = 0.954, π = 0.04765, K = 53.506). Similarly, COI yielded 48 haplotypes (H_d = 0.950, π = 0.03251, K = 36.414). Interspecific comparisons revealed that Culter mongolicus and Culter alburnus exhibited the highest genetic diversity, while Cultrichthys erythropterus showed the lowest. Demographic inferences from neutrality tests and mismatch distribution analyses differed between markers. Based on Cytb, populations of C. erythropterus and C. oxycephaloides appeared to be at neutrality, whereas C. mongolicus, C. alburnus, and C. dabryi significantly deviated, suggesting historical expansion. Mismatch distributions supported recent expansion in C. mongolicus and C. dabryi. In contrast, COI-based neutrality tests indicated expansion in C. mongolicus, C. alburnus, and C. dabryi, with mismatch results confirming this signal for C. dabryi. The negative values of Tajima’s D and Fu’s Fs observed across all five species reflect an accumulation of low-frequency alleles within populations, which may indicate a recent rapid demographic recovery. These findings provide genetic evidence that the genetic diversity of these Cultrinae species has likely been recovering since the fishing ban took effect on 1 January 2020. Further conservation strategies are therefore recommended to promote population recovery and enhance genetic diversity.

Large-water fisheries are central to China’s freshwater aquaculture, but their sustainability is threatened by eutrophication from traditional high-density stocking. Polyculture of grass carp and crucian carp offers an ecologically sound alternative; nevertheless, its direct effects on plankton communities require further study. We conducted monthly sampling from July to December 2023 (over two seasons within a single aquaculture cycle) in polyculture ponds and used eDNA metabarcoding (18S V9) with high-throughput sequencing. We detected 288 planktonic taxa across 28 phyla and 290 genera based on eDNA sequence assignment. Alpha diversity (Chao1, Shannon, Simpson) peaked in autumn and was lowest in winter, with Chao1 showing greater seasonal variation. Beta diversity revealed season as the dominant factor (R² = 0.287, p = 0.012), with significant summer–winter divergence. Null-model analysis indicated stochastic processes (56.3%) slightly exceeded deterministic filtering (43.7%), and stochasticity was higher in summer (67.2%), suggesting fish bioturbation and grazing create heterogeneous microhabitats. Co-occurrence networks were dominated by positive links (87.3%), with Cryptomonas as a central hub, implying mutualism and niche complementarity. This study is the first to integrate eDNA metabarcoding with community assembly theory to elucidate seasonal succession and interactions in this polyculture. Our findings confirm that polyculture sustains diversity and stability via top-down (grazing) and bottom-up (nutrient release) effects, providing eDNA-based taxonomic evidence for management of large-water aquaculture.

Due to overfishing, eutrophication of rivers and lakes, and irrational stocking practices, the diversity of wild native carp populations has declined, leading to germplasm degradation and a decrease in fish quality, thereby affecting the sustainable development of fisheries. In this study, a novel hybrid crucian carp lineage (designated LWR) was successfully established via distant hybridization using Dongting Lake crucian carp (LC, ♀) and Hefang crucian carp (WR, ♂) as parental stocks. Systematic analyses were conducted on the morphology, ploidy, fertility, growth performance, survival rate, and molecular genetics of LWR. The results reveal that LWR is an allodiploid (2n = 100), with a chromosome number identical to that of its parents. Gonadal development in the hybrid progeny (LWR) was normal, with both sexes being fertile and reaching sexual maturity at one year of age. Morphologically, LWR exhibited intermediate traits with a paternal bias, characterized by a deep-bodied and elongated shape. In terms of growth performance, LWR displayed significant heterosis (approximately 145% and 271% higher than the body weight of the maternal parent at 6 months and 1 year). Molecular genetic analysis indicated that the 5S rDNA sequences of LWR were predominantly inherited from the paternal parent WR, with insertions, deletions, recombination, and mutations detected. The mtDNA sequences exhibited 99.78% similarity to those of the maternal parent LC, following maternal inheritance with sporadic nucleotide variations. These findings offer a new paradigm for hybridization and a theoretical foundation for the improvement and sustainable utilization of indigenous crucian carp germplasm resources, the selective breeding of improved aquaculture strains, and the sustainable development of fisheries.

EDNA metabarcoding provides distinct benefits—including non-invasiveness, cost-effectiveness, and high detection sensitivity—that make it particularly appropriate for aquatic ecosystem conservation and fisheries management. An environmental DNA (eDNA) metabarcoding survey was performed in the Cuijiang River to assess the feasibility of this technique for fish diversity monitoring. Fish diversity was evaluated through water collection, eDNA extraction and purification, and subsequent bioinformatics analysis. Our results revealed that the surveyed river section harbours at least 36 fish species, belonging to 30 genera, 13 families, and 6 orders. The fish community was numerically dominated by Cypriniformes. Notably, invasive alien species represented a relatively high proportion (24.72%) of the total operational taxonomic units (OTUs). Alpha diversity indices showed spatial heterogeneity among the monitoring sites, which is likely influenced by anthropogenic activities, land-use patterns, and hydrological connectivity in the sampling areas. Overall, eDNA metabarcoding proves to be an effective approach for fish diversity assessment and can serve as a valuable supplementary tool to conventional methods, with particular utility for the early detection of elusive and invasive species. We therefore recommend its incorporation into ongoing and future aquatic monitoring and conservation frameworks to strengthen early detection, habitat management, and biodiversity protection, thereby offering essential baseline data for future conservation and management of local fish diversity.