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.

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.

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.