The patterns of carbon flow in large rivers influenced by dams are still not well known. We hypothesized that spatial variation in fish assimilation of basal production sources would be affected by heterogeneity of landscape-scale hydrology within a watershed due to the impoundment. We used stable isotope analysis and Bayesian mixing models to estimate relative contributions of basal production sources to fish consumers in a tributary of the Three Gorges Reservoir (TGR) with remarkably heterogeneous habitats between the upper and lower reaches. Model estimates indicated that riparian C₃ plants were the main basal food source irrespective of reaches or feeding groups. Autochthonous algae carbon also appeared to be important as secondary carbon sources. However, the major contributive aquatic algae in the upstream were benthic algae while planktonic algae were important in the downstream, and this difference was related to their distinct hydrological characteristics. The contribution from C₄ plants was comparatively less important to all fish consumers. Our results highlighted the significance of the riparian C₃ carbon source to fish consumers in the TGR tributary and that the difference in landscape-scale characteristics was not enough to influence the pattern, which may be attributed to abundant standing stock of the riparian plants as well as hydrologic regimes in this river.

Food chain length (FCL) is a critical measure of food web complexity that influences the community structure and ecosystem function. The FCL of large subtropical rivers affected by dams and the decisive factors are far beyond clear. In this study, we used stable isotope technology to estimate the FCL of fish in different reaches of the main stream in the Yangtze River and explored the key factors that determined the FCL. The results showed that FCL varied widely among the studied areas with a mean of 4.09 (ranging from 3.69 to 4.31). The variation of FCL among river sections in the upstream of the dam was greater than that in the downstream. Regression analysis and model selection results revealed that the FCL had a significant positive correlation with ecosystem size as well as resource availability, and FCL variation was largely explained by ecosystem size, which represented 72% of the model weight. In summary, our results suggested that ecosystem size plays a key role in determining the FCL in large subtropical rivers and large ecosystems tend to have a longer food chain. Additionally, the construction of the Three Gorges Dam has been speculated to increase the FCL in the impoundment river sections.

Environmental DNA (eDNA) metabarcoding has emerged as a powerful tool for biodiversity monitoring, yet its accuracy is fundamentally constrained by the completeness and taxonomic reliability of reference sequence databases. For the Three Gorges Reservoir (TGR), no integrated multi-marker eDNA reference library exists, hampering standardized fish conservation monitoring under the Yangtze River Ten-Year Fishing Ban. Here, we constructed a comprehensive, multi-marker eDNA reference database for the fish fauna of the TGR, encompassing mitochondrial 12S rRNA, 16S rRNA, and cytochrome c oxidase subunit I (COI) gene sequences from 173 specimens (120 species) collected between 2021 and 2024. After integrating publicly available sequences, the final database comprised 161 species. Then, we quantitatively compared species annotation performance between this local database and public repositories. Results showed that while public databases achieved higher nominal species coverage (94.67%), they exhibited critical deficiencies in annotation accuracy, correctly annotating only 77.97% (12S rRNA), 75.00% (16S rRNA), and 38.14% (COI) of sequences from shared species under controlled conditions. In contrast, the local database exhibited 92.37%, 93.10% and 100% annotation accuracy for the respective markers. Optimal interspecific Kimura 2-parameter (K2P) thresholds for species delimitation were 0.00448 (12S rRNA), 0.00531 (16S rRNA), and 0.00734 (COI). In addition, 15, 0, and 4 species pairs exhibited zero interspecific distance for 12S rRNA, 16S rRNA, and COI, respectively. These limitations reinforce the need for cautious interpretation of eDNA metabarcoding results and the integration of multiple markers or complementary nuclear loci. This study provides preliminary evidence that regionally curated, multi-marker reference libraries could improve taxonomic assignment reliability in eDNA metabarcoding compared to uncurated public repositories, providing a foundational resource for biodiversity conservation.

Freshwater lakes worldwide are undergoing rapid degradation, raising concerns about the effectiveness of recent large-scale conservation interventions. China’s ‘10-year fishing ban’ represents one of the world’s most ambitious fishery moratoria, yet its ecosystem-level consequences remain poorly quantified. Using data from the two seasonal surveys conducted in Dongting Lake in 2019, we applied a mass-balanced Ecopath with Ecosim model to evaluate how fishing closure, and its combination with multi-species stock enhancement, affects trophic structure, energy flows, and system stability from 2021 to 2030. Simulations show that the closure-only scenario nearly doubles total ecosystem production, yet yields limited improvement in maturity indicators, reflecting a slow recovery of food web complexity. Across the tested closure-plus-enhancement scenarios, the highest projected system omnivory index occurred under scenario S5 (from 0.24 to 0.27), whereas the highest projected Shannon diversity index (from 0.59 to 0.64) and total transfer efficiency (from 10.80% to 11.12%) occurred under scenario S1, relative to the 2019 baseline. Based on the level-wise responses of the L9 treatments, a recommended combined scenario consisting of 1.04 t bighead carp, 4.30 t grass carp, and 1.14 t silver carp, with no additional black carp stocking, was constructed. Under this scenario, the model projected enhanced biomass recovery and a shorter restructuring period for key functional groups. Our study provides a reference for predicting ecosystem responses following the ‘10-year fishing ban’ and also provides data for ecosystem-based assessments for stock enhancement.

In order to evaluate food utilization and trophic transfer efficiency of the food chain in the Three Gorges Reservoir, stable carbon and nitrogen isotope methods were employed to investigate the spatiotemporal variations in the energy contribution of four fundamental carbon sources-phytoplankton, C₃, C₄ plants in the riparian zone, and epiphytic algae-to four dominant small-sized fish species, Squalidus argentatus, Saurogobio dabryi, Pseudobrama simoni, and Hemiculter leucisculus. The results indicated significant differences in the δ¹³C and δ¹⁵N values among different carbon source organisms, effectively distinguishing their fundamental carbon sources. The outcomes of the Bayesian mixed model suggested that phytoplankton contributes the highest proportion of energy to the four small fish species. At the hydrological scale, there is no significant difference in the contribution rates of autochthonous and allochthonous carbon sources to the four small fish (P>0.05). However, at the spatial scale, a highly significant difference was observed (P<0.01). This study indicate that autochthonous carbon is the primary energy source for small fish in the reservoir area, while the contribution of allochthonous carbon sources increases noticeably along the longitudinal gradient of the Three Gorges Reservoir. This may be associated with the characteristics of diverse submerged area and the increased sedimentation of exogenous carbon source particles in the quiescent water environment near the reservoir head.