Understanding the biodiversity of aquatic communities and the underlying mechanisms that shape biodiversity patterns and community dynamics is crucial for the effective conservation and management of freshwater ecosystems. However, traditional survey methods often fail to comprehensively capture species diversity, particularly for low-abundance taxa. Moreover, studies integrating both metazoan and fish communities at fine spatial scales remain limited. To address these gaps, we employed a multi-marker eDNA metabarcoding approach, targeting both the 12S and 18S rRNA gene regions, to comprehensively investigate the composition of metazoan and fish communities in the Yujiang River. A total of 12 metazoan orders were detected, encompassing 15 families, 21 genera, and 19 species. For the fish community, 32 species were identified, belonging to 25 genera, 10 families, and 7 orders. Among these, Adula falcatoides and Coptodon zillii were identified as the most prevalent and abundant metazoan and fish species, respectively. Notably, the most prevalent fish species, C. zillii and Oreochromis niloticus, are both recognized as invasive species. The Bray–Curtis distance of metazoa (average: 0.464) was significantly lower than that of fish communities (average: 0.797), suggesting higher community heterogeneity among fish assemblages. Beta-diversity decomposition indicated that variations in the metazoan and fish communities were predominantly driven by species replacement (turnover) (65.4% and 70.9% for metazoa and fish, respectively) rather than nestedness. Mantel tests further revealed that species turnover in metazoan communities was most strongly influenced by water temperature, while fish community turnover was primarily affected by water transparency, likely reflecting the physiological sensitivity of metazoans to thermal gradients and the dependence of fish on visual cues for foraging and habitat selection. In addition, a co-occurrence network of metazoan and fish species was constructed, highlighting potential predator-prey interactions between native species and Corbicula fluminea, which emerged as a potential keystone species. Overall, this study demonstrates the utility of multi-marker eDNA metabarcoding in characterizing aquatic community structures and provides new insights into the spatial dynamics and species interactions within river ecosystems.

Non-fed aquaculture is an important contributor to low environmental impact protein production. However, knowledge of spatiotemporal patterns of the fish community in non-fed fishery systems remains limited, despite their ecological importance for sustainable aquaculture and fisheries. To elucidate the status of the fisheries and their critical drivers in non-fed fishery systems, hydroacoustic surveys were conducted seasonally in Hongchaojiang Reservoir in two seasons (spring and autumn) of two consecutive years: 2018 and 2019. Results showed that the average fish density in Hongchaojiang Reservoir was 121.6 ind./1000 m³. Fish communities varied significantly between geographical locations and seasons. On the temporal scale, fish densities in October were higher than those in April. On the spatial scale, fish densities were higher in the upstream (S1 and S3) than those in the midstream (S2, S4, S5, S6), while the density of S7, S8 and S9 in the downstream was the lowest. Trophic level index, zooplankton, chlorophyll-a, and phytoplankton play vital roles in fish distributional patterns, while the target strength, which reflects fish body size, was highly associated with water temperature, dissolved oxygen, total organic carbon, and phytoplankton. These results suggest that the spatiotemporal distribution of the fish community in Hongchaojiang Reservoir was jointly influenced by biotic and abiotic variables of water bodies, and highlight the importance of water nutrient levels and food availability in shaping fish distribution in the non-fed aquaculture system. This study should improve our understanding of ecological patterns and dominant drivers in fish stocks and provide information for successful sustainable management in non-fed purification fisheries.

Understanding the processes that drive microbial community assembly is a fundamental question in ecology, with important implications for predicting community responses to environmental disturbances. River ecosystems are under growing pressure from human disturbances, jeopardizing their ecological functions. Here, we investigated bacterial and protistan communities along the Yujiang River using environmental DNA metabarcoding. Bacterial communities exhibited significantly greater alpha diversity and broader habitat niches compared to protists. Additionally, a negative correlation was found between alpha diversity and niche breadth for both groups. Protistan communities exhibited significantly higher beta diversity (Bray–Curtis distance) than bacterial communities, with species turnover being the principal factor driving the variations in both communities. Null model results indicated that heterogeneous selection primarily structured bacterial communities, while stochastic processes (drift) mainly governed protist communities. Redundancy analysis and Mantel tests showed significant associations between environmental factors (e.g., temperature and pH) and bacterial community composition. Moreover, the longitude of sampling sites was linked to spatial variations in both bacterial and protistan communities. Further analyses, including distance-decay patterns, variation partitioning, and multiple regression on distance matrices, demonstrated that bacterial communities were driven by both environmental and spatial factors, while protist communities exhibited a stronger response to spatial factors. These results enhance our understanding of microbial community assembly in river ecosystems and provide valuable insights for the conservation and sustainable management of freshwater systems.