The Temporal and Spatial Structure of the Fish Community in the Mountain River Belonging to upper Yangtze River Revealed by Environmental DNA Technology with Analysis of Key Environmental Determinants

The Chishui River, a vital part of the national Nature Reserve for rare endemic species in the upper Yangtze River, maintains a natural hydrological regime due to the absence of dams, underscoring its high conservation value. This study employed environmental DNA (eDNA) techniques to examine spatiotemporal variations in fish community structure across nine sampling sites in Guizhou Province, China, over one year. A total of 93 fish species, predominantly cyprinids, were identified. The fish community was dominated by benthopelagic and omnivorous species, with an increasing presence of exotic species. While fish diversity showed no significant spatial variation, community structure differed markedly between seasons, as revealed by the clustering results in the RDA plot, the sampling sites in the wet season and dry season exhibit a distinct inter-group separation, indicating that season is the primary factor influencing community structure. pH, altitude, and NH3-N are the key drivers of community differentiation, and T(temperature), $${\text{NO}}_{2}^{ - }$$ , $${\text{PO}}_{4}^{{3 - }}$$ , and DO collectively drive community structure. In the context of the Yangtze River basin’s ten-year fishing ban, eDNA analysis proves to be an effective primary survey method. This study elucidates the spatiotemporal dynamics of fish communities in the Chishui River, providing essential data for conservation and management strategies.