Microbial Community Succession Sustains Fish Diversity in the Upper Yangtze River Reserve

Abstract Fish diversity in rivers is critical for aquatic ecosystem sustainability, with multitrophic microbial communities (bacteria, fungi, phytoplankton, zooplankton) playing key roles in energy transfer. This study in the upper Yangtze River's Fish National Nature Reserve (FNNR) used environmental DNA (eDNA) to investigate microbial succession and its relationship with fish diversity. Bacteria showed the highest alpha‐diversity, while zooplankton has the lowest beta‐diversity. Geographic location and total nitrogen emerged as primary drivers of microbial community succession. Bacteria and phytoplankton demonstrated stronger environmental adaptability but lower community turnover compared to fungi and zooplankton. Null model analysis revealed homogenizing processes dominated bacterial and fungal assembly, whereas heterogeneous processes shaped phytoplankton and zooplankton communities. Microbial association networks indicated distinct community structures in different river systems. Path modeling showed that multitrophic microbial communities negatively impacted fish diversity, but cross‐trophic interactions among microorganisms has positive effects. These findings highlight how microbial diversity supports fish communities and provide conservation insights by linking microbial processes to ecosystem health. The study emphasizes the importance of understanding microbial dynamics for adaptive management strategies in biodiversity preservation.