Cascade dams disrupt the river continuum, altering hydrology, biodiversity and nutrient flux. Describing the diversity of multi-trophic microbiota and assessing microbial contributions to the ecosystem processes are prerequisites for the restoration of these aquatic systems. This study investigated the microbial food web structure along a cascade-dammed river, paying special attention to the multi-trophic relationships and the potential role of pelagic-benthic coupling in nutrient cycles. Our results revealed the discontinuity in bacterial and eukaryotic community composition, functional group proportion, as well as α-diversity due to fragmentation by damming. The high microbial dissimilarity along the river, with the total multi-trophic β-diversity was 0.84, was almost completely caused by species replacement. Synchronization among trophic levels suggests potential interactions of the pelagic and the benthic groups, of which the β-diversities were primarily influenced by geographic and environmental factors, respectively. Dam-induced environmental variations, especially hydrological and nutrient variables, potentially influence the microbial food web via both top-down and bottom-up forces. We proposed that the cycles of carbon, nitrogen and phosphorus are influenced by multi-trophic groups through autotrophic and heterotrophic processes, predator-prey relationships, as well as the release of nutrients mainly by microfauna. Our results advance the notion that pelagic-benthic trophic coupling may intensify the accumulation of organic carbon, ammonium and inorganic phosphorus, thereby changing the biogeochemical patterns along river systems. As a consequence, researchers should pay more attention to the multi-trophic studies when assessing the environmental impacts, and to provide the necessary guidance for the ecological conservation and restoration of the dam-regulated systems.

梯级水坝破坏了河流的连续体，改变了水文、生物多样性和养分通量。描述多营养微生物群的多样性和评估微生物对生态系统过程的贡献是恢复这些水生系统的先决条件。本研究调查了沿梯级坝河流的微生物食物网结构，特别关注多营养关系和远洋-底栖耦合在营养循环中的潜在作用。我们的结果揭示了细菌和真核生物群落组成、功能组比例以及由于筑坝造成的碎片而导致的 α 多样性的不连续性。沿河微生物高度差异，总的多营养β-多样性为0.84，几乎完全是由物种更替引起的。营养水平之间的同步表明中上层和底栖群体的潜在相互作用，其中 β 多样性分别主要受地理和环境因素的影响。大坝引起的环境变化，尤其是水文和营养变量，可能通过自上而下和自下而上的力量影响微生物食物网。我们提出碳、氮和磷的循环受到多营养群体的影响，包括自养和异养过程、捕食者-猎物关系以及主要由微型动物释放的养分。我们的研究结果提出了远洋-底栖营养耦合可能会加剧有机碳、铵和无机磷的积累，从而改变河流系统沿线生物地球化学模式的观点。