Summary Despite the essential functions of sedimentary bacterial and fungal communities in biogeochemical cycling, little is known about their biogeographic patterns and driving processes in large rivers. Here we investigated the biogeographic assemblies and co‐occurrence patterns of sedimentary bacterial and fungal communities in the Jinsha River, one of the largest rivers in southwestern China. The mainstream of river was divided into upstream, midstream and downstream. The results showed that both bacterial and fungal communities differed significantly among three sections. For both communities, their composition variations in all sites or each river section were controlled by the combination of dispersal limitation and environmental selection, and dispersal limitation was the dominant factor. Compared with bacteria, fungi had stronger dispersal limitation. Co‐occurrence network analyses revealed higher network connectivity but a lower proportion of positive interaction in the bacterial than fungal network at all sites. In particular, the keystone species belonging to bacterial phyla Proteobacteria and Firmicutes and fungal phyla Ascomycota and Chytridiomycota may play critical roles in maintaining community function. Together, these observations indicate that fungi have a stronger dispersal limitation influence and less network connectivity than bacteria, implying different community assembly mechanisms and ecological functions between bacteria and fungi in large rivers.

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Microeukaryotes are considered critical for biogeochemical cycles and material transformation in river ecosystems, but their biogeography and underlying mechanisms of their assemblages remain poorly understood. We collected 35 water samples and 26 sediment samples covering an 1,148 km reach of the Lancang River, a highly regulated large river in south‐western China. The planktonic and sedimentary microeukaryotic communities were analysed by sequencing the V4 region of eukaryotic 18S rRNA gene. Factors associated with patterns in microeukaryotic communities were assessed by canonical correlation analysis and neutral models. Species interactions and keystone species in microeukaryotic communities were investigated by co‐occurrence network analysis. The results showed that community composition was distinct between planktonic and sedimentary microeukaryotes, as well as between upstream natural sites and regulated sites downstream. Similar environmental (pH, nutrient concentrations) and spatial (altitude, distance) variables were associated with patterns in community composition of planktonic and sedimentary microeukaryote communities, except that turbidity and water temperature were associated only with patterns in planktonic communities. Neutral models were an excellent fit to the distributions of both planktonic (r2 = 0.67) and sedimentary (r2 = 0.50) microeukaryotic communities. The estimated immigration rate (m) from planktonic communities (m = 0.032) was higher than from sedimentary communities (m = 0.022). Co‐occurrence pattern analysis showed that planktonic microeukaryotic networks had more connectivity but a lower proportion of positive interactions than sedimentary microeukaryotic networks. Keystone species, in particular those belonging to phylum Ascomycota, played essential roles in maintaining stability of both planktonic and sedimentary microeukaryotic communities. Our results showed that the composition of planktonic and sedimentary microeukaryote communities differ, and that diversity in both communities was influenced by river regulation. Given the important roles played by microeukaryotes in nutrient cycling and food webs, such impacts may alter other ecosystem processes in rivers.

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