Abstract
Microbial communities play a crucial role in ecosystem functioning, with contributions that can vary among taxonomic domains and size fractions. However, microbial assembly processes for bacteria and eukaryotes are seldom characterized together using size fractionation, especially in flowing waters. Here, we used amplicon sequencing combined with physicochemical measurements to determine how size fractionated (small fraction 0.22–3 μ m; large fraction > 3 μ m) community structure and diversity varied over a subarctic river continuum. We sampled the Sheldrake River, a 25 km river flowing through degrading discontinuous permafrost, from its lacustrine source through subarctic forest shrub tundra to its discharge plume in eastern Hudson Bay (Nunavik, Canada). Microbial community structure differed by size fraction and among habitats, with differences in the variables potentially driving community structure among size fractions and microbial domains. For the small size fraction, colored dissolved organic matter was a significant covariate of community variation for both bacteria and eukaryotes, consistent with the influence of landscape gradients. There were contrasting diversity patterns along the lake–river transect between bacterial size fractions. An abundance‐based approach indicated that for all communities, assembly processes were dominated by homogeneous selection, while an incidence‐based method showed dominance of heterogeneous selection for bacteria and homogenizing dispersal for microbial eukaryotes. Our findings show how different components of riverine microbial communities can have divergent patterns along the downstream continuum to the sea.