River sediments Raw sequence reads. River sediments

Sediment microbial communities drive the biogeochemical cycles that make rivers globally important sources and sinks of carbon (C) and nitrogen (N). The structure of these sediment microbial communities is strongly determined by the local physicochemical environment. However, we currently lack an understanding of the factors that determine microbial community structures at the catchment scale. Here, we show that the contribution of groundwater to total river flow (quantified as base flow index; BFI) predicts the structure and diversity of key C- and N-cycle microbial communities across nine UK rivers spanning a geological BFI gradient from 0.23 (clay sediment) to 0.95 (chalk gravel sediment). For the membrane-bound ammonia monooxygenase enzyme, BFI was also strongly correlated with GC-content (percentage of guanine-cytosine bases in a DNA sequence), codon-usage bias, hydrophobicity of amino acids and net-charge of functional gene sequences, likely reflecting physiological adaptations to modes of life imposed by riverbed sediment structure along the BFI gradient. Our results offer an opportunity to overcome the "paradox of scales" that has seen microbial ecologists focus on small- rather than large-scale environmental variables, enabling us to scale-up our understanding of microbial biogeochemistry to the catchment and beyond.