Stream and lake network position structures freshwater microbial communities across multiple catchments

Streams and lakes form hydrologically connected freshwater networks. Different environmental conditions and dispersal dynamics along the stream to lake continuum potentially affect bacterial community composition, although the strength of such effects may vary among individual catchments. Here, we analysed 224 water samples from 58 streams draining into eight lakes across Switzerland, covering the full continuum from headwaters to lake outlets. Bacterial community composition analyzed via 16S metabarcoding differed between streams and lakes, with a sharp turnover at stream and lake confluence, and this pattern was repeatable across all catchments. Lake communities had lower alpha diversity and lower overall beta dispersion than stream communities, despite hydrological connectivity with a diverse stream microbiome. Community composition in both lakes and streams differed between catchments, but this pattern was more pronounced in lakes. Lake communities were dominated by a small set of widespread and abundant core taxa, primarily established pelagic freshwater genera, that captured the catchment-level differences through shifts in relative abundance. In contrast, stream communities contained a comparatively less abundant core microbiome dominated by soil- and groundwater-associated genera, together with a larger and more diverse peripheral microbiome. Together, these findings show that bacterial community composition changes repeatably across the different positions of hydrological networks.