From soils to lake: Interplay between hydrology and local environmental settings drives species selection across a karst landscape

Terrestrial and aquatic ecosystems are interconnected through runoff and hydrological networks that facilitate the transfer of microbial communities across landscapes. While microbial transport along surface waters is well documented, the role of subsurface hydrological paths in shaping microbial community composition remains poorly understood, particularly in complex karst systems. Here, we studied bacterial communities under stable hydrological conditions across a peri-alpine karst landscape, where mixed limestone-sandstone catchments drain via both surface and subsurface hydrological networks into Lake Thun (Switzerland). We profiled 16S rRNA gene sequences from soils, sediments, surface and subsurface waters, and distinct lake strata. All environments except the lake exhibited high microbial diversity. We observed a clear transitional gradient in bacterial communities along the terrestrial-aquatic interface, with environment type explaining 19% of total variation. Core microbiome analyses revealed both environment-specific and shared taxa, with the strongest overlap between surface and subsurface hydrological networks (63.8–84.6% shared core taxa). Co-occurrence network analysis identified six major modules. Three of them represented distinct metabolic assemblages tightly associated with specific environment types: peat soils, lake strata, and the subsurface network, respectively. One recurrent module spanned multiple environments and was linked to redox-driven processes, including the oxidation of nitrogen compounds, metals, and methane. Two additional modules comprised aquatic copiotrophs associated with streams and soil heterotrophs prone to export and short-term persistence within the hydrological network. Overall, our results demonstrate that specific environmental settings and hydrological connectivity jointly contribute to selection of microbial species within the karst landscape.