Hydrological connectivity shapes microbial community assembly in a karst landscape

Terrestrial and aquatic ecosystems are connected by hydrological networks that transport microbial communities, yet the role of integrated surface–subsurface flow in structuring these communities remains poorly understood, especially in karst systems. We analyzed bacterial communities across a peri-alpine karst landscape draining into Lake Thun, Switzerland, using 16S rRNA gene sequencing from soils, sediments, surface and subsurface waters, and lake strata. Bacterial diversity was high across all environments except the lake, and communities formed a clear terrestrial–aquatic gradient, with environment type explaining 19% of variation. Core microbiome analyses revealed strong connectivity between surface and subsurface hydrological networks, sharing up to 85% of core taxa. Network analyses showed that taxa clustered into seven metabolically distinct modules that transcended habitat boundaries. Core modules were structurally coherent across environments, while associated satellite taxa added habitat-specific functions. These results indicate that karst microbial communities assemble into metabolically cohesive modules linked by subsurface hydrological networks, which integrate microbial diversity across landscapes and contribute to ecosystem stability.