Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes

Subsurface microorganisms make up the majority of Earth's microbial biomass, but ecological processes governing surface communities may not explain community patterns at depth because of burial. Depth constrains dispersal and energy availability, and when combined with geographic isolation across landscapes, may influence community assembly. We sequenced the 16S rRNA gene of bacteria and archaea from 48 sediment cores across 36 lakes in four disconnected mountain ranges in Wyoming, USA and used null models to infer assembly processes across depth, spatial isolation, and varying environments. Although we expected strong dispersal limitations across these isolated settings, community composition was primarily shaped by environmental selection. Communities consistently shifted from domination by organisms that degrade organic matter at the surface to methanogenic, low‐energy adapted taxa in deeper zones. Stochastic processes—like dispersal limitation—contributed to differences among lakes, but because these effects weakened with depth, selection processes ultimately governed subsurface microbial biogeography. Subsurface microbial communities experience extreme energy limitation and become isolated during the burial process. Here, we analysed microbial communities along sediment profiles from 36 lakes in four mountain ranges separated by hundreds of kilometres. Despite large geographic distances, community composition converged at similar sediment depth zones from taxa capable of degrading nutrient‐rich surface sediments to those adapted to the extreme, low‐energy environments of deeper sediments. Assembly processes reflect strong environmental selection shaping microbial communities in subsurface settings.