Microorganisms are found in all environments, including the whole range of the critical zone (CZ), from deep subsurface rock fissures to the surface of leaves of the tallest trees. They play a range of vital roles in the CZ, including facilitating nutrient cycles and decomposition, as well as supporting soil structure in surficial and deep layers of soil profiles. Members of microbial communities differentially respond to natural and anthropogenic gradients, underscoring the role of environmental filtering and niche partitioning in stratifying or structuring microorganisms in the CZ. Microbial energetics drive biogeochemical processes, and in turn, the biogeochemistry of the ecosystem selects for microbial functions. Across a variety of systems, from bedrock to the atmosphere, we must consider the involvement and mechanisms of interaction of microbial communities in order to understand the range of microbial habitats and interactions within the critical zone.