Subsoils below 30 cm store more than half of global soil carbon. Microbial carbon use efficiency (CUE) serves as a key indicator of microbial control over soil carbon turnover, but the general patterns and drivers of microbial CUE across soil depths remain poorly understood. Here, we report a decreasing trend in microbial CUE with increasing soil depths through large-scale soil sampling across 60 sites spanning tropical to boreal forests. Using multiple analytical and statistical approaches complemented by experiments, we further identify depth-dependent drivers of microbial CUE. In the topsoil (0–10 cm), microbial CUE is primarily regulated by microbial diversity, whereas in deep subsoil (70–100 cm), it is predominantly driven by soil physicochemical protections. Our findings underscore the need to incorporate depth-specific microbial CUE drivers into carbon cycle models for more accurate predictions of whole-soil carbon storage and its feedback to climate change.
