Soil proteogenomics uncover microbial strategies for soil depth-specific carbon cycling under whole-soil warming conditions

Soils are Earth’s largest carbon reservoir, yet microbial mechanisms controlling decomposition, and their warming response, remain poorly resolved, especially in subsoils. Using genome-resolved proteogenomics within a replicated whole-soil warming experiment (0–90 cm, +4 °C, 7.5 years) we map microbial traits, their depth stratification, and warming responses. Depth is the dominant driver of microbial community and trait structure. Depth-wise, metabolism converge on low-molecular-weight and C1 compounds, challenging glucose-centric models, with surface soils enriched in methanol oxidation and deep soils in alcohol fermentation, CO oxidation and N₂ fixation. Abundant sialidases in deep soils implicate glycoproteins as a key carbon source. Warming effects are smaller and decrease over time but are depth-specific: surface soils show enhanced amino sugar and sugar alcohol transport, phosphorus mobilization, and stress tolerance, whereas mid- and deep soils exhibit stimulated C1 metabolism, CO oxidation, and altered nitrogen turnover. These depth-specific microbial trait shifts may critically influence soil carbon–climate feedbacks.