Whole-Soil Proteogenomics Uncover Hidden Microbial Strategies for Carbon Cycling Across the Soil Profile Under Deep Soil Warming

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 mapped microbial traits, their depth stratification, and warming responses. Depth was the dominant driver of microbial community and trait structure. Depth-wise, metabolism converged 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 were smaller and decreased over time but were depth-specific: surface soils showed enhanced amino sugar and sugar alcohol transport, phosphorus mobilization, and stress tolerance, whereas mid- and deep soils exhibited stimulated C₁ metabolism, CO oxidation, and altered nitrogen turnover. These depth-specific microbial trait shifts may critically influence soil carbon–climate feedbacks.