Conservation agriculture buffers persistent carbon loss under warming by microbial adaptation.

Microbial carbon use efficiency (CUE) governs soil carbon persistence under warming, with its magnitude highly dependent on how microbial metabolism adapts to varying substrates. How agricultural management mediates this response in agroecosystems remains poorly understood. To address this, we coupled 18O-H2O tracing of community-level CUE with 13C-probing of substrate utilization efficiency (SUE) from substrates differing in apparent bioavailability after 11 years of experimental warming under conventional and conservation agriculture, using glucose as a readily available carbohydrate and vanillin as a less accessible lignin-derived aromatic substrate. Warming stimulated glucose SUE under both management regimes, whereas vanillin SUE declined by 20% exclusively under conservation agriculture. This shift in relative anabolic efficiency (RAE, SUEglucose/SUEvanillin) was associated with warming-induced changes in CUE, primarily through changes in vanillin rather than glucose SUE. Concurrently, conservation agriculture improved substrate quality under warming, reflected by a reduced litter lignocellulose index. In response, microbial communities exhibited distinct functional adaptations, shifting toward copiotrophic taxa with higher rRNA operon copy numbers and a 16% increase in the anabolic-to-catabolic gene ratio, indicating enhanced microbial growth potential and greater investment for labile carbon processing. Structural equation modeling further showed that shifts in substrate quality were a primary driver of RAE, mediated by changes in microbial life-history strategies under conservation agriculture. Together, these results provide a genome-resolved mechanistic framework showing that conservation agriculture enhances soil carbon persistence under warming by reshaping microbial relative anabolic efficiency and metabolic strategies, highlighting metabolic adaptation as a key mechanism regulating soil carbon stability in warming agroecosystems.