Microbial efficiency enhancement drives carbon sequestration in long-term organic farming systems: linking taxonomic succession to carbon use efficiency

Organic farming enhances soil carbon sequestration, which is a critical strategy for climate change mitigation and sustainable agriculture. However, the microbial mechanisms driving carbon accumulation in the soil, particularly the role of metabolic efficiency in long-term organic systems, remain poorly understood. We investigated microbial succession, metabolic efficiency, and carbon stabilization across an organic farming chronosequence (0–5, 5–10, and >10 years) in pepper and cabbage systems. We measured soil carbon fractions, glomalin-related soil proteins, microbial community composition, carbon use efficiency, and extracellular enzyme activities. Organic management beyond a critical 10-year threshold enhanced soil organic matter by 108% and total glomalin-related soil proteins by 4.0-fold compared with conventional farming, with no significant accumulation during the initial 5 years. This non-linear pattern corresponded with a 3.7-fold enhancement in the microbial carbon use efficiency (CUE) measured via dual-isotope approaches ( 13 C-glucose and 18 O-H₂O). Taxonomically coherent succession revealed a positive correlation between Mortierellomycetes proliferation and CUE (rho = 0.67–0.71), whereas inefficient Gammaproteobacteria declined. The eco-enzymatic stoichiometry shifted from 81.7 to 10.1 indicating reduced nitrogen and phosphorus limitation and enhanced carbon acquisition. Correlation network analysis identified CUE as the master regulator linking microbial community structure to carbon stabilization. Our findings establish metabolic efficiency enhancement, rather than biomass accumulation, as the primary mechanism driving soil carbon sequestration under organic management, providing actionable biomarkers for monitoring transition progress and optimizing carbon-smart agricultural practices.