Green manuring outperforms cattle manure in soil carbon sequestration by reshaping dissolved organic matter composition and fungal life strategies

Soil dissolved organic matter (DOM) serves as an important carbon (C) source for microorganisms and is significantly regulated by green manure and cattle manure. However, the molecular mechanisms by which these two organic fertilization practices influence soil C accrual remain unclear. In this study, we used Fourier transform ion cyclotron resonance mass spectrometry and high-throughput sequencing to analyze soil DOM composition and microbial diversity across three soil depths (0–20, 20–40, and 40–60 cm) in a 33-year field fertilization experiment annually treated with chemical fertilizer (CF), cattle manure (CM), and green manure (GM). Compared to CF, both CM and GM promoted soil C sequestration, increasing total soil organic C (SOC) by 53.0–64.8%, dissolved organic C by 61.0–159.4%, and heavy fraction organic C by 47.4–64.7% at the 0–20 cm depth. GM was more efficient than CM in enhancing SOC stock, despite a threefold lower total C input (102.3 vs. 320.1 Mg C ha −1 ). Although both CM and GM significantly altered fungal, rather than bacterial, community structures, CM drove a shift toward r-strategists, while GM favored C-efficient K-strategists at the 0–60 cm depth, and such differences were primarily correlated with exogenous substrate quality. Molecular composition analysis of soil DOM showed that GM increased the relative abundance of plant-derived lignin-like compounds, while CM enhanced tannin and condensed aromatic compounds. Our findings underscore the long-term effects of CM and GM on soil C sequestration in calcareous desert soils, with GM being a more C-efficient fertilization practice for sustainable agricultural development. ● Green manuring enhances soil C stocks and crop yields in calcareous desert soil. ● Green manuring is more efficient in SOC sequestration than cattle manure. ● Green manuring and cattle manure shape divergent DOM composition at 0–60 cm depth. ● Green manuring shifts fungal communities to K-strategists. ● Cattle manure application shifts fungal communities to r-strategists.