Long-term organic fertilization decreases soil carbon biodegradability by mediating molecular transformation of dissolved organic matter

Soil dissolved organic matter (DOM), the most biogeochemically active carbon fraction, plays a critical role in regional and global carbon cycling. However, the DOM molecular transformation pathways through which long-term organic fertilization influences soil carbon stability remain poorly understood. Here, we employed carbon quantification, multiple spectroscopic techniques, and ultra-high resolution mass spectrometry to characterize the quantity and quality of soil DOM across depths of 0–20, 20–40, 40–60, 60–80, and 80–100 cm in a 35-year field experiment with chemical fertilizer (CF), cattle manure (CM), and green manure (GM). Compared to CF, CM and GM increased DOM content by 73.0%–162.8% and 81.4%–101.7%, respectively, in the 0–40 cm layers, with CM also enhancing DOM by 24.9%–69.6% in the 40–100 cm layers. DOM in organic-fertilized soils exhibited higher molecular weights and contained 23.0%–26.2% more nitrogen-containing molecular formulas than in CF-treated soils. Organic fertilization also promoted the accumulation of humic-like fluorescence components and recalcitrant compounds such as lignin-, tannin-, and condensed aromatic-like structures. Transformation network analysis showed that organic fertilization increased total number of DOM molecular transformations by 10.4%–14.1%, with positive net transformations observed in tannin- and condensed aromatic-like compounds, suggesting their formation from lignin-like and aliphatic precursors. A 28-day laboratory incubation further suggested that soil DOM under CM or GM exhibited 10.3%–13.2% lower biodegradability than CF treatment. Collectively, these findings demonstrate that long-term organic fertilization drives DOM molecular transformations toward more chemically stable assemblages, thereby reducing its biodegradability and enhancing the potential for soil carbon sequestration. • Organic fertilization altered soil DOM composition and transformation pathways. • Green manure uniquely exhibited more diverse DOM molecules in subsoil than topsoil. • Soil DOM under organic fertilization exhibited lower biodegradability. • Organic fertilization increased transformation to tannin- and condensed aromatic-like compounds.