Fertilization exerts a profound influence on the formation, turnover and stabilization of soil organic carbon (SOC). However, how long-term fertilization regulates the contribution of plant residues and microbial necromass to SOC sequestration in acidic paddy soil remains unclear. This study aimed to elucidate these mechanisms by determining plant and microbial biomarkers, i.e., lignin phenols and amino sugars, as well as carbon degradation genes in both topsoil (0–15 cm) and subsoil (15–30 cm) within the context of a 10-year paddy field experiment. We investigated four fertilization regimes: no fertilizers (control), chemical fertilizers applied alone (NPK), NPK combined with cattle manure (NPKM), and NPK combined with rice straw (NPKS). Compared to the control, integrated organic-inorganic fertilization increased SOC by 15–21 % and 14–19 % in the topsoil and subsoil, respectively. Specifically, NPKM and NPKS did not alter the contribution of total lignin phenols to SOC in the topsoil but increased that in the subsoil by 63 % and 26 %, respectively. SOC accumulation exhibited a positive correlation with the concentration of total lignin phenols but a negative correlation with the acid to aldehyde ratio of vanillyl, indicating selective preservation of vanillyls. However, NPKM and NPKS decreased the contribution of total microbial residual carbon (MRC) to SOC in the topsoil (13–16 %) but didn't alter that in the subsoil. The decreased MRC contribution of topsoil was mainly reflected in fungal MRC, implying that fungi played a pivotal role in regulating topsoil carbon accumulation. Correlation analyses indicated that soil biotic and abiotic factors jointly affected the sequestration of plant lignin phenols and microbial necromass, and topsoil carbon accumulated with the abundance ratio of hydrolytic to oxidative enzyme-coding genes increasing (r = 0.62, p < 0.05). Combined with Partial Least Squares Path Model, our study revealed that the accumulation of organic carbon in the topsoil was more influenced by plant-derived carbon, whereas in the subsoil, it was co-affected by both plant- and microbially-derived carbon.
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