Manure and chemical fertilization differentially reshape amino compound molecular features and microbial necromass structure in a double-cropping system

It is critical for sustainable agriculture to clarify how long-term fertilization regulates soil carbon (C) and nitrogen (N) sequestration driven by microbial necromass accumulation and turnover of amino compounds (ACs), including amino acids and amino sugars. While fertilization modulates microbial activity to improve soil fertility, the differential effects of manure and chemical fertilization on amino compound molecular profiles (key C/N carriers) and microbial necromass structure (a major soil organic matter component) remain unclear in intensive double-cropping systems. To address this gap, we investigated the long-term (37-year) effects of eight different fertilization regimens: two manure application levels (with or without), combined with four chemical fertilizer regimens (no chemical fertilizer, N, NP, NPK) in a wheat-maize/sweet potato double-cropping system. Results showed that all fertilization treatments significantly increased soil organic C (SOC) and total N (TN) contents, with manure application increasing SOC and TN by 47.52% and 68.37%, respectively. Manure addition was strongly positively correlated with microbial biomass C (MBC; +160.43%) and C/N-degrading enzyme activities (+71.76%), which promoted C and N cycling. Manure application increased SOC and TN by stimulating microbial growth and promoting fungal-dominated necromass accumulation, whereas chemical fertilizers favored fast-growing bacterial communities with lower necromass retention. Specifically, manure application reshaped the molecular composition of the amino acid pool, decreasing the proportion of acidic amino acids and increasing the proportion of hydrophobic amino acids, with N being preferentially retained in low-C/N amino compounds; TN therefore increased proportionally more than SOC, so the bulk C/N ratio was not the highest even though SOC and TN contents were largest. This study highlights that long-term manure application can simultaneously improve the quantity and molecular quality of soil organic matter, providing a sustainable strategy for optimizing long-term C and N sequestration in intensive cropping systems.