Divergent regulation of nitrogen cycling genes under long-term organic and chemical fertilization in plateau cropland soils

The fertilization of agricultural soils has a crucial impact on the microbial communities and nutrient cycling within the soil. However, it remains unclear how long-term fertilization regimes regulate microbial-driven carbon (C) /nitrogen (N) processes in agroecosystems, particularly in ecologically vulnerable plateaus. Here, we integrated metagenomics and quantitative polymerase chain reaction techniques to explore fertilization-induced changes in microbial communities and genes governing C/N cycling, and assessed their linkages to biogeochemical processes in a typical plateau cropland after six-year amendments. The results indicated that among microbial taxa carrying functional genes for C/N cycling, Nocardioides and Phycicoccus were the most significant responses to fertilization. Long-term organic fertilization significantly increased the abundance of genes associated with nitrogen fixation, assimilatory nitrate reduction, and dissimilatory nitrate reduction, enhancing the potential for soil N acquisition and retention, and increasing soil total N content by 47.2 % to 2.84 g kg⁻¹. And long-term application of chemical fertilizer and combinations of chemical and organic fertilizers both enhanced soil methane oxidation potential via increased the abundance of pmoA/B (by 2.0- to 2.7-fold), yet increased N₂O production potential through different pathways: the former promoted incomplete denitrification genes (nirK, norB), while the latter increased nitrification genes (amoA, amoB, nxrB). Additionally, long-term chemical fertilization strengthened the dominance of nar- over nap-mediated nitrate reduction pathways, increasing the narG to napA gene abundance ratio by 85.5 %. In summary, this study revealed the effects of long-term applications of different fertilizer types on the community structures and functions of microorganisms involved in N and C cycling and provides a valuable reference for further understanding of nutrient cycling in agricultural soils.