Differential Responses of Soil Microbial N-Cycling Functional Genes to 35 yr Applications of Chemical Fertilizer and Organic Manure in Wheat Field Soil on Loess Plateau

Fertilization changes nitrogen (N)-cycling processes and associated microbial communities in agricultural ecosystems. However, the long-term responses of N-cycling potential and microbial functional genes to different fertilization sources remain unclear. Soil samples were collected to a depth of 20 cm under winter wheat applied annually with N fertilizer (NF), organic manure (OM), N fertilizer plus organic manure (NM), and a control without fertilization (CK) for 35 yr, and they were analyzed for microbial functional genes involved in soil N cycling using metagenome sequencing in the Loess Plateau of China. Soil N fractions were greater with OM and NM than NF and CK. The total abundances of N-cycling genes were 9.3% (p < 0.05) greater with NM than CK, and 8.2% (p < 0.05) and 12.2% (p < 0.01) higher with OM and NM than NF, respectively. Compared to CK, OM and NM increased the abundance of genes associated with nitrification, denitrification, dissimilatory nitrate reduction, and assimilatory nitrate reduction, but decreased the abundance of genes related to organic N metabolism. However, NF increased the abundance of genes involved in nitrification. Both OM and NM also enhanced the relative abundance of Proteobacteria carrying N-cycling genes but reduced those of Firmicutes and Cyanobacteria. Soil organic carbon, total N, and potential carbon mineralization were the dominant factors affecting the abundances of N-cycling genes. Long-term application of OM and NM can promote N cycling by enhancing gene abundance due to increased soil organic matter and microbial biomass compared to NF and CK.