Response of soil bacterial communities, antibiotic residuals, and crop yields to organic fertilizer substitution in North China under wheat–maize rotation

Manure application can benefit soil quality and sustainable food productivity, but overapplication can spread high levels of antibiotics and antibiotic resistance genes. A two-year field experiment was conducted to evaluate the comprehensive impacts of organic fertilizer substitution in North China under a wheat–maize rotation. Four treatments were conducted: control (ZF), mineral fertilizer (MF), 50% nitrogen (N) mineral fertilizer substituted with organic fertilizer (MOF), and organic fertilizer (OF). Sulfonamide content, abundance of sulfonamide resistance ( sul ) genes, soil bacterial community, crop yield, and grain mineral elements were analyzed. Results showed that the MOF and OF treatments increased grain nutrients (phosphorus, potassium), and enriched sulfonamide residue and sul genes in soil. Additionally, the relative abundances of sul1 and sul2 in MOF and OF soils planted with maize were higher than in those planted with wheat. Compared to MF, the OF treatment decreased soil pH and crop yields but increased soil total nitrogen, phosphorus contents, and the abundance of Firmicutes. However, the MOF treatment significantly increased soil bacterial diversity and maintained yields of both wheat and maize. Increases in potential sul genes source bacteria ( Planifilum ), antibiotics, and soil nutrients accelerated the spread of sul genes in soil. Partial least squares path modeling analysis indicated that the soil bacterial diversity had a strong positive effect on maize yield. These results indicate that substitution of 50% N mineral fertilizer with organic fertilizer has the potential to benefit the stability and sustainability of the soil ecosystem, helping to meet the food demand in North China. However, the risk of antibiotics should be reduced through technical advances. • Organic fertilizer application induced antibiotic pollution in deep soil. • Abundance of sul genes in maize field was higher than that in wheat field. • Substitution (50% N) increased crop yields, nutrients, and soil bacterial diversity. • Organic fertilizer substitution enriched potential sul hosts Planifilum .