Investigation of the Migration of Antibiotic Resistance Genes in Soil–Millet System

The overuse of antibiotics has led to the dissemination of antibiotic resistance genes (ARGs) in agricultural ecosystems, posing a threat to food safety. While current research on ARG transfer in soil–crop systems mainly concerns raw-consumed vegetables like lettuce, its impact on staple crops remains insufficiently studied. This study investigates how organic fertilizer affects ARG dissemination in the soil–millet system. Four fertilization treatments were established: no fertilization (CK), chemical fertilizer only (F), chemical fertilizer combined with manure (FM1), and chemical fertilizer combined with double amount of manure (FM2). Samples were collected from millet rhizosphere soil, roots, stems, leaves, and grains. High-throughput quantitative PCR was employed to investigate the transfer and dissemination of ARGs across the soil–millet system. Results showed that a total of 130 ARGs and 13 mobile genetic elements (MGEs), belonging to 17 gene families, were detected across all samples. The number of unique ARGs was higher in treatments FM1 and FM2 with manure. The accumulated absolute abundances of ARGs, MGEs and gene families all showed an order of FM1 > CK > FM2 > F. Pearson correlation analysis showed a close correlation among ARGs and MGEs. Although organic fertilizer application increased the absolute abundance of ARG-related genes in the rhizosphere soil and millet tissues, posing a potential threat to food safety, the rational strategy employed in the FM1 treatment effectively reduced ARG accumulation in millet leaves and grains. Therefore, this optimized application rate is recommended for millet production.