Impact of half-amount fertilization patterns on antibiotic resistance gene dynamics in a soil-root-crop system on a long-term manure-amended farm

Optimizing manure recycling and mitigating antibiotic resistance gene (ARG) dissemination are critical for sustainable agriculture. This field study evaluated nutrient-matched half-dose fertilization regimes (T1: organic-chemical mix; T2: organic alone; T3: chemical alone) against conventional full-dose fertilization (TF) and a no-current-season-fertilizer control (CK) along the soil-root-crop continuum. Topsoil under T2 maintained a total nitrogen concentration (1.29 g·kg −1 ), showed a comparatively narrow nitrate concentration range (4.59–7.39 mg·kg −1 ), and decreased antibiotic residues by approximately 45% (20.41 μg·kg −1 ) relative to TF. Hierarchical partitioning showed that soil pH (27.20%) and available nitrogen-related variables had the largest relative explanatory contributions to bulk-soil ARG variation. The rhizosphere-root compartment showed strong microbiome filtering, with the highest relative explanatory contributions from Chloroflexi (96.60%) and WD2101_soil_group (98.10%), whereas bacterial profiles in washed edible tissue samples were most strongly associated with Pantoea and Sphingomonas (combined contribution 23.40%) among the measured genera. Under TF, higher nutrient and contaminant loading was associated with greater enrichment of key resistance genes ( fex A, ISCR 1, s tr A, tet Q) in roots and washed edible tissues (BCF Root > 1.0, TF Total > 1.0). Under equal macronutrient inputs, T1 and T2 reduced total bulk-soil ARG abundances by 60%–90% compared with TF ( p < 0.05), with no significant difference between them. T1 reduced the proportion of manure applied through partial synthetic substitution, whereas T2 retained organic substrate inputs at the reduced rate. Both regimes showed low root and tissue enrichment indices (BCF Root ≤ 0.03, TF Total ≤ 0.04), indicating markedly lower relative enrichment than TF. These findings support reduced-input fertilization as a promising strategy for mitigating resistome pressure; regulatory compliance and food-safety implications require separate evaluation.