Long-term nutrient imbalance raises soil antibiotic accumulation and bacterial antibiotic resistance in a Chinese wheat–maize cropping system

Soil microbial communities face intense competition in nutrient-limited environments under fertilizer imbalanced inputs in agriculture, yet how these dynamics drive ecological and evolutionary consequences remain poorly understood. A 35-year field-plot experiment was used to investigate the effects of long-term nutrient imbalance on soil community structure, antibiotic production, and antibiotic resistance gene (ARGs) proliferation under different fertilization regimes, namely, no added nutrients without straw, Ch; PK-only fertilization, PK; NK-only fertilization, NK; NP-only fertilization, NP; NPK fertilization, NPK; and NPK fertilization with straw, SNPK. Metagenomics, UPLC-MS/MS, and HT-qPCR methods revealed that nutrient-imbalanced soils (Ch, PK, NK, NP, NPK) exhibited 14–805 % higher antibiotic concentrations and 11–594 % greater ARGs abundance compared to balanced SNPK soils. Nutrient imbalance intensified microbial competition, evidenced by increased extracellular enzyme activities and negative species correlations in co-occurrence networks. Microbial abundance and α-diversity declined by 8–24 % in nutrient-imbalanced soils, alongside functional specialization (e.g., acetate fermentation and phosphorus storage). Balanced SNPK soils fostered stable microbial networks, efficient nutrient cycling, and lower antibiotic/ARG levels but paradoxically enriched mobile genetic elements, potentially accelerating ARGs spread. These findings underscore that long-term nutrient imbalance exacerbates microbial chemical warfare, elevating antibiotics and ARGs accumulation as adaptive responses to resource scarcity. This work provides actionable insights for policymakers and farmers to optimize fertilization strategies, addressing both agricultural productivity and emerging public health challenges posed by soil resistomes. © 2025 Elsevier B.V.