Pesticide Type Distinctly Shapes Soil Resistomes: A Comparative Analysis of Antibiotic and Non-Antibiotic Agro-Chemicals

Lilan Lyu, Qinyu Lu, Chanchan Huang, Xiyu Zhang, Jinjie Yao, Huaxian Zhao and Chengwu Zou ()
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Lilan Lyu: Guangxi Subtropical Crops Research Institute, Laboratory of Quality Risk Assessment for Agro-Products of Ministry of Agriculture and Rural Affairs (Nanning), Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Quality and Testing Center of Subtropical Fruit and Vegetable of Ministry of Agriculture and Rural Affairs, Nanning 530001, China
Qinyu Lu: Guangxi Subtropical Crops Research Institute, Laboratory of Quality Risk Assessment for Agro-Products of Ministry of Agriculture and Rural Affairs (Nanning), Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Quality and Testing Center of Subtropical Fruit and Vegetable of Ministry of Agriculture and Rural Affairs, Nanning 530001, China
Chanchan Huang: Guangxi Subtropical Crops Research Institute, Laboratory of Quality Risk Assessment for Agro-Products of Ministry of Agriculture and Rural Affairs (Nanning), Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Quality and Testing Center of Subtropical Fruit and Vegetable of Ministry of Agriculture and Rural Affairs, Nanning 530001, China
Xiyu Zhang: Guangxi Subtropical Crops Research Institute, Laboratory of Quality Risk Assessment for Agro-Products of Ministry of Agriculture and Rural Affairs (Nanning), Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Quality and Testing Center of Subtropical Fruit and Vegetable of Ministry of Agriculture and Rural Affairs, Nanning 530001, China
Jinjie Yao: Guangxi Subtropical Crops Research Institute, Laboratory of Quality Risk Assessment for Agro-Products of Ministry of Agriculture and Rural Affairs (Nanning), Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Quality and Testing Center of Subtropical Fruit and Vegetable of Ministry of Agriculture and Rural Affairs, Nanning 530001, China
Huaxian Zhao: Key Laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Guangxi Key Laboratory of Earth Surface Processes and Intelligent Simulation, Nanning Normal University, Nanning 530001, China
Chengwu Zou: College of Agriculture, Guangxi University, Nanning 530001, China

Agriculture, 2025, vol. 15, issue 19, 1-15

Abstract: Agricultural pesticides are significant drivers of antibiotic resistance in soil. However, the differential impacts of antibiotic versus non-antibiotic pesticides on the soil resistome are poorly characterized. Here, we analyzed sequencing data from soils exposed to either antibiotic or non-antibiotic pesticides to compare differences in antibiotic resistance gene (ARG) burden, diversity, assembly processes, network topology, and host taxonomy. Soils exposed to antibiotic pesticides exhibited a significantly higher ARG burden (0.52% vs. 0.27% of total genes), whereas soils exposed to non-antibiotic pesticides showed significantly higher alpha diversity ( p < 0.05). ARG community compositions also differed significantly between antibiotic and non-antibiotic exposures (PERMANOVA, R 2 = 0.215, p < 0.001). Assembly analysis using the modified stochasticity ratio indicated that deterministic processes governed ARG community assembly in both groups, with stronger influence observed in non-antibiotic soils. Co-occurrence network analysis revealed contrasting patterns. A compact, highly centralized network emerged in antibiotic-exposed soils, while a larger, more dispersed network characterized non-antibiotic soils. In both networks, aminoglycoside ARGs served as keystone nodes, accompanied by the β-lactam ARG in antibiotic soils and the macrolide ARG in non-antibiotic soils. Pseudomonadota was the predominant ARG host (>60% contribution) across both exposures, though many other phyla exhibited significance ( p < 0.05) between group differences in their ARG contributions. Non-pathogenic bacteria comprised the majority of ARG hosts in all samples. When examining ARG contributions from pathogenic hosts, zoonotic and animal-associated pathogens contributed significantly ( p < 0.01) more in non-antibiotic soils than in antibiotic soils, whereas the ARG contribution from plant pathogens was comparable between the two pesticide groups. Overall, our study suggests that antibiotic and non-antibiotic pesticides shape distinct ARG network patterns and host–pathogen profiles, posing distinct risks to public health and agricultural ecosystems.

Keywords: antibiotic resistance genes; agricultural soil; antibiotic pesticide; non-antibiotic pesticide; ARG hosts (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2025
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