Global variation in plant-beneficial bacteria in soil under pesticide stress

Danyan Qiu, Yan Wang, Nuohan Xu, Bingfeng Chen, Yuke Zhu, Zhenyan Zhang, Qi Zhang, Tao Lu, Huaping Dong, Jianxin Shou and Haifeng Qian ()
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Danyan Qiu: Shaoxing University, The Institute for Advanced Study
Yan Wang: Zhejiang University of Technology, College of Environment
Nuohan Xu: Shaoxing University, The Institute for Advanced Study
Bingfeng Chen: Zhejiang University of Technology, College of Environment
Yuke Zhu: Zhejiang University of Technology, College of Environment
Zhenyan Zhang: Shaoxing University, The Institute for Advanced Study
Qi Zhang: Shaoxing University, The Institute for Advanced Study
Tao Lu: Zhejiang University of Technology, College of Environment
Huaping Dong: Shaoxing University, College of Chemistry & Chemical Engineering
Jianxin Shou: Shaoxing University, The Institute for Advanced Study
Haifeng Qian: Shaoxing University, The Institute for Advanced Study

Nature Communications, 2025, vol. 16, issue 1, 1-11

Abstract: Abstract The presence of plant-beneficial bacteria (PBB) in soil significantly affects crop production. Excessive agrochemical use in intensive agriculture causes substantial soil residue accumulation, compromising soil health, crop quality, and human health. Understanding changes in beneficial bacteria under pesticide pollution is crucial for guiding sustainable agricultural practices and promoting soil health. We analyze metagenomic data from 1919 soil samples to identify 364 PBBs. We find higher PBB diversity in agricultural soils than in non-agricultural soils; however, pesticide pollution negatively affects the abundance of PBB, particularly those with plant growth-promoting traits. Pesticides not only reduce PBB diversity as individual factors, but they also exert synergistic negative effects with other anthropogenic factors, as determined by Hedges’d effect size and 95% confidence intervals, further accelerating the decline in PBB diversity. Increased pesticide risk also leads to a loss of functional gene diversity in PBB about carbon and nitrogen cycling within essential nutrient cycles, and a reduction in specific amino acid and vitamin synthesis. Artificial application of specific amino acids and vitamins could be an effective strategy to restore PBB in high-pesticide-risk soils. This study provides guidance for regulating pesticide use to mitigate their negative effects on soil PBB and suggests potential remedial measures.

Date: 2025
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DOI: 10.1038/s41467-025-65719-7

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