Research Advances in Microbial Remediation of Soil Pesticide Residues

doi:10.13560/j.cnki.biotech.bull.1985.2025-1011

Abstract

Abstract:

Pesticide residues pose a major challenge to soil ecological security and agricultural product safety. Microbial degradation has emerged as a promising strategy for the remediation to farmland pollution due to its high efficiency and environmental compatibility, demonstrating broad application prospects. This review systematically elucidates the study and application advances in pesticide-degrading microorganisms, covering the following key aspects: In terms of degrading strain screening, various strategies—from traditional enrichment culture to microfluidic single-cell screening—have significantly enhanced both the efficiency and diversity of obtaining efficient degraders. Regarding degradation mechanisms, this review provides an in-depth analysis of key degradation gene functions, catalytic mechanisms of intracellular and extracellular enzymes, and synergistic enhancement of co-metabolic pathways. Concerning ecological processes, this review focuses on the colonization mechanisms of degrading bacteria in the rhizosphere and phyllosphere through chemotaxis and biofilm formation, along with their subsequent functional responses. It further examines both active migration mediated by flagellar motility and passive migration facilitated by environmental factors including hydraulic transport. In application technologies, this review examines the preparation processes of both liquid and solid formulations along with their respective advantages and limitations, and assesses the challenges in practical implementation, such as environmental adaptability, colonization efficiency, and ecological interactions. Finally, the review emphasizes that future efforts should focus on formulation innovations and plant-microbe interactions to enhance field stability and degradation efficacy of inoculants, thereby facilitating large-scale application of this technology and promoting agricultural green development.

Key words: pesticide residues, microbial degradation, degradation mechanism, colonization, degrading inoculant

ZHU Shan-shan, XU Jun, PAN Xing-lu, DONG Feng-shou, ZHENG Yong-quan, WU Xiao-hu. Research Advances in Microbial Remediation of Soil Pesticide Residues[J]. Biotechnology Bulletin, 2025, 41(12): 40-49.

Figures/Tables 1

References 58

[1]	Wang K, Ren YS, Pan XL, et al. Insights on persistent herbicides in cropland soils in northern China: Occurrence, ecological risks, and phytotoxicity to subsequent crops [J]. J Hazard Mater, 2025, 490: 137794.
[2]	Navarro I, Royano S, Alonso C, et al. Environmental exposure and risk assessment of pesticide mixtures in aquatic organisms from the Tagus River Basin [J]. Ecotoxicol Environ Saf, 2025, 305: 119221.
[3]	Sun MJ, Li H, Jaisi DP. Degradation of glyphosate and bioavailability of phosphorus derived from glyphosate in a soil-water system [J]. Water Res, 2019, 163: 114840.
[4]	Zhou Y, Wang LP, Sui JY, et al. Pathway elucidation and key enzymatic processes in the biodegradation of difenoconazole by Pseudomonas putida A-3 [J]. J Agric Food Chem, 2025, 73(8): 4770-4786.
[5]	Yang XY, Wei HY, Zhu CX, et al. Biodegradation of atrazine by the novel Citricoccus sp. strain TT3 [J]. Ecotoxicol Environ Saf, 2018, 147: 144-150.
[6]	Khatoon H, Rai JPN. Optimization studies on biodegradation of atrazine by Bacillus badius ABP6 strain using response surface methodology [J]. Biotechnol Rep, 2020, 26: e00459.
[7]	Li MR, Zhan FD, Chen JJ, et al. Atrazine degradation pathway and genes of Arthrobacter sp. FM326 [J]. Pol J Environ Stud, 2020, 29(5): 3683-3689.
[8]	Chen SM, Li YY, Fan ZW, et al. Soil bacterial community dynamics following bioaugmentation with Paenarthrobacter sp. W11 in atrazine-contaminated soil [J]. Chemosphere, 2021, 282: 130976.
[9]	Cao DT, He SH, Li X, et al. Characterization, genome functional analysis, and detoxification of atrazine by Arthrobacter sp. C2 [J]. Chemosphere, 2021, 264: 128514.
[10]	Zhao WS, Wang C, Xu L, et al. Biodegradation of nicosulfuron by a novel Alcaligenes faecalis strain ZWS11 [J]. J Environ Sci, 2015, 35: 151-162.
[11]	Wang L, Zhang XL, Li YM. Degradation of nicosulfuron by a novel isolated bacterial strain Klebsiella sp. Y1: condition optimization, kinetics and degradation pathway [J]. Water Sci Technol, 2016, 73(12): 2896-2903.
[12]	Zhao HY, Zhu JY, Liu SN, et al. Kinetics study of nicosulfuron degradation by a Pseudomonas nitroreducens strain NSA02 [J]. Biodegradation, 2018, 29(3): 271-283.
[13]	Ma QY, Kong DL, Zhang Q, et al. Microbacterium sulfonylureivorans sp. nov., isolated from sulfonylurea herbicides degrading consortium [J]. Arch Microbiol, 2022, 204(2): 136.
[14]	Chen W, Gao Y, Shi GL, et al. Enhanced degradation of fomesafen by a rhizobial strain Sinorhizobium sp. W16 in symbiotic association with soybean [J]. Appl Soil Ecol, 2023, 187:104847.
[15]	Hao ZY, Zhang S, Shao YX, et al. Preparation and inoculation of Bacillus spp. and Sinorhizobium meliloti strains immobilized on biochar-humic acid improve potted soybean traits and soil parameters [J]. Environ Technol Innov, 2025, 38: 104210.
[16]	Feng ZZ, Li QF, Zhang J, et al. Microbial degradation of fomesafen by a newly isolated strain Pseudomonas zeshuii BY-1 and the biochemical degradation pathway [J]. J Agric Food Chem, 2012, 60(29): 7104-7110.
[17]	Ma LY, Wan Q, Ge J, et al. Growth-promoting bacterium Enterobacter sp. CS8-gfp triggers jasmonate signaling pathway for atrazine and thiamethoxam degradation in rice (Oryza sativa L.) [J]. J Clean Prod, 2025, 522: 146373.
[18]	Ni H, Hu L, Jiang CYZ, et al. Effect of Phanerochaete chrysosporium induced phosphate precipitation on bacterial diversity during the soil remediation process [J]. Environmental Science and Pollution Research, 2024, 31(9): 13523-13534.
[19]	Yin R, Chang MD, Ma R, et al. Insights into the imidaclothiz biodegradation by the white-rot fungus Phanerochaete sordida YK-624 under ligninolytic conditions [J]. J Agric Food Chem, 2025, 73(21): 12877-12886.
[20]	Gupta M, Mathur S, Sharma TK, et al. A study on metabolic prowess of Pseudomonas sp. RPT 52 to degrade imidacloprid, endosulfan and coragen [J]. J Hazard Mater, 2016, 301: 250-258.
[21]	徐丰俊, 刘泽钒, 彭睿琪, 等. 单细胞水平微流体技术筛选北极沉积物中的联苯降解菌 [J]. 环境科学学报, 2022, 42(9): 1-8.
	Xu FJ, Liu ZF, Peng RQ, et al. Isolation of biphenyl-degrading bacteria in Arctic sediments by single-cell level isolation of microfluidics (SLIM) technology [J]. Acta Sci Circumstantiae, 2022, 42(9): 1-8.
[22]	Yu X, Zhou H, Tang J, et al. Degradation kinetics and mechanism of β-cypermethrin and 3-phenoxybenzoic acid by Lysinibacillus pakistanensis VF-2 in soil remediation [J]. J Agric Food Chem, 2025, 73(1): 202-215.
[23]	Gong T, Xu XQ, Dang YL, et al. An engineered Pseudomonas putida can simultaneously degrade organophosphates, pyrethroids and carbamates [J]. Sci Total Environ, 2018, 628/629: 1258-1265.
[24]	Zhao MH, Xiao YF, Yang BB, et al. Enhanced biodegradation potential of Klebsiella michiganensis ES15 for acetochlor: Gene knockout, heterologous expression, molecular docking, and bioremediation [J]. Pestic Biochem Physiol, 2025, 214: 106530.
[25]	Xiao YF, Dong MQ, Wu X, et al. Enrichment, domestication, degradation, adaptive mechanism, and nicosulfuron bioremediation of bacteria consortium YM21 [J]. J Integr Agric, 2025, 24(9): 3529-3545.
[26]	Jiang HY, Yuan PP, Ding JJ, et al. Novel biodegradation pathway of insecticide flonicamid mediated by an amidase and its unusual substrate spectrum [J]. J Hazard Mater, 2023, 441: 129952.
[27]	Zhu SY, Zhang JL, Chen AW, et al. Newly discovered cyanobacteria Nostoc sp. PCC7120 for high efficiency biodegradation of thiamethoxam: Photosynthesis response, enzyme strategies, and molecular mechanisms [J]. Bioresour Technol, 2025, 436: 132979.
[28]	Aswathi A, Pandey A, Madhavan A, et al. Chlorpyrifos induced proteome remodelling of Pseudomonas nitroreducens AR-3 potentially aid efficient degradation of the pesticide [J]. Environ Technol Innov, 2021, 21: 101307.
[29]	Wang BJ, Chen J, Wu S, et al. Reusable carboxylesterase immobilized in ZIF for efficient degradation of chlorpyrifos in enviromental water [J]. Pestic Biochem Physiol, 2023, 194: 105519.
[30]	An TC, Zu L, Li GY, et al. One-step process for debromination and aerobic mineralization of tetrabromobisphenol-a by a novel Ochrobactrum sp. T isolated from an e-waste recycling site [J]. Bioresour Technol, 2011, 102(19): 9148-9154.
[31]	Zhang JJ, Chen YF, Fang T, et al. Co-metabolic degradation of tribenuron methyl, a sulfonylurea herbicide, by Pseudomonas sp. strain NyZ42 [J]. Int Biodeterior Biodegrad, 2013, 76: 36-40.
[32]	Rentz, JA, Alvarez, PJJ, Schnoor, JL. Benzo[α]pyrene co-metabolism in the presence of plant root extracts and exudates: Implications for phytoremediation [J]. Environ Pollut, 2005, 136(3): 477-484.
[33]	Zhao JY, Jia DY, Du J, et al. Substrate regulation on co-metabolic degradation of β-cypermethrin by Bacillus licheniformis B-1 [J]. AMB Express, 2019, 9(1): 83.
[34]	王镔, 蔡凯, 邵汝英, 等. 苯胺高效降解菌的筛选及共代谢机制 [J]. 环境保护科学, 2020, 46(4): 117-121.
	Wang B, Cai K, Shao RY, et al. Study on the screening of aniline-degrading strain and its co-metabolism mechanism [J]. Environ Prot Sci, 2020, 46(4): 117-121.
[35]	Lin ZQ, Pang SM, Zhou Z, et al. Novel pathway of acephate degradation by the microbial consortium ZQ01 and its potential for environmental bioremediation [J]. J Hazard Mater, 2022, 426: 127841.
[36]	Castilla-Alcantara JC, Posada-Baquero R, Ortega-Calvo JJ. Taxis-mediated bacterial transport and its implication for the cometabolism of pyrene in a model aquifer [J]. Water Res, 2024, 248: 120850.
[37]	Perera M, Wijayarathna D, Wijesundera S, et al. Biofilm mediated synergistic degradation of hexadecane by a naturally formed community comprising Aspergillus flavus complex and Bacillus cereus group [J]. BMC Microbiol, 2019, 19(1): 84.
[38]	Li Y, Feng FY, Mu QE, et al. Foliar spraying of chlorpyrifos triggers plant production of linolenic acid recruiting rhizosphere bacterial Sphingomonas sp [J]. Environ Sci Technol, 2023, 57(45): 17312-17323.
[39]	Liu XJ, Sun L, Wang SB, et al. Genomic analysis and phytoprobiotic characteristics of Acinetobacter pittii P09: a p-hydroxybenzoic acid-degrading plant-growth promoting rhizobacteria [J]. Environ Technol Innov, 2025, 38: 104113.
[40]	周慧, 冯红丽, 董彤彤, 等. 胁迫条件下DEHP降解菌的分离及特性研究 [J]. 环境科学与技术, 2022, 45(2): 16-24.
	Zhou H, Feng HL, Dong TT, et al. DEHP degradation bacteria under stress condition: isolation and characterization [J]. Environ Sci Technol, 2022, 45(2): 16-24.
[41]	Wang JL, Liu ZY, Wang XY, et al. Combatting glufosinate-induced pepper toxicity: jasmonic acid recruiting rhizosphere bacterial strain Rhodococcus gordoniae [J]. Microbiome, 2025, 13(1): 158.
[42]	Zhang HH, Liu YP, Wu GW, et al. Bacillus velezensis tolerance to the induced oxidative stress in root colonization contributed by the two-component regulatory system sensor ResE [J]. Plant Cell Environ, 2021, 44(9): 3094-3102.
[43]	Ma KW, Niu YL, Jia Y, et al. Coordination of microbe-host homeostasis by crosstalk with plant innate immunity [J]. Nat Plants, 2021, 7(6): 814-825.
[44]	Liu Y, Tang SK, Wang X, et al. A novel thermostable and salt-tolerant carboxylesterase involved in the initial aerobic degradation pathway for pyrethroids in Glycomyces salinus [J]. J Hazard Mater, 2023, 451: 131128.
[45]	Feng RC, Wang HC, Liu TT, et al. Response of microbial communities in the phyllosphere ecosystem of tobacco exposed to the broad-spectrum copper hydroxide [J]. Front Microbiol, 2023, 14: 1229294.
[46]	Chen XYL, Wicaksono WA, Berg G, et al. Bacterial communities in the plant phyllosphere harbour distinct responders to a broad-spectrum pesticide [J]. Sci Total Environ, 2021, 751: 141799.
[47]	Schulz-Bohm K, Gerards S, Hundscheid M, et al. Calling from distance: attraction of soil bacteria by plant root volatiles [J]. ISME J, 2018, 12(5): 1252-1262.
[48]	Liao QH, Liu H, Lu C, et al. Root exudates enhance the PAH degradation and degrading gene abundance in soils [J]. Sci Total Environ, 2021, 764: 144436.
[49]	Li JL, Hong M, Tang R, et al. Isolation of Diaphorobacter sp. LW2 capable of degrading Phenanthrene and its migration mediated by Pythium ultimum [J]. Environ Technol, 2024, 45(8): 1497-1507.
[50]	Ma YP, Deng YL, Hua HJ, et al. Distinct bacterial population dynamics and disease dissemination after biofilm dispersal and disassembly [J]. ISME J, 2023, 17(8): 1290-1302.
[51]	Li JL, Hong M, Lv J, et al. Enhancement on migration and biodegradation of Diaphorobacter sp. LW2 mediated by Pythium ultimum in soil with different particle sizes [J]. Front Microbiol, 2024, 15: 1391553.
[52]	Elyamine AM, Hu CX. Earthworms and rice straw enhanced soil bacterial diversity and promoted the degradation of phenanthrene [J]. Environ Sci Eur, 2020, 32(1): 124.
[53]	Zhane C, Pan XL, Wu XM, et al. Removal of dimethachlon from soils using immobilized cells and enzymes of a novel potential degrader Providencia stuartii JD [J]. J Hazard Mater, 2019, 378: 120606.
[54]	滕晓, 沈心怡, 张步瑶, 等. 二苯醚类除草剂降解菌Bacillus sp. za微生物制剂的研发与初步应用 [J]. 土壤, 2023, 55(3): 682-688.
	Teng X, Shen XY, Zhang BY, et al. Development and preliminary application of microbial preparation of diphenyl ether herbicede degrading strain Bacillus sp. za [J]. Soils, 2023, 55(3): 682-688.
[55]	Copeland C, Schulze-Lefert P, Ma KW. Potential and challenges for application of microbiomes in agriculture [J]. Plant Cell, 2025, 37(8): koaf185.
[56]	伊国云, 李娟, 程亮, 等. 纤维素降解菌产酶条件优化及其堆肥效果研究 [J]. 福建农业学报, 2025, 40(2): 208-218.
	Yi GY, Li J, Cheng L, et al. Enzyme generation and effect in composting of cellulolytic bacteria [J]. Fujian J Agric Sci, 2025, 40(2): 208-218.
[57]	Sun JQ, Feng YM, Zheng R, et al. Solar-enhanced low-temperature biological wastewater treatment [J]. Nat Sustain, 2025, 8(9): 1048-1057.
[58]	Aluffi ME, Magnoli K, Carranza CS, et al. Ability of mixed fungal cultures to remove glyphosate from soil microcosms under stressful conditions [J]. Biodegradation, 2025, 36(3): 31.