{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T13:09:40Z","timestamp":1788786580655,"version":"build-2803163510"},"reference-count":105,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T00:00:00Z","timestamp":1788739200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>This structured critical narrative review evaluates the bacterial transformation of six selected organophosphate pesticides\u2014chlorpyrifos, methyl parathion, parathion, diazinon, malathion, and phosalone\u2014in relation to chemical, mechanistic, and environmental evidence. Peer-reviewed literature was searched in Scopus and PubMed for the period from 1 January 2020 to 26 August 2026 and was supplemented by backward-reference screening and forward citation tracking of foundational studies. Evidence was assessed across eight domains spanning association, tolerance, controlled dissipation, product-resolved transformation, mechanistic attribution, non-sterile-soil validation, detoxification or ecological recovery, and field readiness. The selected compounds reveal substantial differences in pathway resolution: chlorpyrifos has the most developed parent\u2013product evidence base, methyl parathion and parathion are comparatively well characterized at the hydrolytic and enzyme levels, diazinon and malathion retain important downstream uncertainties, and phosalone remains an unresolved evidence-gap comparator. The synthesis shows that credible soil bioremediation requires convergence among parent\u2013product kinetics, catalytic attribution, transformation-product turnover, performance beyond natural attenuation, toxicity reduction, and recovery of relevant soil or plant functions.<\/jats:p>","DOI":"10.3390\/microorganisms14091974","type":"journal-article","created":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T12:12:25Z","timestamp":1788783145000},"page":"1974","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Metabolite-Resolved Validation of Bacterial Organophosphate Transformation in Soil: A Critical Review of Selected Organophosphate Case Studies"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-0271-1534","authenticated-orcid":false,"given":"Lazzat","family":"Asylbekkyzy","sequence":"first","affiliation":[{"name":"Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050038, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meruyert O.","family":"Bauenova","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050038, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Assemgul K.","family":"Sadvakasova","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050038, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dariga K.","family":"Kirbayeva","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050038, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3892-7920","authenticated-orcid":false,"given":"Bekzhan D.","family":"Kossalbayev","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biochemical Engineering, Satbayev University, 22 Satpaev Street, Almaty 050013, Kazakhstan"},{"name":"Ecology Research Institute, Khoja Akhmet Yassawi International Kazakh-Turkish University, Turkistan 161200, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2265-8861","authenticated-orcid":false,"given":"Fiaz","family":"Ahmad","sequence":"additional","affiliation":[{"name":"Key Laboratory for Space Bioscience & Biotechnology, School of Life Science and Technology, Northwestern Polytechnical University, Chang\u2019an Campus, Xi\u2019an 710072, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dilnaz E.","family":"Zaletova","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050038, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1038\/s41561-021-00712-5","article-title":"Risk of pesticide pollution at the global scale","volume":"14","author":"Tang","year":"2021","journal-title":"Nat. Geosci."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2919","DOI":"10.1021\/acs.est.0c06405","article-title":"Widespread Occurrence of Pesticides in Organically Managed Agricultural Soils\u2014The Ghost of a Conventional Agricultural Past?","volume":"55","author":"Riedo","year":"2021","journal-title":"Environ. Sci. Technol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"108830","DOI":"10.1016\/j.soilbio.2022.108830","article-title":"Soil microbiome signatures are associated with pesticide residues in arable landscapes","volume":"174","author":"Walder","year":"2022","journal-title":"Soil Biol. Biochem."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e2419917122","DOI":"10.1073\/pnas.2419917122","article-title":"Increasing pesticide diversity impairs soil microbial functions","volume":"122","author":"Ni","year":"2025","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1016\/j.jes.2022.04.023","article-title":"Organophosphate pesticides an emerging environmental contaminant: Pollution, toxicity, bioremediation progress, and remaining challenges","volume":"127","author":"Mali","year":"2023","journal-title":"J. Environ. Sci."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1007\/s11274-022-03426-x","article-title":"Potential and limitations for monitoring of pesticide biodegradation at trace concentrations in water and soil","volume":"38","author":"Poursat","year":"2022","journal-title":"World J. Microbiol. Biotechnol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"109465","DOI":"10.1016\/j.microc.2023.109465","article-title":"Analysis of pesticide residues in soil: A review and comparison of methodologies","volume":"195","author":"Brinco","year":"2023","journal-title":"Microchem. J."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"10343","DOI":"10.1021\/acs.est.1c00466","article-title":"Identification of Pesticide Transformation Products in Surface Water Using Suspect Screening Combined with National Monitoring Data","volume":"55","author":"Menger","year":"2021","journal-title":"Environ. Sci. Technol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/s40643-022-00515-5","article-title":"Degradation insight of organophosphate pesticide chlorpyrifos through novel intermediate 2,6-dihydroxypyridine by Arthrobacter sp. HM01","volume":"9","author":"Mali","year":"2022","journal-title":"Bioresour. Bioprocess."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Dar, M.A., and Kaushik, G. (2023). Biodegradation of Malathion in Amended Soil by Indigenous Novel Bacterial Consortia and Analysis of Degradation Pathway. Soil Syst., 7.","DOI":"10.3390\/soilsystems7040081"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"116599","DOI":"10.1016\/j.ecoenv.2024.116599","article-title":"Efficient and harmless removal of insecticide diazinon via the stepwise combination of biodegradation and photodegradation","volume":"281","author":"Geng","year":"2024","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1038\/s41587-020-0548-6","article-title":"PICRUSt2 for prediction of metagenome functions","volume":"38","author":"Douglas","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref_13","first-page":"001203","article-title":"On the limits of 16S rRNA gene-based metagenome prediction and functional profiling","volume":"10","author":"Matchado","year":"2024","journal-title":"Microb. Genom."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"20190249","DOI":"10.1098\/rstb.2019.0249","article-title":"The ecology of heterogeneity: Soil bacterial communities and C dynamics","volume":"375","author":"Nunan","year":"2020","journal-title":"Philos. Trans. R. Soc. B"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"107338","DOI":"10.1016\/j.envint.2022.107338","article-title":"Fate of chlorpyrifos bound residues in paddy soils: Release, transformation, and phytoavailability","volume":"166","author":"Zhong","year":"2022","journal-title":"Environ. Int."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"9591","DOI":"10.1021\/acs.est.1c01354","article-title":"Use of the Dynamic Technique DGT to Determine the Labile Pool Size and Kinetic Resupply of Pesticides in Soils and Sediments","volume":"55","author":"Li","year":"2021","journal-title":"Environ. Sci. Technol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1038\/s43017-020-0080-8","article-title":"The concept and future prospects of soil health","volume":"1","author":"Lehmann","year":"2020","journal-title":"Nat. Rev. Earth Environ."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1038\/s41579-022-00779-w","article-title":"Soil microbiomes and one health","volume":"21","author":"Banerjee","year":"2022","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1038\/s41586-025-09991-z","article-title":"Pesticide residues alter taxonomic and functional biodiversity in soils","volume":"650","author":"Labouyrie","year":"2026","journal-title":"Nature"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"90471","DOI":"10.1007\/s11356-023-28860-8","article-title":"Effect of salinity on the fate of pesticides in irrigated systems: A first overview","volume":"30","author":"Khouni","year":"2023","journal-title":"Environ. Sci. Pollut. Res."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Asylbekkyzy, L., Kossalbayev, B.D., Ahmad, F., Wang, J., Sadvakasova, A.K., Bauenova, M.O., Abseyt, A.A., and Zaletova, D.E. (2026). Environmental Filtering of Bacterial Communities Driven by Pesticide Residue Profiles in the Almaty Region, Kazakhstan. Biology, 15.","DOI":"10.3390\/biology15090712"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1007\/s11157-022-09637-w","article-title":"Microbial bioremediation of pesticides in agricultural soils: An integrative review on natural attenuation, bioaugmentation and biostimulation","volume":"21","author":"Lopes","year":"2022","journal-title":"Rev. Environ. Sci. Bio\/Technol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"114011","DOI":"10.1016\/j.envres.2022.114011","article-title":"Recent advances in assessment methods and mechanism of microbe-mediated chlorpyrifos remediation","volume":"214","author":"Raj","year":"2022","journal-title":"Environ. Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1002\/jrsm.1378","article-title":"Which academic search systems are suitable for systematic reviews or meta-analyses? Evaluating retrieval qualities of Google Scholar, PubMed, and 26 other resources","volume":"11","author":"Gusenbauer","year":"2020","journal-title":"Res. Synth. Methods"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"10320","DOI":"10.1038\/s41598-021-88264-x","article-title":"Biodegradation of chlorpyrifos using isolates from contaminated agricultural soil, its kinetic studies","volume":"11","author":"Farhan","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Kumar, G., Lal, S., Soni, S.K., Maurya, S.K., Shukla, P.K., Chaudhary, P., Bhattacherjee, A.K., and Garg, N. (2022). Mechanism and kinetics of chlorpyrifos co-metabolism by using environment restoring microbes isolated from rhizosphere of horticultural crops under subtropics. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.891870"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"104750","DOI":"10.1016\/j.pestbp.2020.104750","article-title":"Novel degradation pathways for Chlorpyrifos and 3, 5, 6-Trichloro-2-pyridinol degradation by bacterial strain Bacillus thuringiensis MB497 isolated from agricultural fields of Mianwali, Pakistan","volume":"172","author":"Ambreen","year":"2021","journal-title":"Pestic. Biochem. Physiol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"117315","DOI":"10.1016\/j.envres.2023.117315","article-title":"Biodegradation mechanism of chlorpyrifos by Bacillus sp. H27: Degradation enzymes, products, pathways and whole genome sequencing analysis","volume":"239","author":"Liu","year":"2023","journal-title":"Environ. Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"105989","DOI":"10.1016\/j.pestbp.2024.105989","article-title":"Comparative evaluation of biodegradation of chlorpyrifos by various bacterial strains: Kinetics and pathway elucidation","volume":"203","author":"Yadav","year":"2024","journal-title":"Pestic. Biochem. Physiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"105197","DOI":"10.1016\/j.pestbp.2022.105197","article-title":"Proteomic analysis of Burkholderia zhejiangensis CEIB S4\u20133 during the methyl parathion degradation process","volume":"187","year":"2022","journal-title":"Pestic. Biochem. Physiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"124641","DOI":"10.1016\/j.biortech.2020.124641","article-title":"In-depth biochemical identification of a novel methyl parathion hydrolase from Azohydromonas australica and its high effectiveness in the degradation of various organophosphorus pesticides","volume":"323","author":"Zhao","year":"2021","journal-title":"Bioresour. Technol."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Xu, J., Wang, B., Wang, M.-Q., Gao, J.-J., Li, Z.-J., Tian, Y.-S., Peng, R.-H., and Yao, Q.-H. (2022). Metabolic Engineering of Escherichia coli for Methyl Parathion Degradation. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.679126"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1186\/s13568-021-01284-8","article-title":"Biodegradation of p-nitrophenol by engineered strain","volume":"11","author":"Xu","year":"2021","journal-title":"AMB Express"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1016\/j.procbio.2020.04.026","article-title":"Biodegradation of organophosphorus insecticides by two organophosphorus hydrolase genes (opdA and opdE) from isolated Leuconostoc mesenteroides WCP307 of kimchi origin","volume":"94","author":"Haque","year":"2020","journal-title":"Process Biochem."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Wang, G., Li, X., Zheng, J., Li, X., Bai, L., Yue, W., and Jiang, L. (2022). Isolation of a diazinon-degrading strain Sphingobium sp. DI-6 and its novel biodegradation pathway. Front. Microbiol., 13, Correction in Front. Microbiol. 2023, 14, 1219721. https:\/\/doi.org\/10.3389\/fmicb.2023.1219721.","DOI":"10.3389\/fmicb.2022.929147"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1111\/lam.13517","article-title":"Malathion biodegradation by a psychrotolerant bacteria Ochrobactrum sp. M1D and metabolic pathway analysis","volume":"73","author":"Verma","year":"2021","journal-title":"Lett. Appl. Microbiol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"102362","DOI":"10.1016\/j.bcab.2022.102362","article-title":"Optimization of process parameters for biodegradation of malathion by Micrococcus aloeverae MAGK3 using Taguchi methodology and metabolic pathway analysis","volume":"42","author":"Dar","year":"2022","journal-title":"Biocatal. Agric. Biotechnol."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Ma, L., Dai, X., Ai, G., Zheng, X., Zhang, Y., Pan, C., Hu, M., Jiang, C., Wang, L., and Dong, Z. (2022). Isolation and Identification of Efficient Malathion-Degrading Bacteria from Deep-Sea Hydrothermal Sediment. Microorganisms, 10.","DOI":"10.3390\/microorganisms10091797"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Dhakal, G., Thapa Magar, S., and Fujino, T. (2025). Pesticide Degradation by Soil Bacteria: Mechanisms, Bioremediation Strategies, and Implications for Sustainable Agriculture. Environments, 12.","DOI":"10.20944\/preprints202510.0474.v1"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1340","DOI":"10.1111\/sum.12811","article-title":"Soil microbial inoculants for sustainable agriculture: Limitations and opportunities","volume":"38","author":"Ballard","year":"2022","journal-title":"Soil Use Manag."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"3578","DOI":"10.1038\/s41467-024-47755-x","article-title":"Composition and metabolism of microbial communities in soil pores","volume":"15","author":"Li","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"14427","DOI":"10.1021\/acs.est.2c03397","article-title":"Spatial Control of Microbial Pesticide Degradation in Soil: A Model-Based Scenario Analysis","volume":"56","author":"Schwarz","year":"2022","journal-title":"Environ. Sci. Technol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2256","DOI":"10.1039\/D0EM00337A","article-title":"Sorption\u2013desorption of dimethoate in urban soils and potential environmental impacts","volume":"22","author":"Meftaul","year":"2020","journal-title":"Environ. Sci. Process. Impacts"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Karleu\u0161a, R., Marini\u0107, J., Tomi\u0107 Lin\u0161ak, D., Dubrovi\u0107, I., Antunovi\u0107, D., and Brozni\u0107, D. (2025). The Hidden Legacy of Dimethoate: Clay Binding Effects on Decreasing Long-Term Retention and Reducing Environmental Stability in Croatian Soils. Toxics, 13.","DOI":"10.3390\/toxics13030219"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1599","DOI":"10.1007\/s10653-022-01278-w","article-title":"Degradation of four pesticides in five urban landscape soils: Human and environmental health risk assessment","volume":"45","author":"Meftaul","year":"2022","journal-title":"Environ. Geochem. Health"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"104192","DOI":"10.1016\/j.apsoil.2021.104192","article-title":"Natural attenuation and bioremediation of chlorpyrifos and endosulfan in periurban horticultural soils of Buenos Aires (Argentina) using microcosms assays","volume":"169","author":"Cabrera","year":"2022","journal-title":"Appl. Soil Ecol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1007\/s13205-021-02980-9","article-title":"Combined biostimulation and bioaugmentation for chlorpyrifos degradation in laboratory microcosms","volume":"11","author":"Nayak","year":"2021","journal-title":"3 Biotech"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"29358","DOI":"10.1007\/s11356-021-17772-0","article-title":"Evidence for enhanced dissipation of chlorpyrifos in an agricultural soil inoculated with Serratia rubidaea strain ABS 10","volume":"29","author":"Salem","year":"2022","journal-title":"Environ. Sci. Pollut. Res."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"112039","DOI":"10.1016\/j.ecoenv.2021.112039","article-title":"Potential of formulated Dyadobacter jiangsuensis strain 12851 for enhanced bioremediation of chlorpyrifos contaminated soil","volume":"213","author":"Yadav","year":"2021","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1016\/j.jes.2023.07.039","article-title":"Enhanced remediation of chlorpyrifos-contaminated soil by immobilized strain Bacillus H27","volume":"144","author":"Liu","year":"2024","journal-title":"J. Environ. Sci."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"116378","DOI":"10.1016\/j.ecoenv.2024.116378","article-title":"Chlorpyrifos degradation and its impacts on phosphorus bioavailability in microplastic-contaminated soil","volume":"277","author":"Ding","year":"2024","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"127098","DOI":"10.1016\/j.chemosphere.2020.127098","article-title":"Chlorpyrifos inhibits nitrogen fixation in rice-vegetated soil containing Pseudomonas stutzeri A1501","volume":"256","author":"Lu","year":"2020","journal-title":"Chemosphere"},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Lara-Moreno, A., Morillo, E., Merch\u00e1n, F., Madrid, F., and Villaverde, J. (2022). Chlorpyrifos Removal in an Artificially Contaminated Soil Using Novel Bacterial Strains and Cyclodextrin. Evaluation of Its Effectiveness by Ecotoxicity Studies. Agronomy, 12.","DOI":"10.3390\/agronomy12081971"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"103821","DOI":"10.1016\/j.isci.2022.103821","article-title":"The legacy of microbial inoculants in agroecosystems and potential for tackling climate change challenges","volume":"25","author":"Liu","year":"2022","journal-title":"iScience"},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Cyco\u0144, M. (2026). Bioaugmentation as microbiome engineering: A framework for evaluating functional performance, persistence, and safety. Front. Microbiol., 17.","DOI":"10.3389\/fmicb.2026.1835468"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"100608","DOI":"10.1016\/j.cscee.2024.100608","article-title":"Chlorpyrifos degradation by Bacillus sp. strain UPMB10 isolated from polluted environment: Analysis and characterization of the metabolite by GC-MS","volume":"9","author":"Adams","year":"2024","journal-title":"Case Stud. Chem. Environ. Eng."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1186\/s13765-021-00632-3","article-title":"Biodegradable properties of organophosphorus insecticides by the potential probiotic Lactobacillus plantarum WCP931 with a degrading gene (opdC)","volume":"64","author":"Lee","year":"2021","journal-title":"Appl. Biol. Chem."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"101307","DOI":"10.1016\/j.eti.2020.101307","article-title":"Chlorpyrifos induced proteome remodelling of Pseudomonas nitroreducens AR-3 potentially aid efficient degradation of the pesticide","volume":"21","author":"Aswathi","year":"2021","journal-title":"Environ. Technol. Innov."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"104744","DOI":"10.1016\/j.jtice.2023.104744","article-title":"Optimization and elucidation of organophosphorus and pyrethroid degradation pathways by a novel bacterial consortium C3 using RSM and GC-MS-based metabolomics","volume":"144","author":"Malla","year":"2023","journal-title":"J. Taiwan Inst. Chem. Eng."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Haque, M.D.A., Hossain, M.D.S., Ahmad, I., Akbor, M.D.A., Rahman, A., Manir, M.D.S., Patel, H.M., and Cho, K.M. (2022). Unveiling chlorpyrifos mineralizing and tomato plant-growth activities of Enterobacter sp. strain HSTU-ASh6 using biochemical tests, field experiments, genomics, and in silico analyses. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.1060554"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1007\/s10532-026-10328-4","article-title":"Enhancing chlorpyrifos degradation and plant growth through biochar-assisted microbial remediation","volume":"37","author":"Kiran","year":"2026","journal-title":"Biodegradation"},{"key":"ref_62","first-page":"001391","article-title":"Comprehensive genome-wide analysis for the safety assessment of microbial biostimulants in agricultural applications","volume":"11","author":"Bellotti","year":"2025","journal-title":"Microb. Genom."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"120908","DOI":"10.1016\/j.envpol.2022.120908","article-title":"New insights into the effects of chlorpyrifos on soil microbes: Carbon and nitrogen cycle related microbes in wheat\/maize rotation agricultural field","volume":"318","author":"Hou","year":"2023","journal-title":"Environ. Pollut."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"104954","DOI":"10.1016\/j.apsoil.2023.104954","article-title":"Ecological safety evaluation of chlorpyrifos on agricultural soil: Effects on soil microbes","volume":"189","author":"Cheng","year":"2023","journal-title":"Appl. Soil Ecol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"130040","DOI":"10.1016\/j.chemosphere.2021.130040","article-title":"Side effects of traditional pesticides on soil microbial respiration in orchards on the Russian Black Sea coast","volume":"275","author":"Karpun","year":"2021","journal-title":"Chemosphere"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Streletskii, R., Astaykina, A., Krasnov, G., and Gorbatov, V. (2022). Changes in Bacterial and Fungal Community of Soil under Treatment of Pesticides. Agronomy, 12.","DOI":"10.3390\/agronomy12010124"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"126859","DOI":"10.1016\/j.envpol.2025.126859","article-title":"Abrupt versus gradual application of pesticides: Effects on soil bacterial and fungal communities","volume":"383","author":"Riedo","year":"2025","journal-title":"Environ. Pollut."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"12786","DOI":"10.1038\/s41598-021-91755-6","article-title":"Changes in soil microbial community and activity caused by application of dimethachlor and linuron","volume":"11","author":"Medo","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"fiaf052","DOI":"10.1093\/femsec\/fiaf052","article-title":"Impact of pesticides on soil health: Identification of key soil microbial indicators for ecotoxicological assessment strategies through meta-analysis","volume":"101","author":"Swaine","year":"2025","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Khmelevtsova, L., Azhogina, T., Karchava, S., Klimova, M., Polienko, E., Litsevich, A., Chernyshenko, E., Khammami, M., Sazykin, I., and Sazykina, M. (2024). Effect of Mineral Fertilizers and Pesticides Application on Bacterial Community and Antibiotic-Resistance Genes Distribution in Agricultural Soils. Agronomy, 14.","DOI":"10.3390\/agronomy14051021"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"130960","DOI":"10.1016\/j.jhazmat.2023.130960","article-title":"Dissipation kinetics of chlorpyrifos and 3,5,6 trichloro-2-pyridinol under vegetation of different aromatic grasses: Linkage with enzyme kinetics and microbial community of soil","volume":"448","author":"Yadav","year":"2023","journal-title":"J. Hazard. Mater."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1007\/s42773-024-00306-5","article-title":"Effect of biochar on soil microbial community, dissipation and uptake of chlorpyrifos and atrazine","volume":"6","author":"Singh","year":"2024","journal-title":"Biochar"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1016\/j.enceco.2024.05.004","article-title":"Microbe-pesticide interactions: Soil enzyme analysis and bacterial degradation of chlorpyrifos","volume":"6","author":"Srinivasulu","year":"2024","journal-title":"Environ. Chem. Ecotoxicol."},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Kers, J.G., and Saccenti, E. (2022). The Power of Microbiome Studies: Some Considerations on Which Alpha and Beta Metrics to Use and How to Report Results. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.796025"},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Khomich, M., M\u00e5ge, I., Rud, I., and Berget, I. (2021). Analysing microbiome intervention design studies: Comparison of alternative multivariate statistical methods. PLoS ONE, 16.","DOI":"10.21203\/rs.3.rs-910076\/v1"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1038\/s41467-022-28034-z","article-title":"Microbiome differential abundance methods produce different results across 38 datasets","volume":"13","author":"Nearing","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"giab090","DOI":"10.1093\/gigascience\/giab090","article-title":"Inferring microbiota functions from taxonomic genes: A review","volume":"11","author":"Djemiel","year":"2022","journal-title":"GigaScience"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"104129","DOI":"10.1016\/j.apsoil.2021.104129","article-title":"Bacterial functional prediction tools detect but underestimate metabolic diversity compared to shotgun metagenomics in southwest Florida soils","volume":"168","author":"Toole","year":"2021","journal-title":"Appl. Soil Ecol."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"btaf269","DOI":"10.1093\/bioinformatics\/btaf269","article-title":"PICRUSt2-SC: An update to the reference database used for functional prediction within PICRUSt2","volume":"41","author":"Wright","year":"2025","journal-title":"Bioinformatics"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"127081","DOI":"10.1016\/j.micres.2022.127081","article-title":"Metagenomic analysis displays the potential predictive biodegradation pathways of the persistent pesticides in agricultural soil with a long record of pesticide usage","volume":"261","author":"Malla","year":"2022","journal-title":"Microbiol. Res."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1007\/s12010-024-05033-y","article-title":"Repercussions of Prolonged Pesticide Use on Natural Soil Microbiome Dynamics Using Metagenomics Approach","volume":"197","author":"Maharana","year":"2024","journal-title":"Appl. Biochem. Biotechnol."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"141583","DOI":"10.1016\/j.chemosphere.2024.141583","article-title":"Actinomycetota, a central constituent microbe during long-term exposure to diazinon, an organophosphorus insecticide","volume":"354","author":"Jeon","year":"2024","journal-title":"Chemosphere"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1039\/D2EM00095D","article-title":"Identification of chlorpyrifos-degrading microorganisms in farmland soils via cultivation-independent and -dependent approaches","volume":"24","author":"Lian","year":"2022","journal-title":"Environ. Sci. Process. Impacts"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"2687","DOI":"10.1016\/j.csbj.2021.05.001","article-title":"Network analysis methods for studying microbial communities: A mini review","volume":"19","author":"Matchado","year":"2021","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"e00961\u201322","DOI":"10.1128\/msystems.00961-22","article-title":"Inferring microbial co-occurrence networks from amplicon data: A systematic evaluation","volume":"8","author":"Kishore","year":"2023","journal-title":"mSystems"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/s40168-020-00985-9","article-title":"Specialized metabolic functions of keystone taxa sustain soil microbiome stability","volume":"9","author":"Xun","year":"2021","journal-title":"Microbiome"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"106454","DOI":"10.1016\/j.apsoil.2025.106454","article-title":"Microbial network stability in chlorpyrifos-contaminated soils is improved by microbial inoculant application","volume":"215","author":"Wu","year":"2025","journal-title":"Appl. Soil Ecol."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1007\/s10661-024-12494-5","article-title":"Sustainable indigenous bio-mixture for restoration the soil point source pollution with special reference to chlorpyrifos","volume":"196","author":"Mansee","year":"2024","journal-title":"Environ. Monit. Assess."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"e00169\u201322","DOI":"10.1128\/msystems.00169-22","article-title":"Modeling-Guided Amendments Lead to Enhanced Biodegradation in Soil","volume":"7","author":"Dhakar","year":"2022","journal-title":"mSystems"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"149119","DOI":"10.1016\/j.cej.2024.149119","article-title":"Mechanistic understanding of biochar-bacteria system for enhanced chlorpyrifos bioremediation in water and soil medium","volume":"483","author":"Mariyam","year":"2024","journal-title":"Chem. Eng. J."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"e00921-25","DOI":"10.1128\/msystems.00921-25","article-title":"Interactions between native soil microbiome and a synthetic microbial community reveals bacteria with persistent traits","volume":"10","author":"Velte","year":"2025","journal-title":"mSystems"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1007\/s11270-021-05349-z","article-title":"Functional Analysis of Chlorpyrifos Biodegradation in Agricultural Soils Augmented with a Three-Strain Bacterial Consortium","volume":"232","author":"Islam","year":"2021","journal-title":"Water Air Soil Pollut."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"111799","DOI":"10.1016\/j.ecoenv.2020.111799","article-title":"New insights into the biodegradation of chlorpyrifos by a novel bacterial consortium: Process optimization using general factorial experimental design","volume":"209","author":"Uniyal","year":"2021","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"115271","DOI":"10.1016\/j.envres.2023.115271","article-title":"Multi-omics approach reveals elevated potential of bacteria for biodegradation of imidacloprid","volume":"221","author":"Gautam","year":"2023","journal-title":"Environ. Res."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"e01562-21","DOI":"10.1128\/AEM.01562-21","article-title":"A Synergistic Consortium Involved in rac-Dichlorprop Degradation as Revealed by DNA Stable Isotope Probing and Metagenomic Analysis","volume":"87","author":"Hu","year":"2021","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"137428","DOI":"10.1016\/j.jhazmat.2025.137428","article-title":"Dissipation of the insecticide profenofos in tropical agricultural soils (Berambadi catchment, South India): Insight from compound-specific isotope analysis (CSIA)","volume":"488","author":"Masbou","year":"2025","journal-title":"J. Hazard. Mater."},{"key":"ref_97","doi-asserted-by":"crossref","unstructured":"Aziz, H., Wang, X., Murtaza, G., Ashar, A., Hussain, S., Abid, M., Murtaza, B., Saleem, M.H., Fiaz, S., and Ali, S. (2021). Evaluation of Compost and Biochar to Mitigate Chlorpyrifos Pollution in Soil and Their Effect on Soil Enzyme Dynamics. Sustainability, 13.","DOI":"10.3390\/su13179695"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"210","DOI":"10.17221\/106\/2023-PSE","article-title":"Biodegradation of chlorpyrifos by soil bacteria and their effects on growth of rice seedlings under pesticide-contaminated soil","volume":"69","author":"Saengsanga","year":"2023","journal-title":"Plant Soil Environ."},{"key":"ref_99","doi-asserted-by":"crossref","unstructured":"Conde Avila, V., Mart\u00ednez Valenzuela, C., Navarro Noya, Y.E., and Bastidas Bastidas, P.J. (2025). Inoculation With Azotobacter vinelandii Enhanced Chlorpyrifos Degradation and Reduced Cytotoxic and Genotoxic Effects in Soil. Span. J. Soil Sci., 15.","DOI":"10.3389\/sjss.2025.14033"},{"key":"ref_100","doi-asserted-by":"crossref","unstructured":"Tagliabue, F., Marini, E., De Bernardi, A., Vischetti, C., Brunetti, G., and Casucci, C. (2025). A Bioremediation and Soil Fertility Study: Effects of Vermiremediation on Soil Contaminated by Chlorpyrifos. Environments, 12.","DOI":"10.3390\/environments12050136"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"100514","DOI":"10.1016\/j.envadv.2024.100514","article-title":"Simultaneous degradation of chlorpyrifos and profenofos in soils at sublethal concentrations in presence of Eisenia foetida and a native bacterial consortium","volume":"16","year":"2024","journal-title":"Environ. Adv."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"160782","DOI":"10.1016\/j.scitotenv.2022.160782","article-title":"Efficient biodegradation characteristics and detoxification pathway of organophosphorus insecticide profenofos via Cupriavidus nantongensis X1\u1d40 and enzyme OpdB","volume":"862","author":"Fang","year":"2023","journal-title":"Sci. Total Environ."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"127841","DOI":"10.1016\/j.jhazmat.2021.127841","article-title":"Novel pathway of acephate degradation by the microbial consortium ZQ01 and its potential for environmental bioremediation","volume":"426","author":"Lin","year":"2022","journal-title":"J. Hazard. Mater."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"5261","DOI":"10.1021\/acs.jafc.2c07861","article-title":"Rapid Biodegradation of the Organophosphorus Insecticide Acephate by a Novel Strain Burkholderia sp. A11 and Its Impact on the Structure of the Indigenous Microbial Community","volume":"71","author":"Wu","year":"2023","journal-title":"J. Agric. Food Chem."},{"key":"ref_105","doi-asserted-by":"crossref","unstructured":"Aziz, T., Rasheed, S., Shah, A.H., Nasir, H., Fariq, A., Jamil, A., and Jannat, S. (2022). Bioremediation Potential of Plant-Bacterial Consortia for Chlorpyrifos Removal Using Constructed Wetland. Front. Environ. 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