{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T20:32:17Z","timestamp":1790022737439,"version":"4.0.1"},"reference-count":157,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T00:00:00Z","timestamp":1774742400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Sequence-based tools have greatly improved the molecular description of soil bioremediation, but detection alone cannot confirm that a contaminant is being degraded by a defined pathway. In soils, bioavailability limitations, redox microsites, relic DNA, gene mobility, and community restructuring can decouple gene presence from reaction flux. This review synthesizes an operational framework that separates three inferential levels: pathway potential, in situ activity, and verified pathway operation. The framework links inoculant fate, functional gene abundance, gene expression, pathway reconstruction, stable isotope probing, and targeted chemical analysis under explicit quality assurance, quality control, and decision rules. Particular attention is given to distinguishing parent compound loss from mineralization and detoxification and to using isotopic attribution when functional redundancy or inoculant-native overlap obscures agency. Instead of being presented as conceptually new, these principles are organized into a practical workflow for soil systems. This structure clarifies what can be discerned from genes, transcripts, proteins, metabolites, and transformation products at each evidentiary tier and provides a conservative basis for integrating multi-omics with mechanistic and quantitative interpretation.<\/jats:p>","DOI":"10.3390\/ijms27073111","type":"journal-article","created":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T08:22:36Z","timestamp":1774858956000},"page":"3111","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Molecular Monitoring in Soil Bioremediation: From Genetic Potential to Verified Pathway Operation"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7865-6371","authenticated-orcid":false,"given":"Mariusz","family":"Cyco\u0144","sequence":"first","affiliation":[{"name":"Department of Microbiology, Faculty of Pharmaceutical Sciences, Medical University of Silesia, Jagiello\u0144ska 4, 41-200 Sosnowiec, Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,3,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1016\/j.biotechadv.2016.10.006","article-title":"Metagenomics: Probing Pollutant Fate in Natural and Engineered Ecosystems","volume":"34","author":"Bouhajja","year":"2016","journal-title":"Biotechnol. Adv."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1016\/j.mib.2018.01.013","article-title":"The Soil Microbiome\u2014From Metagenomics to Metaphenomics","volume":"43","author":"Jansson","year":"2018","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1007\/s10295-016-1809-8","article-title":"Metagenomic Applications in Environmental Monitoring and Bioremediation","volume":"43","author":"Techtmann","year":"2016","journal-title":"J. Ind. Microbiol. Biotechnol."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Khan, M.F. (2025). Microbial Remediation of Agrochemical-Contaminated Soils: Enzymatic Mechanisms, Quorum Sensing, and Emerging Opportunities. Integr. Environ. Assess. Manag., vjaf167.","DOI":"10.1093\/inteam\/vjaf167"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"142278","DOI":"10.1016\/j.ijbiomac.2025.142278","article-title":"A Holistic Perspective on the Efficiency of Microbial Enzymes in Bioremediation Process: Mechanism and Challenges: A Review","volume":"308","author":"Housseiny","year":"2025","journal-title":"Int. J. Biol. Macromol."},{"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","first-page":"89","article-title":"Bioremediation Techniques for Water and Soil Pollution: Review","volume":"10","author":"Ali","year":"2025","journal-title":"Nat. Eng. Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/s13213-020-01580-x","article-title":"Diagnosing Bioremediation of Crude Oil-Contaminated Soil and Related Geochemical Processes at the Field Scale Through Microbial Community and Functional Genes","volume":"70","author":"Cai","year":"2020","journal-title":"Ann. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"5884","DOI":"10.1128\/AEM.01763-14","article-title":"Dead or Alive: Molecular Assessment of Microbial Viability","volume":"80","author":"Cangelosi","year":"2014","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1186\/s40168-017-0285-3","article-title":"Schr\u00f6dinger\u2019s Microbes: Tools for Distinguishing the Living from the Dead in Microbial Ecosystems","volume":"5","author":"Emerson","year":"2017","journal-title":"Microbiome"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"16242","DOI":"10.1038\/nmicrobiol.2016.242","article-title":"Relic DNA Is Abundant in Soil and Obscures Estimates of Soil Microbial Diversity","volume":"2","author":"Carini","year":"2016","journal-title":"Nat. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e02776-19","DOI":"10.1128\/mBio.02776-19","article-title":"Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities","volume":"11","author":"Carini","year":"2020","journal-title":"mBio"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e00637-18","DOI":"10.1128\/mBio.00637-18","article-title":"How, When, and Where Relic DNA Affects Microbial Diversity","volume":"9","author":"Lennon","year":"2018","journal-title":"mBio"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2977","DOI":"10.1016\/j.soilbio.2007.06.020","article-title":"Cycling of Extracellular DNA in the Soil Environment","volume":"39","author":"Campbell","year":"2007","journal-title":"Soil Biol. Biochem."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1007\/s12088-020-00877-4","article-title":"Atrazine Bioremediation and Its Influence on Soil Microbial Diversity by Metagenomics Analysis","volume":"60","author":"Bhardwaj","year":"2020","journal-title":"Indian J. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Gangola, S., Joshi, S., Bhandari, G., Bhatt, P., Kumar, S., and Pandey, S.C. (2023). Omics Approaches to Pesticide Biodegradation for Sustainable Environment. Advanced Microbial Techniques in Agriculture, Environment, and Health Management, Elsevier.","DOI":"10.1016\/B978-0-323-91643-1.00010-7"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Harirchi, S., Rafieyan, S., Nojoumi, S.A., and Etemadifar, Z. (2022). Microbial Biodegradation and Metagenomics in Remediation of Environmental Pollutants: Enzymes and Mechanisms. Omics Insights in Environmental Bioremediation, Springer Nature.","DOI":"10.1007\/978-981-19-4320-1_21"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1080\/01490451.2023.2261443","article-title":"Application of Microorganisms in Biotransformation and Bioremediation of Environmental Contaminant: A Review","volume":"41","author":"Nag","year":"2024","journal-title":"Geomicrobiol. J."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1007\/s00203-023-03516-w","article-title":"Insights into the Ubiquity, Persistence and Microbial Intervention of Imidacloprid","volume":"205","author":"Bhende","year":"2023","journal-title":"Arch. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Kumar, V., Sharma, J.K., Kumar, S., Gulia, J., Singh, N.P., and Santal, A.R. (2025). Metagenomic and Proteomic Approach for Bioremediation of Environmental Pollutants. Development in Waste Water Treatment Research and Processes, Elsevier.","DOI":"10.1016\/B978-0-443-13615-3.00020-0"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Muhie, S., Gautam, A., Mylroie, J., Sowe, B., Campbell, R., Perkins, E.J., Hammamieh, R., and Garcia-Reyero, N. (2025). Effects of Environmental Chemical Pollutants on Microbiome Diversity: Insights from Shotgun Metagenomics. Toxics, 13.","DOI":"10.3390\/toxics13020142"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e05767","DOI":"10.1016\/j.heliyon.2020.e05767","article-title":"Herbicide Bioremediation: From Strains to Bacterial Communities","volume":"6","author":"Pileggi","year":"2020","journal-title":"Heliyon"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1007\/s00284-020-01916-5","article-title":"Omics Approaches to Pesticide Biodegradation","volume":"77","year":"2020","journal-title":"Curr. Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"bin Salam, M.T., Mahmood, A., Asghar, W., Ito, K., and Kataoka, R. (2024). Phytomicrobiomes: A Potential Approach for Sustainable Pesticide Biodegradation. Appl. Sci., 14.","DOI":"10.3390\/app14072740"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"7361","DOI":"10.1007\/s00253-016-7709-z","article-title":"Application of Biodegradation in Mitigating and Remediating Pesticide Contamination of Freshwater Resources: State of the Art and Challenges for Optimization","volume":"100","author":"Vandermaesen","year":"2016","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1111\/1574-6941.12102","article-title":"Alteration of Microbial Community Structure Affects Diesel Biodegradation in an Arctic Soil","volume":"85","author":"Bell","year":"2013","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"7580","DOI":"10.1021\/es800030f","article-title":"Assessing Soil Microbial Populations Responding to Crude-Oil Amendment at Different Temperatures Using Phylogenetic, Functional Gene (alkB) and Physiological Analyses","volume":"42","author":"Hamamura","year":"2008","journal-title":"Environ. Sci. Technol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"6258","DOI":"10.1128\/AEM.01029-09","article-title":"Microarray and Real-Time PCR Analyses of the Responses of High-Arctic Soil Bacteria to Hydrocarbon Pollution and Bioremediation Treatments","volume":"75","author":"Yergeau","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1016\/j.envpol.2010.10.015","article-title":"Mineralisation of Target Hydrocarbons in Three Contaminated Soils from Former Refinery Facilities","volume":"159","author":"Towell","year":"2011","journal-title":"Environ. Pollut."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1128\/AEM.72.1.59-65.2006","article-title":"Cytochrome P450 Alkane Hydroxylases of the CYP153 Family Are Common in Alkane-Degrading Eubacteria Lacking Integral Membrane Alkane Hydroxylases","volume":"72","author":"Funhoff","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1038\/s41598-020-80631-4","article-title":"Response of Bacterial and Fungal Communities to High Petroleum Pollution in Different Soils","volume":"11","author":"Galitskaya","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1016\/j.chemosphere.2016.07.032","article-title":"Insights into the Biodegradation of Weathered Hydrocarbons in Contaminated Soils by Bioaugmentation and Nutrient Stimulation","volume":"161","author":"Jiang","year":"2016","journal-title":"Chemosphere"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"23012","DOI":"10.1038\/srep23012","article-title":"Metagenomic and Functional Analyses of the Consequences of Reduction of Bacterial Diversity on Soil Functions and Bioremediation in Diesel-Contaminated Microcosms","volume":"6","author":"Jung","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"133647","DOI":"10.1016\/j.biortech.2025.133647","article-title":"Salicylic Acid as a Pathway Inducer for Improved Bioremediation of Oil-Polluted Saline-Alkali Soils by Chemotactic S. stutzeri M3","volume":"441","author":"Li","year":"2026","journal-title":"Bioresour. Technol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"11068","DOI":"10.1038\/srep11068","article-title":"Distribution of Petroleum Degrading Genes and Factor Analysis of Petroleum Contaminated Soil from the Dagang Oilfield, China","volume":"5","author":"Liu","year":"2015","journal-title":"Sci. Rep."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.jes.2019.02.001","article-title":"Vertical Response of Microbial Community and Degrading Genes to Petroleum Hydrocarbon Contamination in Saline Alkaline Soil","volume":"81","author":"Liu","year":"2019","journal-title":"J. Environ. Sci."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1080\/15226514.2015.1109598","article-title":"Breakdown of Low-Level Total Petroleum Hydrocarbons (TPH) in Contaminated Soil Using Grasses and Willows","volume":"18","author":"McIntosh","year":"2016","journal-title":"Int. J. Phytoremediation"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1128\/AEM.02747-12","article-title":"Impact of Long-Term Diesel Contamination on Soil Microbial Community Structure","volume":"79","author":"Sutton","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"136446","DOI":"10.1016\/j.chemosphere.2022.136446","article-title":"Assessment of Bioremediation Potential of Petroleum-Contaminated Soils from the Shanbei Oilfield of China Revealed by qPCR and High Throughput Sequencing","volume":"308","author":"Wu","year":"2022","journal-title":"Chemosphere"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"471","DOI":"10.4014\/jmb.2210.10038","article-title":"Dynamics of Functional Genes and Bacterial Community during Bioremediation of Diesel-Contaminated Soil Amended with Compost","volume":"33","author":"Yang","year":"2023","journal-title":"J. Microbiol. Biotechnol."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Delgado-Balbuena, L., Bello-L\u00f3pez, J.M., Navarro-Noya, Y.E., Rodr\u00edguez-Valent\u00edn, A., Luna-Guido, M.L., and Dendooven, L. (2016). Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0160991"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.apsoil.2011.12.008","article-title":"Bacterial Polycyclic Aromatic Hydrocarbon Ring-Hydroxylating Dioxygenases (PAH-RHD) Encoding Genes in Different Soils from King George Bay, Antarctic Peninsula","volume":"55","author":"Jurelevicius","year":"2012","journal-title":"Appl. Soil. Ecol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.1007\/s00253-006-0423-5","article-title":"Dynamic Changes in nahAc Gene Copy Numbers during Degradation of Naphthalene in PAH-Contaminated Soils","volume":"72","author":"Park","year":"2006","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"3775","DOI":"10.1128\/AEM.00033-15","article-title":"Identification of Anthraquinone-Degrading Bacteria in Soil Contaminated with Polycyclic Aromatic Hydrocarbons","volume":"81","author":"Zhang","year":"2015","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1016\/j.mex.2016.02.005","article-title":"A Quantitative PCR Approach for Quantification of Functional Genes Involved in the Degradation of Polycyclic Aromatic Hydrocarbons in Contaminated Soils","volume":"3","author":"Shahsavari","year":"2016","journal-title":"MethodsX"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1016\/j.jhazmat.2016.07.060","article-title":"Comparative Metagenomic Analysis of PAH Degradation in Soil by a Mixed Microbial Consortium","volume":"318","author":"Zafra","year":"2016","journal-title":"J. Hazard. Mater."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/j.mimet.2008.01.009","article-title":"Real-Time PCR Quantification of PAH-Ring Hydroxylating Dioxygenase (PAH-RHD\u03b1) Genes from Gram Positive and Gram Negative Bacteria in Soil and Sediment Samples","volume":"73","author":"Norini","year":"2008","journal-title":"J. Microbiol. Methods"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"e02399-18","DOI":"10.1128\/AEM.02399-18","article-title":"pahE, a Functional Marker Gene for Polycyclic Aromatic Hydrocarbon-Degrading Bacteria","volume":"85","author":"Liang","year":"2019","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"161233","DOI":"10.1016\/j.scitotenv.2022.161233","article-title":"Distribution of the New Functional Marker Gene (pahE) of Aerobic Polycyclic Aromatic Hydrocarbon (PAHs) Degrading Bacteria in Different Ecosystems","volume":"865","author":"Liang","year":"2023","journal-title":"Sci. Total Environ."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1111\/j.1462-2920.2012.02781.x","article-title":"Comparative Metatranscriptomics Reveals Widespread Community Responses during Phenanthrene Degradation in Soil","volume":"14","author":"Clipson","year":"2012","journal-title":"Environ. Microbiol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"125208","DOI":"10.1016\/j.jenvman.2025.125208","article-title":"Rhizodegradation of Diesel and PAH Contaminated Soils with Miscanthus \u00d7 giganteus: Soil, Plants, Microbes and Pollutants Interactions after Two Seasons","volume":"381","author":"Kwoczynski","year":"2025","journal-title":"J. Environ. Manag."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"2623","DOI":"10.1111\/j.1462-2920.2011.02501.x","article-title":"Stable-isotope Probing of the Polycyclic Aromatic Hydrocarbon-degrading Bacterial Guild in a Contaminated Soil","volume":"13","author":"Jones","year":"2011","journal-title":"Environ. Microbiol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"fiz181","DOI":"10.1093\/femsec\/fiz181","article-title":"DNA Stable Isotope Probing Reveals Contrasted Activity and Phenanthrene-Degrading Bacteria Identity in a Gradient of Anthropized Soils","volume":"95","author":"Lemmel","year":"2019","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.jenvman.2015.03.027","article-title":"Rhizoremediation of Phenanthrene and Pyrene Contaminated Soil Using Wheat","volume":"155","author":"Shahsavari","year":"2015","journal-title":"J. Environ. Manag."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"161139","DOI":"10.1016\/j.scitotenv.2022.161139","article-title":"Different Phenanthrene Degraders between Free-Cell Mediated and Biochar-Immobilization Assisted Soil Bioaugmentation as Identified by RNA-Based Stable Isotope Probing (RNA-SIP)","volume":"864","author":"Teng","year":"2023","journal-title":"Sci. Total Environ."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Toth, C.R.A., Berdugo-Clavijo, C., O\u2019Farrell, C.M., Jones, G.M., Sheremet, A., Dunfield, P.F., and Gieg, L.M. (2018). Stable Isotope and Metagenomic Profiling of a Methanogenic Naphthalene-Degrading Enrichment Culture. Microorganisms, 6.","DOI":"10.3390\/microorganisms6030065"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1016\/j.envpol.2012.07.048","article-title":"Monitoring Bioremediation of Atrazine in Soil Microcosms Using Molecular Tools","volume":"172","author":"Sagarkar","year":"2013","journal-title":"Environ. Pollut."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.ibiod.2012.11.003","article-title":"Bioaugmentation with Arthrobacter sp. Strain DAT1 for Remediation of Heavily Atrazine-Contaminated Soil","volume":"77","author":"Wang","year":"2013","journal-title":"Int. Biodeterior. Biodegrad."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/s13068-018-1113-0","article-title":"Characterisation of an Efficient Atrazine-Degrading Bacterium, Arthrobacter sp. ZXY-2: An Attempt to Lay the Foundation for Potential Bioaugmentation Applications","volume":"11","author":"Zhao","year":"2018","journal-title":"Biotechnol. Biofuels"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Jia, W., Li, N., Yang, T., Dai, W., Jiang, J., Chen, K., and Xu, X. (2021). Bioaugmentation of Atrazine-Contaminated Soil with Paenarthrobacter sp. Strain AT-5 and Its Effect on the Soil Microbiome. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.771463"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1111\/j.1365-294X.2009.04503.x","article-title":"Atz Gene Expressions during Atrazine Degradation in the Soil Drilosphere","volume":"19","author":"Monard","year":"2010","journal-title":"Mol. Ecol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1007\/s10532-012-9574-5","article-title":"Estimating the Biodegradation of Pesticide in Soils by Monitoring Pesticide-Degrading Gene Expression","volume":"24","author":"Monard","year":"2013","journal-title":"Biodegradation"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"18363","DOI":"10.1038\/s41598-019-54978-2","article-title":"Labour Sharing Promotes Coexistence in Atrazine Degrading Bacterial Communities","volume":"9","author":"Billet","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"1048","DOI":"10.1038\/ismej.2010.194","article-title":"Relationship between Bacterial Diversity and Function under Biotic Control: The Soil Pesticide Degraders as a Case Study","volume":"5","author":"Monard","year":"2011","journal-title":"ISME J."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"7846","DOI":"10.1128\/AEM.02478-13","article-title":"The Novel Bacterial N-Demethylase PdmAB Is Responsible for the Initial Step of N,N-Dimethyl-Substituted Phenylurea Herbicide Degradation","volume":"79","author":"Gu","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Khan, M.F., Liao, J., Liu, Z., and Chugh, G. (2025). Bacterial Cytochrome P450 Involvement in the Biodegradation of Fluorinated Pyrethroids. J. Xenobiot., 15.","DOI":"10.3390\/jox15020058"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"103828","DOI":"10.1016\/j.bcab.2025.103828","article-title":"Biodegradation of Fluorinated Beta-Triketone Herbicide Tembotrione by a Bacterial-Fungal Consortium","volume":"70","author":"Khan","year":"2025","journal-title":"Biocatal. Agric. Biotechnol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"e00388-22","DOI":"10.1128\/aem.00388-22","article-title":"Genetic Characterization of the Ibuprofen-Degradative Pathway of Rhizorhabdus wittichii MPO218","volume":"88","author":"Aulestia","year":"2022","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"9159","DOI":"10.1038\/s41598-019-45732-9","article-title":"Features of Diclofenac Biodegradation by Rhodococcus Ruber IEGM 346","volume":"9","author":"Ivshina","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1099\/mic.0.062273-0","article-title":"Genetic and Chemical Characterization of Ibuprofen Degradation by Sphingomonas Ibu-2","volume":"159","author":"Murdoch","year":"2013","journal-title":"Microbiology"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.scitotenv.2010.09.020","article-title":"The Non-Steroidal Anti-Inflammatory Drug Diclofenac Is Readily Biodegradable in Agricultural Soils","volume":"409","author":"Sabourin","year":"2010","journal-title":"Sci. Total Environ."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"9723","DOI":"10.1021\/acs.est.4c02191","article-title":"Sulfamethoxazole Is Metabolized and Mineralized at Extremely Low Concentrations","volume":"58","author":"Lema","year":"2024","journal-title":"Environ. Sci. Technol."},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Cyco\u0144, M., Mrozik, A., and Piotrowska-Seget, Z. (2019). Antibiotics in the Soil Environment\u2014Degradation and Their Impact on Microbial Activity and Diversity. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.00338"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"125306","DOI":"10.1016\/j.envpol.2024.125306","article-title":"Temporal Dynamic of Soil Microbial Communities and Antibiotic Resistance Markers Exposed to Increasing Concentrations of Sulfamethoxazole","volume":"364","author":"Barbieri","year":"2025","journal-title":"Environ. Pollut."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"ycaf246","DOI":"10.1093\/ismeco\/ycaf246","article-title":"Antibiotic-Degrading Bacteria Shape Resistome Dynamics and Horizontal Gene Transfer Potential in Soils with Contrasting Properties","volume":"6","author":"Mei","year":"2026","journal-title":"ISME Commun."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1007\/s11274-017-2284-8","article-title":"Microbial Population Shift Caused by Sulfamethoxazole in Engineered-Soil Aquifer Treatment (e-SAT) System","volume":"33","author":"Rudrashetti","year":"2017","journal-title":"World J. Microbiol. Biotechnol."},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Wang, S., Gao, X., Gao, Y., Li, Y., Cao, M., Xi, Z., Zhao, L., and Feng, Z. (2017). Tetracycline Resistance Genes Identified from Distinct Soil Environments in China by Functional Metagenomics. Front. Microbiol., 8.","DOI":"10.3389\/fmicb.2017.01406"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"138012","DOI":"10.1016\/j.jhazmat.2025.138012","article-title":"Bioremediation Potential of Sulfadiazine-Degrading Bacteria: Impacts on Ryegrass Growth and Soil Functionality","volume":"491","author":"Yin","year":"2025","journal-title":"J. Hazard. Mater."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"11281","DOI":"10.1021\/acs.est.5b01740","article-title":"\u201cOmics\u201d Insights into PAH Degradation Toward Improved Green Remediation Biotechnologies","volume":"49","author":"Dumas","year":"2015","journal-title":"Environ. Sci. Technol."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1007\/s00253-011-3381-5","article-title":"Are Alkane Hydroxylase Genes (alkB) Relevant to Assess Petroleum Bioremediation Processes in Chronically Polluted Coastal Sediments?","volume":"92","author":"Paisse","year":"2011","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"108435","DOI":"10.1016\/j.envint.2024.108435","article-title":"A Multi-Omics Approach to Unravelling the Coupling Mechanism of Nitrogen Metabolism and Phenanthrene Biodegradation in Soil Amended with Biochar","volume":"183","author":"Dong","year":"2024","journal-title":"Environ. Int."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"105144","DOI":"10.1016\/j.apsoil.2023.105144","article-title":"Metagenomic Analysis of Petroleum Biodegradation Coupled to Specific N-Cycling Process in Oil-Contaminated Soil","volume":"193","author":"Kong","year":"2024","journal-title":"Appl. Soil Ecol."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"fiac127","DOI":"10.1093\/femsec\/fiac127","article-title":"Interactions Between Bacterial Inoculants and Native Soil Bacterial Community: The Case of Spore-Forming Bacillus spp.","volume":"98","author":"Mawarda","year":"2022","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"107874","DOI":"10.1016\/j.soilbio.2020.107874","article-title":"Deliberate Introduction of Invisible Invaders: A Critical Appraisal of the Impact of Microbial Inoculants on Soil Microbial Communities","volume":"148","author":"Mawarda","year":"2020","journal-title":"Soil Biol. Biochem."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"122393","DOI":"10.1016\/j.envpol.2023.122393","article-title":"Exposure to Three Herbicide Mixtures Influenced Maize Root-Associated Microbial Community Structure, Function and the Network Complexity","volume":"336","author":"Ma","year":"2023","journal-title":"Environ. Pollut."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"140734","DOI":"10.1016\/j.jhazmat.2025.140734","article-title":"Microplastics Inhibit Oxytetracycline Degradation in Soils: Insights into Biofilm-Enhanced Adsorption and Microbial Community Shifts","volume":"501","author":"Guo","year":"2026","journal-title":"J. Hazard. Mater."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"181331","DOI":"10.1016\/j.scitotenv.2025.181331","article-title":"Microbiome of Soil Waste Dumpsite and Adjacent River Habitat Harbors Dynamic Plastic Degrading Bacterial Diversity and Abundant Functional Enzymes","volume":"1014","author":"Singh","year":"2026","journal-title":"Sci. Total Environ."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"132313","DOI":"10.1016\/j.jhazmat.2023.132313","article-title":"Effect of Microplastics on the Degradation of Tetracycline in a Soil Microbial Electric Field","volume":"460","author":"Wang","year":"2023","journal-title":"J. Hazard. Mater."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"e00169-22","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":"1593","DOI":"10.1002\/ceat.201500479","article-title":"Contaminant-Degrading Microorganisms Identified Using Stable Isotope Probing","volume":"39","author":"Cupples","year":"2016","journal-title":"Chem. Eng. Technol."},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1038\/s41579-018-0029-9","article-title":"Best Practices for Analysing Microbiomes","volume":"16","author":"Knight","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-Resolution Sample Inference from Illumina Amplicon Data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Cao, Y., Yu, M., Dong, G., Chen, B., and Zhang, B. (2020). Digital PCR as an Emerging Tool for Monitoring of Microbial Biodegradation. Molecules, 25.","DOI":"10.3390\/molecules25030706"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"10597","DOI":"10.1007\/s00253-016-7950-5","article-title":"Efficiency and Sensitivity of the Digital Droplet PCR for the Quantification of Antibiotic Resistance Genes in Soils and Organic Residues","volume":"100","author":"Brothier","year":"2016","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"74","DOI":"10.3390\/applmicrobiol1010007","article-title":"Challenges Using Droplet Digital PCR for Environmental Samples","volume":"1","author":"Kokkoris","year":"2021","journal-title":"Appl. Microbiol."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/s13007-014-0042-6","article-title":"Reverse Transcriptase Droplet Digital PCR Shows High Resilience to PCR Inhibitors from Plant, Soil and Water Samples","volume":"10","author":"Dreo","year":"2014","journal-title":"Plant Methods"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1016\/j.envpol.2016.07.041","article-title":"Transformation of Atenolol, Metoprolol, and Carbamazepine in Soils: The Identification, Quantification, and Stability of the Transformation Products and Further Implications for the Environment","volume":"218","author":"Koba","year":"2016","journal-title":"Environ. Pollut."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1016\/j.scitotenv.2016.03.131","article-title":"The Role of Sorption and Biodegradation in the Removal of Acetaminophen, Carbamazepine, Caffeine, Naproxen and Sulfamethoxazole During Soil Contact: A Kinetics Study","volume":"559","author":"Meffe","year":"2016","journal-title":"Sci. Total Environ."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"2984","DOI":"10.1128\/AEM.01942-10","article-title":"Multiple DNA Extractions Coupled with Stable-Isotope Probing of Anthracene-Degrading Bacteria in Contaminated Soil","volume":"77","author":"Jones","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"9387","DOI":"10.1021\/acs.est.0c02124","article-title":"Culture-Independent Analysis of Linuron-Mineralizing Microbiota and Functions in on-Farm Biopurification Systems via DNA-Stable Isotope Probing: Comparison with Enrichment Culture","volume":"54","author":"Lerner","year":"2020","journal-title":"Environ. Sci. Technol."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"fiab051","DOI":"10.1093\/femsec\/fiab051","article-title":"DNA-SIP and Repeated Isolation Corroborate Variovorax as a Key Organism in Maintaining the Genetic Memory for Linuron Biodegradation in an Agricultural Soil","volume":"97","author":"Lerner","year":"2021","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.copbio.2016.04.010","article-title":"Protein-SIP in Environmental Studies","volume":"41","author":"Jehmlich","year":"2016","journal-title":"Curr. Opin. Biotechnol."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/j.mimet.2012.08.007","article-title":"Progress in Understanding Preferential Detection of Live Cells Using Viability Dyes in Combination with DNA Amplification","volume":"91","author":"Fittipaldi","year":"2012","journal-title":"J. Microbiol. Methods"},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"5111","DOI":"10.1128\/AEM.02987-06","article-title":"Use of Propidium Monoazide for Live\/Dead Distinction in Microbial Ecology","volume":"73","author":"Nocker","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"128224","DOI":"10.1016\/j.micres.2025.128224","article-title":"Sources of Variability for Viability PCR Using Propidium Monoazide","volume":"298","author":"Jansriphibul","year":"2025","journal-title":"Microbiol. Res."},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1111\/j.1574-6968.2008.01429.x","article-title":"Novel Approaches Toward Preferential Detection of Viable Cells Using Nucleic Acid Amplification Techniques","volume":"291","author":"Nocker","year":"2009","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_107","doi-asserted-by":"crossref","unstructured":"Pacwa-P\u0142ociniczak, M., Biniecka, P., Bondarczuk, K., and Piotrowska-Seget, Z. (2020). Metagenomic Functional Profiling Reveals Differences in Bacterial Composition and Function During Bioaugmentation of Aged Petroleum-Contaminated Soil. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.02106"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"fiw125","DOI":"10.1093\/femsec\/fiw125","article-title":"Monitoring the Impact of Bioaugmentation with a PAH-Degrading Strain on Different Soil Microbiomes Using Pyrosequencing","volume":"92","author":"Festa","year":"2016","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1186\/s40168-024-01865-2","article-title":"DNA Stable Isotope Probing Reveals the Impact of Trophic Interactions on Bioaugmentation of Soils with Different Pollution Histories","volume":"12","author":"Nieto","year":"2024","journal-title":"Microbiome"},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1007\/s10311-020-01010-z","article-title":"Metagenomic Applications in Microbial Diversity, Bioremediation, Pollution Monitoring, Enzyme and Drug Discovery. A Review","volume":"18","author":"Datta","year":"2020","journal-title":"Environ. Chem. Lett."},{"key":"ref_111","first-page":"9","article-title":"Metatranscriptome Sequencing and Analysis of Agriculture Soil Provided Significant Insights about the Microbial Community Structure and Function","volume":"6","author":"Sharma","year":"2018","journal-title":"Ecol. Genet. Genom."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s43141-019-0006-3","article-title":"Comparative Metatranscriptome Analysis Revealed Broad Response of Microbial Communities in Two Soil Types, Agriculture versus Organic Soil","volume":"17","author":"Sharma","year":"2019","journal-title":"J. Genet. Eng. Biotechnol."},{"key":"ref_113","doi-asserted-by":"crossref","unstructured":"Werner, J., Nour, E., Bunk, B., Spr\u00f6er, C., Smalla, K., Springael, D., and \u00d6zt\u00fcrk, B. (2020). PromA Plasmids Are Instrumental in the Dissemination of Linuron Catabolic Genes Between Different Genera. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.00149"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"4396","DOI":"10.1128\/AEM.01763-09","article-title":"Metagenomic Analysis of Apple Orchard Soil Reveals Antibiotic Resistance Genes Encoding Predicted Bifunctional Proteins","volume":"76","author":"Donato","year":"2010","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1126\/science.1220761","article-title":"The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens","volume":"337","author":"Forsberg","year":"2012","journal-title":"Science"},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1111\/lam.13714","article-title":"Metagenomic and Metatranscriptomic Analyses Reveal That Biobed Systems Can Enrich for Antibiotic Resistance and Genetic Mobility Genes","volume":"75","author":"Russell","year":"2022","journal-title":"Lett. Appl. Microbiol."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1186\/s40168-018-0432-5","article-title":"Trees, Fungi and Bacteria: Tripartite Metatranscriptomics of a Root Microbiome Responding to Soil Contamination","volume":"6","author":"Gonzalez","year":"2018","journal-title":"Microbiome"},{"key":"ref_118","doi-asserted-by":"crossref","first-page":"4177","DOI":"10.1038\/s41598-024-54069-x","article-title":"Survival of a Microbial Inoculant in Soil After Recurrent Inoculations","volume":"14","author":"Papin","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"9762","DOI":"10.1021\/acs.est.3c01240","article-title":"Biodegradation of Amphipathic Fluorinated Peptides Reveals a New Bacterial Defluorinating Activity and a New Source of Natural Organofluorine Compounds","volume":"57","author":"Khan","year":"2023","journal-title":"Environ. Sci. Technol."},{"key":"ref_120","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.2134\/jeq2010.0192","article-title":"Evaluation of PCR-based Quantification Techniques to Estimate the Abundance of Atrazine Chlorohydrolase Gene atzA in Rhizosphere Soils","volume":"39","author":"Thompson","year":"2010","journal-title":"J. Environ. Qual."},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"115636","DOI":"10.1016\/j.envpol.2020.115636","article-title":"Metagenomic Analysis Reveals Mechanisms of Atrazine Biodegradation Promoted by Tree Species","volume":"267","author":"Aguiar","year":"2020","journal-title":"Environ. Pollut."},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"108303","DOI":"10.1016\/j.envint.2023.108303","article-title":"Core Bacteria Carrying the Genes Associated with the Degradation of Atrazine in Different Soils","volume":"181","author":"Liu","year":"2023","journal-title":"Environ. Int."},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1139\/cjm-2020-0033","article-title":"Development of Droplet Digital PCR Assays to Quantify Genes Involved in Nitrification and Denitrification, Comparison with Quantitative Real-Time PCR and Validation of Assays in Vineyard Soil","volume":"67","author":"Voegel","year":"2021","journal-title":"Can. J. Microbiol."},{"key":"ref_124","doi-asserted-by":"crossref","unstructured":"Kareem, H.A., and Khan, M.F. (2026). Current Research Advances and Future Prospects on Microbial Consortia for Sustainable PFAS Remediation. Int. J. Mol. Sci., 27.","DOI":"10.3390\/ijms27042084"},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"fiy026","DOI":"10.1093\/femsec\/fiy026","article-title":"DNA Stable-Isotope Probing Identifies Uncultivated Members of Pseudonocardia Associated with Biodegradation of Pyrene in Agricultural Soil","volume":"94","author":"Chen","year":"2018","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1016\/j.envint.2019.02.001","article-title":"Identification of Dominant Sulfamethoxazole-Degraders in Pig Farm-Impacted Soil by DNA and Protein Stable Isotope Probing","volume":"126","author":"Ouyang","year":"2019","journal-title":"Environ. Int."},{"key":"ref_127","doi-asserted-by":"crossref","unstructured":"Garrido-Sanz, D., Redondo-Nieto, M., Guirado, M., Pindado Jim\u00e9nez, O., Mill\u00e1n, R., Martin, M., and Rivilla, R. (2019). Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil. Genes., 10.","DOI":"10.3390\/genes10060456"},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1186\/s13568-024-01764-7","article-title":"Metagenomic Analyses of a Consortium for the Bioremediation of Hydrocarbons Polluted Soils","volume":"14","author":"Pandolfo","year":"2024","journal-title":"AMB Express"},{"key":"ref_129","doi-asserted-by":"crossref","unstructured":"Bharagava, R.N., Purchase, D., Saxena, G., and Mulla, S.I. (2019). Applications of Metagenomics in Microbial Bioremediation of Pollutants. Microbial Diversity in the Genomic Era, Elsevier.","DOI":"10.1016\/B978-0-12-814849-5.00026-5"},{"key":"ref_130","doi-asserted-by":"crossref","first-page":"125297","DOI":"10.1016\/j.envpol.2024.125297","article-title":"Metagenomic Approaches in Bioremediation of Environmental Pollutants","volume":"363","author":"Chettri","year":"2024","journal-title":"Environ. Pollut."},{"key":"ref_131","doi-asserted-by":"crossref","unstructured":"Fenibo, E.O., Nkuna, R., and Matambo, T. (2025). Metagenomic Insights Into Biopile Remediation of Petroleum-Contaminated Soil Using Chicken Droppings in Rivers State, Nigeria. Bioinform. Biol. Insights, 19.","DOI":"10.1177\/11779322251371117"},{"key":"ref_132","doi-asserted-by":"crossref","unstructured":"Kim, J.-W., Hong, Y.-K., Kim, H.-S., Oh, E.-J., Park, Y.-H., and Kim, S.-C. (2021). Metagenomic Analysis for Evaluating Change in Bacterial Diversity in TPH-Contaminated Soil After Soil Remediation. Toxics, 9.","DOI":"10.3390\/toxics9120319"},{"key":"ref_133","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1007\/s42770-023-01000-7","article-title":"Metagenomics-Metabolomics Analysis of Microbial Function and Metabolism in Petroleum-Contaminated Soil","volume":"54","author":"Li","year":"2023","journal-title":"Braz. J. Microbiol."},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"130690","DOI":"10.1016\/j.chemosphere.2021.130690","article-title":"Plants Exert Beneficial Influence on Soil Microbiome in a HCH Contaminated Soil Revealing Advantage of Microbe-Assisted Plant-Based HCH Remediation of a Dumpsite","volume":"280","author":"Kaur","year":"2021","journal-title":"Chemosphere"},{"key":"ref_135","doi-asserted-by":"crossref","unstructured":"Sangwan, N., Lata, P., Dwivedi, V., Singh, A., Niharika, N., Kaur, J., Anand, S., Malhotra, J., Jindal, S., and Nigam, A. (2012). Comparative Metagenomic Analysis of Soil Microbial Communities Across Three Hexachlorocyclohexane Contamination Levels. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0046219"},{"key":"ref_136","doi-asserted-by":"crossref","unstructured":"Singh, D.P., Prabha, R., Gupta, V.K., and Verma, M.K. (2018). Metatranscriptome Analysis Deciphers Multifunctional Genes and Enzymes Linked with the Degradation of Aromatic Compounds and Pesticides in the Wheat Rhizosphere. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.01331"},{"key":"ref_137","doi-asserted-by":"crossref","first-page":"128246","DOI":"10.1016\/j.jhazmat.2022.128246","article-title":"Exploring an Enhanced Rhizospheric Phenomenon for Pluricontaminated Soil Remediation: Insights from Tripartite Metatranscriptome Analyses","volume":"428","author":"Tartaglia","year":"2022","journal-title":"J. Hazard. Mater."},{"key":"ref_138","doi-asserted-by":"crossref","first-page":"175772","DOI":"10.1016\/j.scitotenv.2024.175772","article-title":"Enhancing Bioremediation of Petroleum-Contaminated Soil by Sophorolipids-Modified Biochar: Combined Metagenomic and Metabolomic Analyses","volume":"951","author":"Chen","year":"2024","journal-title":"Sci. Total Environ."},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"125685","DOI":"10.1016\/j.envpol.2025.125685","article-title":"Long-Term Microbial Functional Responses in Soil Contaminated with Biofuel\/Fossil Fuel Blends Triggered by Different Bioremediation Treatments","volume":"368","author":"Hidalgo","year":"2025","journal-title":"Environ. Pollut."},{"key":"ref_140","doi-asserted-by":"crossref","first-page":"119642","DOI":"10.1016\/j.jece.2025.119642","article-title":"Differential Microbial Mechanisms of TPH Degradation and Detoxification During Stepwise Bioremediation of Petroleum-Contaminated Soil","volume":"13","author":"Ou","year":"2025","journal-title":"J. Environ. Chem. Eng."},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"140640","DOI":"10.1016\/j.jhazmat.2025.140640","article-title":"Metabolism Regulates Spatial Distribution Patterns of Different Microbial Taxonomic Groups in Chlorinated Aliphatic Hydrocarbons Contaminated Soil","volume":"501","author":"Yang","year":"2026","journal-title":"J. Hazard. Mater."},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"131335","DOI":"10.1016\/j.chemosphere.2021.131335","article-title":"Sulfamethoxazole Biodegradation and Impacts on Soil Microbial Communities in a Bolivian Arid High Altitude Catchment","volume":"284","author":"Archundia","year":"2021","journal-title":"Chemosphere"},{"key":"ref_143","doi-asserted-by":"crossref","first-page":"2158","DOI":"10.1007\/s11368-022-03222-y","article-title":"Insights into Structure and Functioning of a Soil Microbial Community Amended with Cattle Manure Digestate and Sulfamethoxazole","volume":"22","author":"Garbini","year":"2022","journal-title":"J. Soils Sediments"},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1021\/acsagscitech.1c00222","article-title":"Metagenomic Insight into Sulfonamide-Induced Variation in Antibiotic Resistome of Soil Associated with Taxonomy, Mobile Genetic Elements (MGEs), and Function","volume":"2","author":"Li","year":"2022","journal-title":"ACS Agric. Sci. Technol."},{"key":"ref_145","doi-asserted-by":"crossref","first-page":"fiad064","DOI":"10.1093\/femsec\/fiad064","article-title":"Effect of Subtherapeutic and Therapeutic Sulfamethazine Concentrations on Transcribed Genes and Translated Proteins Involved in Microbacterium Sp. C448 Resistance and Degradation","volume":"99","author":"Paris","year":"2023","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1093\/bib\/bbx108","article-title":"MAFFT Online Service: Multiple Sequence Alignment, Interactive Sequence Choice and Visualization","volume":"20","author":"Katoh","year":"2019","journal-title":"Brief. Bioinform."},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"1987","DOI":"10.1039\/D5VA00240K","article-title":"Artificial Intelligence Driven Bioinformatics for Sustainable Bioremediation: Integrating Computational Intelligence with Ecological Restoration","volume":"4","author":"Siddique","year":"2025","journal-title":"Environ. Sci. Adv."},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"1020","DOI":"10.1089\/cmb.2019.0345","article-title":"RemeDB: Tool for Rapid Prediction of Enzymes Involved in Bioremediation from High-Throughput Metagenome Data Sets","volume":"27","author":"Balachandran","year":"2020","journal-title":"J. Comput. Biol."},{"key":"ref_149","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_150","first-page":"1","article-title":"Exploring Soil Microbiomes Through Metagenomic Analysis: Taxonomy and Function","volume":"4","year":"2025","journal-title":"Int. Sci. J. Eng. Manag."},{"key":"ref_151","doi-asserted-by":"crossref","first-page":"foaf045","DOI":"10.1093\/femsyr\/foaf045","article-title":"Evolution and Applications of Genome-Scale Metabolic Models in Yeast Systems Biology Studies","volume":"25","author":"He","year":"2025","journal-title":"FEMS Yeast Res."},{"key":"ref_152","doi-asserted-by":"crossref","unstructured":"Jiang, L., Song, M., Luo, C., Zhang, D., and Zhang, G. (2015). Novel Phenanthrene-Degrading Bacteria Identified by DNA-Stable Isotope Probing. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0130846"},{"key":"ref_153","doi-asserted-by":"crossref","first-page":"19232","DOI":"10.1038\/s41598-022-23728-2","article-title":"DNA Stable Isotope Probing on Soil Treated by Plant Biostimulation and Flooding Revealed the Bacterial Communities Involved in PCB Degradation","volume":"12","author":"Vergani","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"124197","DOI":"10.1016\/j.envpol.2024.124197","article-title":"Stable Isotopes and nanoSIMS Single-Cell Imaging Reveals Soil Plastisphere Colonizers Able to Assimilate Sulfamethoxazole","volume":"355","author":"Xiang","year":"2024","journal-title":"Environ. Pollut."},{"key":"ref_155","doi-asserted-by":"crossref","first-page":"lqaf037","DOI":"10.1093\/nargab\/lqaf037","article-title":"XenoBug: Machine Learning-Based Tool to Predict Pollutant-Degrading Enzymes from Environmental Metagenomes","volume":"7","author":"Malwe","year":"2025","journal-title":"NAR Genom. Bioinform."},{"key":"ref_156","doi-asserted-by":"crossref","first-page":"1138","DOI":"10.1016\/j.scitotenv.2018.12.145","article-title":"Carbamazepine, Triclocarban and Triclosan Biodegradation and the Phylotypes and Functional Genes Associated with Xenobiotic Degradation in Four Agricultural Soils","volume":"657","author":"Thelusmond","year":"2019","journal-title":"Sci. Total Environ."},{"key":"ref_157","doi-asserted-by":"crossref","unstructured":"Jeffries, T.C., Rayu, S., Nielsen, U.N., Lai, K., Ijaz, A., Nazaries, L., and Singh, B.K. (2018). Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated Soils. Front. Microbiol., 9.","DOI":"10.3389\/fmicb.2018.00147"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/7\/3111\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T04:29:45Z","timestamp":1775190585000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/7\/3111"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,29]]},"references-count":157,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2026,4]]}},"alternative-id":["ijms27073111"],"URL":"https:\/\/doi.org\/10.3390\/ijms27073111","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,29]]}}}