{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,2]],"date-time":"2026-11-02T01:09:16Z","timestamp":1793581756145,"version":"4.5.0"},"reference-count":103,"publisher":"Elsevier BV","issue":"5","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T00:00:00Z","timestamp":1774396800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100021171","name":"Basic and Applied Basic Research Foundation of Guangdong Province","doi-asserted-by":"publisher","award":["2023B1515020077"],"award-info":[{"award-number":["2023B1515020077"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017610","name":"Shenzhen Science and Technology Innovation Program","doi-asserted-by":"publisher","award":["KCXFZ20240903092800002"],"award-info":[{"award-number":["KCXFZ20240903092800002"]}],"id":[{"id":"10.13039\/501100017610","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017610","name":"Shenzhen Science and Technology Innovation Program","doi-asserted-by":"publisher","award":["SYSPG20241211173609007"],"award-info":[{"award-number":["SYSPG20241211173609007"]}],"id":[{"id":"10.13039\/501100017610","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["52322007"],"award-info":[{"award-number":["52322007"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Fundamental Research"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.1016\/j.fmre.2026.03.011","type":"journal-article","created":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T01:21:02Z","timestamp":1774488062000},"page":"3188-3199","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"title":["Molecular bioindicators for assessing environmental impacts of emerging contaminants"],"prefix":"10.1016","volume":"6","author":[{"given":"Han-Lin","family":"Cui","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi-Jun","family":"Ren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ke","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li-Ying","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan-Qing","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1079-5754","authenticated-orcid":false,"given":"Shu-Hao","family":"Du","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shu-Hong","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ai-Jie","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1235-3498","authenticated-orcid":false,"given":"Bin","family":"Liang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"4","key":"10.1016\/j.fmre.2026.03.011_bib0001","article-title":"Emerging contaminants: A one health perspective","volume":"5","author":"Wang","year":"2024","journal-title":"Innovation"},{"key":"10.1016\/j.fmre.2026.03.011_bib0002","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1038\/s41893-025-01718-2","article-title":"Big data integration for environmental risk assessment of emerging contaminants","volume":"9","author":"Cui","year":"2026","journal-title":"Nat. Sustain."},{"issue":"7","key":"10.1016\/j.fmre.2026.03.011_bib0003","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1007\/s10646-018-1911-y","article-title":"Validity of fish, birds and mammals as surrogates for amphibians and reptiles in pesticide toxicity assessment","volume":"27","author":"Ortiz-Santaliestra","year":"2018","journal-title":"Ecotoxicology"},{"issue":"5","key":"10.1016\/j.fmre.2026.03.011_bib0004","doi-asserted-by":"crossref","first-page":"1459","DOI":"10.1128\/AEM.03351-12","article-title":"Molecular fingerprinting of cyanobacteria from river biofilms as a water quality monitoring tool","volume":"79","author":"Loza","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.fmre.2026.03.011_bib0005","doi-asserted-by":"crossref","DOI":"10.1016\/j.watres.2020.116767","article-title":"Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring","volume":"191","author":"Sagova-Mareckova","year":"2021","journal-title":"Water Res."},{"issue":"7","key":"10.1016\/j.fmre.2026.03.011_bib0006","doi-asserted-by":"crossref","first-page":"3842","DOI":"10.1021\/acs.est.7b06494","article-title":"Omics advances in ecotoxicology","volume":"52","author":"Zhang","year":"2018","journal-title":"Environ. Sci. Technol."},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0007","doi-asserted-by":"crossref","first-page":"5281","DOI":"10.1038\/s41467-020-19006-2","article-title":"Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance","volume":"11","author":"Herold","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.fmre.2026.03.011_bib0008","doi-asserted-by":"crossref","DOI":"10.1016\/j.biotechadv.2024.108458","article-title":"Microbiome regulation for sustainable wastewater treatment","volume":"77","author":"Shi","year":"2024","journal-title":"Biotechnol. Adv."},{"issue":"6278","key":"10.1016\/j.fmre.2026.03.011_bib0009","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1126\/science.aad6359","article-title":"A bacterium that degrades and assimilates poly (ethylene terephthalate)","volume":"351","author":"Yoshida","year":"2016","journal-title":"Science"},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0010","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1021\/acs.est.6b04885","article-title":"Functional characterization of a novel amidase involved in biotransformation of Triclocarban and its dehalogenated congeners in Ochrobactrum sp. TCC-2","volume":"51","author":"Yun","year":"2017","journal-title":"Environ. Sci. Technol."},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0011","doi-asserted-by":"crossref","first-page":"7850","DOI":"10.1038\/s41467-022-35237-x","article-title":"Sourcing thermotolerant poly(ethylene terephthalate) hydrolase scaffolds from natural diversity","volume":"13","author":"Erickson","year":"2022","journal-title":"Nat. Commun."},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0012","doi-asserted-by":"crossref","DOI":"10.1128\/aem.01547-22","article-title":"Molecular mechanism of chloramphenicol and thiamphenicol resistance mediated by a novel oxidase, CmO, in sphingomonadaceae","volume":"89","author":"Ma","year":"2023","journal-title":"Appl. Environ. Microbiol."},{"issue":"6","key":"10.1016\/j.fmre.2026.03.011_bib0013","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1038\/s41589-018-0052-1","article-title":"Shared strategies for \u03b2-lactam catabolism in the soil microbiome","volume":"14","author":"Crofts","year":"2018","journal-title":"Nat. Chem. Biol."},{"issue":"6476","key":"10.1016\/j.fmre.2026.03.011_bib0014","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1126\/science.aay3164","article-title":"The exposome and health: Where chemistry meets biology","volume":"367","author":"Vermeulen","year":"2020","journal-title":"Science"},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0015","article-title":"Roles of Hsp70s in stress responses of microorganisms, plants, and animals","volume":"2015","author":"Yu","year":"2015","journal-title":"Biomed. Res. Int."},{"issue":"3","key":"10.1016\/j.fmre.2026.03.011_bib0016","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1002\/ieam.1530","article-title":"The role of biomarkers in the assessment of aquatic ecosystem health","volume":"10","author":"Hook","year":"2014","journal-title":"Integr. Environ. Assess. Manag."},{"issue":"9","key":"10.1016\/j.fmre.2026.03.011_bib0017","doi-asserted-by":"crossref","first-page":"5612","DOI":"10.1021\/acs.chemrev.2c00644","article-title":"Enzymes\u2019 Power for plastics degradation","volume":"123","author":"Tournier","year":"2023","journal-title":"Chem. Rev."},{"key":"10.1016\/j.fmre.2026.03.011_bib0018","doi-asserted-by":"crossref","DOI":"10.1016\/j.copbio.2024.103170","article-title":"Bacterial degradation of perfluoroalkyl acids","volume":"88","author":"Smorada","year":"2024","journal-title":"Curr. Opin. Biotechnol."},{"issue":"7998","key":"10.1016\/j.fmre.2026.03.011_bib0019","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1038\/s41586-023-06955-z","article-title":"Functional and evolutionary significance of unknown genes from uncultivated taxa","volume":"626","author":"Rodr\u00edguez del R\u00edo","year":"2024","journal-title":"Nature"},{"key":"10.1016\/j.fmre.2026.03.011_bib0020","doi-asserted-by":"crossref","DOI":"10.1016\/j.watres.2026.125619","article-title":"PDG_DB: A comprehensive database unveils environmental distribution patterns of plastic-degrading genes via large-scale multi-omic data analysis","volume":"296","author":"Zhang","year":"2026","journal-title":"Water Res."},{"issue":"D1","key":"10.1016\/j.fmre.2026.03.011_bib0021","doi-asserted-by":"crossref","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: Expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database","volume":"51","author":"Alcock","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.fmre.2026.03.011_bib0022","doi-asserted-by":"crossref","DOI":"10.1016\/j.ecolind.2024.112723","article-title":"Soil macrofauna are important bioindicators of soil quality in agroecosystems under different management","volume":"167","author":"Mamabolo","year":"2024","journal-title":"Ecol. Indic."},{"issue":"6525","key":"10.1016\/j.fmre.2026.03.011_bib0023","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1126\/science.abd6951","article-title":"A ubiquitous tire rubber\u2013derived chemical induces acute mortality in coho salmon","volume":"371","author":"Tian","year":"2021","journal-title":"Science"},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0024","doi-asserted-by":"crossref","first-page":"2817","DOI":"10.1038\/s41467-024-46663-4","article-title":"Data-driven identification of predictive risk biomarkers for subgroups of osteoarthritis using interpretable machine learning","volume":"15","author":"Nielsen","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.fmre.2026.03.011_bib0025","doi-asserted-by":"crossref","DOI":"10.1016\/j.compbiolchem.2024.108268","article-title":"Key genes and pathways in the molecular landscape of pancreatic ductal adenocarcinoma: A bioinformatics and machine learning study","volume":"113","author":"Eyuboglu","year":"2024","journal-title":"Comput. Biol. Chem."},{"issue":"3","key":"10.1016\/j.fmre.2026.03.011_bib0026","doi-asserted-by":"crossref","DOI":"10.1016\/j.jece.2025.116637","article-title":"The distribution of functional nitrogen cycle gene in river and their response to nitrogen concentrations","volume":"13","author":"He","year":"2025","journal-title":"J. Environ. Chem. Eng."},{"key":"10.1016\/j.fmre.2026.03.011_bib0027","doi-asserted-by":"crossref","DOI":"10.1016\/j.ecolind.2023.110369","article-title":"Influence of microplastic-associated biofilms on the bioavailability of a mixture of cadmium and benzo[a]pyrene by the analysis of biomarker gene expression in larval zebrafish","volume":"152","author":"Di Natale","year":"2023","journal-title":"Ecol. Indic."},{"issue":"6476","key":"10.1016\/j.fmre.2026.03.011_bib0028","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1126\/science.aay6636","article-title":"Tracking complex mixtures of chemicals in our changing environment","volume":"367","author":"Escher","year":"2020","journal-title":"Science"},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0029","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1038\/s41545-020-00086-y","article-title":"Emerging contaminants affect the microbiome of water systems\u2014strategies for their mitigation","volume":"3","author":"Gomes","year":"2020","journal-title":"npj Clean Water"},{"issue":"19","key":"10.1016\/j.fmre.2026.03.011_bib0030","doi-asserted-by":"crossref","first-page":"7490","DOI":"10.1021\/acs.est.2c08732","article-title":"Complementary biotransformation of antimicrobial triclocarban obviously mitigates nitrous oxide emission toward sustainable microbial denitrification","volume":"57","author":"Zhang","year":"2023","journal-title":"Environ. Sci. Technol."},{"issue":"13","key":"10.1016\/j.fmre.2026.03.011_bib0031","doi-asserted-by":"crossref","first-page":"2937","DOI":"10.1111\/mec.15472","article-title":"Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap","volume":"30","author":"Cordier","year":"2021","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.fmre.2026.03.011_bib0032","doi-asserted-by":"crossref","DOI":"10.1016\/j.aquatox.2021.106035","article-title":"Relationships between gene transcription and contaminant concentrations in Baltic ringed seals: A comparison between tissue matrices","volume":"242","author":"Ometere Boyi","year":"2022","journal-title":"Aquatic Toxicol."},{"key":"10.1016\/j.fmre.2026.03.011_bib0033","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1016\/j.scitotenv.2018.05.403","article-title":"Diclofenac, carbamazepine and triclocarban biodegradation in agricultural soils and the microorganisms and metabolic pathways affected","volume":"640","author":"Thelusmond","year":"2018","journal-title":"Sci. Total Environ."},{"issue":"2","key":"10.1016\/j.fmre.2026.03.011_bib0034","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1093\/toxsci\/kfx097","article-title":"The role of omics in the application of adverse outcome pathways for chemical risk assessment","volume":"158","author":"Brockmeier","year":"2017","journal-title":"Toxicol. Sci."},{"issue":"3","key":"10.1016\/j.fmre.2026.03.011_bib0035","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1002\/etc.34","article-title":"Adverse outcome pathways: A conceptual framework to support ecotoxicology research and risk assessment","volume":"29","author":"Ankley","year":"2010","journal-title":"Environ. Toxicol. Chem."},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0036","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1038\/s42004-024-01154-x","article-title":"The reaction mechanism of the Ideonella sakaiensis PETase enzyme","volume":"7","author":"Burgin","year":"2024","journal-title":"Commun. Chem."},{"issue":"5","key":"10.1016\/j.fmre.2026.03.011_bib0037","doi-asserted-by":"crossref","first-page":"3270","DOI":"10.1021\/acs.est.0c06687","article-title":"Microbial interactions drive the complete catabolism of the antibiotic sulfamethoxazole in activated sludge microbiomes","volume":"55","author":"Qi","year":"2021","journal-title":"Environ. Sci. Technol."},{"issue":"31","key":"10.1016\/j.fmre.2026.03.011_bib0038","doi-asserted-by":"crossref","first-page":"13833","DOI":"10.1021\/acs.est.4c02845","article-title":"Triclosan dioxygenase: A novel two-component Rieske Nonheme iron ring-hydroxylating dioxygenase initiates Triclosan degradation","volume":"58","author":"Yin","year":"2024","journal-title":"Environ. Sci. Technol."},{"issue":"12","key":"10.1016\/j.fmre.2026.03.011_bib0039","doi-asserted-by":"crossref","first-page":"4268","DOI":"10.1128\/AEM.02457-10","article-title":"Facilitation of bacterial adaptation to chlorothalonil-contaminated sites by horizontal transfer of the chlorothalonil hydrolytic dehalogenase gene","volume":"77","author":"Liang","year":"2011","journal-title":"Appl. Environ. Microbiol."},{"issue":"6","key":"10.1016\/j.fmre.2026.03.011_bib0040","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1111\/mmi.12332","article-title":"Molecular characterization of the enzymes involved in the degradation of a brominated aromatic herbicide","volume":"89","author":"Chen","year":"2013","journal-title":"Mol. Microbiol."},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0041","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-019-46901-6","article-title":"Targeted detection of Dehalococcoides mccartyi microbial protein biomarkers as indicators of reductive dechlorination activity in contaminated groundwater","volume":"9","author":"Solis","year":"2019","journal-title":"Sci. Rep."},{"key":"10.1016\/j.fmre.2026.03.011_bib0042","doi-asserted-by":"crossref","DOI":"10.1016\/j.envpol.2022.119326","article-title":"Effects of heavy metals pollution on the co-selection of metal and antibiotic resistance in urban rivers in UK and India","volume":"306","author":"Gupta","year":"2022","journal-title":"Environ. Pollut."},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0043","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/ismej.2014.106","article-title":"Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology","volume":"9","author":"Gibson","year":"2014","journal-title":"ISME J."},{"key":"10.1016\/j.fmre.2026.03.011_bib0044","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1016\/j.envpol.2017.10.061","article-title":"Ecological risk assessment of a contaminated stream using multi-level integrated biomarker response in Carassius auratus","volume":"233","author":"Samanta","year":"2018","journal-title":"Environ. Pollut."},{"key":"10.1016\/j.fmre.2026.03.011_bib0045","doi-asserted-by":"crossref","DOI":"10.1016\/j.marpolbul.2024.116398","article-title":"Biochemical and molecular biomarkers and their association with anthropogenic chemicals in wintering Manx shearwaters (Puffinus puffinus)","volume":"203","author":"Serafini","year":"2024","journal-title":"Mar. Pollut. Bull."},{"key":"10.1016\/j.fmre.2026.03.011_bib0046","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1016\/j.aquatox.2013.09.010","article-title":"Transcription patterns of genes encoding four metallothionein homologs in Daphnia pulex exposed to copper and cadmium are time- and homolog-dependent","volume":"142-143","author":"Asselman","year":"2013","journal-title":"Aquatic Toxicol."},{"key":"10.1016\/j.fmre.2026.03.011_bib0047","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1016\/j.envpol.2019.02.056","article-title":"The utility of vitellogenin as a biomarker of estrogenic endocrine disrupting chemicals in molluscs","volume":"248","author":"Tran","year":"2019","journal-title":"Environ. Pollut."},{"key":"10.1016\/j.fmre.2026.03.011_bib0048","doi-asserted-by":"crossref","DOI":"10.1016\/j.marenvres.2021.105315","article-title":"Vitellogenin gene expression in marine mussels exposed to ethinylestradiol: No induction at the transcriptional level","volume":"168","author":"Fern\u00e1ndez-Gonz\u00e1lez","year":"2021","journal-title":"Mar. Environ. Res."},{"key":"10.1016\/j.fmre.2026.03.011_bib0049","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1007\/s10646-025-02920-w","article-title":"Quantification of soil microbial functional genes as potential new method in environmental risk assessment of pesticides","volume":"34","author":"Stache","year":"2025","journal-title":"Ecotoxicology"},{"key":"10.1016\/j.fmre.2026.03.011_bib0050","doi-asserted-by":"crossref","DOI":"10.1016\/j.marpolbul.2020.111621","article-title":"Effects of environmental factors on denitrifying bacteria and functional genes in sediments of Bohai Sea, China","volume":"160","author":"Chen","year":"2020","journal-title":"Mar. Pollut. Bull."},{"key":"10.1016\/j.fmre.2026.03.011_bib0051","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2024.177057","article-title":"Effects of warming and fertilization on nirK-, nirS- and nosZ-type denitrifier communities in paddy soil","volume":"955","author":"Deng","year":"2024","journal-title":"Sci. Total Environ."},{"issue":"9","key":"10.1016\/j.fmre.2026.03.011_bib0052","doi-asserted-by":"crossref","first-page":"5957","DOI":"10.1128\/AEM.00439-06","article-title":"Abundance of narG, nirS, nirK, and nosZ genes of denitrifying bacteria during primary successions of a glacier foreland","volume":"72","author":"Kandeler","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.fmre.2026.03.011_bib0053","doi-asserted-by":"crossref","DOI":"10.1016\/j.jhazmat.2022.129281","article-title":"Antibiotics sulfamethoxazole alter nitrous oxide production and pathways in estuarine sediments: Evidenced by the N15-O18 isotopes tracing","volume":"437","author":"Chen","year":"2022","journal-title":"J. Hazard. Mater."},{"key":"10.1016\/j.fmre.2026.03.011_bib0054","doi-asserted-by":"crossref","first-page":"baac008","DOI":"10.1093\/database\/baac008","article-title":"PlasticDB: A database of microorganisms and proteins linked to plastic biodegradation","volume":"2022","author":"Gambarini","year":"2022","journal-title":"Database"},{"key":"10.1016\/j.fmre.2026.03.011_bib0055","doi-asserted-by":"crossref","first-page":"fuae031","DOI":"10.1093\/femsre\/fuae031","article-title":"Microbial functional diversity and redundancy: Moving forward","volume":"49","author":"Ramond","year":"2024","journal-title":"FEMS Microbiol. Rev."},{"issue":"7553","key":"10.1016\/j.fmre.2026.03.011_bib0056","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1038\/nature14485","article-title":"Counteraction of antibiotic production and degradation stabilizes microbial communities","volume":"521","author":"Kelsic","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.fmre.2026.03.011_bib0057","doi-asserted-by":"crossref","DOI":"10.1016\/j.jhazmat.2023.132644","article-title":"Integrated transcriptomic and biochemical characterization of the mechanisms governing stress responses in soil-dwelling invertebrate (Folsomia candida) upon exposure to dibutyl phthalate","volume":"462","author":"Zheng","year":"2024","journal-title":"J. Hazard. Mater."},{"issue":"3","key":"10.1016\/j.fmre.2026.03.011_bib0058","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1093\/bfgp\/elx021","article-title":"The differential expression of Chironomus spp genes as useful tools in the search for pollution biomarkers in freshwater ecosystems","volume":"17","author":"Mantilla","year":"2017","journal-title":"Brief. Funct. Genomics"},{"issue":"10","key":"10.1016\/j.fmre.2026.03.011_bib0059","doi-asserted-by":"crossref","first-page":"e00104","DOI":"10.1128\/AEM.00104-17","article-title":"Degradation of diphenyl ether in sphingobium phenoxybenzoativorans SC_3 is initiated by a novel ring cleavage dioxygenase","volume":"83","author":"Cai","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0060","doi-asserted-by":"crossref","DOI":"10.1038\/srep38430","article-title":"Insights into functional and evolutionary analysis of carbaryl metabolic pathway from Pseudomonas sp. strain C5pp","volume":"6","author":"Trivedi","year":"2016","journal-title":"Sci. Rep."},{"issue":"13","key":"10.1016\/j.fmre.2026.03.011_bib0061","doi-asserted-by":"crossref","first-page":"3774","DOI":"10.1128\/AEM.00046-16","article-title":"Identification of a third Mn(II) oxidase enzyme in Pseudomonas putida GB-1","volume":"82","author":"Geszvain","year":"2016","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.fmre.2026.03.011_bib0062","doi-asserted-by":"crossref","first-page":"2625","DOI":"10.1007\/s00253-013-5207-0","article-title":"Isolation, transposon mutagenesis, and characterization of the novel nicotine-degrading strain Shinella sp. HZN7","volume":"98","author":"Ma","year":"2014","journal-title":"Appl. Microbiol. Biotechnol."},{"issue":"24","key":"10.1016\/j.fmre.2026.03.011_bib0063","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."},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0064","doi-asserted-by":"crossref","first-page":"10.25.1","DOI":"10.1002\/0471142727.mb1025s88","article-title":"Preparation of proteins and peptides for mass spectrometry analysis in a bottom-up proteomics workflow","volume":"90","author":"Gundry","year":"2010","journal-title":"Curr. Protoc. Mol. Biol."},{"issue":"6","key":"10.1016\/j.fmre.2026.03.011_bib0065","doi-asserted-by":"crossref","first-page":"2182","DOI":"10.1128\/AEM.03764-14","article-title":"Involvement of the cytochrome P450 system EthBAD in the N-deethoxymethylation of acetochlor by Rhodococcus sp. strain T3-1","volume":"81","author":"Wang","year":"2015","journal-title":"Appl. Environ. Microbiol."},{"issue":"24","key":"10.1016\/j.fmre.2026.03.011_bib0066","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/elps.202100163","article-title":"Affinity monolith chromatography: A review of general principles and recent developments","volume":"42","author":"Poddar","year":"2021","journal-title":"Electrophoresis"},{"issue":"11","key":"10.1016\/j.fmre.2026.03.011_bib0067","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1016\/j.jgg.2024.08.011","article-title":"Whole-genome sequencing identifies functional genes for environmental adaptation in Chinese sheep","volume":"51","author":"Niu","year":"2024","journal-title":"J. Genet. Genomics"},{"issue":"2","key":"10.1016\/j.fmre.2026.03.011_bib0068","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1007\/s10142-021-00768-x","article-title":"Whole-genome sequencing, genome mining, metabolic reconstruction and evolution of pentachlorophenol and other xenobiotic degradation pathways in Bacillus tropicus strain AOA-CPS1","volume":"21","author":"Aregbesola","year":"2021","journal-title":"Funct. Integr. Genomics"},{"issue":"W1","key":"10.1016\/j.fmre.2026.03.011_bib0069","doi-asserted-by":"crossref","first-page":"W81","DOI":"10.1093\/nar\/gkz310","article-title":"antiSMASH 5.0: Updates to the secondary metabolite genome mining pipeline","volume":"47","author":"Blin","year":"2019","journal-title":"Nucleic Acids Res."},{"issue":"4","key":"10.1016\/j.fmre.2026.03.011_bib0070","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.01822-22","article-title":"Whole-genome sequencing of a chlorimuron-ethyl-degrading strain: Chenggangzhangella methanolivorans CHL1 and its degrading enzymes","volume":"10","author":"Yu","year":"2022","journal-title":"Microbiol. Spectr."},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0071","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST server: Rapid annotations using subsystems technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"issue":"5","key":"10.1016\/j.fmre.2026.03.011_bib0072","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1038\/s41396-017-0040-6","article-title":"Novel hydrogenases from deep-sea hydrothermal vent metagenomes identified by a recently developed activity-based screen","volume":"12","author":"Adam","year":"2018","journal-title":"ISME J."},{"issue":"11","key":"10.1016\/j.fmre.2026.03.011_bib0073","doi-asserted-by":"crossref","DOI":"10.1128\/AEM.00170-21","article-title":"Coinducible catabolism of 1-naphthol via synergistic regulation of the initial hydroxylase genes in Sphingobium sp. strain B2","volume":"87","author":"Huang","year":"2021","journal-title":"Appl. Environ. Microbiol."},{"issue":"4","key":"10.1016\/j.fmre.2026.03.011_bib0074","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1038\/s41396-021-01139-x","article-title":"Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane","volume":"16","author":"McKay","year":"2022","journal-title":"ISME J."},{"issue":"11","key":"10.1016\/j.fmre.2026.03.011_bib0075","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1038\/s41564-017-0012-7","article-title":"Recovery of nearly 8000 metagenome-assembled genomes substantially expands the tree of life","volume":"2","author":"Parks","year":"2017","journal-title":"Nat. Microbiol."},{"issue":"10","key":"10.1016\/j.fmre.2026.03.011_bib0076","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btv033","article-title":"MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"issue":"5","key":"10.1016\/j.fmre.2026.03.011_bib0077","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1101\/gr.213959.116","article-title":"metaSPAdes: A new versatile metagenomic assembler","volume":"27","author":"Nurk","year":"2017","journal-title":"Genome Res."},{"issue":"8","key":"10.1016\/j.fmre.2026.03.011_bib0078","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/nbt.3893","article-title":"Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea","volume":"35","author":"Bowers","year":"2017","journal-title":"Nat. Biotechnol."},{"issue":"7","key":"10.1016\/j.fmre.2026.03.011_bib0079","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1038\/s41564-018-0171-1","article-title":"Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy","volume":"3","author":"Sieber","year":"2018","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.fmre.2026.03.011_bib0080","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2020.140435","article-title":"Exploring novel Cr(VI) remediation genes for Cr(VI)-contaminated industrial wastewater treatment by comparative metatranscriptomics and metagenomics","volume":"742","author":"Pei","year":"2020","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.fmre.2026.03.011_bib0081","doi-asserted-by":"crossref","DOI":"10.1016\/j.envpol.2022.120772","article-title":"Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation","volume":"317","author":"Dell\u2019Anno","year":"2023","journal-title":"Environ. Pollut."},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0082","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: Prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"issue":"D1","key":"10.1016\/j.fmre.2026.03.011_bib0083","doi-asserted-by":"crossref","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Huerta-Cepas","year":"2018","journal-title":"Nucleic Acids Res."},{"issue":"16","key":"10.1016\/j.fmre.2026.03.011_bib0084","doi-asserted-by":"crossref","first-page":"8883","DOI":"10.1093\/nar\/gkaa621","article-title":"DRAM for distilling microbial metabolism to automate the curation of microbiome function","volume":"48","author":"Shaffer","year":"2020","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0085","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1186\/s40168-019-0670-1","article-title":"Identification and reconstruction of novel antibiotic resistance genes from metagenomes","volume":"7","author":"Berglund","year":"2019","journal-title":"Microbiome"},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0086","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/s40168-018-0401-z","article-title":"DeepARG: A deep learning approach for predicting antibiotic resistance genes from metagenomic data","volume":"6","author":"Arango-Argoty","year":"2018","journal-title":"Microbiome"},{"issue":"4","key":"10.1016\/j.fmre.2026.03.011_bib0087","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"Patro","year":"2017","journal-title":"Nat. Methods"},{"issue":"3","key":"10.1016\/j.fmre.2026.03.011_bib0088","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"issue":"5","key":"10.1016\/j.fmre.2026.03.011_bib0089","doi-asserted-by":"crossref","DOI":"10.1002\/imt2.70075","article-title":"Unveiling soil microbial diversity through ultra-deep short-read metagenomic sequencing and co-assembly","volume":"4","author":"Johansen","year":"2025","journal-title":"iMeta"},{"issue":"9","key":"10.1016\/j.fmre.2026.03.011_bib0090","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1038\/nbt.3935","article-title":"Shotgun metagenomics, from sampling to analysis","volume":"35","author":"Quince","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.fmre.2026.03.011_bib0091","doi-asserted-by":"crossref","DOI":"10.1016\/j.chemosphere.2021.129566","article-title":"Metagenomics analysis identifies nitrogen metabolic pathway in bioremediation of diesel contaminated soil","volume":"271","author":"Gao","year":"2021","journal-title":"Chemosphere"},{"key":"10.1016\/j.fmre.2026.03.011_bib0092","doi-asserted-by":"crossref","DOI":"10.1038\/s41587-023-02033-x","article-title":"Discovery of sparse, reliable omic biomarkers with stabl","author":"H\u00e9dou","year":"2024","journal-title":"Nat. Biotechnol."},{"issue":"6","key":"10.1016\/j.fmre.2026.03.011_bib0093","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1038\/s41587-022-01226-0","article-title":"Identification of antimicrobial peptides from the human gut microbiome using deep learning","volume":"40","author":"Ma","year":"2022","journal-title":"Nat. Biotechnol."},{"issue":"2","key":"10.1016\/j.fmre.2026.03.011_bib0094","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1038\/s41564-017-0062-x","article-title":"Detecting macroecological patterns in bacterial communities across independent studies of global soils","volume":"3","author":"Ramirez","year":"2018","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.fmre.2026.03.011_bib0095","doi-asserted-by":"crossref","first-page":"baaf013","DOI":"10.1093\/database\/baaf013","article-title":"Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database","volume":"2025","author":"Wiegers","year":"2025","journal-title":"Database"},{"issue":"1","key":"10.1016\/j.fmre.2026.03.011_bib0096","doi-asserted-by":"crossref","first-page":"vbag028","DOI":"10.1093\/bioadv\/vbag028","article-title":"Empowering biological knowledgebases: Advances in human-in-the-loop AI-driven literature curation","volume":"6","author":"Wood","year":"2026","journal-title":"Bioinformatics Adv."},{"key":"10.1016\/j.fmre.2026.03.011_bib0097","doi-asserted-by":"crossref","DOI":"10.1016\/j.watres.2023.119981","article-title":"Predictive in silico models for aquatic toxicity of cosmetic and personal care additive mixtures","volume":"236","author":"Yang","year":"2023","journal-title":"Water Res."},{"issue":"7873","key":"10.1016\/j.fmre.2026.03.011_bib0098","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"issue":"3","key":"10.1016\/j.fmre.2026.03.011_bib0099","doi-asserted-by":"crossref","DOI":"10.1002\/qub2.70002","article-title":"Revolutionizing multi-omics analysis with artificial intelligence and data processing","volume":"13","author":"Yetgin","year":"2025","journal-title":"Quant. Biol."},{"issue":"D1","key":"10.1016\/j.fmre.2026.03.011_bib0100","doi-asserted-by":"crossref","first-page":"D693","DOI":"10.1093\/nar\/gkab1016","article-title":"Rhea, the reaction knowledgebase in 2022","volume":"50","author":"Bansal","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.fmre.2026.03.011_bib0101","doi-asserted-by":"crossref","first-page":"baz119","DOI":"10.1093\/database\/baz119","article-title":"PMBD: A comprehensive plastics microbial biodegradation database","volume":"2019","author":"Gan","year":"2019","journal-title":"Database"},{"issue":"D1","key":"10.1016\/j.fmre.2026.03.011_bib0102","doi-asserted-by":"crossref","first-page":"D445","DOI":"10.1093\/nar\/gkz862","article-title":"The MetaCyc database of metabolic pathways and enzymes - a 2019 update","volume":"48","author":"Caspi","year":"2019","journal-title":"Nucleic Acids Res."},{"issue":"D1","key":"10.1016\/j.fmre.2026.03.011_bib0103","doi-asserted-by":"crossref","first-page":"D457","DOI":"10.1093\/nar\/gkv1070","article-title":"KEGG as a reference resource for gene and protein annotation","volume":"44","author":"Kanehisa","year":"2015","journal-title":"Nucleic Acids Res."}],"container-title":["Fundamental Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667325826001883?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667325826001883?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T21:59:05Z","timestamp":1790805545000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2667325826001883"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":103,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2026,9]]}},"alternative-id":["S2667325826001883"],"URL":"https:\/\/doi.org\/10.1016\/j.fmre.2026.03.011","relation":{},"ISSN":["2667-3258"],"issn-type":[{"value":"2667-3258","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Molecular bioindicators for assessing environmental impacts of emerging contaminants","name":"articletitle","label":"Article Title"},{"value":"Fundamental Research","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.fmre.2026.03.011","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Publishing Services by Elsevier B.V. on behalf of KeAi Communications Co. Ltd.","name":"copyright","label":"Copyright"}]}}