{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T09:15:01Z","timestamp":1773738901351,"version":"3.50.1"},"reference-count":66,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2025,2,14]],"date-time":"2025-02-14T00:00:00Z","timestamp":1739491200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"DOI":"10.13039\/100015911","name":"Joint Genome Institute","doi-asserted-by":"publisher","award":["1243"],"award-info":[{"award-number":["1243"]}],"id":[{"id":"10.13039\/100015911","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000097","name":"NIH National Center for Research Resources","doi-asserted-by":"crossref","award":["5P20RR016480-12"],"award-info":[{"award-number":["5P20RR016480-12"]}],"id":[{"id":"10.13039\/100000097","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["P20 GM103451-12"],"award-info":[{"award-number":["P20 GM103451-12"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>The North Railroad Avenue Plume (NRAP) Superfund site in New Mexico, USA exemplifies successful chlorinated solvent bioremediation. NRAP was the result of leakage from a dry-cleaning that operated for 37 years. The presence of tetrachloroethene biodegradation byproducts, organohalide respiring genera (OHRG), and reductive dehalogenase (<jats:italic>rdh<\/jats:italic>) genes detected in groundwater samples indicated that enhanced reductive dechlorination (ERD) was the remedy of choice. This was achieved through biostimulation by mixing emulsified vegetable oil into the contaminated aquifer. This report combines metagenomic techniques with site monitoring metadata to reveal new details of ERD. DNA extracts from groundwater samples collected prior to and at four, 23 and 39 months after remedy implementation were subjected to whole metagenome sequencing (WMS) and 16S rRNA gene amplicon (16S) analyses. The response of the indigenous NRAP microbiome to ERD protocols is consistent with results obtained from microcosms, dechlorinating consortia, and observations at other contaminated sites. WMS detects three times as many phyla and six times as many genera as 16S. Both techniques reveal abundance changes in <jats:italic>Dehalococcoides<\/jats:italic> and <jats:italic>Dehalobacter<\/jats:italic> that reflect organohalide form and availability. Methane was not detected before biostimulation but appeared afterwards, corresponding to an increase in methanogenic <jats:italic>Archaea<\/jats:italic>. Assembly of WMS reads produced scaffolds containing <jats:italic>rdh<\/jats:italic> genes from <jats:italic>Dehalococcoides<\/jats:italic>, <jats:italic>Dehalobacter<\/jats:italic>, <jats:italic>Dehalogenimonas<\/jats:italic>, <jats:italic>Desulfocarbo<\/jats:italic>, and <jats:italic>Desulfobacula<\/jats:italic>. Anaerobic and aerobic cometabolic organohalide degrading microbes that increase in abundance include methanogenic <jats:italic>Archaea<\/jats:italic>, methanotrophs, <jats:italic>Dechloromonas<\/jats:italic>, and <jats:italic>Xanthobacter<\/jats:italic>, some of which contain hydrolytic dehalogenase genes. Aerobic cometabolism may be supported by oxygen gradients existing in aquifer microenvironments or by microbes that produce O<jats:sub>2<\/jats:sub> via microbial dismutation. The NRAP model for successful ERD is consistent with the established pathway and identifies new taxa and processes that support this syntrophic process. This project explores the potential of metagenomic tools (MGT) as the next advancement in bioremediation.<\/jats:p>","DOI":"10.1371\/journal.pone.0306503","type":"journal-article","created":{"date-parts":[[2025,2,14]],"date-time":"2025-02-14T18:22:05Z","timestamp":1739557325000},"page":"e0306503","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Whole metagenome sequencing and 16S rRNA gene amplicon analyses reveal the complex microbiome responsible for the success of enhanced in-situ reductive dechlorination (ERD) of a tetrachloroethene-contaminated Superfund site"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9884-0440","authenticated-orcid":true,"given":"Rebecca A.","family":"Reiss","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter A.","family":"Guerra","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Oleg","family":"Makhnin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8310-7078","authenticated-orcid":true,"given":"Matthew","family":"Kellom","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2025,2,14]]},"reference":[{"key":"pone.0306503.ref001","doi-asserted-by":"crossref","first-page":"638082","DOI":"10.3389\/fpubh.2021.638082","article-title":"Perchloroethylene and dry cleaning: It\u2019s time to move the industry to safer alternatives","volume":"9","author":"DM Ceballos","year":"2021","journal-title":"Front Public Health"},{"issue":"1","key":"pone.0306503.ref002","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1353\/tech.2004.0022","article-title":"Recognizing emerging environmental problems: The case of chlorinated solvents in groundwater","volume":"45","author":"RE Jackson","year":"2004","journal-title":"Technol Cult"},{"key":"pone.0306503.ref003","unstructured":"Toxic Substances Portal. Agency for Toxic Substances and Disease Registry. Centers for Disease Control. 2023 [cited 7\/24\/2023]. https:\/\/wwwn.cdc.gov\/TSP\/index.aspx."},{"key":"pone.0306503.ref004","unstructured":"EPA. trans-1,2-Dichloroethylene: Integrated Risk Information System (IRIS); 2010 [https:\/\/iris.epa.gov\/ChemicalLanding\/&substance_nmbr=314."},{"key":"pone.0306503.ref005","unstructured":"EPA. cis-1,2-Dichloroethylene: Integrated Risk Information System (IRIS); 2010 [https:\/\/iris.epa.gov\/ChemicalLanding\/&substance_nmbr=418."},{"key":"pone.0306503.ref006","unstructured":"EPA. 1,1-Dichloroethylene (1,1-DCE): Integrated Risk Information System (IRIS); 2002 [https:\/\/cfpub.epa.gov\/ncea\/iris2\/chemicalLanding.cfm?substance_nmbr=39."},{"issue":"11","key":"pone.0306503.ref007","doi-asserted-by":"crossref","first-page":"2479","DOI":"10.1021\/es015611l","article-title":"Natural formation of vinyl chloride in the terrestrial environment","volume":"36","author":"F Keppler","year":"2002","journal-title":"Environ Sci Technol"},{"key":"pone.0306503.ref008","doi-asserted-by":"crossref","first-page":"3079","DOI":"10.3389\/fmicb.2018.03079","article-title":"Microbial synthesis and transformation of inorganic and organic chlorine compounds","volume":"9","author":"S Atashgahi","year":"2018","journal-title":"Front Microbiol"},{"issue":"5","key":"pone.0306503.ref009","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1111\/gbi.12513","article-title":"The biogeochemical cycling of chlorine","volume":"20","author":"TP Barnum","year":"2022","journal-title":"Geobiology"},{"issue":"8","key":"pone.0306503.ref010","doi-asserted-by":"crossref","first-page":"5619","DOI":"10.1021\/acs.chemrev.6b00571","article-title":"Enzymatic halogenation and dehalogenation reactions: pervasive and mechanistically diverse","volume":"117","author":"V Agarwal","year":"2017","journal-title":"Chemical Reviews"},{"key":"pone.0306503.ref011","doi-asserted-by":"crossref","first-page":"116332","DOI":"10.1016\/j.watres.2020.116332","article-title":"Natural attenuation of a chlorinated ethene plume discharging to a stream: Integrated assessment of hydrogeological, chemical and microbial interactions","volume":"186","author":"CB Ottosen","year":"2020","journal-title":"Water Research"},{"issue":"D1","key":"pone.0306503.ref012","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: The protein families database in 2021","volume":"49","author":"J Mistry","year":"2020","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"pone.0306503.ref013","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1128\/AEM.72.1.428-436.2006","article-title":"Growth of Dehalobacter and Dehalococcoides spp. during degradation of chlorinated ethanes","volume":"72","author":"A Grostern","year":"2006","journal-title":"Appl Environ Microbiol"},{"issue":"3","key":"pone.0306503.ref014","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1111\/1574-6976.12019","article-title":"Microbial syntrophy: interaction for the common good","volume":"37","author":"BEL Morris","year":"2013","journal-title":"FEMS Microbiology Reviews"},{"key":"pone.0306503.ref015","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/bs.ampbs.2019.02.007","article-title":"The electrifying physiology of Geobacter bacteria, 30 years on","volume":"74","author":"G Reguera","year":"2019","journal-title":"Adv Microb Physiol"},{"issue":"D1","key":"pone.0306503.ref016","doi-asserted-by":"crossref","first-page":"D957","DOI":"10.1093\/nar\/gkac974","article-title":"Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9","volume":"51","author":"S Mukherjee","year":"2022","journal-title":"Nucleic Acids Research"},{"issue":"3","key":"pone.0306503.ref017","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1099\/ijs.0.63408-0","article-title":"Reclassification of Trichlorobacter thiogenes as Geobacter thiogenes comb. nov","volume":"57","author":"KP Nevin","year":"2007","journal-title":"International Journal of Systematic and Evolutionary Microbiology"},{"issue":"18","key":"pone.0306503.ref018","doi-asserted-by":"crossref","first-page":"6630","DOI":"10.1128\/AEM.01535-12","article-title":"Unexpected specificity of interspecies cobamide transfer from Geobacter spp. to organohalide-respiring Dehalococcoides mccartyi strains","volume":"78","author":"J Yan","year":"2012","journal-title":"Appl Environ Microbiol"},{"issue":"5","key":"pone.0306503.ref019","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1007\/s11274-017-2258-x","article-title":"The organohalide-respiring bacterium Sulfurospirillum multivorans: a natural source for unusual cobamides","volume":"33","author":"T. Schubert","year":"2017","journal-title":"World J Microbiol Biotechnol"},{"issue":"5","key":"pone.0306503.ref020","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.2166\/wst.2022.068","article-title":"Interspecies transfer of biosynthetic cobalamin for complete dechlorination of trichloroethene by Dehalococcoides mccartyi","volume":"85","author":"H Li","year":"2022","journal-title":"Water Sci Technol"},{"issue":"15","key":"pone.0306503.ref021","doi-asserted-by":"crossref","first-page":"13262","DOI":"10.1007\/s11356-017-8867-y","article-title":"Microbial degradation of chloroethenes: a review","volume":"24","author":"I Dolinova","year":"2017","journal-title":"Environ Sci Pollut Res Int"},{"issue":"12","key":"pone.0306503.ref022","doi-asserted-by":"crossref","first-page":"2976","DOI":"10.1128\/aem.54.12.2976-2980.1988","article-title":"Dependence of tetrachloroethylene dechlorination on methanogenic substrate consumption by Methanosarcina sp. strain DCM","volume":"54","author":"BZ Fathepure","year":"1988","journal-title":"Appl Environ Microbiol"},{"key":"pone.0306503.ref023","doi-asserted-by":"crossref","first-page":"1053169","DOI":"10.3389\/fmicb.2022.1053169","article-title":"Recent advances and trends of trichloroethylene biodegradation: A critical review","volume":"13","author":"Z Wu","year":"2022","journal-title":"Front Microbiol"},{"issue":"9","key":"pone.0306503.ref024","doi-asserted-by":"crossref","first-page":"5917","DOI":"10.1021\/acs.est.0c08631","article-title":"Potential role of methanogens in microbial reductive dechlorination of organic chlorinated pollutants in situ","volume":"55","author":"J Yuan","year":"2021","journal-title":"Environ Sci Technol"},{"issue":"9","key":"pone.0306503.ref025","doi-asserted-by":"crossref","first-page":"2469","DOI":"10.1016\/j.biortech.2008.12.022","article-title":"Biodegradation of trichloroethylene (TCE) by methanotrophic community","volume":"100","author":"AK Shukla","year":"2009","journal-title":"Bioresour Technol"},{"issue":"2","key":"pone.0306503.ref026","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1007\/s10532-019-09875-w","article-title":"Evaluation of methanotrophic bacterial communities capable of biodegrading trichloroethene (TCE) in acidic aquifers","volume":"30","author":"Y Shao","year":"2019","journal-title":"Biodegradation"},{"key":"pone.0306503.ref027","doi-asserted-by":"crossref","first-page":"115431","DOI":"10.1016\/j.watres.2019.115431","article-title":"Potential for co-metabolic oxidation of TCE and evidence for its occurrence in a large-scale aquifer survey","volume":"171","author":"A Gafni","year":"2020","journal-title":"Water Res"},{"key":"pone.0306503.ref028","doi-asserted-by":"crossref","first-page":"116310","DOI":"10.1016\/j.watres.2020.116310","article-title":"Two distinct Dehalobacter strains sequentially dechlorinate 1,1,1-trichloroethane and 1,1-dichloroethane at a field site treated with granular zero valent iron and guar gum","volume":"186","author":"MI Yang","year":"2020","journal-title":"Water Res"},{"issue":"5","key":"pone.0306503.ref029","doi-asserted-by":"crossref","first-page":"728","DOI":"10.3390\/w13050728","article-title":"1,2-DCA natural attenuation evaluation in groundwater: Insight by dual isotope 13C\/37Cl and molecular analysis approach","volume":"13","author":"G Carpani","year":"2021","journal-title":"Water"},{"key":"pone.0306503.ref030","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/1475-2859-9-12","article-title":"Bacterial diversity and reductive dehalogenase redundancy in a 1,2-dichloroethane-degrading bacterial consortium enriched from a contaminated aquifer","volume":"9","author":"M Marzorati","year":"2010","journal-title":"Microb Cell Fact"},{"issue":"1","key":"pone.0306503.ref031","doi-asserted-by":"crossref","first-page":"3194","DOI":"10.1038\/s41467-023-38523-4","article-title":"Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems","volume":"14","author":"SE Ruff","year":"2023","journal-title":"Nat Commun"},{"key":"pone.0306503.ref032","unstructured":"EPA. First Five-Year Review Report for North Railroad Avenue Plume Superfund Site Espanola, Rio Arriba County, New Mexico. Report NMD986670156 Washington DC. U.S. Environmental Protection Agency, Region 6; 2010. https:\/\/semspub.epa.gov\/work\/HQ\/180310.pdf."},{"key":"pone.0306503.ref033","unstructured":"EPA. Second Five Year Review Report for North Railroad Avenue Plume Superfund Site Espa\u00f1ola Rio Arriba County, New Mexico. Report 9899774. Washington, DC. U.S. Environmental Protection Agency, Region 6; 2015. https:\/\/semspub.epa.gov\/work\/06\/9899774.pdf."},{"key":"pone.0306503.ref034","unstructured":"EPA. Third Five Year Review Report for North Railroad Avenue Plume Superfund Site Espa\u00f1ola Rio Arriba County, New Mexico. Report 100021780. Washington, DC. U.S. Environmental Protection Agency, Region 6; 2020. https:\/\/semspub.epa.gov\/work\/06\/100021780.pdf."},{"issue":"21","key":"pone.0306503.ref035","doi-asserted-by":"crossref","first-page":"10005","DOI":"10.3390\/app112110005","article-title":"In situ bioremediation of a chlorinated hydrocarbon plume: A superfund site field pilot test","volume":"11","author":"P Guerra","year":"2021","journal-title":"Applied Sciences"},{"key":"pone.0306503.ref036","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1186\/s40793-016-0209-z","article-title":"Metagenome phylogenetic profiling of microbial community evolution in a tetrachloroethene-contaminated aquifer responding to enhanced reductive dechlorination protocols","volume":"11","author":"RA Reiss","year":"2016","journal-title":"Stand Genomic Sci"},{"key":"pone.0306503.ref037","first-page":"83","volume-title":"Chlorinated Solvent Source Zone Remediation","author":"RA Deeb","year":"2014"},{"issue":"7459","key":"pone.0306503.ref038","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/nature12352","article-title":"Insights into the phylogeny and coding potential of microbial dark matter","volume":"499","author":"C Rinke","year":"2013","journal-title":"Nature"},{"issue":"8","key":"pone.0306503.ref039","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":"RM Bowers","year":"2017","journal-title":"Nat Biotechnol"},{"key":"pone.0306503.ref040","doi-asserted-by":"crossref","first-page":"13219","DOI":"10.1038\/ncomms13219","article-title":"Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system","volume":"7","author":"K Anantharaman","year":"2016","journal-title":"Nat Commun"},{"issue":"D1","key":"pone.0306503.ref041","doi-asserted-by":"crossref","first-page":"D723","DOI":"10.1093\/nar\/gkac976","article-title":"The IMG\/M data management and analysis system v.7: content updates and new features","volume":"51","author":"I-MA Chen","year":"2022","journal-title":"Nucleic Acids Research"},{"issue":"15","key":"pone.0306503.ref042","doi-asserted-by":"crossref","first-page":"5361","DOI":"10.1128\/AEM.00063-11","article-title":"Design and verification of a pangenome microarray oligonucleotide probe set for Dehalococcoides spp","volume":"77","author":"LA Hug","year":"2011","journal-title":"Appl Environ Microbiol"},{"key":"pone.0306503.ref043","volume":"1243","author":"RA Reiss","year":"2013","journal-title":"Whole metagenomic analysis of microbial community evolution within a tetrachloroethene-contaminated EPA Superfund site undergoing remediation by enhanced reductive dechlorination"},{"issue":"3","key":"pone.0306503.ref044","doi-asserted-by":"crossref","DOI":"10.1128\/mSystems.00804-20","article-title":"DOE JGI Metagenome Workflow","volume":"6","author":"A Clum","year":"2021","journal-title":"mSystems"},{"issue":"10","key":"pone.0306503.ref045","doi-asserted-by":"crossref","DOI":"10.1099\/ijsem.0.005056","article-title":"Valid publication of the names of forty-two phyla of prokaryotes","volume":"71","author":"A Oren","year":"2021","journal-title":"Int J Syst Evol Microbiol"},{"issue":"11","key":"pone.0306503.ref046","doi-asserted-by":"crossref","first-page":"5607","DOI":"10.1099\/ijsem.0.004332","article-title":"List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ","volume":"70","author":"AC Parte","year":"2020","journal-title":"Int J Syst Evol Microbiol"},{"issue":"17","key":"pone.0306503.ref047","doi-asserted-by":"crossref","first-page":"2271","DOI":"10.1093\/bioinformatics\/btp393","article-title":"IMG ER: a system for microbial genome annotation expert review and curation","volume":"25","author":"VM Markowitz","year":"2009","journal-title":"Bioinformatics"},{"issue":"12","key":"pone.0306503.ref048","doi-asserted-by":"crossref","first-page":"e0044322","DOI":"10.1128\/aem.00443-22","article-title":"Dehalogenation of chlorinated ethenes to ethene by a novel isolate, \"Candidatus Dehalogenimonas etheniformans\"","volume":"88","author":"G Chen","year":"2022","journal-title":"Appl Environ Microbiol"},{"key":"pone.0306503.ref049","doi-asserted-by":"crossref","first-page":"1806","DOI":"10.3389\/fmicb.2020.01806","article-title":"Methanosarcina acetivorans: A model for mechanistic understanding of aceticlastic and reverse methanogenesis","volume":"11","author":"JG Ferry","year":"2020","journal-title":"Front Microbiol"},{"issue":"4","key":"pone.0306503.ref050","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1021\/es00016a017","article-title":"Reductive dechlorination catalyzed by bacterial transition-metal coenzymes","volume":"25","author":"CJ Gantzer","year":"1991","journal-title":"Environ Sci Technol"},{"issue":"10","key":"pone.0306503.ref051","doi-asserted-by":"crossref","first-page":"5770","DOI":"10.1021\/es404122y","article-title":"Bioremediation of chlorinated ethenes in fractured bedrock and associated changes in dechlorinating and nondechlorinating microbial populations","volume":"48","author":"A P\u00e9rez-de-Mora","year":"2014","journal-title":"Environ Sci Technol"},{"key":"pone.0306503.ref052","doi-asserted-by":"crossref","first-page":"89","DOI":"10.3389\/fmicb.2019.00089","article-title":"Functional genes and bacterial communities during organohalide respiration of chloroethenes in microcosms of multi-contaminated groundwater","volume":"10","author":"L Hermon","year":"2019","journal-title":"Front Microbiol"},{"issue":"1","key":"pone.0306503.ref053","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1186\/1471-2164-13-200","article-title":"Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae","volume":"13","author":"DD Wagner","year":"2012","journal-title":"BMC Genomics"},{"issue":"8","key":"pone.0306503.ref054","doi-asserted-by":"crossref","first-page":"2850","DOI":"10.1128\/aem.62.8.2850-2853.1996","article-title":"Characterization of chloroethylene dehalogenation by cell extracts of Desulfomonile tiedjei and its relationship to chlorobenzoate dehalogenation","volume":"62","author":"GT Townsend","year":"1996","journal-title":"Appl Environ Microbiol"},{"key":"pone.0306503.ref055","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1007\/978-3-662-49875-0_15","volume-title":"Organohalide-Respiring Bacteria","author":"T Kruse","year":"2016"},{"issue":"3","key":"pone.0306503.ref056","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1016\/j.copbio.2013.02.014","article-title":"Genomic insights into organohalide respiration","volume":"24","author":"RE Richardson","year":"2013","journal-title":"Current Opinion in Biotechnology"},{"issue":"23","key":"pone.0306503.ref057","doi-asserted-by":"crossref","first-page":"3130","DOI":"10.1128\/JB.00419-16","article-title":"The MarR-type regulator Rdh2r regulates rdh gene transcription in Dehalococcoides mccartyi strain CBDB1","volume":"198","author":"L Krasper","year":"2016","journal-title":"J Bacteriol"},{"issue":"12","key":"pone.0306503.ref058","doi-asserted-by":"crossref","first-page":"8257","DOI":"10.1128\/AEM.71.12.8257-8264.2005","article-title":"Multiple reductive-dehalogenase-homologous genes are simultaneously transcribed during dechlorination by Dehalococcoides-containing cultures","volume":"71","author":"AS Waller","year":"2005","journal-title":"Appl Environ Microbiol"},{"issue":"3","key":"pone.0306503.ref059","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1039\/C9EM00605B","article-title":"Insights into origins and function of the unexplored majority of the reductive dehalogenase gene family as a result of genome assembly and ortholog group classification","volume":"22","author":"O Molenda","year":"2020","journal-title":"Environ Sci Process Impacts"},{"issue":"7","key":"pone.0306503.ref060","doi-asserted-by":"crossref","DOI":"10.1093\/femsec\/fiac067","article-title":"Combined read- and assembly-based metagenomics to reconstruct a Dehalococcoides mccartyi genome from PCB-contaminated sediments and evaluate functional differences among organohalide-respiring consortia in the presence of different halogenated contaminants","volume":"98","author":"JM Ewald","year":"2022","journal-title":"FEMS Microbiol Ecol"},{"issue":"4","key":"pone.0306503.ref061","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1038\/s41564-022-01319-1","article-title":"Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota","volume":"8","author":"CO Seymour","year":"2023","journal-title":"Nat 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