{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T12:18:46Z","timestamp":1791893926478,"version":"4.3.4"},"reference-count":61,"publisher":"American Society for Microbiology","issue":"6","license":[{"start":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T00:00:00Z","timestamp":1718668800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/doi.org\/10.1128\/ASMCopyrightv2"},{"start":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T00:00:00Z","timestamp":1718668800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100008762","name":"Genome Canada","doi-asserted-by":"crossref","award":["BCB 285MPR"],"award-info":[{"award-number":["BCB 285MPR"]}],"id":[{"id":"10.13039\/100008762","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Canadian Government | Natural Sciences and Engineering Research Council of Canada","award":["CGS-D"],"award-info":[{"award-number":["CGS-D"]}]},{"DOI":"10.13039\/100013873","name":"Government of Ontario","doi-asserted-by":"crossref","award":["OGS"],"award-info":[{"award-number":["OGS"]}],"id":[{"id":"10.13039\/100013873","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Canadian Government | Natural Sciences and Engineering Research Council of Canada","award":["Discovery"],"award-info":[{"award-number":["Discovery"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2024,6,18]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Chloroform (CF) and dichloromethane (DCM) are groundwater contaminants of concern due to their high toxicity and inhibition of important biogeochemical processes such as methanogenesis. Anaerobic biotransformation of CF and DCM has been well documented but typically independently of one another. CF is the electron acceptor for certain organohalide-respiring bacteria that use reductive dehalogenases (RDases) to dechlorinate CF to DCM. In contrast, known DCM degraders use DCM as their electron donor, which is oxidized using a series of methyltransferases and associated proteins encoded by the\n                      <jats:italic>mec<\/jats:italic>\n                      cassette to facilitate the entry of DCM to the Wood\u2013Ljungdahl pathway. The SC05 culture is an enrichment culture sold commercially for bioaugmentation, which transforms CF via DCM to CO\n                      <jats:sub>2<\/jats:sub>\n                      . This culture has the unique ability to dechlorinate CF to DCM using electron equivalents provided by the oxidation of DCM to CO\n                      <jats:sub>2<\/jats:sub>\n                      . Here, we use metagenomic and metaproteomic analyses to identify the functional genes involved in each of these transformations. Though 91 metagenome-assembled genomes were assembled, the genes for an RDase\u2014named\n                      <jats:italic>acdA<\/jats:italic>\n                      \u2014and a complete\n                      <jats:italic>mec<\/jats:italic>\n                      cassette were found to be encoded on a single contig belonging to\n                      <jats:italic>Dehalobacter<\/jats:italic>\n                      . AcdA and critical Mec proteins were also highly expressed by the culture. Heterologously expressed AcdA dechlorinated CF and other chloroalkanes but had 100-fold lower activity on DCM. Overall, the high expression of Mec proteins and the activity of AcdA suggest a\n                      <jats:italic>Dehalobacter<\/jats:italic>\n                      capable of dechlorination of CF to DCM and subsequent mineralization of DCM using the\n                      <jats:italic>mec<\/jats:italic>\n                      cassette.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Chloroform (CF) and dichloromethane (DCM) are regulated groundwater contaminants. A cost-effective approach to remove these pollutants from contaminated groundwater is to employ microbes that transform CF and DCM as part of their metabolism, thus depleting the contamination as the microbes continue to grow. In this work, we investigate bioaugmentation culture SC05, a mixed microbial consortium that effectively and simultaneously degrades both CF and DCM coupled to the growth of\n                      <jats:italic>Dehalobacter<\/jats:italic>\n                      . We identified the functional genes responsible for the transformation of CF and DCM in SC05. These genetic biomarkers provide a means to monitor the remediation process in the field.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/aem.00732-24","type":"journal-article","created":{"date-parts":[[2024,5,31]],"date-time":"2024-05-31T09:00:30Z","timestamp":1717146030000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":18,"title":["From\n                    <i>mec<\/i>\n                    cassette to\n                    <i>rdhA<\/i>\n                    : a key\n                    <i>Dehalobacter<\/i>\n                    genomic neighborhood in a chloroform and dichloromethane\u2013transforming microbial consortium"],"prefix":"10.1128","volume":"90","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1691-6892","authenticated-orcid":false,"given":"Olivia","family":"Bulka","sequence":"first","affiliation":[{"name":"Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3525-2366","authenticated-orcid":true,"given":"Katherine","family":"Picott","sequence":"additional","affiliation":[{"name":"Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Radhakrishnan","family":"Mahadevan","sequence":"additional","affiliation":[{"name":"Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8071-338X","authenticated-orcid":true,"given":"Elizabeth A.","family":"Edwards","sequence":"additional","affiliation":[{"name":"Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada"},{"name":"Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1007\/s11157-014-9345-3"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4419-1401-9_1"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1002\/j.1551-8833.1974.tb02129.x"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-211-99323-1"},{"key":"e_1_3_4_6_2","unstructured":"Agency for Toxic Substances and Disease Registry (ATSDR). 1997. Toxicological profile for chloroform. Atlanta GA"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1289\/ehp.1308030"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/s0043-1354(02)00151-3"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.copbio.2006.05.001"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6941.2000.tb00696.x"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2009.02150.x"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.13287"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00253-017-8236-2"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.biotechadv.2018.03.018"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.12387"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ese.2022.100199"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1021\/es403582f"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2021.152659"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2012.0322"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1039\/c9em00605b"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01873-12"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1111\/1751-7915.12745"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1111\/1462-2920.16464"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.1111\/gcb.16068"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.64.2.646-650.1998"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1007\/s002030050362"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.7775"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-020-00881-y"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1007\/s11356-023-28144-1"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-019-0579-5"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.07325-11"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.syapm.2016.12.001"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2011.02656.x"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.est.3c06686"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01970-21"},{"key":"e_1_3_4_36_2","article-title":"Metagenomic sequences from two subcultures of an anaerobic chloroform and dichloromethane degrading microbial community","author":"Bulka O","year":"2024","unstructured":"Bulka O, Edwards EA. 2024. Metagenomic sequences from two subcultures of an anaerobic chloroform and dichloromethane degrading microbial community. Microbiol Resour Announc (Submitted.)","journal-title":"Microbiol Resour Announc (Submitted.)"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.1319"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2016.00100"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.4056\/sigs.3787426"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/femsec\/fiac072"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.est.8b03717"},{"key":"e_1_3_4_42_2","volume-title":"Battelle 2023 Bioremediation Symposium","author":"Picott K","year":"2023","unstructured":"Picott K, Bowers C, Edwards EA. 2023. Tools for the characterization and manipulation of reductive dehalogenases for bioremediation of chlorinated solvents Battelle 2023 Bioremediation Symposium"},{"key":"e_1_3_4_43_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01993-21"},{"key":"e_1_3_4_44_2","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.001039"},{"key":"e_1_3_4_45_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01269-06"},{"key":"e_1_3_4_46_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-018-0333-4"},{"key":"e_1_3_4_47_2","doi-asserted-by":"publisher","DOI":"10.1098\/rstb.2012.0325"},{"key":"e_1_3_4_48_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10532-013-9662-1"},{"key":"e_1_3_4_49_2","doi-asserted-by":"publisher","DOI":"10.1021\/es4044769"},{"key":"e_1_3_4_50_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1074675"},{"key":"e_1_3_4_51_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00115297"},{"key":"e_1_3_4_52_2","doi-asserted-by":"publisher","DOI":"10.1007\/s002030050577"},{"key":"e_1_3_4_53_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_3_4_54_2","volume-title":"FastQC. A quality control tool for high throughput sequence data","author":"Andrews S","year":"2010","unstructured":"Andrews S, Krueger F, Seconds-Pichon A, Biggins F, Wingett S. 2010. FastQC. A quality control tool for high throughput sequence data. Babraham Bioinformatics."},{"key":"e_1_3_4_55_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv688"},{"key":"e_1_3_4_56_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-020-00834-3"},{"key":"e_1_3_4_57_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02195-w"},{"key":"e_1_3_4_58_2","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2019.00999"},{"key":"e_1_3_4_59_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_3_4_60_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-13-299"},{"key":"e_1_3_4_61_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.biochem.7b01205"},{"key":"e_1_3_4_62_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00496-19"}],"container-title":["Applied and Environmental Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/aem.00732-24","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/aem.00732-24","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T09:06:24Z","timestamp":1718701584000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/aem.00732-24"}},"subtitle":[],"editor":[{"given":"Pablo Ivan","family":"Nikel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2024,6,18]]},"references-count":61,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2024,6,18]]}},"alternative-id":["10.1128\/aem.00732-24"],"URL":"https:\/\/doi.org\/10.1128\/aem.00732-24","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.11.10.566631","asserted-by":"object"}]},"ISSN":["0099-2240","1098-5336"],"issn-type":[{"value":"0099-2240","type":"print"},{"value":"1098-5336","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,6,18]]},"assertion":[{"value":"2024-04-16","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-05-20","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-05-31","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00732-24"}}