{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T17:26:35Z","timestamp":1790702795569,"version":"4.1.0"},"reference-count":102,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,12,7]],"date-time":"2022-12-07T00:00:00Z","timestamp":1670371200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["LP160100610"],"award-info":[{"award-number":["LP160100610"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Dichloromethane (DCM; CH\n                    <jats:sub>2<\/jats:sub>\n                    Cl\n                    <jats:sub>2<\/jats:sub>\n                    ) is a widespread pollutant with anthropogenic and natural sources. Anaerobic DCM-dechlorinating bacteria use the Wood\u2013Ljungdahl pathway, yet dechlorination reaction mechanisms remain unclear and the enzyme(s) responsible for carbon-chlorine bond cleavage have not been definitively identified. Of the three bacterial taxa known to carry out anaerobic dechlorination of DCM, \u2018\n                    <jats:italic>Candidatus<\/jats:italic>\n                    Formimonas warabiya\u2019 strain DCMF is the only organism that can also ferment non-chlorinated substrates, including quaternary amines (i.e., choline and glycine betaine) and methanol. Strain DCMF is present within enrichment culture DFE, which was derived from an organochlorine-contaminated aquifer. We utilized the metabolic versatility of strain DCMF to carry out comparative metaproteomics of cultures grown with DCM or glycine betaine. This revealed differential abundance of numerous proteins, including a methyltransferase gene cluster (the\n                    <jats:italic>mec<\/jats:italic>\n                    cassette) that was significantly more abundant during DCM degradation, as well as highly conserved amongst anaerobic DCM-degrading bacteria. This lends strong support to its involvement in DCM dechlorination. A putative glycine betaine methyltransferase was also discovered, adding to the limited knowledge about the fate of this widespread osmolyte in anoxic subsurface environments. Furthermore, the metagenome of enrichment culture DFE was assembled, resulting in five high quality and two low quality draft metagenome-assembled genomes. Metaproteogenomic analysis did not reveal any genes or proteins for utilization of DCM or glycine betaine in the cohabiting bacteria, supporting the previously held idea that they persist\n                    <jats:italic>via<\/jats:italic>\n                    necromass utilization.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2022.1035247","type":"journal-article","created":{"date-parts":[[2022,12,7]],"date-time":"2022-12-07T00:08:28Z","timestamp":1670371708000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":7,"title":["Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by \u2018Candidatus Formimonas warabiya\u2019 strain DCMF"],"prefix":"10.3389","volume":"13","author":[{"given":"Sophie I.","family":"Holland","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xabier","family":"V\u00e1zquez-Campos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haluk","family":"Ertan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard J.","family":"Edwards","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael J.","family":"Manefield","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2022,12,7]]},"reference":[{"key":"ref1","volume-title":"Toxicological profile for methylene chloride","year":"2000"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"2805","DOI":"10.1093\/bioinformatics\/bti418","article-title":"MEDS and PocR are novel domains with a predicted role in sensing simple hydrocarbon derivatives in prokaryotic signal transduction systems","volume":"21","author":"Anantharaman","year":"2005","journal-title":"Bioinformatics"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1186\/s40168-019-0665-y","article-title":"Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data","volume":"7","author":"Arumugam","year":"2019","journal-title":"Microbiome"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/0010-406X(67)90109-0","article-title":"The species distribution of some naturally occurring quaternary ammonium compounds","volume":"21","author":"Beers","year":"1967","journal-title":"Comp. 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