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Cited by 10Microbial bioremediation and biosurfactantsChromium effects and bioremediationEnvironmental remediation with nanomaterials

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Long-term survival of Dehalococcoides mccartyi strains in mixed cultures under electron acceptor and ammonium limitation

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Morson, Nadia, Molenda, Olivia, Picott, Katherine J, Richardson, Ruth E, Edwards, Elizabeth A·2022·FEMS Microbes
DOI 10.1093/femsmc/xtac021PMC PMC10117805

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Abstract

Few strains of Dehalococcoides mccartyi harbour and express the vinyl chloride reductase (VcrA) that catalyzes the dechlorination of vinyl chloride (VC), a carcinogenic soil and groundwater contaminant. The vcrA operon is found on a Genomic Island (GI) and, therefore, believed to participate in horizontal gene transfer (HGT). To try to induce HGT of the vcrA-GI, we blended two enrichment cultures in medium without ammonium while providing VC. We hypothesized that these conditions would select for a mutant strain of D. mccartyi that could both fix nitrogen and respire VC. However, after more than 4 years of incubation, we found no evidence for HGT of the vcrA-GI. Rather, we observed VC-dechlorinating activity attributed to the trichloroethene reductase TceA. Sequencing and protein modelling revealed a mutation in the predicted active site of TceA, which may have influenced substrate specificity. We also identified two nitrogen-fixing D. mccartyi strains in the KB-1 culture. The presence of multiple strains of D. mccartyi with distinct phenotypes is a feature of natural environments and certain enrichment cultures (such as KB-1), and may enhance bioaugmentation success. The fact that multiple distinct strains persist in the culture for decades and that we could not induce HGT of the vcrA-GI suggests that it is not as mobile as predicted, or that mobility is restricted in ways yet to be discovered to specific subclades of Dehalococcoides.

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Research works printed but not linked: 54

  1. Almagro Armenteros, 2019, SignalP 5.0 improves signal peptide predictions using deep neural networks, Nat Biotechnol, 37, 420, 10.1038/s41587-019-0036-z · DOI
  2. Birrell, 2016, Importance of hydrogen bonding in fine tuning the [2Fe-2S] cluster redox potential of HydC from Thermotoga maritima, Biochemistry, 55, 4344, 10.1021/acs.biochem.6b00341 · DOI
  3. Bommer, 2014, Structural basis for organohalide respiration, Science, 346, 455, 10.1126/science.1258118 · DOI
  4. Chen, 2010, MolProbity: all-atom structure validation for macromolecular crystallography, Acta Crystallogr Sect D Biol Crystallogr, 66, 12, 10.1107/S0907444909042073 · DOI · Paper page
  5. Chovancova, 2012, CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures, PLoS Comput Biol, 8, 23, 10.1371/journal.pcbi.1002708 · DOI
  6. Doherty, 2000, A history of the production and use of carbon tetrachloride, tetrachloroethylene, trichloroethylene and 1,1,1-trichloroethane in the United States: part 1 - historical background; carbon tetrachloride and tetrachloroethylene, Environ Forensics, 1, 69, 10.1006/enfo.2000.0010 · DOI
  7. Duhamel, 2007, Growth and yields of dechlorinators, acetogens, and methanogens during reductive dechlorination of chlorinated ethenes and dihaloelimination of 1,2-dichloroethane, Environ Sci Technol, 41, 2303, 10.1021/es062010r · DOI
  8. Duhamel, 2006, Microbial composition of chlorinated ethene-degrading cultures dominated by Dehalococcoides, FEMS Microbiol Ecol, 58, 538, 10.1111/j.1574-6941.2006.00191.x · DOI
  9. Duhamel, 2004, Characterization of a highly enriched Dehalococcoides - containing culture that grows on vinyl chloride and, Appl Environ Microbiol, 70, 5538, 10.1128/AEM.70.9.5538-5545.2004 · DOI
  10. Duhamel, 2002, Comparison of anaerobic dechlorinating enrichment cultures maintained on tetrachloroethene, trichloroethene, cis-dichloroethene and vinyl chloride, Water Res, 36, 4193, 10.1016/S0043-1354(02)00151-3 · DOI
  11. Edgar, 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, 32, 1792, 10.1093/nar/gkh340 · DOI · Paper page
  12. Edwards, 1994, Anaerobic degradation of toluene and o-xylene by a methanogenic consortium, Appl Environ Microbiol, 60, 313, 10.1128/aem.60.1.313-322.1994 · DOI
  13. Fennell, 1997, Comparison of butyric acid, ethanol, lactic acid, and propionic acid as hydrogen donors for the reductive dechlorination of tetrachloroethene, Environ Sci Technol, 31, 918, 10.1021/es960756r · DOI
  14. Field, 2016, Natural production of organohalide compounds in the environment, 7, 10.1007/978-3-662-49875-0_2 · DOI
  15. Freedman, 1989, Biological reductive dechlorination of tetrachloroethylene and trichloroethylene to ethylene under methanogenic conditions, Appl Environ Microbiol, 55, 2144, 10.1128/aem.55.9.2144-2151.1989 · DOI
  16. Fung, 2007, Expression of reductive dehalogenase genes in Dehalococcoides ethenogenes strain 195 growing on tetrachloroethene, trichloroethene, or 2,3-dichlorophenol, Appl Environ Microbiol, 73, 4439, 10.1128/AEM.00215-07 · DOI
  17. Hendrickson, 2002, Molecular analysis of Dehalococcoides 16S ribosomal DNA from throughout North America and Europe, Appl Environ Microbiol, 68, 485, 10.1128/AEM.68.2.485-495.2002 · DOI
  18. Hug, 2013, Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases, Philos Trans R Soc B Biol Sci, 368, 20120322, 10.1098/rstb.2012.0322 · DOI
  19. Johnson, 2008, Temporal transcriptomic microarray analysis of “Dehalococcoides ethenogenes” strain 195 during the transition into stationary phase, Appl Environ Microbiol, 74, 2864, 10.1128/AEM.02208-07 · DOI
  20. Kaya, 2019, Impact of fixed nitrogen availability on Dehalococcoides mccartyi reductive dechlorination activity, Environ Sci Technol, 53, 14548, 10.1021/acs.est.9b04463 · DOI
  21. Kearse, 2012, Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinformatics, 28, 1647, 10.1093/bioinformatics/bts199 · DOI
  22. Kelley, 2015, The phyre2 web portal for protein modeling, prediction and analysis, Nat Protoc, 10, 845, 10.1038/nprot.2015.053 · DOI · Paper page
  23. Kokkonen, 2019, Engineering enzyme access tunnels, Biotechnol Adv, 37, 107386, 10.1016/j.biotechadv.2019.04.008 · DOI
  24. Kube, 2005, Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1, Nat Biotechnol, 23, 1269, 10.1038/nbt1131 · DOI
  25. Langen, 1992, Protein control of iron-sulfur cluster redox potentials, J Biol Chem, 267, 25625, 10.1016/S0021-9258(18)35647-3 · DOI
  26. Lee, 2009, Evidence for nitrogen fixation by “Dehalococcoides ethenogenes” strain 195, Appl Environ Microbiol, 75, 7551, 10.1128/AEM.01886-09 · DOI
  27. Leigh, 2007, Nitrogen regulation in bacteria and archaea, Annu Rev Microbiol, 61, 349, 10.1146/annurev.micro.61.080706.093409 · DOI
  28. Liang, 2015, Identity and substrate specificity of reductive dehalogenases expressed in Dehalococcoides-containing enrichment cultures maintained on different chlorinated ethenes, Appl Environ Microbiol, 81, 4626, 10.1128/AEM.00536-15 · DOI
  29. Löffler, 2006, Harnessing microbial activities for environmental cleanup, Curr Opin Biotechnol, 17, 274, 10.1016/j.copbio.2006.05.001 · DOI
  30. Löffler, 2013, Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi, Int J Syst Evol Microbiol, 63, 625, 10.1099/ijs.0.034926-0 · DOI
  31. McMurdie, 2011, Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides, BMC Genomics, 12, 287, 10.1186/1471-2164-12-287 · DOI
  32. Major, 2002, Field demonstration of successful bioaugmentation to achieve dechlorination of tetrachloroethene to ethene, Environ Sci Technol, 36, 5106, 10.1021/es0255711 · DOI
  33. Molenda, 2020, 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, Environ Sci Process Impacts, 22, 663, 10.1039/C9EM00605B · DOI
  34. Molenda, 2016, Dehalogenimonas sp. strain WBC-2 genome and identification of its trans-dichloroethene reductive dehalogenase, tdrA, Appl Environ Microbiol, 82, 40, 10.1128/AEM.02017-15 · DOI
  35. Molenda, 2019, Extrachromosomal circular elements targeted by CRISPR-Cas in Dehalococcoides mccartyi are linked to mobilization of reductive dehalogenase genes, ISME J, 13, 24, 10.1038/s41396-018-0254-2 · DOI
  36. Moran, 2007, Chlorinated solvents in groundwater of the United States, Environ Sci Technol, 41, 74, 10.1021/es061553y · DOI
  37. Müller, 2004, Molecular identification of the catabolic vinyl chloride reductase from Dehalococcoides sp. strain VS and its environmental distribution, Appl Environ Microbiol, 70, 4880, 10.1128/AEM.70.8.4880-4888.2004 · DOI
  38. Perez-de-Mora, 2017, Chlorinated electron acceptor availability selects for specific Dehalococcoides populations in dechlorinating enrichment cultures and in groundwater, Front Microbiol, 44
  39. Pöritz, 2013, Genome sequences of two dehalogenation specialists - Dehalococcoides mccartyi strains BTF08 and DCMB5 enriched from the highly polluted bitterfeld region, FEMS Microbiol Lett, 343, 101, 10.1111/1574-6968.12160 · DOI
  40. Rahm, 2008, Dehalococcoides’ gene transcripts as quantitative bioindicators of tetrachloroethene, trichloroethene, and cis-1,2-dichloroethene dehalorespiration rates, Environ Sci Technol, 42, 5099, 10.1021/es702912t · DOI
  41. Raymond, 2004, The natural history of nitrogen fixation, Mol Biol Evol, 21, 541, 10.1093/molbev/msh047 · DOI
  42. Regeard, 2005, Indications for acquisition of reductive dehalogenase genes through horizontal gene transfer by Dehalococcoides ethenogenes strain 195, Appl Environ Microbiol, 71, 2955, 10.1128/AEM.71.6.2955-2961.2005 · DOI
  43. Roy, 2010, I-TASSER: a unified platform for automated protein structure and function prediction, Nat Protoc, 5, 725, 10.1038/nprot.2010.5 · DOI
  44. Smatlak, 1996, Comparative kinetics of hydrogen utilization for reductive dechlorination of tetrachloroethene and methanogenesis in an anaerobic enrichment culture, Environ Sci Technol, 30, 2850, 10.1021/es9602455 · DOI
  45. Song, 2013, High-resolution comparative modeling with RosettaCM, Structure, 21, 1735, 10.1016/j.str.2013.08.005 · DOI
  46. Stephens, 1996, Protein control of redox potentials of iron-sulfur proteins, Chem Rev, 96, 2491, 10.1021/cr950045w · DOI
  47. Studer, 2020, QMEANDisCo-distance constraints applied on model quality estimation, Bioinformatics, 36, 1765, 10.1093/bioinformatics/btz828 · DOI
  48. Sung, 2006, Quantitative PCR confirms purity of strain GT, a novel trichloroethene-to-ethene-respiring Dehalococcoides isolate, Appl Environ Microbiol, 72, 1980, 10.1128/AEM.72.3.1980-1987.2006 · DOI
  49. Tang, 2013, Functional characterization of reductive dehalogenases by using blue native polyacrylamide gel electrophoresis, Appl Environ Microbiol, 79, 974, 10.1128/AEM.01873-12 · DOI
  50. Trott, 2009, AutoDock vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading, J Comput Chem, 32, 174
  51. Untergasser, 2012, Primer3-new capabilities and interfaces, Nucleic Acids Res, 40, e115, 10.1093/nar/gks596 · DOI
  52. Waller, 2012, Transcriptional analysis of a Dehalococcoides-containing microbial consortium reveals prophage activation, Appl Environ Microbiol, 78, 1178, 10.1128/AEM.06416-11 · DOI
  53. Wang, 2014, Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls, Proc Natl Acad Sci, 111, 12103, 10.1073/pnas.1404845111 · DOI
  54. Yan, 2021, Respiratory vinyl chloride reductive dechlorination to ethene in TceA-expressing Dehalococcoides mccartyi, Environ Sci Technol, 55, 4831, 10.1021/acs.est.0c07354 · DOI

Metadata

Authors
Morson, N., Molenda, O., Picott, K. J., Richardson, R. E., & Edwards, E. A.
Affiliations
  • University of Toronto (CA)
  • Cornell University (US)
Corresponding author
Edwards, Elizabeth A
ORCID
Venue
FEMS Microbes
Publisher
Oxford University Press (OUP)
Published
2022
Volume
3
Pages
xtac021-xtac021
ISSN
2633-6685 (ISSN-L)
DOI
10.1093/femsmc/xtac021
PMC
PMC10117805
OpenAlex
W4284971694
Cited by
10
References
1
Citations by year
2026: 4 · 2025: 1 · 2024: 3 · 2023: 2
FWCI
0.36
Type
journal article
Language
en
Open access
Licence
Locations
  • FEMS Microbes (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Ontario Genomics Institute (2009-OGI-ABC-1405)
  • Natural Sciences and Engineering Research Council of Canada
  • Strategic Environmental Research and Development Program (W912HQ-07-C-0036, ER-1586)
Topics
  • Physical Sciences › Environmental Science › Pollution › Microbial bioremediation and biosurfactants
  • Physical Sciences › Environmental Science › Health, Toxicology and Mutagenesis › Chromium effects and bioremediation
  • Physical Sciences › Environmental Science › Environmental Engineering › Environmental remediation with nanomaterials
Keywords
Dehalococcoides mccartyi, genomic islands, horizontal gene transfer, nitrogen fixation, ammonium limitation, strain persistence, bioaugmentation

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