CoChat
Sign Up
PreprintCited by 10Microbial bioremediation and biosurfactantsChromium effects and bioremediationEnvironmental remediation with nanomaterials

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

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

Open access
Morson, Nadia, Molenda, Olivia, Picott, Katherine J., Richardson, Ruth E., Edwards, Elizabeth A.·2020·FEMS Microbes
DOI 10.1101/2020.12.18.423565PMC PMC10117805

Preprint — published as 10.1093/femsmc/xtac021 · Paper page

Open this paper in CoChat — free accountOpen PDF

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. To try to induce horizontal gene transfer 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 horizontal gene transfer 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 horizontal gene transfer 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 sub-clades of Dehalococcoides . TOC Art:

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2020.12.18.423565

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 54

  1. 10.1038/s41587-019-0036-z · DOI
  2. 10.1021/acs.biochem.6b00341 · DOI
  3. 10.1126/science.1258118 · DOI
  4. 10.1107/S0907444909042073 · DOI · Paper page
  5. 10.1371/journal.pcbi.1002708 · DOI
  6. 10.1006/enfo.2000.0010 · DOI
  7. 10.1111/j.1574-6941.2006.00191.x · DOI
  8. 10.1021/es062010r · DOI
  9. 10.1128/AEM.70.9.5538-5545.2004 · DOI
  10. 10.1016/S0043-1354(02)00151-3 · DOI
  11. 10.1093/nar/gkh340 · DOI · Paper page
  12. 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. 10.1021/es960756r · DOI
  14. Field JA . Natural production of organohalide compounds in the environment. In: Loffler FE , Adrian L (eds.). Organohalide-Respiring Bacteria. Berlin, Heidelberg: Springer Berlin Heidelberg, 2016, 7–30. · DOI
  15. 10.1128/AEM.55.9.2144-2151.1989 · DOI
  16. 10.1128/AEM.00215-07 · DOI
  17. 10.1128/AEM.68.2.485-495.2002 · DOI
  18. 10.1098/rstb.2012.0322 · DOI
  19. 10.1128/AEM.02208-07 · DOI
  20. 2019, Impact of Fixed Nitrogen Availability on Dehalococcoides mccartyi Reductive Dechlorination Activity, Environ Sci Technol, 53, 14548, 10.1021/acs.est.9b04463 · DOI
  21. 10.1093/bioinformatics/bts199 · DOI
  22. 10.1038/nprot.2015.053 · DOI · Paper page
  23. 2019, Engineering enzyme access tunnels, Biotechnol Adv, 37, 107386, 10.1016/j.biotechadv.2019.04.008 · DOI
  24. 10.1038/nbt1131 · DOI
  25. 1992, Protein control of iron-sulfur cluster redox potentials, J Biol Chem, 267, 25625, 10.1016/S0021-9258(18)35647-3 · DOI
  26. 10.1128/AEM.01886-09 · DOI
  27. 10.1146/annurev.micro.61.080706.093409 · DOI
  28. 10.1128/AEM.00536-15 · DOI
  29. 10.1016/j.copbio.2006.05.001 · DOI
  30. 10.1099/ijs.0.034926-0 · DOI
  31. 10.1021/es0255711 · DOI
  32. 10.1186/1471-2164-12-287 · DOI
  33. 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. 10.1128/AEM.02017-15 · DOI
  35. 10.1038/s41396-018-0254-2 · DOI
  36. 10.1021/es061553y · DOI
  37. 10.1128/AEM.70.8.4880-4888.2004 · DOI
  38. Perez-de-Mora A , Lacourt A , McMaster ML et al. Chlorinated electron acceptor availability selects for specific Dehalococcoides populations in dechlorinating enrichment cultures and in groundwater. 2017:44. · DOI
  39. 10.1111/1574-6968.12160 · DOI
  40. 10.1021/es702912t · DOI
  41. 10.1093/molbev/msh047 · DOI
  42. 10.1128/AEM.71.6.2955-2961.2005 · DOI
  43. 10.1038/nprot.2010.5 · DOI
  44. 10.1021/es9602455 · DOI
  45. 10.1016/j.str.2013.08.005 · DOI
  46. 10.1021/cr950045w · DOI
  47. 10.1093/bioinformatics/btz828 · DOI
  48. 10.1128/AEM.72.3.1980-1987.2006 · DOI
  49. 10.1128/AEM.01873-12 · DOI
  50. 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. 10.1093/nar/gkr648 · DOI
  52. 10.1128/AEM.06416-11 · DOI
  53. 10.1073/pnas.1404845111 · DOI
  54. 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
openRxiv
Published
2020-12-20
Volume
3
Pages
xtac021-xtac021
ISSN
2633-6685 (ISSN-L)
DOI
10.1101/2020.12.18.423565
PMC
PMC10117805
OpenAlex
W4284971694
Cited by
10
References
1
Citations by year
2026: 4 · 2025: 1 · 2024: 3 · 2023: 2
FWCI
0.35
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
  • U.S. Department of Defense
  • Genome Canada (2009-OGI-ABC-1405)
  • Ontario Genomics
  • Government of Ontario (ORF-GL2)
  • Government of Canada
  • Ontario Genomics Institute (2009‐OGI‐ABC‐1405)
  • University of Toronto
  • Strategic Environmental Research and Development Program (W912HQ-07-C-0036, ER-1586)
  • Natural Sciences and Engineering Research Council of Canada (2009-OGI-ABC-1405)
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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review