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Dehalococcoides

Dehalococcoides is a genus of bacteria within class Dehalococcoidia that obtain energy via the oxidation of hydrogen and subsequent reductive dehalogenation of halogenated organic compounds in a mode of anaerobic respiration called organohalide respiration.[2] They are well known for their great potential to remediate halogenated ethenes and aromatics. They are the only bacteria known to transform highly chlorinated dioxins, PCBs. In addition, they are the only known bacteria to transform tetrachloroethene (perchloroethene, PCE) to ethene.

Dehalococcoides
Scientific classification Edit this classification
Domain: Bacteria
Phylum: Chloroflexota
Class: Dehalococcoidia
Order: Dehalococcoidales
Family: Dehalococcoidaceae
Genus: Dehalococcoides
Löffler et al. 2013[1]
Type species
Dehalococcoides mccartyi
Löffler et al. 2013
Species
  • D. mccartyi Löffler et al. 2013
Synonyms
  • "Dehalococcoides" Maymo-Gatell et al. 1997
  • "Dehalococcoides ethenogenes" Maymo-Gatell et al. 1997

Microbiology

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The first member of the genus Dehalococcoides was described in 1997 as Dehalococcoides ethenogenes strain 195 (nom. inval.). Additional Dehalococcoides members were later described as strains CBDB1,[3] BAV1, FL2, VS, and GT. In 2012 all yet-isolated Dehalococcoides strains were summarized under the new taxonomic name D. mccartyi, with strain 195 as the type strain.[4]

GTDB release 202 clusters the genus into three species, all labeled Dehalococcoides mccartyi in their NCBI accession.[5]

Activities

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Dehalococcoides are obligately organohalide-respiring bacteria,[4] meaning that they can only grow by using halogenated compounds as electron acceptors. Currently, hydrogen (H2) is often regarded as the only known electron donor to support growth of dehalococcoides bacteria.[6][7][8] However, studies have shown that using various electron donors such as formate,[9] and methyl viologen,[7] have also been effective in promoting growth for various species of dehalococcoides. In order to perform reductive dehalogenation processes, electrons are transferred from electron donors through dehydrogenases, and ultimately used to reduce halogenated compounds,[4] many of which are human-synthesized chemicals acting as pollutants.[10] Furthermore, it has been shown that a majority of reductive dehalogenase activities lie within the extracellular and membranous components of D. ethenogenes, indicating that dechlorination processes may function semi-independently from intracellular systems.[7] Currently, all known dehalococcoides strains require acetate for producing cellular material, however, the underlying mechanisms are not well understood as they appear to lack fundamental enzymes that complete biosynthesis cycles found in other organisms.[8]

Dehalococcoides can transform many persistent compounds. This includes tetrachloroethylene (PCE) and trichloroethylene (TCE) which are transformed to ethylene, and chlorinated dioxins, vinyl chloride, benzenes, polychlorinated biphenyls (PCBs), phenols and many other aromatic contaminants.[11][12][13]

Applications

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Dehalococcoides can uniquely transform many highly toxic and/or persistent compounds that are not transformed by any other known bacteria, in addition to halogenated compounds that other common organohalide respirers use.[10][14] For example, common compounds such as chlorinated dioxins, benzenes, PCBs, phenols and many other aromatic substrates can be reduced into less harmful chemical forms.[10] However, dehalococcoides are currently the only known dechlorinating bacteria with the unique ability to degrade the highly recalcitrant, tetrachloroethene (PCE) and Trichloroethylene (TCE) compounds into more suitable for environmental conditions, and thus used in bioremediation.[10][15][9] Their capacity to grow by using contaminants allows them to proliferate in contaminated soil or groundwater, offering promise for in situ decontamination efforts.

The process of transforming halogenated pollutants to non-halogenated compounds involves different reductive enzymes. D. mccartyi strain BAV1 is able to reduce vinyl chloride, a contaminant that usually originates from landfills, to ethene by using a special vinyl chloride reductase thought to be coded for by the bvcA gene.[16] A chlorobenzene reductive dehalogenase has also been identified in the strain CBDB1.[17]

Several companies worldwide now use Dehalococcoides-containing mixed cultures in commercial remediation efforts. In mixed cultures, other bacteria present can augment the dehalogenation process by producing metabolic products that can be used by Dehalococcoides and others involved in the degradation process.[11][18] For example, Dehalococcoides sp. strain WL can work alongside Dehalobacter in a step-wise manner to degrade vinyl chloride: Dehalobacter converts 1,1,2-TCA to vinyl chloride, which is subsequently degraded by Dehalococcoides.[19] Also, the addition of electron acceptors is needed – they are converted to hydrogen in situ by other bacteria present, which can then be used as an electron source by Dehalococcoides.[14][11] MEAL (a methanol, ethanol, acetate, and lactate mixture) is documented to have been used as substrate.[20] In the US, BAV1 was patented for the in situ reductive dechlorination of vinyl chlorides and dichloroethylenes in 2007.[21] D. mccartyi in high-density dechlorinating bioflocs have also been used in ex situ bioremediation.[22]

Although dehalococcoides have been shown to reduce contaminants such as PCE and TCE, it appears that individual species have various dechlorinating capabilities which contributes to the degree that these compounds are reduced. This could have implications on the effects of bioremediation tactics.[15] For example, particular strains of dehalococcoides have shown preference to produce more soluble, intermediates such as 1,2–dichloroethene isomers and vinyl chloride that contrasts against bioremediation goals, primarily due to their harmful nature.[6][10] Therefore, an important aspect of current bioremediation tactics involves the use of multiple dechlorinating organisms to promote symbiotic relationships within a mixed culture to ensure complete reduction to ethene.[15] As a result, studies have focused upon metabolic pathways and environmental factors that regulate reductive dehalogenative processes in order to better implement dehalococcoides for bioremediation tactics.[10]

However, not all members of Dehalococcoides can reduce all halogenated contaminants. Certain strains cannot use PCE or TCE as electron acceptors (e.g. CBDB1) and some cannot use vinyl chloride as an electron acceptor (e.g. FL2).[16] D. mccartyi strains 195 and SFB93 are inhibited by high concentrations of acetylene (which builds up in contaminated groundwater sites as a result of TCE degradation) via changes in gene expression that likely disrupt normal electron transport chain function.[11] Even when D. mccartyi strains work well to turn toxic chemicals into harmless ones, treatment times range from months to decades.[23] When selecting Dehalococcoides strains for bioremediation use, it is important to consider their metabolic capabilities and their sensitivities to different chemicals.

In 2022, the United States National Aeronautics and Space Administration (NASA) co-funded a US$1.9 million multi-year project with Arizona State University, the University of Arizona, and the Florida Institute of Technology to reduce perchlorates (such as those found in the regolith of Mars) to a useful form of soil for growing plants.[23]

Genomes

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Several strains of Dehalococcoides sp. has been sequenced.[24][25][26] They contain between 14 and 36 reductive dehalogenase homologous (rdh) operons each consisting of a gene for the active dehalogenases (rdhA) and a gene for a putative membrane anchor (rdhB). Most rdh-operons in Dehalococcoides genomes are preceded by a regulator gene, either of the marR-type (rdhR) or a two-component system (rdhST). Dehalococcoides have very small genomes of about 1.4–1.5 Mio base pairs. This is one of the smallest values for free-living organisms.

Biochemistry

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Dehalococcoides strains do not seem to encode quinones but respire with a novel protein-bound electron transport chain.[27]

See also

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References

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  1. ^ Löffler FE, Yan J, Ritalahti KM, Adrian L, Edwards EA, Konstantinidis KT, Muller JA, Fullerton H, Zinder SH, Spormann AM. (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 (Pt 2): 625–635. doi:10.1099/ijs.0.034926-0. PMID 22544797.
  2. ^ "Dehalococcoides". NCIB Taxonomy Browser.
  3. ^ Adrian L, Szewzyk U, Wecke J, Görisch H (2000). "Bacterial dehalorespiration with chlorinated benzenes". Nature. 408 (6812): 580–583. Bibcode:2000Natur.408..580A. doi:10.1038/35046063. PMID 11117744. S2CID 4350003.
  4. ^ a b c Loffler, F. E.; Yan, J.; Ritalahti, K. M.; Adrian, L.; Edwards, E. A.; Konstantinidis, K. T.; Muller, J. A.; Fullerton, H.; Zinder, S. H.; Spormann, A. M. (2012). "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". International Journal of Systematic and Evolutionary Microbiology. 63 (Pt 2): 625–635. doi:10.1099/ijs.0.034926-0. ISSN 1466-5026. PMID 22544797.
  5. ^ "GTDB - Tree". gtdb.ecogenomic.org.
  6. ^ a b Cheng, Dan; He, Jianzhong (15 September 2009). "Isolation and Characterization of "Dehalococcoides" sp. Strain MB, Which Dechlorinates Tetrachloroethene to trans-1,2-Dichloroethene". Applied and Environmental Microbiology. 75 (18): 5910–5918. Bibcode:2009ApEnM..75.5910C. doi:10.1128/AEM.00767-09. PMC 2747852. PMID 19633106.
  7. ^ a b c Nijenhuis, Ivonne; Zinder, Stephen H. (1 March 2005). "Characterization of Hydrogenase and Reductive Dehalogenase Activities of Dehalococcoides ethenogenes Strain 195". Applied and Environmental Microbiology. 71 (3): 1664–1667. Bibcode:2005ApEnM..71.1664N. doi:10.1128/AEM.71.3.1664-1667.2005. PMC 1065153. PMID 15746376.
  8. ^ a b Tang, Yinjie J.; Yi, Shan; Zhuang, Wei-Qin; Zinder, Stephen H.; Keasling, Jay D.; Alvarez-Cohen, Lisa (15 August 2009). "Investigation of Carbon Metabolism in "Dehalococcoides ethenogenes" Strain 195 by Use of Isotopomer and Transcriptomic Analyses". Journal of Bacteriology. 191 (16): 5224–5231. doi:10.1128/JB.00085-09. PMC 2725585. PMID 19525347.
  9. ^ a b Mayer-Blackwell, Koshlan; Azizian, Mohammad F.; Green, Jennifer K.; Spormann, Alfred M.; Semprini, Lewis (7 February 2017). "Survival of Vinyl Chloride Respiring dehalococcoides mccartyi under Long-Term Electron Donor Limitation". Environmental Science & Technology. 51 (3): 1635–1642. Bibcode:2017EnST...51.1635M. doi:10.1021/acs.est.6b05050. PMID 28002948.
  10. ^ a b c d e f Maphosa, Farai; Lieten, Shakti H.; Dinkla, Inez; Stams, Alfons J.; Smidt, Hauke; Fennell, Donna E. (2 October 2012). "Ecogenomics of microbial communities in bioremediation of chlorinated contaminated sites". Frontiers in Microbiology. 3: 351. doi:10.3389/fmicb.2012.00351. PMC 3462421. PMID 23060869.
  11. ^ a b c d Mao, Xinwei; Oremland, Ronald S.; Liu, Tong; Gushgari, Sara; Landers, Abigail A.; Baesman, Shaun M.; Alvarez-Cohen, Lisa (2017-02-21). "Acetylene Fuels TCE Reductive Dechlorination by Defined Dehalococcoides/Pelobacter Consortia". Environmental Science & Technology. 51 (4): 2366–2372. Bibcode:2017EnST...51.2366M. doi:10.1021/acs.est.6b05770. ISSN 0013-936X. PMC 6436540. PMID 28075122.
  12. ^ Lu, Gui-Ning; Tao, Xue-Qin; Huang, Weilin; Dang, Zhi; Li, Zhong; Liu, Cong-Qiang (2010). "Dechlorination pathways of diverse chlorinated aromatic pollutants conducted by Dehalococcoides sp. strain CBDB1". Science of the Total Environment. 408 (12): 2549–2554. Bibcode:2010ScTEn.408.2549L. doi:10.1016/j.scitotenv.2010.03.003. PMID 20346484.
  13. ^ Fennell, Donna E.; Nijenhuis, Ivonne; Wilson, Susan F.; Zinder, Stephen H.; Häggblom, Max M. (2004-04-01). "Dehalococcoides ethenogenes Strain 195 Reductively Dechlorinates Diverse Chlorinated Aromatic Pollutants". Environmental Science & Technology. 38 (7): 2075–2081. Bibcode:2004EnST...38.2075F. doi:10.1021/es034989b. ISSN 0013-936X. PMID 15112809.
  14. ^ a b Maymó-Gatell, Xavier; Chien, Yueh-tyng; Gossett, James M.; Zinder, Stephen H. (1997-06-06). "Isolation of a Bacterium That Reductively Dechlorinates Tetrachloroethene to Ethene". Science. 276 (5318): 1568–1571. doi:10.1126/science.276.5318.1568. ISSN 0036-8075. PMID 9171062.
  15. ^ a b c Grostern, Ariel; Edwards, Elizabeth A. (2006). "Growth of Dehalobacter and Dehalococcoides spp. during Degradation of Chlorinated Ethanes". Applied and Environmental Microbiology. 72 (1): 428–436. Bibcode:2006ApEnM..72..428G. doi:10.1128/AEM.72.1.428-436.2006. PMC 1352275. PMID 16391074.
  16. ^ a b Krajmalnik-Brown, Rosa; Hölscher, Tina; Thomson, Ivy N.; Saunders, F. Michael; Ritalahti, Kirsti M.; Löffler, Frank E. (2004-10-01). "Genetic Identification of a Putative Vinyl Chloride Reductase in Dehalococcoides sp. Strain BAV1". Applied and Environmental Microbiology. 70 (10): 6347–6351. Bibcode:2004ApEnM..70.6347K. doi:10.1128/aem.70.10.6347-6351.2004. ISSN 0099-2240. PMC 522117. PMID 15466590.
  17. ^ Adrian, Lorenz; Rahnenführer, Jan; Gobom, Johan; Hölscher, Tina (2007-12-01). "Identification of a Chlorobenzene Reductive Dehalogenase in Dehalococcoides sp. Strain CBDB1". Applied and Environmental Microbiology. 73 (23): 7717–7724. Bibcode:2007ApEnM..73.7717A. doi:10.1128/aem.01649-07. ISSN 0099-2240. PMC 2168065. PMID 17933933.
  18. ^ Duhamel, Melanie; Edwards, Elizabeth A. (2006-12-01). "Microbial composition of chlorinated ethene-degrading cultures dominated by Dehalococcoides". FEMS Microbiology Ecology. 58 (3): 538–549. doi:10.1111/j.1574-6941.2006.00191.x. ISSN 0168-6496. PMID 17117995.
  19. ^ Grostern, Ariel; Edwards, Elizabeth A. (2006-01-01). "Growth of Dehalobacter and Dehalococcoides spp. during Degradation of Chlorinated Ethanes". Applied and Environmental Microbiology. 72 (1): 428–436. Bibcode:2006ApEnM..72..428G. doi:10.1128/aem.72.1.428-436.2006. ISSN 0099-2240. PMC 1352275. PMID 16391074.
  20. ^ McKinsey, P.C. (February 20, 2003). "Bioremediation of Trichloroethylene-Contaminated Sediments Augmented with a Dehalococcoides Consortia". Retrieved October 8, 2017.
  21. ^ Loeffler, Frank (May 3, 2007). "United States Patent Application 20070099284". Archived from the original on 2018-08-27. Retrieved 2017-10-09.
  22. ^ Fajardo-Williams, Devyn (2015). "Coupling Bioflocculation of Dehalococcoides to High-Dechlorination Rates for Ex situ and In situ Bioremediation". ProQuest. ProQuest 1718184775.
  23. ^ a b Brown, David W. (November 2024). "Red Mars, green Mars". MIT Technology Review. 127 (6). Massachusetts Institute of Technology: 24–26.
  24. ^ Kube, M.; Beck, A.; Zinder, SH.; Kuhl, H.; Reinhardt, R.; Adrian, L. (Oct 2005). "Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1". Nat Biotechnol. 23 (10): 1269–73. doi:10.1038/nbt1131. PMID 16116419.
  25. ^ Seshadri, R.; Adrian, L.; Fouts, DE.; Eisen, JA.; Phillippy, AM.; Methe, BA.; Ward, NL.; Nelson, WC.; et al. (Jan 2005). "Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes". Science. 307 (5706): 105–8. Bibcode:2005Sci...307..105S. doi:10.1126/science.1102226. PMID 15637277. S2CID 15601443.
  26. ^ Pöritz, M.; Goris, T.; Wubet, T.; Tarkka, MT.; Buscot, F.; Nijenhuis, I.; Lechner, U.; Adrian, L. (Jun 2013). "Genome sequences of two dehalogenation specialists – Dehalococcoides mccartyi strains BTF08 and DCMB5 enriched from the highly polluted Bitterfeld region". FEMS Microbiol Lett. 343 (2): 101–4. doi:10.1111/1574-6968.12160. PMID 23600617.
  27. ^ Kublik, Anja; Deobald, Darja; Hartwig, Stefanie; Schiffmann, Christian L.; Andrades, Adarelys; von Bergen, Martin; Sawers, R. Gary; Adrian, Lorenz (2016-09-01). "Identification of a multi-protein reductive dehalogenase complex in Dehalococcoides mccartyi strain CBDB1 suggests a protein-dependent respiratory electron transport chain obviating quinone involvement". Environmental Microbiology. 18 (9): 3044–3056. doi:10.1111/1462-2920.13200. ISSN 1462-2920. PMID 26718631.
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