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

Volumn 63, Issue PART2, 2013, Pages 625-635

  Löffler, Frank E ^a,b,c   Yan, Jun ^a,b   Ritalahti, Kirsti M ^a,c   Adrian, Lorenz ^d   Edwards, Elizabeth A ^e   Konstantinidis, Konstantinos T ^f   Müller, Jochen A ^d   Fullerton, Heather ^g   Zinder, Stephen H ^g   Spormann, Alfred M ^h  

^a UNIVERSITY OF TENNESSEE   (United States)

^b University of Tennessee Knoxville   (United States)

^c OAK RIDGE NATIONAL LABORATORY   (United States)

^d HELMHOLTZ CENTRE FOR ENVIRONMENTAL RESEARCH UFZ   (Germany)

^e UNIVERSITY OF TORONTO   (Canada)

^f Georgia Institute of Technology   (United States)

^g Department of Obstetrics Gynecology   (United States)

^h STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

8 (5 HEXYL 2 FURYL)OCTANOATE; 9 (5 PENTYL 2 FURYL)NONANOATE; ACETIC ACID; BROMINE; CHLORINE; FATTY ACID; FURAN DERIVATIVE; HALOGEN; HYDROGEN; ORGANOHALOGEN DERIVATIVE; RNA 16S; SOLVENT; UNCLASSIFIED DRUG;

ANAEROBIC BACTERIUM; AQUIFER; ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL METABOLISM; BACTERIAL STRAIN; BACTERIUM ISOLATE; BIOREMEDIATION; CARBON SOURCE; CHLOROFLEXI; CLASSIFICATION; CONCENTRATION (PARAMETERS); CONTAMINATION; CONTROLLED STUDY; DEBROMINATION; DECHLORINATION; DEHALOCOCCOIDACEAE; DEHALOCOCCOIDALES; DEHALOCOCCOIDES MCCARTYI; DEHALOCOCCOIDIA CLASSIS; DNA BASE COMPOSITION; MORPHOLOGY; NEW GENUS; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYLUM; PRIORITY JOURNAL; RIVER; RNA GENE; RNA SEQUENCE; SEDIMENT; SEQUENCE HOMOLOGY; SLUDGE; TAXONOMIC IDENTIFICATION; TEMPERATURE;

BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; BIODEGRADATION, ENVIRONMENTAL; CHLOROFLEXI; DNA, BACTERIAL; FATTY ACIDS; HALOGENS; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEWAGE;

EID: 84874041126     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.034926-0     Document Type: Article

References (51)

1. Adrian, L., Szewzyk, U., Wecke, J. & Gorisch, H. (2000). Bacterial dehalorespiration with chlorinated benzenes. Nature 408, 580-583.
2. Adrian, L., Hansen, S. K., Fung, J. M., Gorisch, H. & Zinder, S. H. (2007). Growth of Dehalococcoides strains with chlorophenols as electron acceptors. Environ Sci Technol 41, 2318-2323.
3. Amos, B. K., Ritalahti, K. M., Cruz-Garcia, C., Padilla-Crespo, E. & Loffler, F. E. (2008). Oxygen effect on Dehalococcoides viability and biomarker quantification. Environ Sci Technol 42, 5718-5726.
4. Amos, B. K., Suchomel, E. J., Pennell, K. D. & Loffler, F. E. (2009). Spatial and temporal distributions of Geobacter lovleyi and Dehalococcoides spp. during bioenhanced PCE-NAPL dissolution. Environ Sci Technol 43, 1977-1985.
5. Cheng, D. & He, J. (2009). Isolation and characterization of "Dehalococcoides" sp. strain MB, which dechlorinates tetrachloroethene to trans-1,2-dichloroethene. Appl Environ Microbiol 75, 5910-5918.
6. Cupples, A. M., Spormann, A. M. & McCarty, P. L. (2003). Growth of a Dehalococcoides-like microorganism on vinyl chloride and cisdichloroethene as electron acceptors as determined by competitive PCR. Appl Environ Microbiol 69, 953-959.
7. de Jong, E., Field, J. A., Spinnler, H.-E., Wijnberg, J. B. P. A. & de Bont, J. A. M. (1994). Significant biogenesis of chlorinated aromatics by fungi in natural environments. Appl Environ Microbiol 60, 264-270.
8. Duhamel, M., Mo, K. & Edwards, E. A. (2004). Characterization of a highly enriched Dehalococcoides-containing culture that grows on vinyl chloride and trichloroethene. Appl Environ Microbiol 70, 5538-5545.
9. Ehrenreich, A. & Widdel, F. (1994). Anaerobic oxidation of ferrous iron by purple bacteria, a new type of phototrophic metabolism. Appl Environ Microbiol 60, 4517-4526.
10. Goris, J., Konstantinidis, K. T., Klappenbach, J. A., Coenye, T., Vandamme, P. & Tiedje, J. M. (2007). DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57, 81-91.
11. Gribble, G. W. (2003). The diversity of naturally produced organohalogens. Chemosphere 52, 289-297.
12. He, J., Sung, Y., Dollhopf, M. E., Fathepure, B. Z., Tiedje, J. M. & Loffler, F. E. (2002). Acetate versus hydrogen as direct electron donors to stimulate the microbial reductive dechlorination process at chloroethene-contaminated sites. Environ Sci Technol 36, 3945-3952.
13. He, J., Ritalahti, K. M., Yang, K.-L., Koenigsberg, S. S. & Loffler, F. E. (2003). Detoxification of vinyl chloride to ethene coupled to growth of an anaerobic bacterium. Nature 424, 62-65.
14. He, J., Sung, Y., Krajmalnik-Brown, R., Ritalahti, K. M. & Loffler, F. E. (2005). Isolation and characterization of Dehalococcoides sp. strain FL2, a trichloroethene (TCE) and 1,2-dichloroethene-respiring anaerobe. Environ Microbiol 7, 1442-1450.
15. Hendrickson, E. R., Payne, J. A., Young, R. M., Starr, M. G., Perry, M. P., Fahnestock, S., Ellis, D. E. & Ebersole, R. C. (2002). Molecular analysis of Dehalococcoides 16S ribosomal DNA from chloroethenecontaminated sites throughout North America and Europe. Appl Environ Microbiol 68, 485-495.
16. Hoekstra, E. J., de Leer, E. W. B. & Brinkman, U. A. Th. (1999). Findings supporting the natural formation of trichloroacetic acid in soil. Chemosphere 38, 2875-2883.
17. Hug, L. A., Salehi, M., Nuin, P., Tillier, E. R. & Edwards, E. A. (2011). Design and verification of a pangenome microarray oligonucleotide probe set for Dehalococcoides spp. Appl Environ Microbiol 77, 5361-5369.
18. Hugenholtz, P. & Stackebrandt, E. (2004). Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). Int J Syst Evol Microbiol 54, 2049-2051.
19. Jayachandran, G., Gorisch, H. & Adrian, L. (2003). Dehalorespiration with hexachlorobenzene and pentachlorobenzene by Dehalococcoides sp. strain CBDB1. Arch Microbiol 180, 411-416.
20. Kandler, O. (1993). Cell wall biochemistry and three-domain concept of life. Syst Appl Microbiol 16, 501-509.
21. Kittelmann, S. & Friedrich, M. W. (2008). Identification of novel perchloroethene-respiring microorganisms in anoxic river sediment by RNA-based stable isotope probing. Environ Microbiol 10, 31-46.
22. Konstantinidis, K. T., Ramette, A. & Tiedje, J. M. (2006). The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci 361, 1929-1940.
23. Krzmarzick, M. J., Crary, B. B., Harding, J. J., Oyerinde, O. O., Leri, A. C., Myneni, S. C. & Novak, P. J. (2012). Natural niche for organohalide-respiring Chloroflexi. Appl Environ Microbiol 78, 393-401.
24. Kube, M., Beck, A., Zinder, S. H., Kuhl, H., Reinhardt, R. & Adrian, L. (2005). Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1. Nat Biotechnol 23, 1269-1273.
25. Kubitschek, H. E. (1990). Cell volume increase in Escherichia coli after shifts to richer media. J Bacteriol 172, 94-101.
26. Lee, P. K., Cheng, D., Hu, P., West, K. A., Dick, G. J., Brodie, E. L., Andersen, G. L., Zinder, S. H., He, J. & Alvarez-Cohen, L. (2011). Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray. ISME J 5, 1014-1024.
27. Lendvay, J. M., Loffler, F. E., Dollhopf, M., Aiello, M. R., Daniels, G., Fathepure, B. Z., Gebhard, M., Heine, R., Helton, R. & other authors (2003). Bioreactive barriers: bioaugmentation and biostimulation for chlorinated solvent remediation. Environ Sci Technol 37, 1422-1431.
28. Loffler, F. E. & Edwards, E. A. (2006). Harnessing microbial activities for environmental cleanup. Curr Opin Biotechnol 17, 274-284.
29. Loffler, F. E., Tiedje, J. M. & Sanford, R. A. (1999). Fraction of electrons consumed in electron acceptor reduction and hydrogen thresholds as indicators of halorespiratory physiology. Appl Environ Microbiol 65, 4049-4056.
30. Loffler, F. E., Sanford, R. A. & Ritalahti, K. M. (2005). Enrichment, cultivation, and detection of reductively dechlorinating bacteria. Methods Enzymol 397, 77-111.
31. Loffler, F. E., Ritalahti, K. M. & Zinder, S. H. (2013). Dehalococcoides and reductive dechlorination of chlorinated solvents. In Bioaugmentation for Groundwater Remediation (SERDP ESTCP Remediation Technology, vol. 5), pp. 39-88. Edited by H. F. Stroo, A. Leeson & C. H. Ward. New York: Springer.
32. Marco-Urrea, E., Nijenhuis, I. & Adrian, L. (2011). Transformation and carbon isotope fractionation of tetraand trichloroethene to trans-dichloroethene by Dehalococcoides sp. strain CBDB1. Environ Sci Technol 45, 6216.
33. May, H. D., Miller, G. S., Kjellerup, B. V. & Sowers, K. R. (2008). Dehalorespiration with polychlorinated biphenyls by an anaerobic ultramicrobacterium. Appl Environ Microbiol 74, 2089-2094.
34. Maymó-Gatell, X., Chien, Y.-T., Gossett, J. M. & Zinder, S. H. (1997). Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276, 1568-1571.
35. McMurdie, P. J., Behrens, S. F., Muller, J. A., Goke, J., Ritalahti, K. M., Wagner, R., Goltsman, E., Lapidus, A., Holmes, S. & other authors (2009). Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS Genet 5, e1000714.
36. Moe, W. M., Yan, J., Nobre, M. F., da Costa, M. S. & Rainey, F. A. (2009). Dehalogenimonas lykanthroporepellens gen. nov., sp. nov., a reductively dehalogenating bacterium isolated from chlorinated solvent-contaminated groundwater. Int J Syst Evol Microbiol 59, 2692-2697.
37. Moench, T. T. & Zeikus, J. G. (1983). An improved preparation method for a titanium (III) media reductant. J Microbiol Methods 1, 199-202.
38. Morris, R. M., Sowell, S., Barofsky, D., Zinder, S. H. & Richardson, R. E. (2006). Transcription and mass-spectroscopic proteomic studies of electron transport oxidoreductases in Dehalococcoides ethenogenes. Environ Microbiol 8, 1499-1509.
39. Muller, J. A., Rosner, B. M., Von Abendroth, G., Meshulam-Simon, G., McCarty, P. L. & Spormann, A. M. (2004). Molecular identification of the catabolic vinyl chloride reductase from Dehalococcoides sp. strain VS and its environmental distribution. Appl Environ Microbiol 70, 4880-4888.
40. Oberg, G. (2002). The natural chlorine cycle fitting the scattered pieces. Appl Microbiol Biotechnol 58, 565-581.
41. Rappé, M. S., Connon, S. A., Vergin, K. L. & Giovannoni, S. J. (2002). Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418, 630-633.
42. Ritalahti, K. M., Amos, B. K., Sung, Y., Wu, Q., Koenigsberg, S. S. & Loffler, F. E. (2006). Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains. Appl Environ Microbiol 72, 2765-2774.
43. Rosner, B. M., McCarty, P. L. & Spormann, A. M. (1997). In vitro studies on reductive vinyl chloride dehalogenation by an anaerobic mixed culture. Appl Environ Microbiol 63, 4139-4144.
44. Schink, B. (2006). Microbially driven redox reactions in anoxic environments: pathways, energetics, and biochemical consequences. Eng Life Sci 6, 228-233.
45. Seshadri, R., Adrian, L., Fouts, D. E., Eisen, J. A., Phillippy, A. M., Methe, B. A., Ward, N. L., Nelson, W. C., Deboy, R. T. & other authors (2005). Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science 307, 105-108.
46. Sung, Y., Ritalahti, K. M., Apkarian, R. P. & Loffler, F. E. (2006). Quantitative PCR confirms purity of strain GT, a novel trichloroethene-to-ethene-respiring Dehalococcoides isolate. Appl Environ Microbiol 72, 1980-1987.
47. White, D. C., Geyer, R., Peacock, A. D., Hedrick, D. B., Koenigsberg, S. S., Sung, Y., He, J. & Loffler, F. E. (2005). Phospholipid furan fatty acids and ubiquinone-8: lipid biomarkers that may protect Dehalococcoides strains from free radicals. Appl Environ Microbiol 71, 8426-8433.
48. Wolin, E. A., Wolfe, R. S. & Wolin, M. J. (1964). Viologen dye inhibition of methane formation by Methanobacillus omelianskii. J Bacteriol 87, 993-998.
49. Yamada, T., Sekiguchi, Y., Hanada, S., Imachi, H., Ohashi, A., Harada, H. & Kamagata, Y. (2006). Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Microbiol 56, 1331-1340.
50. Yan, J., Rash, B. A., Rainey, F. A. & Moe, W. M. (2009). Isolation of novel bacteria within the Chloroflexi capable of reductive dechlorination of 1,2,3-trichloropropane. Environ Microbiol 11, 833-843.
51. Zehnder, A. J. B. & Wuhrmann, K. (1976). Titanium (III) citrate as a nontoxic oxidation-reduction buffering system for the culture of obligate anaerobes. Science 194, 1165-1166.