Advertisement

Overview of Known Organohalide-Respiring Bacteria—Phylogenetic Diversity and Environmental Distribution

  • Siavash Atashgahi
  • Yue Lu
  • Hauke SmidtEmail author
Chapter

Abstract

To date, organohalide respiration (OHR) has been restricted to the bacterial domain of life. Known organohalide-respiring bacteria (OHRB) are spread among several phyla comprising both Gram-positive and Gram-negative bacteria. As a unique trait, OHRB benefit from reductive dehalogenase enzymes enabling them to use different organohalides as terminal electron acceptors and occupy a wide range of terrestrial and aquatic environments. This chapter comprises three sections: First, we give an overview of phylogeny of known OHRB and briefly discuss physiological and genetic characteristics of each group. Second, the environmental distribution of OHRB is presented. Owing to the application of molecular diagnostic approaches, OHRB are being increasingly detected not only from organohalide-contaminated groundwaters and sediments but also from pristine environments, including deep oceanic sediments and soils that are ample sources of naturally occurring organohalides. Finally, we highlight important factors that impact the ecology of OHRB and their interaction with other microbial guilds.

Keywords

Riverbed Sediment Reductive Dehalogenation Tidal Flat Sediment Chlorinate Ethene RDase Gene 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgement

The authors thank the BE-Basic Foundation (project MicroControl (8.004.01)) for financial support. Yue Lu was sponsored by a CSC Fellowship.

References

  1. Abe Y, Aravena R, Zopfi J, Parker B, Hunkeler D (2009) Evaluating the fate of chlorinated ethenes in streambed sediments by combining stable isotope, geochemical and microbial methods. J Contam Hydrol 107(1):10–21PubMedCrossRefGoogle Scholar
  2. Abelson PH (1990) Inefficient remediation of ground-water pollution. Science 250(4982)Google Scholar
  3. Adrian L, Manz W, Szewzyk U, Görisch H (1998) Physiological characterization of a bacterial consortium reductively dechlorinating 1,2,3- and 1,2,4-trichlorobenzene. Appl Environ Microbiol 64(2):496–503PubMedPubMedCentralGoogle Scholar
  4. Adrian L, Szewzyk U, Wecke J, Görisch H (2000) Bacterial dehalorespiration with chlorinated benzenes. Nature 408:580–583PubMedCrossRefGoogle Scholar
  5. Adrian L, Rahnenführer J, Gobom J, Hölscher T (2007) Identification of a chlorobenzene reductive dehalogenase in Dehalococcoides sp. strain CBDB1. Appl Environ Microbiol 73(23):7717–7724PubMedPubMedCentralCrossRefGoogle Scholar
  6. Ahn Y-B, Rhee S-K, Fennell DE, Kerkhof LJ, Hentschel U, Häggblom MM (2003) Reductive dehalogenation of brominated phenolic compounds by microorganisms associated with the marine sponge Aplysina aerophoba. Appl Environ Microbiol 69(7):4159–4166PubMedPubMedCentralCrossRefGoogle Scholar
  7. Ahn Y-B, Häggblom MM, Kerkhof LJ (2007) Comparison of anaerobic microbial communities from estuarine sediments amended with halogenated compounds to enhance dechlorination of 1,2,3,4-tetrachlorodibenzo-p-dioxin. FEMS Microbiol Ecol 61(2):362–371PubMedCrossRefGoogle Scholar
  8. Ahn Y-B, Kerkhof LJ, Häggblom MM (2009) Desulfoluna spongiiphila sp. nov., a dehalogenating bacterium in the Desulfobacteraceae from the marine sponge Aplysina aerophoba. Int J Syst Evol Microbiol 59(9):2133–2139PubMedCrossRefGoogle Scholar
  9. Atashgahi S, Maphosa F, Doğan E, Smidt H, Springael D, Dejonghe W (2013) Small-scale oxygen distribution determines the vinyl chloride biodegradation pathway in surficial sediments of riverbed hyporheic zones. FEMS Microbiol Ecol 84(1):133–142PubMedCrossRefGoogle Scholar
  10. Atashgahi S, Maphosa F, De Vrieze J, Haest PJ, Boon N, Smidt H, Springael D, Dejonghe W (2014) Evaluation of solid polymeric organic materials for use in bioreactive sediment capping to stimulate the degradation of chlorinated aliphatic hydrocarbons. Appl Microbiol Biotechnol 98(5):2255–2266PubMedCrossRefGoogle Scholar
  11. Aulenta F, Di Maio V, Ferri T, Majone M (2010) The humic acid analogue antraquinone-2, 6-disulfonate (AQDS) serves as an electron shuttle in the electricity-driven microbial dechlorination of trichloroethene to cis-dichloroethene. Bioresour Technol 101(24):9728–9733PubMedCrossRefGoogle Scholar
  12. Baxter-Plant V, Mikheenko I, Robson M, Harrad S, Macaskie L (2004) Dehalogenation of chlorinated aromatic compounds using a hybrid bioinorganic catalyst on cells of Desulfovibrio desulfuricans. Biotechnol Lett 26(24):1885–1890PubMedCrossRefGoogle Scholar
  13. Bedard DL, Bailey JJ, Reiss BL, Jerzak GVS (2006) Development and characterization of stable sediment-free anaerobic bacterial enrichment cultures that dechlorinate Aroclor 1260. Appl Environ Microbiol 72(4):2460–2470PubMedPubMedCentralCrossRefGoogle Scholar
  14. Berkaw M, Sowers KR, May HD (1996) Anaerobic ortho dechlorination of polychlorinated biphenyls by estuarine sediments from Baltimore harbor. Appl Environ Microbiol 62(7):2534–2539PubMedPubMedCentralGoogle Scholar
  15. Bouchard B, Beaudet R, Villemur R, McSween G, Lepine F, Bisaillon J-G (1996) Isolation and characterization of Desulfitobacterium frappieri sp. nov., an anaerobic bacterium which reductively dechlorinates pentachlorophenol to 3-chlorophenol. Int J Syst Bacteriol 46(4):1010–1015PubMedCrossRefGoogle Scholar
  16. Bowman KS, Nobre MF, da Costa MS, Rainey FA, Moe WM (2013) Dehalogenimonas alkenigignens sp. nov., a chlorinated-alkane-dehalogenating bacterium isolated from groundwater. Int J Syst Evol Microbiol 63 (Pt 4):1492–1498Google Scholar
  17. Boyle AW, Häggblom MM, Young LY (1999a) Dehalogenation of lindane (γ-hexachlorocyclohexane) by anaerobic bacteria from marine sediments and by sulfate-reducing bacteria. FEMS Microbiol Ecol 29(4):379–387Google Scholar
  18. Boyle AW, Phelps CD, Young L (1999b) Isolation from estuarine sediments of a Desulfovibrio strain which can grow on lactate coupled to the reductive dehalogenation of 2,4,6-tribromophenol. Appl Environ Microbiol 65(3):1133–1140PubMedPubMedCentralGoogle Scholar
  19. Breitenstein A, Saano A, Salkinoja-Salonen M, Andreesen JR, Lechner U (2001) Analysis of a 2,4,6-trichlorophenol-dehalogenating enrichment culture and isolation of the dehalogenating member Desulfitobacterium frappieri strain TCP-A. Arch Microbiol 175:133–142PubMedCrossRefGoogle Scholar
  20. Bunge M, Lechner U (2009) Anaerobic reductive dehalogenation of polychlorinated dioxins. Appl Microbiol Biotechnol 84(3):429–444PubMedCrossRefGoogle Scholar
  21. Bunge M, Wagner A, Fischer M, Andreesen JR, Lechner U (2008) Enrichment of a dioxin-dehalogenating Dehalococcoides species in two-liquid phase cultures. Environ Microbiol 10(10):2670–2683PubMedCrossRefGoogle Scholar
  22. Chang YC, Hatsu M, Jung K, Yoo YS, Takamizawa K (1998) Degradation of a variety of halogenated aliphatic compounds by an anaerobic mixed culture. J Ferment Bioeng 86(4):410–412CrossRefGoogle Scholar
  23. Chen K, Huang L, Xu C, Liu X, He J, Zinder SH, Li S, Jiang J (2013) Molecular characterization of the enzymes involved in the degradation of a brominated aromatic herbicide. Mol Microbiol 89(6):1121–1139PubMedCrossRefGoogle Scholar
  24. 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(18):5910–5918PubMedPubMedCentralCrossRefGoogle Scholar
  25. Cheng D, Chow WL, He J (2009) A Dehalococcoides-containing co-culture that dechlorinates tetrachloroethene to trans-1,2-dichloroethene. ISME J 4(1):88–97PubMedCrossRefGoogle Scholar
  26. Chow WL, Cheng D, Wang S, He J (2010) Identification and transcriptional analysis of trans-DCE-producing reductive dehalogenases in Dehalococcoides species. ISME J 4(8):1020–1030PubMedCrossRefGoogle Scholar
  27. Christiansen N, Ahring BK (1996) Desulfitobacterium hafniense sp. nov., an anaerobic, reductively dechlorinating bacterium. Int J Syst Bacteriol 46(2):442–448CrossRefGoogle Scholar
  28. Cole JR, Cascarelli AL, Mohn WW, Tiedje JM (1994) Isolation and characterization of a novel bacterium growing via reductive dehalogenation of 2-chlorophenol. Appl Environ Microbiol 60(10):3536–3542PubMedPubMedCentralGoogle Scholar
  29. Conant B, Cherry JA, Gillham RW (2004) A PCE groundwater plume discharging to a river: influence of the streambed and near-river zone on contaminant distributions. J Contam Hydrol 73(1):249–279PubMedCrossRefGoogle Scholar
  30. Cordova CD, Schicklberger MF, Yu Y, Spormann AM (2011) Partial functional replacement of CymA by SirCD in Shewanella oneidensis MR-1. J Bacteriol 193(9):2312–2321PubMedPubMedCentralCrossRefGoogle Scholar
  31. Cornelissen G, Gustafsson Ö, Bucheli TD, Jonker MT, Koelmans AA, van Noort PC (2005) Extensive sorption of organic compounds to black carbon, coal, and kerogen in sediments and soils: mechanisms and consequences for distribution, bioaccumulation, and biodegradation. Environ Sci Technol 39(18):6881–6895PubMedCrossRefGoogle Scholar
  32. Courbet C, Rivière A, Jeannottat S, Rinaldi S, Hunkeler D, Bendjoudi H, de Marsily G (2011) Complementing approaches to demonstrate chlorinated solvent biodegradation in a complex pollution plume: mass balance, PCR and compound-specific stable isotope analysis. J Contam Hydrol 126(3):315–329PubMedCrossRefGoogle Scholar
  33. Cutter LA, Watts JE, Sowers KR, May HD (2001) Identification of a microorganism that links its growth to the reductive dechlorination of 2,3,5,6-chlorobiphenyl. Environ Microbiol 3(11):699–709PubMedCrossRefGoogle Scholar
  34. Damgaard I, Bjerg PL, Bælum J, Scheutz C, Hunkeler D, Jacobsen CS, Tuxen N, Broholm MM (2013) Identification of chlorinated solvents degradation zones in clay till by high resolution chemical, microbial and compound specific isotope analysis. J Contam Hydrol 146:37–50PubMedCrossRefGoogle Scholar
  35. De Wever H, Cole JR, Fettig MR, Hogan DA, Tiedje JM (2000) Reductive dehalogenation of trichloroacetic acid by Trichlorobacter thiogenes gen. nov., sp. nov. Appl Environ Microbiol 66(6):2297–2301PubMedPubMedCentralCrossRefGoogle Scholar
  36. De Wildeman S, Diekert G, Van Langenhove H, Verstraete W (2003) Stereoselective microbial dehalorespiration with vicinal dichlorinated alkanes. Appl Environ Microbiol 69(9):5643–5647PubMedPubMedCentralCrossRefGoogle Scholar
  37. Delgado AG, Kang D-W, Nelson KG, Fajardo-Williams D, Miceli JF III, Done HY, Popat SC, Krajmalnik-Brown R (2014) Selective enrichment yields robust ethene-producing dechlorinating cultures from microcosms stalled at cis-dichloroethene. PLoS ONE 9(6):e100654PubMedPubMedCentralCrossRefGoogle Scholar
  38. Deplanche K, Snape T, Hazrati S, Harrad S, Macaskie L (2009) Versatility of a new bioinorganic catalyst: palladized cells of Desulfovibrio desulfuricans and application to dehalogenation of flame retardant materials. Environ Technol 30(7):681–692PubMedCrossRefGoogle Scholar
  39. DeWeerd KA, Mandelco L, Tanner RS, Woese CR, Suflita JM (1990) Desulfomonile tiedjei gen. nov. and sp. nov., a novel anaerobic, dehalogenating, sulfate-reducing bacterium. Arch Microbiol 154(1):23–30CrossRefGoogle Scholar
  40. DeWeerd K, Concannon F, Suflita JM (1991) Relationship between hydrogen consumption, dehalogenation, and the reduction of sulfur oxyanions by Desulfomonile tiedjei. Appl Environ Microbiol 57(7):1929–1934PubMedPubMedCentralGoogle Scholar
  41. Ding C, Zhao S, He J (2014) A Desulfitobacterium sp. strain PR reductively dechlorinates both 1,1,1-trichloroethane and chloroform. Environ Microbiol 16(11):3387–3397PubMedCrossRefGoogle Scholar
  42. Drzyzga O, Gottschal JC (2002) Tetrachloroethene dehalorespiration and growth of Desulfitobacterium frappieri TCE1 in strict dependence on the activity of Desulfovibrio fructosivorans. Appl Environ Microbiol 68(2):642–649PubMedPubMedCentralCrossRefGoogle Scholar
  43. Drzyzga O, Gerritse J, Dijk JA, Elissen H, Gottschal JC (2001) Coexistence of a sulphate-reducing Desulfovibrio species and the dehalorespiring Desulfitobacterium frappieri TCE1 in defined chemostat cultures grown with various combinations of sulphate and tetrachloroethene. Environ Microbiol 3(2):92–99PubMedCrossRefGoogle Scholar
  44. Duhamel M, Edwards EA (2006) Microbial composition of chlorinated ethene-degrading cultures dominated by Dehalococcoides. FEMS Microbiol Ecol 58(3):538–549PubMedCrossRefGoogle Scholar
  45. Duret A, Holliger C, Maillard J (2012) The physiological opportunism of Desulfitobacterium hafniense strain TCE1 towards organohalide respiration with tetrachloroethene. Appl Environ Microbiol 78(17):6121–6127PubMedPubMedCentralCrossRefGoogle Scholar
  46. Edmunds W, Shand P, Hart P, Ward R (2003) The natural (baseline) quality of groundwater: a UK pilot study. Sci Total Environ 310(1):25–35PubMedCrossRefGoogle Scholar
  47. Emmanuel E, Pierre MG, Perrodin Y (2009) Groundwater contamination by microbiological and chemical substances released from hospital wastewater: Health risk assessment for drinking water consumers. Environ Int 35(4):718–726PubMedCrossRefGoogle Scholar
  48. Fagervold SK, Watts JE, May HD, Sowers KR (2005) Sequential reductive dechlorination of meta-chlorinated polychlorinated biphenyl congeners in sediment microcosms by two different Chloroflexi phylotypes. Appl Environ Microbiol 71(12):8085–8090PubMedPubMedCentralCrossRefGoogle Scholar
  49. Fagervold SK, May HD, Sowers KR (2007) Microbial reductive dechlorination of Aroclor 1260 in Baltimore Harbor sediment microcosms is catalyzed by three phylotypes within the phylum Chloroflexi. Appl Environ Microbiol 73(9):3009–3018PubMedPubMedCentralCrossRefGoogle Scholar
  50. Fennell DE, Gossett JM (1998) Modeling the production of and competition for hydrogen in a dechlorinating culture. Environ Sci Technol 32(16):2450–2460CrossRefGoogle Scholar
  51. Fennell DE, Carroll AB, Gossett JM, Zinder SH (2001) Assessment of indigenous reductive dechlorinating potential at a TCE-contaminated site using microcosms, polymerase chain reaction analysis, and site data. Environ Sci Technol 35(9):1830–1839PubMedCrossRefGoogle Scholar
  52. Finneran KT, Forbush HM, VanPraagh CVG, Lovley DR (2002) Desulfitobacterium metallireducens sp. nov., an anaerobic bacterium that couples growth to the reduction of metals and humic acids as well as chlorinated compounds. Int J Sys Evol Microbiol 52(6):1929–1935Google Scholar
  53. Fletcher KE, Ritalahti KM, Pennell KD, Takamizawa K, Löffler FE (2008) Resolution of culture Clostridium bifermentans DPH-1 into two populations, a Clostridium sp. and tetrachloroethene-dechlorinating Desulfitobacterium hafniense strain JH1. Appl Environ Microbiol 74(19):6141–6143PubMedPubMedCentralCrossRefGoogle Scholar
  54. Futagami T, Morono Y, Terada T, Kaksonen AH, Inagaki F (2009) Dehalogenation activities and distribution of reductive dehalogenase homologous genes in marine subsurface sediments. Appl Environ Microbiol 75(21):6905–6909PubMedPubMedCentralCrossRefGoogle Scholar
  55. Futagami T, Morono Y, Terada T, Kaksonen AH, Inagaki F (2013) Distribution of dehalogenation activity in subseafloor sediments of the Nankai Trough subduction zone. Phil Trans R Soc B 368(1616):20120249PubMedPubMedCentralCrossRefGoogle Scholar
  56. Gerritse J, Renard V, Pedro G, Lawson PA, Collins MD, Gottschal JC (1996) Desulfitobacterium sp. strain PCE1, an anaerobic bacterium that can grow by reductive dechlorination of tetrachloroethene or ortho- chlorinated phenols. Arch Microbiol 165:132–140PubMedCrossRefGoogle Scholar
  57. Gerritse J, Drzyzga O, Kloetstra G, Keijmel M, Wiersum LP, Hutson R, Collins MD, Gottschal JC (1999) Influence of different electron donors and acceptors on dehalorespiration of tetrachloroethene by Desulfitobacterium frappieri TCE1. Appl Environ Microbiol 65(12):5212–5221PubMedPubMedCentralGoogle Scholar
  58. Goris T, Hornung B, Kruse T, Reinhold A, Westermann M, Schaap PJ, Smidt H, Diekert G (2015) Draft genome sequence and characterization of Desulfitobacterium hafniense PCE-S. Stand Genomic Sci 10(1):15PubMedPubMedCentralCrossRefGoogle Scholar
  59. Gribble GW (2010) Naturally occurring organohalogen compounds-a comprehensive update. Progress in the chemistry of organic natural products, vol 91. Springer/Wien, GermanyGoogle Scholar
  60. Grøn C (1991) Organic halogens in Danish groundwaters. Lect Notes in Earth Sci 33:495–506CrossRefGoogle Scholar
  61. Grostern A, Edwards EA (2006) Growth of Dehalobacter and Dehalococcoides spp. during degradation of chlorinated ethanes. Appl Environ Microbiol 72(1):428–436PubMedPubMedCentralCrossRefGoogle Scholar
  62. Grostern A, Duhamel M, Dworatzek S, Edwards EA (2010) Chloroform respiration to dichloromethane by a Dehalobacter population. Environ Microbiol 12(4):1053–1060PubMedCrossRefGoogle Scholar
  63. Hamonts K, Kuhn T, Maesen M, Bronders J, Lookman R, Kalka H, Diels L, Meckenstock RU, Springael D, Dejonghe W (2009) Factors determining the attenuation of chlorinated aliphatic hydrocarbons in eutrophic river sediment impacted by discharging polluted groundwater. Environ Sci Technol 43(14):5270–5275PubMedCrossRefGoogle Scholar
  64. Hamonts K, Kuhn T, Vos J, Maesen M, Kalka H, Smidt H, Springael D, Meckenstock RU, Dejonghe W (2012) Temporal variations in natural attenuation of chlorinated aliphatic hydrocarbons in eutrophic river sediments impacted by a contaminated groundwater plume. Water Res 46(6):1873–1888PubMedCrossRefGoogle Scholar
  65. Hamonts K, Ryngaert A, Smidt H, Springael D, Dejonghe W (2014) Determinants of the microbial community structure of eutrophic, hyporheic river sediments polluted with chlorinated aliphatic hydrocarbons. FEMS Microbiol Ecol 87(3):715–732PubMedCrossRefGoogle Scholar
  66. He J, Ritalahti KM, Aiello MR, Löffler FE (2003) Complete detoxification of vinyl chloride by an anaerobic enrichment culture and identification of the reductively dechlorinating population as a Dehalococcoides species. Appl Environ Microbiol 69(2):996–1003PubMedPubMedCentralCrossRefGoogle Scholar
  67. He J, Sung Y, Krajmalnik-Brown R, Ritalahti KM, Löffler FE (2005) Isolation and characterization of Dehalococcoides sp. strain FL2, a trichloroethene (TCE)-and 1,2-dichloroethene-respiring anaerobe. Environ Microbiol 7(9):1442–1450PubMedCrossRefGoogle Scholar
  68. Hendrickson ER, Payne JA, Young RM, Starr MG, Perry MP, Fahnestock S, Ellis DE, Ebersole RC (2002) Molecular analysis of Dehalococcoides 16S ribosomal DNA from chloroethene-contaminated sites throughout North America and Europe. Appl Environ Microbiol 68(2):485–495PubMedPubMedCentralCrossRefGoogle Scholar
  69. Holliger C, Schraa G, Stams AJ, Zehnder AJB (1993) A highly purified enrichment culture couples the reductive dechlorination of tetrachloroethene to growth. Appl Environ Microbiol 59(9):2991–2997PubMedPubMedCentralGoogle Scholar
  70. Holliger C, Hahn D, Harmsen H, Ludwig W, Schumacher W, Tindall B, Vazquez F, Weiss N, Zehnder AJB (1998a) Dehalobacter restrictus gen. nov. and sp. nov., a strictly anaerobic bacterium that reductively dechlorinates tetra- and trichloroethene in an anaerobic respiration. Arch Microbiol 169(4):313–321PubMedCrossRefGoogle Scholar
  71. Holliger C, Wohlfarth G, Diekert G (1998b) Reductive dechlorination in the energy metabolism of anaerobic bacteria. FEMS Microbiol Rev 22(5):383–398CrossRefGoogle Scholar
  72. Horowitz A, Suflita JM, Tiedje JM (1983) Reductive dehalogenations of halobenzoates by anaerobic lake sediment microorganisms. Appl Environ Microbiol 45(5):1459–1465PubMedPubMedCentralGoogle Scholar
  73. Hosseinkhani B, Hennebel T, Van Nevel S, Verschuere S, Yakimov MM, Cappello S, Blaghen M, Boon N (2014) Biogenic nanopalladium based remediation of chlorinated hydrocarbons in marine environments. Environ Sci Technol 48(1):550–557PubMedCrossRefGoogle Scholar
  74. Hug LA, Beiko RG, Rowe AR, Richardson RE, Edwards EA (2012) Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community. BMC Genom 13(1):327CrossRefGoogle Scholar
  75. Hug LA, Castelle CJ, Wrighton KC, Thomas BC, Sharon I, Frischkorn KR, Williams KH, Tringe SG, Banfield JF (2013a) Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. Microbiome 1(1):22PubMedPubMedCentralCrossRefGoogle Scholar
  76. Hug LA, Maphosa F, Leys D, Löffler FE, Smidt H, Edwards EA, Adrian L (2013b) Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases. Phil Trans R Soc B 368(1616)Google Scholar
  77. Inagaki F, Suzuki M, Takai K, Oida H, Sakamoto T, Aoki K, Nealson KH, Horikoshi K (2003) Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl Environ Microbiol 69(12):7224–7235PubMedPubMedCentralCrossRefGoogle Scholar
  78. Johnson RL, Brillante SM, Isabella LM, Houck JE, Pankow JF (1985) Migration of chlorophenolic compounds at the chemical waste disposal site at Alkali Lake, Oregon—2. Contaminant distributions, transport, and retardation. Groundwater 23(5):652–666Google Scholar
  79. Jorgensen SL, Hannisdal B, Lanzén A, Baumberger T, Flesland K, Fonseca R, Øvreås L, Steen IH, Thorseth IH, Pedersen RB, Schleper C (2012) Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge. Proc Natl Acad Sci USA 109(42):E2846–E2855PubMedPubMedCentralCrossRefGoogle Scholar
  80. Justicia-Leon SD, Ritalahti KM, Mack EE, Löffler FE (2012) Dichloromethane fermentation by a Dehalobacter sp. in an enrichment culture derived from pristine river sediment. Appl Environ Microbiol 78(4):1288–1291PubMedPubMedCentralCrossRefGoogle Scholar
  81. Kaster A-K, Mayer-Blackwell K, Pasarelli B, Spormann AM (2014) Single cell genomic study of Dehalococcoidetes species from deep-sea sediments of the Peruvian Margin. ISME J 8:1831–1842PubMedPubMedCentralCrossRefGoogle Scholar
  82. Kawai M, Futagami T, Toyoda A, Takaki Y, Nishi S, Hori S, Arai W, Tsubouchi T, Morono Y, Uchiyama I, Ito T, Fujiyama A, Inagaki F, Takami H (2014) High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes. Front Microbiol 5:80PubMedPubMedCentralCrossRefGoogle Scholar
  83. Keller S, Ruetz M, Kunze C, Kräutler B, Diekert G, Schubert T (2013) Exogenous 5, 6-dimethylbenzimidazole caused production of a non-functional tetrachloroethene reductive dehalogenase in Sulfurospirillum multivorans. Environ Microbiol 16(11):3361–3369PubMedCrossRefGoogle Scholar
  84. Kim S-H, Harzman C, Davis JK, Hutcheson R, Broderick JB, Marsh TL, Tiedje JM (2012) Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction. BMC Microbiol 12(1):21PubMedPubMedCentralCrossRefGoogle Scholar
  85. King GM (1988) Dehalogenation in marine sediments containing natural sources of halophenols. Appl Environ Microbiol 54(12):3079–3085PubMedPubMedCentralGoogle Scholar
  86. Kittelmann S, Friedrich MW (2008a) Identification of novel perchloroethene-respiring microorganisms in anoxic river sediment by RNA-based stable isotope probing. Environ Microbiol 10(1):31–46PubMedGoogle Scholar
  87. Kittelmann S, Friedrich MW (2008b) Novel uncultured Chloroflexi dechlorinate perchloroethene to trans-dichloroethene in tidal flat sediments. Environ Microbiol 10(6):1557–1570PubMedCrossRefGoogle Scholar
  88. Kjellerup BV, Paul P, Ghosh U, May HD, Sowers KR (2012) Spatial distribution of PCB dechlorinating bacteria and activities in contaminated soil. Appl Environ Soil Sci 2012:584970CrossRefGoogle Scholar
  89. Krajmalnik-Brown R, Hölscher T, Thomson IN, Saunders FM, Ritalahti KM, Löffler FE (2004) Genetic identification of a putative vinyl chloride reductase in Dehalococcoides sp. strain BAV1. Appl Environ Microbiol 70(10):6347–6351PubMedPubMedCentralCrossRefGoogle Scholar
  90. Krajmalnik-Brown R, Sung Y, Ritalahti KM, Michael Saunders F, Löffler FE (2007) Environmental distribution of the trichloroethene reductive dehalogenase gene (tceA) suggests lateral gene transfer among Dehalococcoides. FEMS Microbiol Ecol 59(1):206–214PubMedCrossRefGoogle Scholar
  91. Kranzioch I, Stoll C, Holbach A, Chen H, Wang L, Zheng B, Norra S, Bi Y, Schramm K-W, Tiehm A (2013) Dechlorination and organohalide-respiring bacteria dynamics in sediment samples of the Yangtze Three Gorges Reservoir. Environ Sci Poll R 20(10):7046–7056CrossRefGoogle Scholar
  92. Kräutler B, Fieber W, Ostermann S, Fasching M, Ongania K-H, Gruber K, Kratky C, Mikl C, Siebert A, Diekert G (2003) The cofactor of tetrachloroethene reductive dehalogenase of Dehalospirillum multivorans is norpseudo-B12, a new type of a natural corrinoid. Helv Chim Acta 86(11):3698–3716CrossRefGoogle Scholar
  93. Krumholz LR (1997) Desulfuromonas chloroethenica sp. nov. uses tetrachloroethylene and trichloroethylene as electron acceptors. Int J Syst Bacteriol 47(4):1262–1263CrossRefGoogle Scholar
  94. Krumholz LR, Sharp R, Fishbain SS (1996) A freshwater anaerobe coupling acetate oxidation to tetrachloroethylene dehalogenation. Appl Environ Microbiol 62(11):4108–4113PubMedPubMedCentralGoogle Scholar
  95. Krzmarzick MJ, Crary BB, Harding JJ, Oyerinde OO, Leri AC, Myneni SC, Novak PJ (2012) Natural niche for organohalide-respiring Chloroflexi. Appl Environ Microbiol 78(2):393–401PubMedPubMedCentralCrossRefGoogle Scholar
  96. Krzmarzick MJ, Miller HR, Yan T, Novak PJ (2014) Novel Firmicutes group implicated in the dechlorination of two chlorinated xanthones, analogues of natural organochlorines. Appl Environ Microbiol 80(3):1210–1218PubMedPubMedCentralCrossRefGoogle Scholar
  97. Kube M, Beck A, Zinder SH, Kuhl H, Reinhardt R, Adrian L (2005) Genome sequence of the chlorinated compound–respiring bacterium Dehalococcoides species strain CBDB1. Nat Biotechnol 23(10):1269–1273PubMedCrossRefGoogle Scholar
  98. Lanthier M, Villemur R, Lépine F, Bisaillon J-G, Beaudet R (2001) Geographic distribution of Desulfitobacterium frappieri PCP-1 and Desulfitobacterium spp. in soils from the province of Quebec, Canada. FEMS Microbiol Ecol 36(2–3):185–191PubMedCrossRefGoogle Scholar
  99. LaRoe SL, Fricker AD, Bedard DL (2014) Dehalococcoides mccartyi strain JNA in pure culture extensively dechlorinates aroclor 1260 according to polychlorinated biphenyl (PCB) Dechlorination Process N. Environ Sci Technol 48(16):9187–9196PubMedCrossRefGoogle Scholar
  100. Lee PK, Macbeth TW, Sorenson KS, Deeb RA, Alvarez-Cohen L (2008) Quantifying genes and transcripts to assess the in situ physiology of “Dehalococcoides” spp. in a trichloroethene-contaminated groundwater site. Appl Environ Microbiol 74(9):2728–2739PubMedPubMedCentralCrossRefGoogle Scholar
  101. Lee PKH, Cheng D, Hu P, West KA, Dick GJ, Brodie EL, Andersen GL, Zinder SH, He J, Alvarez-Cohen L (2011) Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray. ISME J 5(6):1014–1024PubMedPubMedCentralCrossRefGoogle Scholar
  102. Lee M, Low A, Zemb O, Koenig J, Michaelsen A, Manefield M (2012) Complete chloroform dechlorination by organochlorine respiration and fermentation. Environ Microbiol 14(4):883–894PubMedCrossRefGoogle Scholar
  103. Lee PKH, Cheng D, West KA, Alvarez-Cohen L, He J (2013) Isolation of two new Dehalococcoides mccartyi strains with dissimilar dechlorination functions and their characterization by comparative genomics via microarray analysis. Environ Microbiol 15(8):2293–2305PubMedCrossRefGoogle Scholar
  104. Lendvay JM, Dean SM, Adriaens P (1998) Temporal and spatial trends in biogeochemical conditions at a groundwater-surface water interface: Implications for natural bioattenuation. Environ Sci Technol 32(22):3472–3478CrossRefGoogle Scholar
  105. Lendvay J, Löffler FE, Dollhopf M, Aiello M, Daniels G, Fathepure B, Gebhard M, Heine R, Helton R, Shi J, Krajmalnik-Brown R, Major CL, Barcelona MJ, Petrovskis E, Hickey R, Tiedje JM, Adriaens P (2003) Bioreactive barriers: a comparison of bioaugmentation and biostimulation for chlorinated solvent remediation. Environ Sci Technol 37(7):1422–1431CrossRefGoogle Scholar
  106. Lévesque M-J, La Boissière S, Thomas J-C, Beaudet R, Villemur R (1997) Rapid method for detecting Desulfitobacterium frappieri strain PCP-1 in soil by the polymerase chain reaction. Appl Environ Microbiol 47(6):719–725Google Scholar
  107. Leys D, Adrian L, Smidt H (2013) Organohalide respiration: microbes breathing chlorinated molecules. Phil Trans R Soc B 368(1616):20120316PubMedPubMedCentralCrossRefGoogle Scholar
  108. Li Z, Yoshida N, Wang A, Nan J, Liang B, Zhang C, Zhang D, Suzuki D, Zhou X, Xiao Z, Katayama A (2015) Anaerobic mineralization of 2, 4, 6-tribromophenol to CO2 by a synthetic microbial community comprising Clostridium, Dehalobacter, and Desulfatiglans. Bioresour Technol 176:225–232PubMedCrossRefGoogle Scholar
  109. Linkfield T, Tiedje J (1990) Characterization of the requirements and substrates for reductive dehalogenation by strain DCB-1. J Ind Microbiol 5(1):9–15PubMedCrossRefGoogle Scholar
  110. Löffler FE, Champine JE, Ritalahti KM, Sprague SJ, Tiedje JM (1997a) Complete reductive dechlorination of 1,2-dichloropropane by anaerobic bacteria. Appl Environ Microbiol 63(7):2870–2875PubMedPubMedCentralGoogle Scholar
  111. Löffler FE, Ritalahti KM, Tiedje JM (1997b) Dechlorination of chloroethenes is inhibited by 2-bromoethanesulfonate in the absence of methanogens. Appl Environ Microbiol 63(12):4982–4985PubMedPubMedCentralGoogle Scholar
  112. Löffler FE, Sun Q, Li J, Tiedje JM (2000) 16S rRNA gene-based detection of tetrachloroethene-dechlorinating Desulfuromonas and Dehalococcoides species. Appl Environ Microbiol 66(4):1369–1374PubMedPubMedCentralCrossRefGoogle Scholar
  113. Löffler FE, Yan J, Ritalahti KM, Adrian L, Edwards EA, Konstantinidis KT, Müller 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):625–635Google Scholar
  114. Lohner ST, Spormann AM (2013) Identification of a reductive tetrachloroethene dehalogenase in Shewanella sediminis. Phil Trans R Soc B 368(1616):20120326PubMedPubMedCentralCrossRefGoogle Scholar
  115. Lookman R, Paulus D, Marnette E, Pijls C, Ryngaert A, Diels L, Volkering F (2007) Ground water transfer initiates complete reductive dechlorination in a PCE-contaminated aquifer. Ground Water Monit Remediat 27(3):65–74CrossRefGoogle Scholar
  116. Lorah MM, Olsen LD (1999) Natural attenuation of chlorinated volatile organic compounds in a freshwater tidal wetland: field evidence of anaerobic biodegradation. Water Res 35(12):3811–3827CrossRefGoogle Scholar
  117. Lovley DR, Giovannoni SJ, White DC, Champine JE, Phillips E, Gorby YA, Goodwin S (1993) Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. Arch Microbiol 159(4):336–344PubMedCrossRefGoogle Scholar
  118. Luijten ML, de Weert J, Smidt H, Boschker HT, de Vos WM, Schraa G, Stams AJ (2003) Description of Sulfurospirillum halorespirans sp. nov., an anaerobic, tetrachloroethene-respiring bacterium, and transfer of Dehalospirillum multivorans to the genus Sulfurospirillum as Sulfurospirillum multivorans comb. nov. Int J Syst Evol Microbiol 53 (3):787–793Google Scholar
  119. Madsen T, Licht D (1992) Isolation and characterization of an anaerobic chlorophenol-transforming bacterium. Appl Environ Microbiol 58(9):2874–2878PubMedPubMedCentralGoogle Scholar
  120. Mägli A, Wendt M, Leisinger T (1996) Isolation and characterization of Dehalobacterium formicoaceticum gen. nov. sp. nov., a strictly anaerobic bacterium utilizing dichloromethane as source of carbon and energy. Arch Microbiol 166(2):101–108CrossRefGoogle Scholar
  121. Magnuson JK, Stern RV, Gossett JM, Zinder SH, Burris DR (1998) Reductive dechlorination of tetrachloroethene to ethene by a two-component enzyme pathway. Appl Environ Microbiol 64(4):1270–1275PubMedPubMedCentralGoogle Scholar
  122. Magnuson JK, Romine MF, Burris DR, Kingsley MT (2000) Trichloroethene reductive dehalogenase from Dehalococcoides ethenogenes: Sequence of tceA and substrate range characterization. Appl Environ Microbiol 66(12):5141–5147PubMedPubMedCentralCrossRefGoogle Scholar
  123. Maillard J, Schumacher W, Vazquez F, Regeard C, Hagen WR, Holliger C (2003) Characterization of the corrinoid iron-sulfur protein tetrachloroethene reductive dehalogenase of Dehalobacter restrictus. Appl Environ Microbiol 69(8):4628–4638PubMedPubMedCentralCrossRefGoogle Scholar
  124. Maillard J, Charnay MP, Regeard C, Rohrbach-Brandt E, Rouzeau-Szynalski K, Rossi P, Holliger C (2011) Reductive dechlorination of tetrachloroethene by a stepwise catalysis of different organohalide respiring bacteria and reductive dehalogenases. Biodegradation 22(5):949–960PubMedCrossRefGoogle Scholar
  125. Major DW, McMaster ML, Cox EE, Edwards EA, Dworatzek SM, Hendrickson ER, Starr MG, Payne JA, Buonamici LW (2002) Field demonstration of successful bioaugmentation to achieve dechlorination of tetrachloroethene to ethene. Environ Sci Technol 36(23):5106–5116PubMedCrossRefGoogle Scholar
  126. Maphosa F, de Vos WM, Smidt H (2010) Exploiting the ecogenomics toolbox for environmental diagnostics of organohalide-respiring bacteria. Trends Biotechnol 28(6):308–316PubMedCrossRefGoogle Scholar
  127. Maphosa F, van Passel MWJ, de Vos WM, Smidt H (2012) Metagenome analysis reveals yet unexplored reductive dechlorinating potential of Dehalobacter sp. E1 growing in co-culture with Sedimentibacter sp. Environ Microbiol Reports 4 (6):604–616Google Scholar
  128. Marzorati M, De Ferra F, Van Raemdonck H, Borin S, Allifranchini E, Carpani G, Serbolisca L, Verstraete W, Boon N, Daffonchio D (2007) A novel reductive dehalogenase, identified in a contaminated groundwater enrichment culture and in Desulfitobacterium dichloroeliminans strain DCA1, is linked to dehalogenation of 1, 2-dichloroethane. Appl Environ Microbiol 73(9):2990–2999PubMedPubMedCentralCrossRefGoogle Scholar
  129. May HD, Miller GS, Kjellerup BV, Sowers KR (2008) Dehalorespiration with polychlorinated biphenyls by an anaerobic ultramicrobacterium. Appl Environ Microbiol 74(7):2089–2094PubMedPubMedCentralCrossRefGoogle Scholar
  130. Maymo-Gatell X, Y-t Chien, Gossett JM, Zinder SH (1997) Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276(5318):1568–1571PubMedCrossRefGoogle Scholar
  131. McMurdie PJ, Behrens SF, Müller JA, Göke J, Ritalahti KM, Wagner R, Goltsman E, Lapidus A, Holmes S, Löffler FE, Spormann AM (2009) Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS Genet 5(11):e1000714PubMedPubMedCentralCrossRefGoogle Scholar
  132. McMurdie PJ, Hug LA, Edwards EA, Holmes S, Spormann AM (2011) Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides. BMC Genom 12(1):287CrossRefGoogle Scholar
  133. McNamara PJ, Krzmarzick MJ (2013) Triclosan enriches for Dehalococcoides-like Chloroflexi in anaerobic soil at environmentally relevant concentrations. FEMS Microbiol Lett 344(1):48–52PubMedCrossRefGoogle Scholar
  134. Men Y, Lee PK, Harding KC, Alvarez-Cohen L (2013) Characterization of four TCE-dechlorinating microbial enrichments grown with different cobalamin stress and methanogenic conditions. Appl Microbiol Biotechnol 97:1–12CrossRefGoogle Scholar
  135. Men Y, Seth EC, Yi S, Crofts TS, Allen RH, Taga ME, Alvarez-Cohen L (2014) Identification of specific corrinoids reveals corrinoid modification in dechlorinating microbial communities. Environ Microbiol 17(12):4873–4884PubMedCrossRefGoogle Scholar
  136. Miller E, Wohlfarth G, Diekert G (1997) Comparative studies on tetrachloroethene reductive dechlorination mediated by Desulfitobacterium sp. strain PCE-S. Arch Microbiol 168(6):513–519PubMedCrossRefGoogle Scholar
  137. Miller E, Wohlfarth G, Diekert G (1998) Purification and characterization of the tetrachloroethene reductive dehalogenase of strain PCE-S. Arch Microbiol 169(6):497–502PubMedCrossRefGoogle Scholar
  138. Miller GS, Milliken CE, Sowers KR, May HD (2005) Reductive dechlorination of tetrachloroethene to trans-dichloroethene and cis-dichloroethene by PCB-dechlorinating bacterium DF-1. Environ Sci Technol 39(8):2631–2635PubMedCrossRefGoogle Scholar
  139. Moe WM, Yan J, Nobre MF, da Costa MS, Rainey FA (2009) Dehalogenimonas lykanthroporepellens gen. nov., sp. nov., a reductively dehalogenating bacterium isolated from chlorinated solvent-contaminated groundwater. Int J Syst Evol Microbiol 59(11):2692–2697Google Scholar
  140. Mukherjee K, Bowman KS, Rainey FA, Siddaramappa S, Challacombe JF, Moe WM (2014) Dehalogenimonas lykanthroporepellens BL-DC-9T simultaneously transcribes many rdhA genes during organohalide respiration with 1,2-DCA, 1,2-DCP and 1,2,3-TCP as electron acceptors. FEMS Microbiol Lett 351:111–118CrossRefGoogle Scholar
  141. Müller JA, Rosner BM, Von Abendroth G, Meshulam-Simon G, McCarty PL, Spormann AM (2004) Molecular identification of the catabolic vinyl chloride reductase from Dehalococcoides sp. strain VS and its environmental distribution. Appl Environ Microbiol 70(8):4880–4888PubMedPubMedCentralCrossRefGoogle Scholar
  142. Nelson JJJ, Zinder S (2014) Dehalogenation of chlorobenzenes, dichlorotoluene, and tetrachloroethene by three Dehalobacter spp. Environ Sci Technol 48(7):3776–3782PubMedCrossRefGoogle Scholar
  143. Nelson JL, Fung JM, Cadillo-Quiroz H, Cheng X, Zinder SH (2011) A role for Dehalobacter spp. in the reductive dehalogenation of dichlorobenzenes and monochlorobenzene. Environ Sci Technol 45(16):6806–6813Google Scholar
  144. Niggemyer A, Spring S, Stackebrandt E, Rosenzweig RF (2001) Isolation and characterization of a novel As (V)-reducing bacterium: implications for arsenic mobilization and the genus Desulfitobacterium. Appl Environ Microbiol 67(12):5568–5580PubMedPubMedCentralCrossRefGoogle Scholar
  145. Nijenhuis I, Nikolausz M, Köth A, Felföldi T, Weiss H, Drangmeister J, Großmann J, Kästner M, Richnow H-H (2007) Assessment of the natural attenuation of chlorinated ethenes in an anaerobic contaminated aquifer in the Bitterfeld/Wolfen area using stable isotope techniques, microcosm studies and molecular biomarkers. Chemosphere 67(2):300–311PubMedCrossRefGoogle Scholar
  146. Nonaka H, Keresztes G, Shinoda Y, Ikenaga Y, Abe M, Naito K, Inatomi K, Furukawa K, Inui M, Yukawa H (2006) Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195. J Bacteriol 188(6):2262–2274PubMedPubMedCentralCrossRefGoogle Scholar
  147. Øfjord G, Puhakka JA, Ferguson JF (1994) Reductive dechlorination of Aroclor 1254 by marine sediment cultures. Environ Sci Technol 28(13):2286–2294CrossRefGoogle Scholar
  148. Padilla-Crespo E, Yan J, Swift C, Wagner DD, Chourey K, Hettich RL, Ritalahti KM, Löffler FE (2014) Identification and environmental distribution of dcpA, which encodes the reductive dehalogenase catalyzing the dichloroelimination of 1,2-dichloropropane to propene in organohalide-respiring Chloroflexi. Appl Environ Microbiol 80(3):808–818PubMedPubMedCentralCrossRefGoogle Scholar
  149. Parthasarathy A, Stich TA, Lohner ST, Lesnefsky A, Britt RD, Spormann AM (2015) Biochemical and EPR-spectroscopic investigation into heterologously expressed vinyl chloride reductive dehalogenase (VcrA) from Dehalococcoides mccartyi strain VS. J Am Chem Soc 137(10):3525–3532PubMedPubMedCentralCrossRefGoogle Scholar
  150. Payne RB, May HD, Sowers KR (2011) Enhanced reductive dechlorination of polychlorinated biphenyl impacted sediment by bioaugmentation with a dehalorespiring bacterium. Environ Sci Technol 45(20):8772–8779PubMedPubMedCentralCrossRefGoogle Scholar
  151. Payne KA, Quezada CP, Fisher K, Dunstan MS, Collins FA, Sjuts H, Levy C, Hay S, Rigby SE, Leys D (2014) Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation. Nature 517:513–516PubMedPubMedCentralCrossRefGoogle Scholar
  152. Pöritz M, Goris T, Wubet T, Tarkka MT, Buscot F, Nijenhuis I, Lechner U, Adrian L (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):101–104PubMedCrossRefGoogle Scholar
  153. Richardson RE (2013) Genomic insights into organohalide respiration. Curr Opin Biotechnol 24:498–505PubMedCrossRefGoogle Scholar
  154. Richardson RE, Bhupathiraju VK, Song DL, Goulet TA, Alvarez-Cohen L (2002) Phylogenetic characterization of microbial communities that reductively dechlorinate TCE based upon a combination of molecular techniques. Environ Sci Technol 36(12):2652–2662PubMedCrossRefGoogle Scholar
  155. Ritalahti KM, Löffler FE (2004) Populations implicated in anaerobic reductive dechlorination of 1,2-dichloropropane in highly enriched bacterial communities. Appl Environ Microbiol 70(7):4088–4095PubMedPubMedCentralCrossRefGoogle Scholar
  156. Ritalahti KM, Amos BK, Sung Y, Wu Q, Koenigsberg SS, Löffler FE (2006) Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains. Appl Environ Microbiol 72(4):2765–2774PubMedPubMedCentralCrossRefGoogle Scholar
  157. Rosner B, McCarty P, Spormann A (1997) In vitro studies on reductive vinyl chloride dehalogenation by an anaerobic mixed culture. Appl Environ Microbiol 63(11):4139–4144PubMedPubMedCentralGoogle Scholar
  158. Rotaru DEH, Franks AE, Orellana R, Risso C, Nevin KP (2011) Geobacter: the microbe electric’s physiology, ecology, and practical applications. Adv Microb Physiol 59:1PubMedCrossRefGoogle Scholar
  159. Rouzeau-Szynalski K, Maillard J, Holliger C (2011) Frequent concomitant presence of Desulfitobacterium spp. and “Dehalococcoides” spp. in chloroethene-dechlorinating microbial communities. Appl Microbiol Biotechnol 90(1):361–368PubMedCrossRefGoogle Scholar
  160. Rowe AR, Lazar BJ, Morris RM, Richardson RE (2008) Characterization of the community structure of a dechlorinating mixed culture and comparisons of gene expression in planktonic and biofloc-associated “Dehalococcoides” and Methanospirillum species. Appl Environ Microbiol 74(21):6709–6719PubMedPubMedCentralCrossRefGoogle Scholar
  161. Rupakula A, Kruse T, Boeren S, Holliger C, Smidt H, Maillard J (2013) The restricted metabolism of the obligate organohalide respiring bacterium Dehalobacter restrictus: lessons from tiered functional genomics. Phil Trans R Soc B 368 (1616)Google Scholar
  162. Rupakula A, Lu Y, Kruse T, Boeren S, Holliger C, Smidt H, Maillard J (2014) Functional genomics of corrinoid starvation in the organohalide-respiring bacterium Dehalobacter restrictus strain PER-K23. Front Microbiol 5:751PubMedGoogle Scholar
  163. Sanford RA, Cole JR, Löffler FE, Tiedje JM (1996) Characterization of Desulfitobacterium chlororespirans sp. nov., which grows by coupling the oxidation of lactate to the reductive dechlorination of 3-chloro-4-hydroxybenzoat. Appl Environ Microbiol 62(10):3800–3808PubMedPubMedCentralGoogle Scholar
  164. Sanford RA, Cole JR, Tiedje JM (2002) Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium. Appl Environ Microbiol 68(2):893–900PubMedPubMedCentralCrossRefGoogle Scholar
  165. Scheutz C, Durant Nd, Dennis P, Hansen MH, Jørgensen T, Jakobsen R, Ee Cox, Bjerg PL (2008) Concurrent ethene generation and growth of Dehalococcoides containing vinyl chloride reductive dehalogenase genes during an enhanced reductive dechlorination field demonstration. Environ Sci Technol 42(24):9302–9309PubMedCrossRefGoogle Scholar
  166. Schneidewind U, Haest PJ, Atashgahi S, Maphosa F, Hamonts K, Maesen M, Calderer M, Seuntjens P, Smidt H, Springael D, Dejonghe W (2014) Kinetics of dechlorination by Dehalococcoides mccartyi using different carbon sources. J Contam Hydrol 157:25–36PubMedCrossRefGoogle Scholar
  167. Scholz-Muramatsu H, Neumann A, Messmer M, Moore E, Diekert G (1995) Isolation and characterization of Dehalospirillum multivorans gen. nov., sp. nov., a tetrachloroethene-utilizing, strictly anaerobic bacterium. Arch Microbiol 163(1):48–56CrossRefGoogle Scholar
  168. Schumacher W, Kroneck PM, Pfennig N (1992) Comparative systematic study on “Spirillum” 5175. Campylobacter and Wolinella species. Arch Microbiol 158(4):287–293CrossRefGoogle Scholar
  169. Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, Kolonay JF, Dodson RJ, Daugherty SC, Brinkac LM, Sullivan SA, Madupu R, Nelson KE, Kang KH, Impraim M, Tran K, Robinson JM, Forberger HA, Fraser CM, Zinder SH, Heidelberg JF (2005) Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science 307(5706):105–108PubMedCrossRefGoogle Scholar
  170. Shani N, Rossi P, Holliger C (2013) Correlations between environmental variables and bacterial community structures suggest Fe (III) and vinyl chloride reduction as antagonistic terminal electron-accepting processes. Environ Sci Technol 47(13):6836–6845PubMedGoogle Scholar
  171. Shelobolina ES, Vanpraagh CG, Lovley DR (2003) Use of ferric and ferrous iron containing minerals for respiration by Desulfitobacterium frappieri. Geomicrobiol J 20(2):143–156Google Scholar
  172. Shelton DR, Tiedje JM (1984) Isolation and partial characterization of bacteria in an anaerobic consortium that mineralizes 3-chlorobenzoic acid. Appl Environ Microbiol 48(4):840–848PubMedPubMedCentralGoogle Scholar
  173. Siddaramappa S, Challacombe JF, Delano SF, Green LD, Daligault H, Bruce D, Detter C, Tapia R, Han S, Goodwin L, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Miriam L, Yun-Juan C, Kyrpides NC, Ovchinnikova G, Hauser L, Lapidus A, Yan J, Bowman KS, da Costa MS, Rainey FA, Moe WM (2012) Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9T) and comparison to “Dehalococcoides” strains. Stand Genomic Sci 6(2):251PubMedPubMedCentralCrossRefGoogle Scholar
  174. Smatlak CR, Gossett JM, Zinder SH (1996) Comparative kinetics of hydrogen utilization for reductive dechlorination of tetrachloroethene and methanogenesis in an anaerobic enrichment culture. Environ Sci Technol 30(9):2850–2858CrossRefGoogle Scholar
  175. Smits TH, Devenoges C, Szynalski K, Maillard J, Holliger C (2004) Development of a real-time PCR method for quantification of the three genera Dehalobacter, Dehalococcoides, and Desulfitobacterium in microbial communities. J Microbiol Methods 57(3):369–378PubMedCrossRefGoogle Scholar
  176. Stams AJ, Plugge CM (2009) Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat Rev Microbiol 7(8):568–577PubMedCrossRefGoogle Scholar
  177. Suflita JM, Horowitz A, Shelton DR, Tiedje JM (1982) Dehalogenation: a novel pathway for the anaerobic biodegradation of haloaromatic compounds. Science 218(4577):1115–1117PubMedCrossRefGoogle Scholar
  178. Sun B, Cole JR, Sanford RA, Tiedje JM (2000) Isolation and characterization of Desulfovibrio dechloracetivorans sp. nov., a marine dechlorinating bacterium growing by coupling the oxidation of acetate to the reductive dechlorination of 2-chlorophenol. Appl Environ Microbiol 66(6):2408–2413PubMedPubMedCentralCrossRefGoogle Scholar
  179. Sun B, Cole JR, Tiedje JM (2001) Desulfomonile limimaris sp. nov., an anaerobic dehalogenating bacterium from marine sediments. Int J Syst Evol Microbiol 51(2):365–371PubMedCrossRefGoogle Scholar
  180. Sun B, Griffin BM, Ayala-del-Rio HL, Hashsham SA, Tiedje JM (2002) Microbial dehalorespiration with 1,1,1-trichloroethane. Science 298(5595):1023–1025PubMedCrossRefGoogle Scholar
  181. Sung Y, Ritalahti KM, Sanford RA, Urbance JW, Flynn SJ, Tiedje JM, Löffler FE (2003) Characterization of two tetrachloroethene-reducing, acetate-oxidizing anaerobic bacteria and their description as Desulfuromonas michiganensis sp. nov. Appl Environ Microbiol 69(5):2964–2974PubMedPubMedCentralCrossRefGoogle Scholar
  182. Sung Y, Fletcher KE, Ritalahti KM, Apkarian RP, Ramos-Hernández N, Sanford RA, Mesbah NM, Löffler FE (2006a) Geobacter lovleyi sp. nov. strain SZ, a novel metal-reducing and tetrachloroethene-dechlorinating bacterium. Appl Environ Microbiol 72(4):2775–2782PubMedPubMedCentralCrossRefGoogle Scholar
  183. Sung Y, Ritalahti K, Apkarian R, Loffler F (2006b) Quantitative PCR confirms purity of strain GT, a novel trichloroethene-to-ethene-respiring Dehalococcoides isolate. Appl Environ Microbiol 72(3):1980–1987PubMedPubMedCentralCrossRefGoogle Scholar
  184. Suyama A, Iwakiri R, Kai K, Tokunaga T, Sera N, Furukawa K (2001) Isolation and characterization of Desulfitobacterium sp strain Y51 capable of efficient dehalogenation of tetrachloroethene and polychloroethanes. Biosci Biotechnol Biochem 65(7):1474–1481PubMedCrossRefGoogle Scholar
  185. Suyama A, Yamashita M, Yoshino S, Furukawa K (2002) Molecular characterization of the PceA reductive dehalogenase of Desulfitobacterium sp. strain Y51. J Bacteriol 184(13):3419–3425PubMedPubMedCentralCrossRefGoogle Scholar
  186. Suzuki D, Ueki A, Amaishi A, Ueki K (2008) Desulfoluna butyratoxydans gen. nov., sp. nov., a novel Gram-negative, butyrate-oxidizing, sulfate-reducing bacterium isolated from an estuarine sediment in Japan. Int J Syst Evol Microbiol 58(4):826–832PubMedCrossRefGoogle Scholar
  187. Taş N, Van Eekert MH, Schraa G, Zhou J, De Vos WM, Smidt H (2009) Tracking functional guilds:“Dehalococcoides” spp. in European river basins contaminated with hexachlorobenzene. Appl Environ Microbiol 75(14):4696–4704PubMedPubMedCentralCrossRefGoogle Scholar
  188. Thibodeau J, Gauthier A, Duguay M, Villemur R, Lépine F, Juteau P, Beaudet R (2004) Purification, cloning, and sequencing of a 3, 5-dichlorophenol reductive dehalogenase from Desulfitobacterium frappieri PCP-1. Appl Environ Microbiol 70(8):4532–4537PubMedPubMedCentralCrossRefGoogle Scholar
  189. Thomas SH, Wagner RD, Arakaki AK, Skolnick J, Kirby JR, Shimkets LJ, Sanford RA, Löffler FE (2008) The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-Proteobacteria. PLoS ONE 3(5):e2103PubMedPubMedCentralCrossRefGoogle Scholar
  190. Thornton SF, Bright MI, Lerner DN, Tellam JH (2000) Attenuation of landfill leachate by UK Triassic Sandstone aquifer materials: 2. Sorption and degradation of organic pollutants in laboratory columns. J Contam Hydrol 43(3):355–383CrossRefGoogle Scholar
  191. Tobiszewski M, Namieśnik J (2012) Abiotic degradation of chlorinated ethanes and ethenes in water. Environ Sci Poll R 19(6):1994–2006CrossRefGoogle Scholar
  192. Tsukagoshi N, Ezaki S, Uenaka T, Suzuki N, Kurane R (2006) Isolation and transcriptional analysis of novel tetrachloroethene reductive dehalogenase gene from Desulfitobacterium sp. strain KBC1. Appl Microbiol Biotechnol 69(5):543–553PubMedCrossRefGoogle Scholar
  193. Utkin I, Woese C, Wiegel J (1994) Isolation and characterization of Desulfitobacterium dehalogenans gen. nov., sp. nov., an anaerobic bacterium which reductively dechlorinates chlorophenolic compounds. Int J Syst Bacteriol 44(4):612–619PubMedCrossRefGoogle Scholar
  194. van de Pas BA, Smidt H, Hagen WR, van der Oost J, Schraa G, Stams AJ, de Vos WM (1999) Purification and molecular characterization of ortho-chlorophenol reductive dehalogenase, a key enzyme of halorespiration in Desulfitobacterium dehalogenans. J Biol Chem 274(29):20287–20292PubMedCrossRefGoogle Scholar
  195. van de Pas BA, Gerritse J, de Vos WM, Schraa G, Stams AJ (2001) Two distinct enzyme systems are responsible for tetrachloroethene and chlorophenol reductive dehalogenation in Desulfitobacterium strain PCE1. Arch Microbiol 176(3):165–169PubMedCrossRefGoogle Scholar
  196. van der Zaan B, Hannes F, Hoekstra N, Rijnaarts H, de Vos WM, Smidt H, Gerritse J (2010) Correlation of Dehalococcoides 16S rRNA and chloroethene-reductive dehalogenase genes with geochemical conditions in chloroethene-contaminated groundwater. Appl Environ Microbiol 76(3):843–850PubMedCrossRefGoogle Scholar
  197. Van der Zee FP, Cervantes FJ (2009) Impact and application of electron shuttles on the redox (bio) transformation of contaminants: a review. Biotechnol Adv 27(3):256–277PubMedCrossRefGoogle Scholar
  198. van Doesburg W, Eekert MH, Middeldorp PJ, Balk M, Schraa G, Stams AJ (2005) Reductive dechlorination of β-hexachlorocyclohexane (β-HCH) by a Dehalobacter species in coculture with a Sedimentibacter sp. FEMS Microbiol Ecol 54(1):87–95PubMedCrossRefGoogle Scholar
  199. Villemur R, Lanthier M, Beaudet R, Lépine F (2006) The Desulfitobacterium genus. FEMS Microbiol Rev 30(5):706–733PubMedCrossRefGoogle Scholar
  200. Wagner DD, Hug LA, Hatt JK, Spitzmiller MR, Padilla-Crespo E, Ritalahti KM, Edwards EA, Konstantinidis KT, Löffler FE (2012) Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae. BMC Genom 13(1):200CrossRefGoogle Scholar
  201. Wang S, He J (2013a) Dechlorination of commercial PCBs and other multiple halogenated compounds by a sediment-free culture containing Dehalococcoides and Dehalobacter. Environ Sci Technol 47(18):10526–10534PubMedGoogle Scholar
  202. Wang S, He J (2013b) Phylogenetically distinct bacteria involve extensive dechlorination of Aroclor 1260 in sediment-free cultures. PLoS ONE 8(3):e59178PubMedPubMedCentralCrossRefGoogle Scholar
  203. Wang S, Chng KR, Wilm A, Zhao S, Yang K-L, Nagarajan N, He J (2014a) Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls. Proc Natl Acad Sci USA 111(33):12103–12108PubMedPubMedCentralCrossRefGoogle Scholar
  204. Wang S, Zhang W, Yang K-L, He J (2014b) Isolation and characterization of a novel Dehalobacter species strain TCP1 that reductively dechlorinates 2,4,6-trichlorophenol. Biodegradation 25(2):313–323PubMedCrossRefGoogle Scholar
  205. Wasmund K, Schreiber L, Lloyd KG, Petersen DG, Schramm A, Stepanauskas R, Jørgensen BB, Adrian L (2014) Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi. ISME J 8(2):383–397PubMedCrossRefGoogle Scholar
  206. Wasmund K, Algora C, Müller J, Krüger M, Lloyd KG, Reinhard R, Adrian L (2015) Development and application of primers for the class Dehalococcoidia (phylum Chloroflexi) reveals highly diverse and stratified sub-group distributions in the marine subsurface. Environ Microbiol 17(10):3540–3556PubMedCrossRefGoogle Scholar
  207. Watts JE, Fagervold SK, May HD, Sowers KR (2005) A PCR-based specific assay reveals a population of bacteria within the Chloroflexi associated with the reductive dehalogenation of polychlorinated biphenyls. Microbiol 151(6):2039–2046CrossRefGoogle Scholar
  208. Webster G, Parkes RJ, Cragg BA, Newberry CJ, Weightman AJ, Fry JC (2006) Prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin. FEMS Microbiol Ecol 58(1):65–85PubMedCrossRefGoogle Scholar
  209. Wild A, Hermann R, Leisinger T (1996) Isolation of an anaerobic bacterium which reductively dechlorinates tetrachloroethene and trichloroethene. Biodegradation 7(6):507–511PubMedCrossRefGoogle Scholar
  210. Wu Q, Sowers KR, May HD (2000) Establishment of a polychlorinated biphenyl-dechlorinating microbial consortium, specific for doubly flanked chlorines, in a defined, sediment-free medium. Appl Environ Microbiol 66(1):49–53PubMedPubMedCentralCrossRefGoogle Scholar
  211. Wu Q, Milliken CE, Meier GP, Watts JE, Sowers KR, May HD (2002a) Dechlorination of chlorobenzenes by a culture containing bacterium DF-1, a PCB dechlorinating microorganism. Environ Sci Technol 36(15):3290–3294PubMedCrossRefGoogle Scholar
  212. Wu Q, Watts JE, Sowers KR, May HD (2002b) Identification of a bacterium that specifically catalyzes the reductive dechlorination of polychlorinated biphenyls with doubly flanked chlorines. Appl Environ Microbiol 68(2):807–812PubMedPubMedCentralCrossRefGoogle Scholar
  213. Yan J, Rash B, Rainey F, Moe W (2009) Isolation of novel bacteria within the Chloroflexi capable of reductive dechlorination of 1,2,3-trichloropropane. Environ Microbiol 11(4):833–843PubMedCrossRefGoogle Scholar
  214. Yan J, Ritalahti KM, Wagner DD, Löffler FE (2012) Unexpected specificity of interspecies cobamide transfer from Geobacter spp. to organohalide-respiring Dehalococcoides mccartyi strains. Appl Environ Microbiol 78(18):6630–6636PubMedPubMedCentralCrossRefGoogle Scholar
  215. Yi S, Seth EC, Men Y-J, Stabler SP, Allen RH, Alvarez-Cohen L, Taga ME (2012) Versatility in corrinoid salvaging and remodeling pathways supports corrinoid-dependent metabolism in Dehalococcoides mccartyi. Appl Environ Microbiol 78(21):7745–7752PubMedPubMedCentralCrossRefGoogle Scholar
  216. Yoshida N, Asahi K, Sakakibara Y, Miyake K, Katayama A (2007a) Isolation and quantitative detection of tetrachloroethene (PCE)-dechlorinating bacteria in unsaturated subsurface soils contaminated with chloroethenes. J Biosci Bioeng 104(2):91–97PubMedCrossRefGoogle Scholar
  217. Yoshida N, Yoshida Y, Handa Y, Kim H-K, Ichihara S, Katayama A (2007b) Polyphasic characterization of a PCP-to-phenol dechlorinating microbial community enriched from paddy soil. Sci Total Environ 381(1):233–242PubMedCrossRefGoogle Scholar
  218. Yoshida N, Ye L, Baba D, Katayama A (2009) A novel Dehalobacter species is involved in extensive 4,5,6,7-tetrachlorophthalide dechlorination. Appl Environ Microbiol 75(8):2400–2405PubMedPubMedCentralCrossRefGoogle Scholar
  219. Zanaroli G, Balloi A, Negroni A, Borruso L, Daffonchio D, Fava F (2012) A Chloroflexi bacterium dechlorinates polychlorinated biphenyls in marine sediments under in situ-like biogeochemical conditions. J Hazard Mater 209:449–457PubMedCrossRefGoogle Scholar
  220. Zhang C, Katayama A (2012) Humin as an electron mediator for microbial reductive dehalogenation. Environ Sci Technol 46(12):6575–6583PubMedCrossRefGoogle Scholar
  221. Zhao JS, Spain J, Thiboutot S, Ampleman G, Greer C, Hawari J (2004) Phylogeny of cyclic nitramine-degrading psychrophilic bacteria in marine sediment and their potential role in the natural attenuation of explosives. FEMS Microbiol Ecol 49(3):349–357PubMedCrossRefGoogle Scholar
  222. Zhao J-S, Manno D, Beaulieu C, Paquet L, Hawari J (2005) Shewanella sediminis sp. nov., a novel Na+-requiring and hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading bacterium from marine sediment. Int J Syst Evol Microbiol 55(4):1511–1520PubMedCrossRefGoogle Scholar
  223. Zhao J-S, Deng Y, Manno D, Hawari J (2010) Shewanella spp. genomic evolution for a cold marine lifestyle and in-situ explosive biodegradation. PLoS ONE 5(2):e9109PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Laboratory of MicrobiologyWageningen UniversityWageningenThe Netherlands

Personalised recommendations