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Organohalide-Respiring Bacteria as Members of Microbial Communities: Catabolic Food Webs and Biochemical Interactions

  • Ruth E. RichardsonEmail author
Chapter

Abstract

Organohalide-respiring bacteria (OHRB) have been isolated from a wide range of anoxic environments worldwide and can easily be enriched in the laboratory. Obligate OHRB generally thrive best in mixed communities as part of anaerobic food webs that typically involve interspecies hydrogen (H2) transfer from fermenters to OHRB, and often OHRB compete for H2 with hydrogenotrophic methanogens. In laboratory enrichments, the community composition of the non-OHRB fraction of the communities is dependent on which electron donor is used for enrichment as well as other factors (e.g., the concentrations of organohalide substrate). In addition to catabolic food webs, other biochemical interactions in these communities include provision of key cofactors (e.g., corrinoids), relief of toxicity due to reactive oxygen species, as well as the organohalides themselves. Multiple OHRB often coexist stably in enrichment cultures and environmental communities. This diversity in OHRB populations creates complex interactions among different OHRB—with the partially dehalogenated end product of one population serving as substrate for other populations. Recent broad surveys of bacterial and archaeal community structure at sites undergoing in situ bioremediation are confirming that fermenters, methanogens, and OHRB are all stimulated by enhanced bioremediation efforts but that aerobes including methanotrophs and organohalide-oxidizing aerobes are also stimulated—especially in downgradient plume regions. The chapter will also discuss roles of OHRB populations in pristine environments including soils and sediments where they dehalogenate naturally produced halogenated organic matter and may compete with sulfate reducers and iron reducers when appropriate electron acceptors are available.

Keywords

Electron Donor Clone Library Enrichment Culture Hydrogenotrophic Methanogen Acetoclastic Methanogen 
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.

Abbreviations

Dhc

Dehalococcoides

OHRB

Organohalide-respiring bacteria

Dhb

Dehalobacter

RDase

Reductive dehalogenase

PCE

Tetrachloroethene

TCE

Trichloroethene

cis-DCE

cis-1,2-dichloroethene

VC

Vinyl chloride

DNAPL

Dense nonaqueous phase liquid

PCBs

Polychlorinated biphenyls

Notes

Acknowledgments

The author acknowledges the collective work of many researchers worldwide and the public and private funding agencies that have made this area of research possible. Thanks to Elizabeth Edwards and Cresten Mansfeldt for input on the chapter content.

References

  1. Adrian L, Manz W, Szewzyk U, Gorisch 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
  2. Adrian L, Szewzyk U, Gorisch H (2000a) Bacterial growth based on reductive dechlorination of trichlorobenzenes. Biodegradation 11(1):73–81PubMedCrossRefGoogle Scholar
  3. Adrian L, Szewzyk U, Wecke J, Gorisch H (2000b) Bacterial dehalorespiration with chlorinated benzenes. Nature 408(6812):580–583PubMedCrossRefGoogle Scholar
  4. Aeppli C, Bastviken D, Andersson P, Gustafsson Ö (2013) Chlorine isotope effects and composition of naturally produced organochlorines from chloroperoxidases, flavin-dependent halogenases, and in forest soil. Environ Sci Technol 47(13):6864–6871. doi: 10.1021/es3037669 PubMedGoogle Scholar
  5. Ahn YB, Rhee SK, 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
  6. Ahn Y-B, Haggblom 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):362–371. doi: 10.1111/j.1574-6941.2007.00342.x PubMedCrossRefGoogle Scholar
  7. Arp DJ, Yeager CM, Hyman MR (2001) Molecular and cellular fundamentals of aerobic cometabolism of trichloroethylene. Biodegradation 12(2):81–103. doi: 10.1023/a:1012089908518 PubMedCrossRefGoogle Scholar
  8. Asplund G, Grimvall A (1991) Organohalogens in nature. Environ Sci Technol 25(8):1346–1350CrossRefGoogle Scholar
  9. Aulenta F, Majone M, Verbo P, Tandoi V (2002) Complete dechlorination of tetrachloroethene to ethene in presence of methanogenesis and acetogenesis by an anaerobic sediment microcosm. Biodegradation 13(6):411–424Google Scholar
  10. Aulenta F, Gossett JM, Papini MP, Rossetti S, Majone M (2005) Comparative study of methanol, butyrate, and hydrogen as electron donors for long-term dechlorination of tetrachloroethene in mixed anerobic cultures. Biotechnol Bioeng 91(6):743–753PubMedCrossRefGoogle Scholar
  11. Aulenta F, Catervi A, Majone M, Panero S, Reale P, Rossetti S (2007) Electron transfer from a solid-state electrode assisted by methyl viologen sustains efficient microbial reductive dechlorination of TCE. Environ Sci Technol 41(7):2554–2559PubMedCrossRefGoogle Scholar
  12. Baelum J, Chambon JC, Scheutz C, Binning PJ, Laier T, Bjerg PL, Jacobsen CS (2013) A conceptual model linking functional gene expression and reductive dechlorination rates of chlorinated ethenes in clay rich groundwater sediment. Water Res 47(7):2467–2478. doi: 10.1016/j.watres.2013.02.016 PubMedCrossRefGoogle Scholar
  13. Baelum J, Scheutz C, Chambon JC, Jensen CM, Brochmann RP, Dennis P, Laier T, Broholm MM, Bjerg PL, Binning PJ, Jacobsen CS (2014) The impact of bioaugmentation on dechlorination kinetics and on microbial dechlorinating communities in subsurface clay till. Environ Pollut 186:149–157. doi: 10.1016/j.envpol.2013.11.013 PubMedCrossRefGoogle Scholar
  14. Ballerstedt H, Hantke J, Bunge M, Werner B, Gerritse J, Andreesen JR, Lechner U (2004) Properties of a trichlorodibenzo-p-dioxin-dechlorinating mixed culture with a Dehalococcoides as putative dechlorinating species. FEMS Microbiol Ecol 47(2):223–234PubMedCrossRefGoogle Scholar
  15. Bastviken D, Thomsen F, Svensson T, Karlsson S, Sanden P, Shaw G, Matucha M, Oberg G (2007) Chloride retention in forest soil by microbial uptake and by natural chlorination of organic matter. Geochim Cosmochim Acta 71(13):3182–3192. doi: 10.1016/j.gca.2007.04.028 CrossRefGoogle Scholar
  16. Bastviken D, Svensson T, Karlsson S, Sanden P, Oberg G (2009) Temperature sensitivity indicates that chlorination of organic matter in forest soil is primarily biotic. Environ Sci Technol 43(10):3569–3573. doi: 10.1021/es8035779 PubMedCrossRefGoogle Scholar
  17. Becker JG (2006) A modeling study and implications of competition between Dehalococcoides ethenogenes and other tetrachloroethene-respiring bacteria. Environ Sci Technol 40(14):4473–4480PubMedCrossRefGoogle Scholar
  18. Becker JG, Seagren EA (2009) Modeling the effects of microbial competition and hydrodynamics on the dissolution and detoxification of dense nonaqueous phase liquid contaminants. Environ Sci Technol 43(3):870–877. doi: 10.1021/es801616f PubMedCrossRefGoogle Scholar
  19. Bedard DL, Bailey JJ, Reiss BL, Jerzak GV (2006) Development and characterization of stable sediment-free anaerobic bacterial enrichment cultures that dechlorinate aroclor 1260. Appl Environ Microbiol 72(4):2460–2470PubMedPubMedCentralCrossRefGoogle Scholar
  20. Bedard DL, Ritalahti KA, Lӧffler FE (2007) The Dehalococcoides population in sediment-free mixed cultures metabolically dechlorinates the commercial polychlorinated biphenyl mixture aroclor 1260. Appl Environ Microbiol 73(8):2513–2521. doi: 10.1128/aem.02909-06 PubMedPubMedCentralCrossRefGoogle Scholar
  21. Bengtson P, Bastviken D, de Boer W, Oberg G (2009) Possible role of reactive chlorine in microbial antagonism and organic matter chlorination in terrestrial environments. Environ Microbiol 11(6):1330–1339. doi: 10.1111/j.1462-2920.2009.01915.x PubMedCrossRefGoogle Scholar
  22. Bowman KS, Moe WM, Rash BA, Bae HS, Rainey FA (2006) Bacterial diversity of an acidic Louisiana groundwater contaminated by dense nonaqueous-phase liquid containing chloroethanes and other solvents. FEMS Microbiol Ecol 58(1):120–133PubMedCrossRefGoogle Scholar
  23. 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 63:1492–1498. doi: 10.1099/ijs.0.045054-0 PubMedCrossRefGoogle Scholar
  24. Brisson VL, West KA, Lee PKH, Tringe SG, Brodie EL, Alvarez-Cohen L (2012) Metagenomic analysis of a stable trichloroethene-degrading microbial community. ISME J 6(9):1702–1714. doi: 10.1038/ismej.2012.15 PubMedPubMedCentralCrossRefGoogle Scholar
  25. Bunge M, Lechner U (2009) Anaerobic reductive dehalogenation of polychlorinated dioxins. Appl Microbiol Biotechnol 84(3):429–444. doi: 10.1007/s00253-009-2084-7 PubMedCrossRefGoogle Scholar
  26. Chambon JC, Bjerg PL, Scheutz C, Baelum J, Jakobsen R, Binning PJ (2013) Review of reactive kinetic models describing reductive dechlorination of chlorinated ethenes in soil and groundwater. Biotechnol Bioeng 110(1):1–23. doi: 10.1002/bit.24714 PubMedCrossRefGoogle Scholar
  27. Chen MJ, Abriola LM, Amos BK, Suchomel EJ, Pennell KD, Lӧffler FE, Christ JA (2013) Microbially enhanced dissolution and reductive dechlorination of PCE by a mixed culture: Model validation and sensitivity analysis. J Contam Hydrol 151:117–130. doi: 10.1016/j.jconhyd.2013.05.005 PubMedCrossRefGoogle Scholar
  28. Cheng D, Chow WL, He J (2010) A Dehalococcoides-containing co-culture that dechlorinates tetrachloroethene to trans-1,2-dichloroethene. ISME J 4(1). doi: 10.1038/ismej.2009.90
  29. Clarke N, Fuksova K, Gryndler M, Lachmanova Z, Liste HH, Rohlenova J, Schroll R, Schroder P, Matucha M (2009) The formation and fate of chlorinated organic substances in temperate and boreal forest soils. Environ Sci Pollut Res 16(2):127–143. doi: 10.1007/s11356-008-0090-4 CrossRefGoogle Scholar
  30. Coleman NV, Mattes TE, Gossett JM, Spain JC (2002a) Biodegradation of cis-dichloroethene as the sole carbon source by a beta-proteobacterium. Appl Environ Microbiol 68(6):2726–2730PubMedPubMedCentralCrossRefGoogle Scholar
  31. Coleman NV, Mattes TE, Gossett JM, Spain JC (2002b) Phylogenetic and kinetic diversity of aerobic vinyl chloride-assimilating bacteria from contaminated sites. Appl Environ Microbiol 68(12):6162–6171PubMedPubMedCentralCrossRefGoogle Scholar
  32. Conrad ME, Brodie EL, Radtke CW, Bill M, Delwiche ME, Lee MH, Swift DL, Colwell FS (2010) Field evidence for co-metabolism of trichloroethene stimulated by addition of electron donor to groundwater. Environ Sci Technol 44(12):4697–4704. doi: 10.1021/es903535j PubMedCrossRefGoogle Scholar
  33. Cord-Ruwisch R, Lovley DR, Schink B (1998) Growth of Geobacter sulfurreducens with acetate in syntrophic cooperation with hydrogen-oxidizing anaerobic partners. Appl Environ Microbiol 64(6):2232–2236PubMedPubMedCentralGoogle Scholar
  34. Cupples AM, Spormann AM, McCarty PL (2003) Growth of a Dehalococcoides-like microorganism on vinyl chloride and cis-dichloroethene as electron acceptors as determined by competitive PCR. Appl Environ Microbiol 69(2):953–959PubMedPubMedCentralCrossRefGoogle Scholar
  35. 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
  36. Daprato RC, Lӧffler FE, Hughes JB (2007) Comparative analysis of three tetrachloroethene to ethene halorespiring consortia suggests functional redundancy. Environ Sci Technol 41(7):2261–2269PubMedCrossRefGoogle Scholar
  37. 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
  38. Delgado AG, Fajardo-Williams D, Popat SC, Torres CI, Krajmalnik-Brown R (2014) Successful operation of continuous reactors at short retention times results in high-density, fast-rate Dehalococcoides dechlorinating cultures. Appl Microbiol Biotechnol 98(6):2729–2737. doi: 10.1007/s00253-013-5263-5 PubMedCrossRefGoogle Scholar
  39. Diekert G, Wohlfarth G (1994) Metabolism of homoacetogens. Antonie Van Leeuwenhoek 66(1–3):209–221. doi: 10.1007/BF00871640 PubMedCrossRefGoogle Scholar
  40. Ding C, Zhao S, He J (2014) A Desulfitobacterium sp. strain PR reductively dechlorinates both 1,1,1-trichloroethane and chloroform: strain PR dechlorinates TCA and chloroform. Environ Microbiol 16(11):3387–3397. doi: 10.1111/1462-2920.12387 PubMedCrossRefGoogle Scholar
  41. DiStefano TD, Gossett JM, Zinder SH (1991) Reductive dechlorination of high concentrations of tetrachloroethene to ethene by an anaerobic enrichment culture in the absence of methanogenesis. Appl Environ Microbiol 57(8):2287–2292PubMedPubMedCentralGoogle Scholar
  42. Dojka MA, Hugenholtz P, Haack SK, Pace NR (1998) Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl Environ Microbiol 64(10):3869–3877PubMedPubMedCentralGoogle Scholar
  43. Dolfing J, Tiedje JM (1991) Kinetics of two complementary hydrogen sink reactions in a defined 3-chlorobenzoate degrading methanogenic co-culture. FEMS Microbiol Lett 86(1):25–32. doi: 10.1111/j.1574-6968.1991.tb04792.x CrossRefGoogle Scholar
  44. Dugat-Bony E, Biderre-Petit C, Jaziri F, David MM, Denonfoux J, Lyon DY, Richard J-Y, Curvers C, Boucher D, Vogel TM, Peyretaillade E, Peyret P (2012) In situ TCE degradation mediated by complex dehalorespiring communities during biostimulation processes. Microb Biotechnol 5(5):642–653. doi: 10.1111/j.1751-7915.2012.00339.x PubMedPubMedCentralCrossRefGoogle Scholar
  45. Duhamel M, Edwards EA (2006) Microbial composition of chlorinated ethene-degrading cultures dominated by Dehalococcoides. FEMS Microbiol Ecol 58(3):538–549PubMedCrossRefGoogle Scholar
  46. Duhamel M, Edwards EA (2007) Growth and yields of dechlorinators, acetogens, and methanogens during reductive dechlorination of chlorinated ethenes and dihaloelimination of 1,2-dichloroethane. Environ Sci Technol 41(7):2303–2310PubMedCrossRefGoogle Scholar
  47. Duhamel M, Wehr SD, Yu L, Rizvi H, Seepersad D, Dworatzek S, Cox EE, Edwards EA (2002) Comparison of anaerobic dechlorinating enrichment cultures maintained on tetrachloroethene, trichloroethene, cis-dichloroethene and vinyl chloride. Water Res 36(17):4193–4202PubMedCrossRefGoogle Scholar
  48. Ellis DE, Lutz EJ, Odom JM, Buchanan RJ, Bartlett CL, Lee MD, Harkness MR, Deweerd KA (2000) Bioaugmentation for accelerated in situ anaerobic bioremediation. Environ Sci Technol 34(11):2254–2260CrossRefGoogle 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):3009–3018. doi: 10.1128/Aem.02958-06 PubMedPubMedCentralCrossRefGoogle 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, Gossett JM, Zinder SH (1997) Comparison of butyric kid, ethanol, lactic acid, and propionic acid as hydrogen donors for the reductive dechlorination of tetrachloroethene. Environ Sci Technol 31(3):918–926CrossRefGoogle Scholar
  52. Freeborn RA, West KA, Bhupathiraju VK, Chauhan S, Rahm BG, Richardson RE, Alvarez-Cohen L (2005) Phylogenetic analysis of TCE-dechlorinating consortia enriched on a variety of electron donors. Environ Sci Technol 39(21):8358–8368PubMedCrossRefGoogle Scholar
  53. Fung JM, Weisenstein BP, Mack EE, Vidumsky JE, Ei TA, Zinder SH (2009) Reductive dehalogenation of dichlorobenzenes and monochlorobenzene to benzene in microcosms. Environ Sci Technol 43(7):2302–2307. doi: 10.1021/es802131d PubMedCrossRefGoogle Scholar
  54. Futagami T, Yamaguchi T, Nakayama SI, Goto M, Furukawa K (2006) Effects of chloromethanes on growth of and deletion of the pce gene cluster in dehalorespiring Desulfitobacterium hafniense strain Y51. Appl Environ Microbiol 72(9):5998–6003. doi: 10.1128/aem.00979-06 PubMedPubMedCentralCrossRefGoogle Scholar
  55. Gerritse J, Renard V, Pedro Gomes TM, 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(2):132–140Google Scholar
  56. Gossett JM (2010) Sustained aerobic oxidation of vinyl chloride at low oxygen concentrations. Environ Sci Technol 44(4):1405–1411. doi: 10.1021/es9033974 PubMedCrossRefGoogle Scholar
  57. Gribble GW (1994) The natural production of chlorinated compounds. Environ Sci Technol 28(7):A310–A319CrossRefGoogle Scholar
  58. Gribble GW (2003) The diversity of naturally produced organohalogens. Chemosphere 52(2):289–297. doi: 10.1016/S0045-6535(03)00207-8 PubMedCrossRefGoogle Scholar
  59. Grostern A, Edwards EA (2006a) A 1,1,1-trichloroethane-degrading anaerobic mixed microbial culture enhances biotransformation of mixtures of chlorinated ethenes and ethanes. Appl Environ Microbiol 72(12):7849–7856PubMedPubMedCentralCrossRefGoogle Scholar
  60. Grostern A, Edwards EA (2006b) Growth of Dehalobacter and Dehalococcoides spp. during degradation of chlorinated ethanes. Appl Environ Microbiol 72(1):428–436. doi: 10.1128/aem.72.1.428-436.2006 PubMedPubMedCentralCrossRefGoogle Scholar
  61. Grostern A, Edwards EA (2009) Characterization of a Dehalobacter coculture that dechlorinates 1,2-dichloroethane to ethene and identification of the putative reductive dehalogenase gene. Appl Environ Microbiol 75(9):2684–2693PubMedPubMedCentralCrossRefGoogle Scholar
  62. Grostern A, Chan WW, Edwards EA (2009) 1,1,1-trichloroethane and 1,1-dichloroethane reductive dechlorination kinetics and co-contaminant effects in a Dehalobacter-containing mixed culture. Environ Sci Technol 43(17):6799–6807PubMedCrossRefGoogle Scholar
  63. Grostern A, Duhamel M, Dworatzek S, Edwards EA (2010) Chloroform respiration to dichloromethane by a Dehalobacter population. Environ Microbiol 12(4):1053–1060. doi: 10.1111/j.1462-2920.2009.02150.x PubMedCrossRefGoogle Scholar
  64. Gu AZ, Hedlund BP, Staley JT, Strand SE, Stensel HD (2004) Analysis and comparison of the microbial community structures of two enrichment cultures capable of reductively dechlorinating TCE and cis-DCE. Environ Microbiol 6(1):45Google Scholar
  65. Gustavsson M, Karlsson S, Öberg G, Sandén P, Svensson T, Valinia S, Thiry Y, Bastviken D (2012) Organic matter chlorination rates in different boreal soils: the role of soil organic matter content. Environ Sci Technol 46(3):1504–1510. doi: 10.1021/es203191r PubMedCrossRefGoogle Scholar
  66. Haest PJ, Springael D, Smolders E (2010a) Dechlorination kinetics of TCE at toxic TCE concentrations: assessment of different models. Water Res 44(1):331–339. doi: 10.1016/j.watres.2009.09.033 PubMedCrossRefGoogle Scholar
  67. Haest PJ, Springael D, Smolders E (2010b) Modelling reactive CAH transport using batch experiment degradation kinetics. Water Res 44(9):2981–2989. doi: 10.1016/j.watres.2010.02.031 PubMedCrossRefGoogle Scholar
  68. Hatt JK, Loffler FE (2012) Quantitative real-time PCR (qPCR) detection chemistries affect enumeration of the Dehalococcoides 16S rRNA gene in groundwater. J Microbiol Methods 88(2):263–270. doi: 10.1016/j.mimet.2011.12.005 PubMedCrossRefGoogle Scholar
  69. He J, Sung Y, Dollhopf ME, Fathepure BZ, Tiedje JM, Lӧffler FE (2002) Acetate versus hydrogen as direct electron donors to stimulate the microbial reductive dechlorination process at chloroethene-contaminated sites. Environ Sci Technol 36(18):3945–3952PubMedCrossRefGoogle Scholar
  70. He J, Sung Y, Krajmalnik-Brown R, Ritalahti KM, Lӧffler 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
  71. He JZ, Robrock KR, Alvarez-Cohen L (2006) Microbial reductive debromination of polybrominated diphenyl ethers (PBDEs). Environ Sci Technol 40(14):4429–4434PubMedCrossRefGoogle Scholar
  72. He J, Holmes VF, Lee PK, Alvarez-Cohen L (2007) Influence of vitamin B12 and cocultures on the growth of Dehalococcoides isolates in defined medium. Appl Environ Microbiol 73(9):2847–2853PubMedPubMedCentralCrossRefGoogle Scholar
  73. Heavner GLW (2013) Biokinetic modeling, laboratory examination and field analysis of DNA, RNA and protein as robust molecular biomarkers of chloroethene reductive dechlorination in Dehalococcoides mccartyi. Ph.D. Disseration, Cornell UniversityGoogle Scholar
  74. Heavner GLW, Rowe AR, Mansfeldt CB, Pan JK, Gossett JM, Richardson RE (2013) Molecular biomarker-based biokinetic modeling of a PCE-dechlorinating and methanogenic mixed culture. Environ Sci Technol 47(8):3724–3733. doi: 10.1021/es303517s PubMedCrossRefGoogle Scholar
  75. Heimann AC, Batstone DJ, Jakobsen R (2006) Methanosarcina spp. drive vinyl chloride dechlorination via interspecies hydrogen transfer. Appl Environ Microbiol 72(4):2942–2949PubMedPubMedCentralCrossRefGoogle Scholar
  76. 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
  77. Holliger C, Hahn D, Harmsen H, Ludwig W, Schumacher W, Tindall B, Vazquez F, Weiss N, Zehnder AJB (1998) 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):313–321. doi: 10.1007/s002030050577 PubMedCrossRefGoogle Scholar
  78. Holoman TRP, Elberson MA, Cutter LA, May HD, Sowers KR (1998) Characterization of a defined 2,3,5,6-tetrachlorobiphenyl-ortho-dechlorinating microbial community by comparative sequence analysis of genes coding for 16S rRNA. Appl Environ Microbiol 64(9):3359–3367PubMedGoogle Scholar
  79. 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 Genomics 13. doi: 10.1186/1471-2164-13-327
  80. Jennings LK, Chartrand MMG, Lacrampe-Couloume G, Lollar BS, Spain JC, Gossett JM (2009) Proteomic and transcriptomic analyses reveal genes upregulated by cis-dichloroethene in Polaromonas sp strain JS666. Appl Environ Microbiol 75(11):3733–3744. doi: 10.1128/aem.00031-09 PubMedPubMedCentralCrossRefGoogle Scholar
  81. Johnson DR, Nemir A, Andersen GL, Zinder SH, Alvarez-Cohen L (2009) Transcriptomic microarray analysis of corrinoid responsive genes in Dehalococcoides ethenogenes strain 195. FEMS Microbiol Lett 294(2):198–206PubMedCrossRefGoogle Scholar
  82. Jones EJP, Voytek MA, Lorah MM, Kirshtein JD (2006) Characterization of a microbial consortium capable of rapid and simultaneous dechlorination of 1,1,2,2-tetrachloroethane and chlorinated ethane and ethene intermediates. Bioremediat J 10(4):153–168. doi: 10.1080/10889860601021399 CrossRefGoogle Scholar
  83. Justicia-Leon SD, Ritalahti KM, Mack EE, Lӧffler FE (2012) Dichloromethane fermentation by a Dehalobacter sp in an enrichment culture derived from pristine river sediment. Appl Environ Microbiol 78(4):1288–1291. doi: 10.1128/aem.07325-11 PubMedPubMedCentralCrossRefGoogle Scholar
  84. Justicia-Leon SD, Higgins S, Mack EE, Griffiths DR, Tang S, Edwards EA, Löffler FE (2014) Bioaugmentation with distinct Dehalobacter strains achieves chloroform detoxification in microcosms. Environ Sci Technol 48:1851–1858. doi: 10.1021/es403582f PubMedCrossRefGoogle Scholar
  85. Kjellerup BV, Sun X, Ghosh U, May HD, Sowers KR (2008) Site-specific microbial communities in three PCB-impacted sediments are associated with different in situ dechlorinating activities. Environ Microbiol 10(5):1296–1309. doi: 10.1111/j.1462-2920.2007.01543.x PubMedCrossRefGoogle Scholar
  86. Kotik M, Davidova A, Voriskova J, Baldrian P (2013) Bacterial communities in tetrachloroethene-polluted groundwaters: a case study. Sci Total Environ 454–455:517–527. doi: 10.1016/j.scitotenv.2013.02.082 PubMedCrossRefGoogle Scholar
  87. Krzmarzick MJ, Crary BB, Harding JJ, Oyerinde OO, Leri AC, Myneni SCB, Novak PJ (2012) Natural niche for organohalide-respiring chloroflexi. Appl Environ Microbiol 78(2):393–401. doi: 10.1128/aem.06510-11 PubMedPubMedCentralCrossRefGoogle Scholar
  88. 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
  89. Kulkarni G, Kridelbaugh DM, Guss AM, Metcalf WW (2009) Hydrogen is a preferred intermediate in the energy-conserving electron transport chain of Methanosarcina barkeri. Proc Natl Acad Sci USA 106(37):15915–15920. doi: 10.1073/pnas.0905914106 PubMedPubMedCentralCrossRefGoogle Scholar
  90. Lai YJ, Becker JG (2013) Compounded effects of chlorinated ethene inhibition on ecological interactions and population abundance in a Dehalococcoides—Dehalobacter coculture. Environ Sci Technol 47(3):1518–1525. doi: 10.1021/es3034582 PubMedGoogle Scholar
  91. Lee PKH, 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):2728–2739. doi: 10.1128/aem.02199-07 PubMedPubMedCentralCrossRefGoogle Scholar
  92. Lee PKH, He JZ, Zinder SH, Alvarez-Cohen L (2009) Evidence for nitrogen fixation by “Dehalococcoides ethenogenes” strain 195. Appl Environ Microbiol 75(23):7551–7555. doi: 10.1128/aem.01886-09 PubMedPubMedCentralCrossRefGoogle Scholar
  93. Lee J, Lee TK, Lӧffler FE, Park J (2011a) Characterization of microbial community structure and population dynamics of tetrachloroethene-dechlorinating tidal mudflat communities. Biodegradation 22(4):687–698. doi: 10.1007/s10532-010-9429-x PubMedCrossRefGoogle Scholar
  94. Lee LK, Ding C, Yang KL, He JZ (2011b) Complete debromination of tetra- and penta-brominated diphenyl ethers by a coculture consisting of Dehalococcoides and Desulfovibrio species. Environ Sci Technol 45(19):8475–8482. doi: 10.1021/es201559g PubMedCrossRefGoogle Scholar
  95. Lee M, Low A, Zemb O, Koenig J, Michaelsen A, Manefield M (2012a) Complete chloroform dechlorination by organochlorine respiration and fermentation. Environ Microbiol 14(4):883–894. doi: 10.1111/j.1462-2920.2011.02656.x PubMedCrossRefGoogle Scholar
  96. Lee PKH, Dill BD, Louie TS, Shah M, VerBerkmoes NC, Andersen GL, Zinder SH, Alvarez-Cohen L (2012b) Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation. Appl Environ Microbiol 78(5):1424–1436. doi: 10.1128/aem.06792-11 PubMedPubMedCentralCrossRefGoogle Scholar
  97. Lee PKH, Warnecke F, Brodie EL, Macbeth TW, Conrad ME, Andersen GL, Alvarez-Cohen L (2012c) Phylogenetic microarray analysis of a microbial community performing reductive dechlorination at a TCE-contaminated site. Environ Sci Technol 46(2):1044–1054. doi: 10.1021/es203005k PubMedCrossRefGoogle Scholar
  98. Lendvay JM, Löffler FE, Dollhopf M, Aiello MR, Daniels G, Fathepure BZ, 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
  99. Leri AC, Marcus MA, Myneni SCB (2007) X-ray spectromicroscopic investigation of natural organochlorine distribution in weathering plant material. Geochim Cosmochim Acta 71(23):5834–5846. doi: 10.1016/j.gca.2007.09.001 CrossRefGoogle Scholar
  100. Liu H, Park JW, Haggblom MM (2014) Enriching for microbial reductive dechlorination of polychlorinated dibenzo-p-dioxins and dibenzofurans. Environ Pollut 184:222–230. doi: 10.1016/j.envpol.2013.08.019 PubMedCrossRefGoogle Scholar
  101. Löffler FE, Yan JY, Ritalahti KM, Adrian L, Edwards EA, Konstantinidis KT, Mueller JA, Fullerton H, Zinder SH, Spormann AM (2013) Dehalococcoides mccartyi gen. nov., sp. nov., obligate organohalide-respiring anaerobic bacteria, relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidetes classis nov., within the phylum Chloroflexi. Int J Syst Evol Microbiol 63:625–635. doi: 10.1099/ijs.0.034926-0 CrossRefGoogle Scholar
  102. Löffler FE, Sanford RA (2005) Analysis of trace hydrogen metabolism. In: Methods in enzymology, vol 397. Academic Press, New York, pp 222–237. doi:http://dx.doi.org/10.1016/S0076-6879(05)97013-4
  103. Lovley DR, Ferry JG (1985) Production and consumption of H2 during growth of Methanosarcina spp. on acetate. Appl Environ Microbiol 49(1):247–249PubMedPubMedCentralGoogle Scholar
  104. Lowe M, Madsen EL, Schindler K, Smith C, Emrich S, Robb F, Halden RU (2002) Geochemistry and microbial diversity of a trichloroethene-contaminated Superfund site undergoing intrinsic in situ reductive dechlorination. FEMS Microbiol Ecol 40(2):123–134PubMedCrossRefGoogle Scholar
  105. Lu XX, Wilson JT, Kampbell DH (2006) Relationship between Dehalococcoides DNA in ground water and rates of reductive dechlorination at field scale. Water Res 40(16):3131–3140PubMedCrossRefGoogle Scholar
  106. Macbeth TW, Cummings DE, Spring S, Petzke LM, Sorenson KS (2004) Molecular characterization of a dechlorinating community resulting from in situ biostimulation in a trichloroethene-contaminated deep, fractured basalt aquifer and comparison to a derivative laboratory culture. Appl Environ Microbiol 70(12):7329–7341PubMedPubMedCentralCrossRefGoogle Scholar
  107. 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
  108. 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
  109. Manchester MJ, Hug LA, Zarek M, Zila A, Edwards EA (2012) Discovery of a trans-dichloroethene-respiring Dehalogenimonas species in the 1,1,2,2-tetrachloroethane-dechlorinating WBC-2 consortium. Appl Environ Microbiol 78(15):5280–5287. doi: 10.1128/AEM.00384-12 PubMedPubMedCentralCrossRefGoogle Scholar
  110. Mansfeldt CB, Rowe AR, Heavner GLW, Zinder SH, Richardson RE (2014) Meta-analyses of Dehalococcoides mccartyi strain 195 transcriptomic profiles identify a respiration rate-related gene expression transition point and interoperon recruitment of a key oxidoreductase subunit. Appl Environ Microbiol 80(19):6062–6072. doi: 10.1128/AEM.02130-14 PubMedPubMedCentralCrossRefGoogle Scholar
  111. Maphosa F, Smidt H, De Vos WM, Roling WFM (2010) Microbial community- and metabolite dynamics of an anoxic dechlorinating bioreactor. Environ Sci Technol 44(13):4884–4890. doi: 10.1021/es903721s PubMedCrossRefGoogle Scholar
  112. 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 Rep 4(6):604–616. doi: 10.1111/j.1758-2229.2012.00376.x PubMedGoogle Scholar
  113. Marco-Urrea E, Seifert J, von Bergen M, Adrian L (2012) Stable isotope peptide mass spectrometry to decipher Amino Acid Metabolism in Dehalococcoides Strain CBDB1. J Bacteriol 194:4169–4177. doi: 10.1128/jb.00049-12 PubMedPubMedCentralCrossRefGoogle Scholar
  114. Marshall IPG, Berggren DRV, Azizian MF, Burow LC, Semprini L, Spormann AM (2012) The hydrogenase chip: a tiling oligonucleotide DNA microarray technique for characterizing hydrogen-producing and -consuming microbes in microbial communities. ISME J 6(4):814–826. doi: 10.1038/ismej.2011.136 PubMedCrossRefGoogle Scholar
  115. 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):2990–2999. doi: 10.1128/AEM.02748-06 PubMedPubMedCentralCrossRefGoogle Scholar
  116. Mathai PP, Zitomer DH, Maki JS (2015) Quantitative detection of syntrophic fatty acid-degrading bacterial communities in methanogenic environments. Microbiology 161:1189–1197. doi: 10.1099/mic.0.000085 PubMedCrossRefGoogle Scholar
  117. Mattes TE, Alexander AK, Coleman NV (2010) Aerobic biodegradation of the chloroethenes: pathways, enzymes, ecology, and evolution. FEMS Microbiol Rev 34(4):445–475. doi: 10.1111/j.1574-6976.2010.00210.x PubMedCrossRefGoogle Scholar
  118. Matturro B, Heavner GL, Richardson RE, Rossetti S (2013) Quantitative estimation of Dehalococcoides mccartyi at laboratory and field scale: comparative study between CARD-FISH and real time PCR. J Microbiol Methods 93(2):127–133. doi: 10.1016/j.mimet.2013.02.011 PubMedCrossRefGoogle Scholar
  119. Maymó-Gatell X, Chien Y, Gossett JM, Zinder SH (1997) Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276(5318):1568–1571PubMedCrossRefGoogle Scholar
  120. Men YJ, Feil H, VerBerkmoes NC, Shah MB, Johnson DR, Lee PKH, West KA, Zinder SH, Andersen GL, Alvarez-Cohen L (2012) Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses. ISME J 6(2):410–421. doi: 10.1038/ismej.2011.111 PubMedCrossRefGoogle Scholar
  121. Men Y, Lee PKH, 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(14):6439–6450. doi: 10.1007/s00253-013-4896-8 PubMedCrossRefGoogle Scholar
  122. Men YJ, Seth EC, Yi S, Allen RH, Taga ME, Alvarez-Cohen L (2014) Sustainable growth of Dehalococcoides mccartyi 195 by corrinoid salvaging and remodeling in defined lactate-fermenting consortia. Appl Environ Microbiol 80(7):2133–2141. doi: 10.1128/aem.03477-13 PubMedPubMedCentralCrossRefGoogle Scholar
  123. 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 59:2692–2697. doi: 10.1099/ijs.0.011502-0 PubMedCrossRefGoogle Scholar
  124. Mohn WW, Tiedje JM (1992) Microbial reductive dehalogenation. Microbiol Rev 56(3):482–507PubMedPubMedCentralGoogle Scholar
  125. Morris RM, Sowell S, Barofsky D, Zinder S, Richardson R (2006) Transcription and mass-spectroscopic proteomic studies of electron transport oxidoreductases in Dehalococcoides ethenogenes. Environ Microbiol 8(9):1499–1509PubMedCrossRefGoogle Scholar
  126. Morris RM, Fung JM, Rahm BG, Zhang S, Freedman DL, Zinder SH, Richardson RE (2007) Comparative proteomics of Dehalococcoides spp. reveals strain-specific peptides associated with activity. Appl Environ Microbiol 73(1):320–326. doi: 10.1128/AEM.02129-06 PubMedCrossRefGoogle Scholar
  127. Morris BEL, Henneberger R, Huber H, Moissl-Eichinger C (2013) Microbial syntrophy: interaction for the common good. FEMS Microbiol Rev 37:384–406. doi: 10.1111/1574-6976.12019 PubMedCrossRefGoogle Scholar
  128. 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):6806–6813. doi: 10.1021/es200480k PubMedCrossRefGoogle Scholar
  129. Nelson JL, Jiang J, Zinder SH (2014) Dehalogenation of chlorobenzenes, dichlorotoluenes, and tetrachloroethene by three Dehalobacter spp. Environ Sci Technol 48(7):3776–3782. doi: 10.1021/es4044769 PubMedCrossRefGoogle Scholar
  130. Nemir A, David MM, Perrussel R, Sapkota A, Simonet P, Monier J-M, Vogel TM (2010) Comparative phylogenetic microarray analysis of microbial communities in TCE-contaminated soils. Chemosphere 80(5):600–607. doi: 10.1016/j.chemosphere.2010.03.036 PubMedCrossRefGoogle Scholar
  131. Oba Y, Futagami T, Amachi S (2014) Enrichment of a microbial consortium capable of reductive deiodination of 2,4,6-triiodophenol. J Biosci Bioeng 117(3):310–317. doi: 10.1016/j.jbiosc.2013.08.011 PubMedCrossRefGoogle Scholar
  132. Oberg G, Holm M, Sanden P, Svensson T, Parikka M (2005) The role of organic-matter-bound chlorine in the chlorine cycle: a case study of the Stubbetorp catchment, Sweden. Biogeochemistry 75(2):241–269. doi: 10.1007/s10533-004-7259-9 CrossRefGoogle Scholar
  133. Oelgeschläger E, Rother M (2008) Carbon monoxide-dependent energy metabolism in anaerobic bacteria and archaea. Arch Microbiol 190:257–269. doi: 10.1007/s00203-008-0382-6 PubMedCrossRefGoogle Scholar
  134. Pérez-de-Mora A, Zila A, McMaster ML, Edwards EA (2014) Bioremediation of chlorinated ethenes in fractured bedrock and associated changes in dechlorinating and nondechlorinating microbial populations. Environ Sci Technol 48(10):5770–5779. doi: 10.1021/es404122y PubMedCrossRefGoogle Scholar
  135. Rahm BG, Richardson RE (2008) Correlation of respiratory gene expression levels and pseudo-steady-state PCE respiration rates in Dehalococcoides ethenogenes. Environ Sci Technol 42(2):416–421. doi: 10.1021/es071455s PubMedCrossRefGoogle Scholar
  136. Rahm BG, Chauhan S, Holmes VF, Macbeth TW, Sorenson KS Jr, Alvarez-Cohen L (2006) Molecular characterization of microbial populations at two sites with differing reductive dechlorination abilities. Biodegradation 17(6):523–534. doi: 10.1007/s10532-005-9023-9 PubMedCrossRefGoogle Scholar
  137. Redon P-O, Abdelouas A, Bastviken D, Cecchini S, Nicolas M, Thiry Y (2011) Chloride and organic chlorine in forest soils: storage, residence times, and influence of ecological conditions. Environ Sci Technol 45(17):7202–7208. doi: 10.1021/es2011918 PubMedCrossRefGoogle Scholar
  138. 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
  139. Ritalahti KM, Amos BK, Sung Y, Wu QZ, Koenigsberg SS, Lӧffler FE (2006) Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains. Appl Environ Microbiol 72(4):2765–2774. doi: 10.1128/aem.72.4.2765-27774.2006 PubMedPubMedCentralCrossRefGoogle Scholar
  140. Rohlenova J, Gryndler M, Forczek ST, Fuksova K, Handova V, Matucha M (2009) Microbial chlorination of organic matter in forest soil: investigation using Cl-36-chloride and its methodology. Environ Sci Technol 43(10):3652–3655. doi: 10.1021/es803300f PubMedCrossRefGoogle Scholar
  141. 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):6709–6719. doi: 10.1128/aem.00445-08 PubMedPubMedCentralCrossRefGoogle Scholar
  142. Rowe AR, Heavner GL, Mansfeldt CB, Werner JJ, Richardson RE (2012) Relating chloroethene respiration rates in Dehalococcoides to protein and mRNA biomarkers. Environ Sci Technol 46(17):9388–9397. doi: 10.1021/es300996c PubMedCrossRefGoogle Scholar
  143. Rowe AR, Mansfeldt CB, Heavner GL, Richardson RE (2013) Methanospirillum respiratory mRNA biomarkers correlate with hydrogenotrophic methanogenesis rate during growth and competition for hydrogen in an organochlorine-respiring mixed culture. Environ Sci Technol 47(1):372–381. doi: 10.1021/es303061y PubMedCrossRefGoogle Scholar
  144. 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. Philos Trans R Soc Lond Ser B Biol Sci 368(1616). doi: 10.1098/rstb.2012.0325
  145. Rupakula A, Lu Y, Kruse T, Boeren S, Holliger C, Smidt H, Maillard J (2015) Functional genomics of corrinoid starvation in the organohalide-respiring bacterium Dehalobacter restrictus strain PER-K23. Frontiers in Microbiology 5. doi: 10.3389/fmicb.2014.00761
  146. Schaefer CE, Condee CW, Vainberg S, Steffan RJ (2009) Bioaugmentation for chlorinated ethenes using Dehalococcoides sp.: comparison between batch and column experiments. Chemosphere 75(2):141–148. doi: 10.1016/j.chemosphere.2008.12.041
  147. Schink B, Stams AJM (2013) Syntrophism among prokaryotes. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The Prokaryotes. Springer, Berlin, pp 471–493CrossRefGoogle Scholar
  148. Schipp CJ, Marco-Urrea E, Kublik A, Seifert J, Adrian L (2013) Organic cofactors in the metabolism of Dehalococcoides mccartyi strains. Philos Trans R Soc B-Biol Sci 368(1616). doi: 10.1098/rstb.2012.0321
  149. 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 157:25–36. doi: 10.1016/j.jconhyd.2013.10.006 PubMedCrossRefGoogle Scholar
  150. 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):48–56. doi: 10.1007/BF00262203 CrossRefGoogle Scholar
  151. 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 KT, 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
  152. 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):6836–6845. doi: 10.1021/es304017s PubMedGoogle Scholar
  153. 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
  154. Sieber JR, Le HM, McInerney MJ (2014) The importance of hydrogen and formate transfer for syntrophic fatty, aromatic and alicyclic metabolism: importance of interspecies hydrogen and formate transfer. Environ Microbiol 16:177–188. doi: 10.1111/1462-2920.12269 PubMedCrossRefGoogle Scholar
  155. Sleep BE, Brown AJ, Lollar BS (2005) Long-term tetrachlorethene degradation sustained by endogenous cell decay. J Environ Eng Sci 4(1):11–17CrossRefGoogle Scholar
  156. 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
  157. Sun BL, Griffin BM, Ayala-del-Rio HL, Hashsham SA, Tiedje JM (2002) Microbial dehalorespiration with 1,1,1-trichloroethane. Science 298(5595):1023–1025PubMedCrossRefGoogle Scholar
  158. Tang YJJ, Yi S, Zhuang WQ, Zinder SH, Keasling JD, Alvarez-Cohen L (2009) Investigation of carbon metabolism in “Dehalococcoides ethenogenes” strain 195 by use of isotopomer and transcriptomic analyses. J Bacteriol 191(16):5224–5231. doi: 10.1128/jb.00085-09 PubMedPubMedCentralCrossRefGoogle Scholar
  159. Tang S, Gong Y, Edwards EA (2012) Semi-automatic in silico gap closure enabled de novo assembly of two Dehalobacter genomes from metagenomic data. PLoS ONE 7(12):e52038. doi: 10.1371/journal.pone.0052038 PubMedPubMedCentralCrossRefGoogle Scholar
  160. Tas N, van Eekert MHA, 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):4696–4704. doi: 10.1128/AEM.02829-08
  161. Tas N, van Eekert MHA, Wagner A, Schraa G, de Vos WM, Smidt H (2011) Role of “Dehalococcoides” spp. in the anaerobic transformation of hexachlorobenzene in European rivers. Appl Environ Microbiol 77(13):4437–4445. doi: 10.1128/aem.01940-10
  162. Thomas SH, Wagner RD, Arakaki AK, Skolnick J, Kirby JR, Shimkets LJ, Sanford RA, Loffler FE (2008) The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-Proteobacteria. Plos One 3(5). doi: 10.1371/journal.pone.0002103
  163. van Doesburg W, van Eekert MHA, Middeldorp PJM, Balk M, Schraa G, Stams AJM (2005) Reductive dechlorination of beta-hexachlorocyclohexane (beta-HCH) by a Dehalobacter species in coculture with a Sedimentibacter sp. FEMS Microbiol Ecol 54(1):87–95. doi: 10.1016/j.femsec.2005.03.003 PubMedCrossRefGoogle Scholar
  164. Vandermeeren P, Herrmann S, Cichocka D, Busschaert P, Lievens B, Richnow HH, Springael D (2014) Diversity of dechlorination pathways and organohalide respiring bacteria in chlorobenzene dechlorinating enrichment cultures originating from river sludge. Biodegradation 25(5):757–776. doi: 10.1007/s10532-014-9697-y PubMedCrossRefGoogle Scholar
  165. Wagner DD, Hug LA, Hatt JK, Spitzmiller MR, Padilla-Crespo E, Ritalahti KM, Edwards EA, Konstantinidis KT, Lӧffler FE (2012) Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae. BMC Genomics 13. doi: 10.1186/1471-2164-13-200
  166. Watts JE, Wu Q, Schreier SB, May HD, Sowers KR (2001) Comparative analysis of polychlorinated biphenyl-dechlorinating communities in enrichment cultures using three different molecular screening techniques. Environ Microbiol 3(11):710–719PubMedCrossRefGoogle Scholar
  167. Werner JJ, Ptak AC, Rahm BG, Zhang S, Richardson RE (2009) Absolute quantification of Dehalococcoides proteins: enzyme bioindicators of chlorinated ethene dehalorespiration. Environ Microbiol 11(10):2687–2697. doi: 10.1111/j.1462-2920.2009.01996.x PubMedCrossRefGoogle Scholar
  168. Wu Q, Watts JEM, Sowers KR, May HD (2002) 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
  169. Yan T, LaPara TM, Novak PJ (2006) The reductive dechlorination of 2,3,4,5-tetrachlorobiphenyl in three different sediment cultures: evidence for the involvement of phylogenetically similar Dehalococcoides-like bacterial populations. FEMS Microbiol Ecol 55(2):248–261PubMedPubMedCentralCrossRefGoogle Scholar
  170. Yan J, Ritalahti KM, Wagner DD, Lӧffler FE (2012) Unexpected specificity of interspecies cobamide transfer from Geobacter spp. to organohalide-respiring Dehalococcoides mccartyi strains. Appl Environ Microbiol 78(18):6630–6636. doi: 10.1128/aem.01535-12 PubMedPubMedCentralCrossRefGoogle Scholar
  171. Yan J, Im J, Yang Y, Lӧffler FE (2013) Guided cobalamin biosynthesis supports Dehalococcoides mccartyi reductive dechlorination activity. Philos Trans R Soc B-Biol Sci 368(1616). doi: 10.1098/rstb.2012.0320
  172. Yang YR, McCarty PL (1998) Competition for hydrogen within a chlorinated solvent dehalogenating anaerobic mixed culture. Environ Sci Technol 32(22):3591–3597CrossRefGoogle Scholar
  173. Yang YR, Pesaro M, Sigler W, Zeyer J (2005) Identification of microorganisms involved in reductive dehalogenation of chlorinated ethenes in an anaerobic microbial community. Water Res 39(16):3954–3966PubMedCrossRefGoogle Scholar
  174. Yi S, Seth EC, Men YJ, 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):7745–7752. doi: 10.1128/aem.02150-12 PubMedPubMedCentralCrossRefGoogle Scholar
  175. Yoshida N, Takahashi N, Hiraishi A (2005) Phylogenetic characterization of a polychlorinated-dioxin-dechlorinating microbial community by use of microcosm studies. Appl Environ Microbiol 71(8):4325–4334PubMedPubMedCentralCrossRefGoogle Scholar
  176. Yu S, Semprini L (2004) Kinetics and modeling of reductive dechlorination at high PCE and TCE concentrations. Biotechnol Bioeng 88(4):451–464. doi: 10.1002/bit.20260 PubMedCrossRefGoogle Scholar
  177. Yu ZT, Smith GB (2000) Inhibition of methanogenesis by C-1- and C-2-polychlorinated aliphatic hydrocarbons. Environ Toxicol Chem 19(9):2212–2217CrossRefGoogle Scholar
  178. Yu SH, Dolan ME, Semprini L (2005) Kinetics and inhibition of reductive dechlorination of chlorinated ethylenes by two different mixed cultures. Environ Sci Technol 39(1):195–205. doi: 10.1021/es0496773 PubMedCrossRefGoogle Scholar
  179. Zhang H, Ziv-El M, Rittmann BE, Krajmalnik-Brown R (2010) Effect of dechlorination and sulfate reduction on the microbial community structure in denitrifying membrane-biofilm reactors. Environ Sci Technol 44(13):5159–5164. doi: 10.1021/es100695n PubMedCrossRefGoogle Scholar
  180. Zhuang WQ, Yi S, Feng XY, Zinder SH, Tang YJJ, Alvarez-Cohen L (2011) Selective utilization of exogenous amino acids by Dehalococcoides ethenogenes strain 195 and its effects on growth and dechlorination activity. Appl Environ Microbiol 77(21):7797–7803. doi: 10.1128/aem.05676-11 PubMedPubMedCentralCrossRefGoogle Scholar
  181. Zhuang WQ, Yi S, Bill M, Brisson VL, Feng XY, Men YJ, Conrad ME, Tang YJJ, Alvarez-Cohen L (2014) Incomplete Wood-Ljungdahl pathway facilitates one-carbon metabolism in organohalide-respiring Dehalococcoides mccartyi. Proc Natl Acad Sci USA 111(17):6419–6424. doi: 10.1073/pnas.1321542111 PubMedPubMedCentralCrossRefGoogle Scholar
  182. Zinder SH, Anguish T (1992) Carbon monoxide, hydrogen, and formate metabolism during methanogenesis from acetate by thermophilic cultures of Methanosarcina and Methanothrix strains. Grostern, Ariel Edwards, Elizabeth A, Research Support, Non-US Govt Research Support, US Govt, Non-PHS United States. Appl Environ Microbiol 75(9):2684–2693 (2009 May); 58(10):3323–3329 (Epub 6 Mar 2009)Google Scholar
  183. Ziv-El M, Delgado AG, Yao Y, Kang DW, Nelson KG, Halden RU, Krajmalnik-Brown R (2011) Development and characterization of DehaloR2, a novel anaerobic microbial consortium performing rapid dechlorination of TCE to ethene. Appl Microbiol Biotechnol 92(5):1063–1071. doi: 10.1007/s00253-011-3388-y PubMedCrossRefGoogle Scholar
  184. Ziv-El M, Popat SC, Parameswaran P, Kang DW, Polasko A, Halden RU, Rittmann BE, Krajmalnik-Brown R (2012) Using electron balances and molecular techniques to assess trichoroethene-induced shifts to a dechlorinating microbial community. Biotechnol Bioeng 109(9):2230–2239. doi: 10.1002/Bit.24504 PubMedCrossRefGoogle Scholar

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© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.School of Civil and Environmental EngineeringCornell UniversityIthacaUSA

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