Skip to main content

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

  • Chapter
  • First Online:

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.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

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

References

  • 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):496–503

    CAS  PubMed  PubMed Central  Google Scholar 

  • Adrian L, Szewzyk U, Gorisch H (2000a) Bacterial growth based on reductive dechlorination of trichlorobenzenes. Biodegradation 11(1):73–81

    Article  CAS  PubMed  Google Scholar 

  • Adrian L, Szewzyk U, Wecke J, Gorisch H (2000b) Bacterial dehalorespiration with chlorinated benzenes. Nature 408(6812):580–583

    Article  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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):4159–4166

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Asplund G, Grimvall A (1991) Organohalogens in nature. Environ Sci Technol 25(8):1346–1350

    Article  CAS  Google Scholar 

  • 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):411–424

    Google Scholar 

  • 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):743–753

    Article  CAS  PubMed  Google Scholar 

  • 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):2554–2559

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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):223–234

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Becker JG (2006) A modeling study and implications of competition between Dehalococcoides ethenogenes and other tetrachloroethene-respiring bacteria. Environ Sci Technol 40(14):4473–4480

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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):2460–2470

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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):120–133

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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):2726–2730

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):6162–6171

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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):2232–2236

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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):953–959

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):699–709

    Article  CAS  PubMed  Google Scholar 

  • Daprato RC, Lӧffler FE, Hughes JB (2007) Comparative analysis of three tetrachloroethene to ethene halorespiring consortia suggests functional redundancy. Environ Sci Technol 41(7):2261–2269

    Article  CAS  PubMed  Google Scholar 

  • De Wildeman S, Diekert G, Van Langenhove H, Verstraete W (2003) Stereoselective microbial dehalorespiration with vicinal dichlorinated alkanes. Appl Environ Microbiol 69(9):5643–5647

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Diekert G, Wohlfarth G (1994) Metabolism of homoacetogens. Antonie Van Leeuwenhoek 66(1–3):209–221. doi:10.1007/BF00871640

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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):2287–2292

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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):3869–3877

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Duhamel M, Edwards EA (2006) Microbial composition of chlorinated ethene-degrading cultures dominated by Dehalococcoides. FEMS Microbiol Ecol 58(3):538–549

    Article  CAS  PubMed  Google Scholar 

  • 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):2303–2310

    Article  CAS  PubMed  Google Scholar 

  • 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):4193–4202

    Article  CAS  PubMed  Google Scholar 

  • 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):2254–2260

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fennell DE, Gossett JM (1998) Modeling the production of and competition for hydrogen in a dechlorinating culture. Environ Sci Technol 32(16):2450–2460

    Article  CAS  Google Scholar 

  • 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):918–926

    Article  CAS  Google Scholar 

  • 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):8358–8368

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):132–140

    Google Scholar 

  • Gossett JM (2010) Sustained aerobic oxidation of vinyl chloride at low oxygen concentrations. Environ Sci Technol 44(4):1405–1411. doi:10.1021/es9033974

    Article  CAS  PubMed  Google Scholar 

  • Gribble GW (1994) The natural production of chlorinated compounds. Environ Sci Technol 28(7):A310–A319

    Article  Google Scholar 

  • Gribble GW (2003) The diversity of naturally produced organohalogens. Chemosphere 52(2):289–297. doi:10.1016/S0045-6535(03)00207-8

    Article  CAS  PubMed  Google Scholar 

  • 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):7849–7856

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):2684–2693

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):6799–6807

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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):45

    Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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):3945–3952

    Article  CAS  PubMed  Google Scholar 

  • 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):1442–1450

    Article  CAS  PubMed  Google Scholar 

  • He JZ, Robrock KR, Alvarez-Cohen L (2006) Microbial reductive debromination of polybrominated diphenyl ethers (PBDEs). Environ Sci Technol 40(14):4429–4434

    Article  CAS  PubMed  Google Scholar 

  • 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):2847–2853

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 University

    Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Heimann AC, Batstone DJ, Jakobsen R (2006) Methanosarcina spp. drive vinyl chloride dechlorination via interspecies hydrogen transfer. Appl Environ Microbiol 72(4):2942–2949

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):485–495

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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):3359–3367

    CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):198–206

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):1269–1273

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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):1422–1431

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Google Scholar 

  • Lovley DR, Ferry JG (1985) Production and consumption of H2 during growth of Methanosarcina spp. on acetate. Appl Environ Microbiol 49(1):247–249

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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):123–134

    Article  CAS  PubMed  Google Scholar 

  • 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):3131–3140

    Article  CAS  PubMed  Google Scholar 

  • 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):7329–7341

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):5141–5147

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):5106–5116

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Maymó-Gatell X, Chien Y, Gossett JM, Zinder SH (1997) Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276(5318):1568–1571

    Article  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Mohn WW, Tiedje JM (1992) Microbial reductive dehalogenation. Microbiol Rev 56(3):482–507

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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):1499–1509

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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):2652–2662

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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

  • 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

    Google Scholar 

  • 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 471–493

    Chapter  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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):105–108

    Article  CAS  PubMed  Google Scholar 

  • 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

    CAS  PubMed  Google Scholar 

  • 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):840–848

    CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Sleep BE, Brown AJ, Lollar BS (2005) Long-term tetrachlorethene degradation sustained by endogenous cell decay. J Environ Eng Sci 4(1):11–17

    Article  CAS  Google Scholar 

  • 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):2408–2413

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sun BL, Griffin BM, Ayala-del-Rio HL, Hashsham SA, Tiedje JM (2002) Microbial dehalorespiration with 1,1,1-trichloroethane. Science 298(5595):1023–1025

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Google Scholar 

  • 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):710–719

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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):807–812

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):248–261

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Google Scholar 

  • Yang YR, McCarty PL (1998) Competition for hydrogen within a chlorinated solvent dehalogenating anaerobic mixed culture. Environ Sci Technol 32(22):3591–3597

    Article  CAS  Google Scholar 

  • 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):3954–3966

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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):4325–4334

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Yu ZT, Smith GB (2000) Inhibition of methanogenesis by C-1- and C-2-polychlorinated aliphatic hydrocarbons. Environ Toxicol Chem 19(9):2212–2217

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ruth E. Richardson .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Richardson, R. (2016). Organohalide-Respiring Bacteria as Members of Microbial Communities: Catabolic Food Webs and Biochemical Interactions. In: Adrian, L., Löffler, F. (eds) Organohalide-Respiring Bacteria. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-49875-0_14

Download citation

Publish with us

Policies and ethics