Applied Microbiology and Biotechnology

, Volume 92, Issue 5, pp 1063–1071 | Cite as

Development and characterization of DehaloR^2, a novel anaerobic microbial consortium performing rapid dechlorination of TCE to ethene

  • Michal Ziv-El
  • Anca G. Delgado
  • Ying Yao
  • Dae-Wook Kang
  • Katherine G. Nelson
  • Rolf U. Halden
  • Rosa Krajmalnik-Brown
Environmental Biotechnology

Abstract

A novel anaerobic consortium, named DehaloR^2, that performs rapid and complete reductive dechlorination of trichloroethene (TCE) to ethene is described. DehaloR^2 was developed from estuarine sediment from the Back River of the Chesapeake Bay and has been stably maintained in the laboratory for over 2 years. Initial sediment microcosms showed incomplete reduction of TCE to DCE with a ratio of trans- to cis- isomers of 1.67. However, complete reduction to ethene was achieved within 10 days after transfer of the consortium to sediment-free media and was accompanied by a shift to cis-DCE as the prevailing intermediate metabolite. The microbial community shifted from dominance of the Proteobacterial phylum in the sediment to Firmicutes and Chloroflexi in DehaloR^2, containing the genera Acetobacterium, Clostridium, and the dechlorinators Dehalococcoides. Also present were Spirochaetes, possible acetogens, and Geobacter which encompass previously described dechlorinators. Rates of TCE to ethene reductive dechlorination reached 2.83 mM Cl d−1 in batch bottles with a Dehalococcoides sp. density of 1.54E+11 gene copies per liter, comparing favorably to other enrichment cultures described in the literature and identifying DehaloR^2 as a promising consortium for use in bioremediation of chlorinated ethene-impacted environments.

Keywords

Dehalococcoides Chlorinated ethenes Sediment microorganisms Reductive dechlorination 

References

  1. Abelson PH (1990) Inefficient remediation of groundwater pollution. Science 250:733CrossRefGoogle Scholar
  2. Abrahamsson K, Ekdahl A, Collen J, Pedersen M (1995) Marine algae—a source of trichloroethylene and perchloroethylene. Limnol Oceanogr 40:1321–1326CrossRefGoogle Scholar
  3. Amos BK, Ritalahti KM, Cruz-Garcia C, Padilla-Crespo E, Loffler FE (2008) Oxygen effect on Dehalococcoides viability and biomarker quantification. Environ Sci Technol 42:5718–5726CrossRefGoogle Scholar
  4. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2006) New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol 72:5734–5741CrossRefGoogle Scholar
  5. Cummings DE, Snoeyenbos-West OL, Newby DT, Niggemyer AM, Lovley DR, Achenbach LA, Rosenzweig RF (2003) Diversity of Geobacteraceae species inhabiting metal-polluted freshwater lake sediments ascertained by 16S rRNA gene analyses. Microb Ecol 46:257–269Google Scholar
  6. Cupples AM, Spormann AM, McCarty PL (2004) Comparative evaluation of chloroethene dechlorination to ethene by Dehalococcoides-like microorganisms. Environ Sci Technol 38:4768–4774CrossRefGoogle Scholar
  7. DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL (2006) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34:W394–W399CrossRefGoogle Scholar
  8. Duhamel M, Edwards EA (2006) Microbial composition of chlorinated ethene-degrading cultures dominated by Dehalococcoides. FEMS Microbiol Ecol 58:538–549CrossRefGoogle Scholar
  9. 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 41:2303–2310CrossRefGoogle Scholar
  10. 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 39:8358–8368CrossRefGoogle Scholar
  11. Haest PJ, Springael D, Smolder E (2010) Dechlorination kinetics of TCE at toxic TCE concentrations: Assessment of different models. Water Research 44:331–339CrossRefGoogle Scholar
  12. Griffin BM, Tiedje JM, Loffler FE (2004) Anaerobic microbial reductive dechlorination of tetrachloroethene to predominately trans-1,2-dichloroethene. Environ Sci Technol 38:4300–4303CrossRefGoogle Scholar
  13. Heidler J, Sapkota A, Halden RU (2006) Partitioning, persistence, and accumulation in digested sludge of the topical antiseptic triclocarban during wastewater treatment. Environ Sci Technol 40:3634–3639CrossRefGoogle Scholar
  14. Holmes VF, He JZ, Lee PKH, Alvarez-Cohen L (2006) Discrimination of multiple Dehalococcoides strains in a trichloroethene enrichment by quantification of their reductive dehalogenase genes. Appl Environ Microbiol 72:5877–5883CrossRefGoogle Scholar
  15. Huber T, Faulkner G, Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317–2319CrossRefGoogle Scholar
  16. 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 294:198–206CrossRefGoogle Scholar
  17. Kittelmann S, Friedrich MW (2008a) Identification of novel perchloroethene-respiring microorganisms in anoxic river sediment by RNA-based stable isotope probing. Environ Microbiol 10:31–46CrossRefGoogle Scholar
  18. Kittelmann S, Friedrich MW (2008b) Novel uncultured Chloroflexi dechlorinate perchloroethene to trans-dichloroethene in tidal flat sediments. Environ Microbiol 10:1557–1570CrossRefGoogle Scholar
  19. 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 74:2728–2739CrossRefGoogle Scholar
  20. Loffler FE, Sun Q, Li JR, Tiedje JM (2000) 16S rRNA gene-based detection of tetrachloroethene-dechlorinating Desulfuromonas and Dehalococcoides species. Appl Environ Microbiol 66:1369–1374CrossRefGoogle Scholar
  21. Loffler FE, Sanford RA, Ritalahti KM (2005) Enrichment, cultivation, and detection of reductively dechlorinating bacteria. Environ Microbiol 397:77–111Google Scholar
  22. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar BA, Lai T, Steppi S, Jobb G, Forster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Konig A, Liss T, Lubmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer KH (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371CrossRefGoogle Scholar
  23. 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 70:7329–7341CrossRefGoogle Scholar
  24. McCarty PL (1997) Microbiology—breathing with chlorinated solvents. Science 276:1521–1522CrossRefGoogle Scholar
  25. Miller GS, Milliken CE, Sowers KR, May HD (2005) Reductive dechlorination of tetrachloroethene to trans-dichloroethene and cis-dichloroethene by PCB-dechlorinating bacterium DF-1. Environ Sci Technol 39:2631–2635CrossRefGoogle Scholar
  26. Miller TR, Heidler J, Chillrud SN, DeLaguild A, Ritchie JC, Mihalic JN, Bopp R, Halden RU (2008) Fate of triclosan and evidence for reductive dechlorination of triclocarban in estuarine sediments. Environ Sci Technol 42:4570–4576CrossRefGoogle Scholar
  27. 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 36:2652–2662CrossRefGoogle Scholar
  28. Ritalahti KM, Amos BK, Sung Y, Wu QZ, Koenigsberg SS, Loffler FE (2006) Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains. Appl Environ Microbiol 72:2765–2774CrossRefGoogle Scholar
  29. Schaefer CE, Condee CW, Vainberg S, Steffan RJ (2009) Bioaugmentation for chlorinated ethenes using Dehalococcoides sp.: comparison between batch and column experiments. Chemosphere 75:141–148CrossRefGoogle Scholar
  30. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541CrossRefGoogle Scholar
  31. Schlotelburg C, von Wintzingerode C, Hauck R, von Wintzingerode F, Hegemann W, Gobel UB (2002) Microbial structure of an anaerobic bioreactor population that continuously dechlorinates 1,2-dichloropropane. FEMS Microbiol Ecol 39:229–237CrossRefGoogle Scholar
  32. Taş N, Eekert MHA, Vos WM, Smidt H (2009) The little bacteria that can—diversity, genomics and ecophysiology of ‘Dehalococcoides’ spp. in contaminated environments. Microb Biotechnol 3:389–402CrossRefGoogle Scholar
  33. Torres CI, Krajmalnik-Brown R, Parameswaran P, Marcus AK, Wanger G, Gorby YA, Rittmann BE (2009) Selecting anode-respiring bacteria based on anode potential: phylogenetic, electrochemical, and microscopic characterization. Environ Sci Technol 43:9519–9524CrossRefGoogle Scholar
  34. Vainberg S, Condee CW, Steffan RJ (2009) Large-scale production of bacterial consortia for remediation of chlorinated solvent-contaminated groundwater. J Ind Microbiol Biotechnol 36:1189–1197CrossRefGoogle Scholar
  35. Wolcott RD, Gontcharova V, Sun Y, Dowd SE (2009) Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and titanium amplicon pyrosequencing and metagenomic approaches. BMC Microbiol 9:226CrossRefGoogle Scholar
  36. Xiu ZM, Jin ZH, Li TL, Mahendra S, Lowry GV, Alvarez PJJ (2010) Effects of nano-scale zero-valent iron particles on a mixed culture dechlorinating trichloroethylene. Bioresour Technol 101:1141–1146CrossRefGoogle Scholar
  37. Zhang H, Banaszak JE, Parameswaran P, Alder J, Krajmalnik-Brown R, Rittmann BE (2009) Focused-pulsed sludge pre-treatment increases the bacterial diversity and relative abundance of acetoclastic methanogens in a full-scale anaerobic digester. Water Res 43:4517–4526CrossRefGoogle Scholar
  38. Zhang HS, 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 44:5159–5164CrossRefGoogle Scholar
  39. Zhao YG, Ren NQ, Wang AJ (2008) Contributions of fermentative acidogenic bacteria and sulfate-reducing bacteria to lactate degradation and sulfate reduction. Chemosphere 72:233–242CrossRefGoogle Scholar
  40. Zhou JZ, Davey ME, Figueras JB, Rivkina E, Gilichinsky D, Tiedje JM (1997) Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA. Microbiology-Uk 143:3913–3919CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Michal Ziv-El
    • 1
  • Anca G. Delgado
    • 1
  • Ying Yao
    • 1
  • Dae-Wook Kang
    • 1
  • Katherine G. Nelson
    • 1
  • Rolf U. Halden
    • 1
  • Rosa Krajmalnik-Brown
    • 1
  1. 1.Swette Center for Environmental BiotechnologyBiodesign Institute at Arizona State UniversityTempeUSA

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