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Characterization of four TCE-dechlorinating microbial enrichments grown with different cobalamin stress and methanogenic conditions

  • Applied microbial and cell physiology
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Abstract

To investigate the important supportive microorganisms responsible for trichloroethene (TCE) bioremediation under specific environmental conditions and their relationship with Dehalococcoides (Dhc), four stable and robust enrichment cultures were generated using contaminated groundwater. Enrichments were maintained under four different conditions exploring two parameters: high and low TCE amendments (resulting in inhibited and uninhibited methanogenic activity, respectively) and with and without vitamin B12 amendment. Lactate was supplied as the electron donor. All enrichments were capable of reductively dechlorinating TCE to vinyl chloride and ethene. The dechlorination rate and ethene generation were higher, and the proportion of electrons used for dechlorination increased when methanogenesis was inhibited. Biologically significant cobalamin biosynthesis was detected in the enrichments without B12 amendment. Comparative genomics using a genus-wide microarray revealed a Dhc genome similar to that of strain 195 in all enrichments, a strain that lacks the major upstream corrin ring biosynthesis pathway. Seven other bacterial operational taxonomic units (OTUs) were detected using clone libraries. OTUs closest to Pelosinus, Dendrosporobacter, and Sporotalea (PDS) were most dominant. The Clostridium-like OTU was most affected by B12 amendment and active methanogenesis. Principal component analysis revealed that active methanogenesis, rather than vitamin B12 limitation, exerted a greater effect on the community structures even though methanogens did not seem to play an essential role in providing corrinoids to Dhc. In contrast, acetogenic bacteria that were abundant in the enrichments, such as PDS and Clostridium sp., may be potential corrinoid providers for Dhc.

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References

  • 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 6:1702–1714

    Article  CAS  Google Scholar 

  • Chen M, Wolin MJ (1981) Influence of heme and vitamin B12 on growth and fermentations of Bacteroides species. J Bacteriol 145:466–471

    CAS  Google Scholar 

  • Croft MT, Lawrence AD, Raux-Deery E, Warren MJ, Smith AG (2005) Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature 438:90–93

    Article  CAS  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 69:953–959

    Article  CAS  Google Scholar 

  • Cupples AM, Spormann AM, McCarty PL (2004) Comparative evaluation of chloroethene dechlorination to ethene by Dehalococcoides-like microorganisms. Environ Sci Technol 38:4768–4774

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Distefano TD, Gossett JM, Zinder SH (1992) Hydrogen as an electron donor for dechlorination of tetrachloroethene by an anaerobic mixed culture. Appl Environ Microbiol 58:3622–3629

    CAS  Google Scholar 

  • Doherty RE (2000) A history of the production and use of carbon tetrachloride, tetrachloroethylene, trichloroethylene and 1,1,1-trichloroethane in the United States: part 1—historical background; carbon tetrachloride and tetrachloroethylene. Environ Forensics 1:69–81

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Duhamel M, Mo K, Edwards EA (2004) Characterization of a highly enriched Dehalococcoides-containing culture that grows on vinyl chloride and trichloroethene. Appl Environ Microbiol 70:5538–5545

    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 39:8358–8368

    Article  CAS  Google Scholar 

  • Futamata H, Yoshida N, Kurogi T, Kaiya S, Hiraishi A (2007) Reductive dechlorination of chloroethenes by Dehalococcoides-containing cultures enriched from a polychlorinated-dioxin-contaminated microcosm. ISME J 1:471–479

    Article  CAS  Google Scholar 

  • Gray MJ, Escalante-Semerena JC (2009) In vivo analysis of cobinamide salvaging in Rhodobacter sphaeroides strain 2.4.1. J Bacteriol 191:3842–3851

    Article  CAS  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 6:45–54

    Article  CAS  Google Scholar 

  • Guimaraes DH, Weber A, Klaiber I, Vogler B, Renz P (1994) Guanylcobamide and hypoxanthylcobamide—corrinoids formed by Desulfovibrio vulgaris. Arch Microbiol 162:272–276

    Google Scholar 

  • He J, Sung Y, Krajmalnik-Brown R, Ritalahti KM, Löffler FE (2005) Isolation and characterization of Dehalococcoides sp strain FL2, a trichloroethene (TCE)- and 1,2-dichloroethene-respiring anaerobe. Environ Microbiol 7:1442–1450

    Article  CAS  Google Scholar 

  • He JZ, Holmes VF, Lee PKH, Alvarez-Cohen L (2007) Influence of vitamin B12 and cocultures on the growth of Dehalococcoides isolates in defined medium. Appl Environ Microbiol 73:2847–2853

    Article  CAS  Google Scholar 

  • He JZ, Ritalahti KM, Aiello MR, Löffler FE (2003a) Complete detoxification of vinyl chloride by an anaerobic enrichment culture and identification of the reductively dechlorinating population as a Dehalococcoides species. Appl Environ Microbiol 69:996–1003

    Article  CAS  Google Scholar 

  • He JZ, Ritalahti KM, Yang KL, Koenigsberg SS, Löffler FE (2003b) Detoxification of vinyl chloride to ethene coupled to growth of an anaerobic bacterium. Nature 424:62–65

    Article  CAS  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 68:485–495

    Article  CAS  Google Scholar 

  • 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 72:5877–5883

    Article  CAS  Google Scholar 

  • Janssen PH (1991) Isolation of Clostridium propionicum strain 19acry3 and further characteristics of the species. Arch Microbiol 155:566–571

    Article  CAS  Google Scholar 

  • Johnson DR, Brodie EL, Hubbard AE, Andersen GL, Zinder SH, Alvarez-Cohen L (2008) Temporal transcriptomic microarray analysis of “Dehalococcoides ethenogenes” strain 195 during the transition into stationary phase. Appl Environ Microbiol 74:2864–2872

    Article  CAS  Google Scholar 

  • Lee PKH, Cheng D, Hu P, West KA, Dick GJ, Brodie EL, Andersen GL, Zinder SH, He JZ, Alvarez-Cohen L (2011) Comparative genomics of two newly isolated Dehalococcoides strains and an enrichment using a genus microarray. ISME J 5:1014–1024

    Article  CAS  Google Scholar 

  • Lee PKH, Johnson DR, Holmes VF, He JZ, Alvarez-Cohen L (2006) Reductive dehalogenase gene expression as a biomarker for physiological activity of Dehalococcoides spp. Appl Environ Microbiol 72:6161–6168

    Article  CAS  Google Scholar 

  • Löffler FE, Ritalahti KM, Tiedje JM (1997) Dechlorination of chloroethenes is inhibited by 2-bromoethanesulfonate in the absence of methanogens. Appl Environ Microbiol 63:4982–4985

    Google Scholar 

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

    Article  Google Scholar 

  • McCarty PL (1997) Microbiology: breathing with chlorinated solvents. Science 276:1521–1522

    Article  CAS  Google Scholar 

  • McMurdie PJ, Behrens SF, Müller JA, Goke J, Ritalahti KM, Wagner R, Goltsman E, Lapidus A, Holmes S, Löffler FE, Spormann AM (2009) Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS Genet 5:e1000714

    Article  Google Scholar 

  • Men Y, 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 6:410–421

    Article  CAS  Google Scholar 

  • Moe WM, Stebbing RE, Rao JU, Bowman KS, Nobre MF, da Costa MS, Rainey FA (2012) Pelosinus defluvii sp. nov., isolated from chlorinated solvent contaminated groundwater, emended description of the genus Pelosinus, and transfer of Sporotalea propionica to Pelosinus propionicus comb. nov. IJSEM 62:1369–1376

    CAS  Google Scholar 

  • Moran MJ, Zogorski JS, Squillace PJ (2007) Chlorinated solvents in groundwater of the United States. Environ Sci Technol 41:74–81

    Article  CAS  Google Scholar 

  • Mosher JJ, Phelps TJ, Podar M, Hurt RA, Campbell JH, Drake MM, Moberly JG, Schadt CW, Brown SD, Hazen TC, Arkin AP, Palumbo AV, Faybishenko BA, Elias DA (2012) Microbial community succession during lactate amendment and electron-acceptor limitation reveals a predominance of metal-reducing Pelosinus spp. Appl Environ Microbiol 78:2082–2091

    Article  CAS  Google Scholar 

  • Ray AE, Bargar JR, Sivaswamy V, Dohnalkova AC, Fujita Y, Peyton BM, Magnuson TS (2011) Evidence for multiple modes of uranium immobilization by an anaerobic bacterium. Geochim Cosmochim Acta 75:2684–2695

    Article  CAS  Google Scholar 

  • Ray AE, Connon SA, Sheridan PP, Gilbreath J, Shields M, Newby DT, Fujita Y, Magnuson TS (2010) Intragenomic heterogeneity of the 16S rRNA gene in strain UFO1 caused by a 100-bp insertion in helix 6. FEMS Microbiol Ecol 72:343–353

    Article  CAS  Google Scholar 

  • Renz P (1999) Biosynthesis of the 5,6-dimethylbenzimidazole moiety of cobalamin and of the other bases found in natural corrinoids. In: Banerjee R (ed) Chemistry and biochemistry of B12. Wiley, New York, pp 557–575

    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 36:2652–2662

    Article  CAS  Google Scholar 

  • Ritalahti KM, Löffler FE (2004) Populations implicated in anaerobic reductive dechlorination of 1,2-dichloropropane in highly enriched bacterial communities. Appl Environ Microbiol 70:4088–4095

    Article  CAS  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 74:6709–6719

    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 307:105–108

    Article  CAS  Google Scholar 

  • Shelobolina ES, Nevin KP, Blakeney-Hayward JD, Johnsen CV, Plaia TW, Krader P, Woodard T, Holmes DE, VanPraagh CG, Lovley DR (2007) Geobacter pickeringii sp nov., Geobacter argillaceus sp nov and Pelosinus fermentans gen. nov., sp nov., isolated from subsurface kaolin lenses. IJSEM 57:126–135

    CAS  Google Scholar 

  • Sieber JR, Sims DR, Han C, Kim E, Lykidis A, Lapidus AL, McDonnald E, Rohlin L, Culley DE, Gunsalus R, McInerney MJ (2010) The genome of Syntrophomonas wolfei: new insights into syntrophic metabolism and biohydrogen production. Environ Microbiol 12:2289–2301

    CAS  Google Scholar 

  • Siebert A, Neumann A, Schubert T, Diekert G (2002) A non-dechlorinating strain of Dehalospirillum multivorans: evidence for a key role of the corrinoid cofactor in the synthesis of an active tetrachloroethene dehalogenase. Arch Microbiol 178:443–449

    Article  CAS  Google Scholar 

  • Strömpl C, Tindall BJ, Lunsdorf H, Wong TY, Moore ERB, Hippe H (2000) Reclassification of Clostridium quercicolum as Dendrosporobacter quercicolus gen. nov., comb. nov. IJSEM 50:101–106

    Google Scholar 

  • Stupperich E, Eisinger HJ, Krautler B (1988) Diversity of corrinoids in acetogenic bacteria P-cresolylcobamide from Sporomusa ovata, 5-methoxy-6-methylbenzimidazolylcobamide from Clostridium formicoaceticum and vitamin B12 from Acetobacterium woodii. Eur J Biochem 172:459–464

    Article  CAS  Google Scholar 

  • Stupperich E, Steiner I, Ruhlemann M (1986) Isolation and analysis of bacterial cobamides by high-performance liquid-chromatography. Anal Biochem 155:365–370

    Article  CAS  Google Scholar 

  • Sung Y, Ritalahti KM, Apkarian RP, Löffler FE (2006) Quantitative PCR confirms purity of strain GT, a novel trichloroethene-to-ethene-respiring Dehalococcoides isolate. Appl Environ Microbiol 72:1980–1987

    Article  CAS  Google Scholar 

  • Walker CB, He ZL, Yang ZK, Ringbauer JA, He Q, Zhou JH, Voordouw G, Wall JD, Arkin AP, Hazen TC, Stolyar S, Stahl DA (2009) The electron transfer system of syntrophically grown Desulfovibrio vulgaris. J Bacteriol 191:5793–5801

    Article  CAS  Google Scholar 

  • West KA, Johnson DR, Hu P, DeSantis TZ, Brodie EL, Lee PKH, Feil H, Andersen GL, Zinder SH, Alvarez-Cohen L (2008) Comparative genomics of “Dehalococcoides ethenogenes” 195 and an enrichment culture containing unsequenced “Dehalococcoides” strains. Appl Environ Microbiol 74:3533–3540

    Article  CAS  Google Scholar 

  • Wolin EA, Wolin MJ, Wolfe RS (1963) Formation of methane by bacterial extracts. J Biol Chem 238:2882–2886

    CAS  Google Scholar 

  • Wu CW, Whang LM, Cheng HH, Chan KC (2012) Fermentative biohydrogen production from lactate and acetate. Bioresour Technol 113:30–36

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Yi S, Seth EC, Men YJ, Allen RH, Alvarez-Cohen L, Taga ME (2012) Versatility in corrinoid salvaging and remodeling pathways supports the corrinoid-dependent metabolism of Dehalococcoides mccartyi. Appl Environ Microbiol 78:7745–7752

    Article  CAS  Google Scholar 

  • Yu ZT, Smith GB (2000) Inhibition of methanogenesis by C1- and C2-polychlorinated aliphatic hydrocarbons. Environ Toxicol Chem 19:2212–2217

    CAS  Google Scholar 

Download references

Acknowledgments

This research was supported by the Strategic Environmental Research and Development Program through grant ER-1587 and the National Institute of Environmental Health Sciences Superfund P42ES004705. We would like to give our thanks to Dr. Gary Andersen for microarray development, to Vanessa Brisson for the primer design of up-stream corrin ring biosynthesis genes, and to Ben Stenuit for the thoughtful discussion.

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Authors and Affiliations

  1. Department of Civil and Environmental Engineering, University of California, 207 O’Brien Hall, Berkeley, CA, 94720-1710, USA

    Yujie Men

  2. Department of Civil and Environmental Engineering, University of California, 209 O’Brien Hall, Berkeley, CA, 94720-1710, USA

    Patrick K. H. Lee & Katie C. Harding

  3. Department of Civil and Environmental Engineering, University of California, 726 Davis Hall, Berkeley, CA, 94720-1710, USA

    Lisa Alvarez-Cohen

  4. School of Energy and Environment, City University of Hong Kong, Room 506, Biotech Centre 1, 9 Science Park West Avenue, Hong Kong Science Park, Shatin, N.T., Hong Kong, China

    Patrick K. H. Lee

  5. Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA

    Lisa Alvarez-Cohen

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  1. Yujie Men
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  2. Patrick K. H. Lee
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Correspondence to Lisa Alvarez-Cohen.

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Men, Y., Lee, P.K.H., Harding, K.C. et al. Characterization of four TCE-dechlorinating microbial enrichments grown with different cobalamin stress and methanogenic conditions. Appl Microbiol Biotechnol 97, 6439–6450 (2013). https://doi.org/10.1007/s00253-013-4896-8

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  • DOI: https://doi.org/10.1007/s00253-013-4896-8

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