Detection and Quantification of Dehalococcoides-Related Bacteria in a Chlorinated Ethene-Contaminated Aquifer Undergoing Natural Attenuation

REFERENCES

• Adrian , L. , Szewzyk , U. , Wecke , J. and Görisch , H. 2000 . Bacterial dehalorespiration with chlorinated benzenes . Nature , 408 : 580 – 583 .
   PubMed Web of Science ®Google Scholar
• Alfreider , A. , Vogt , C. and Babel , W. 2002 . Microbial diversity in an in situ reactor system treating monochlorobenzene contaminated groundwater as revealed by 16S ribosomal DNA analysis . Syst. Appl. Microbiol. , 25 : 232 – 240 .
   PubMed Web of Science ®Google Scholar
• Altschul , S. F. , Madden , T. L. , Schäffer , A. A. , Zhang , J. , Zhang , Z. , Miller , W. and Lipman , D. J. 1997 . Gapped BLAST and PSI-BLAST: A new generation of protein database search programs . Nucleic Acids Res. , 25 : 3389 – 3402 .
   PubMed Web of Science ®Google Scholar
• Amann , R. , Fuchs , B. M. and Behrens , S. 2001 . The identification of microorganisms by fluorescence in situ hybridization . Curr. Opin. Biotechnol. , 12 : 231 – 236 .
   PubMed Web of Science ®Google Scholar
• Amann , R. I. , Ludwig , W. and Schleifer , K.-H. 1995 . Phylogenetic identification and in situ detection of individual microbial cells without cultivation . Microbiol. Rev. , 59 : 143 – 169 .
   PubMedGoogle Scholar
• Aulenta , F. , Rossetti , S. , Majone , M. and Tandoi , V. 2004 . Detection and quantitative estimation of Dehalococcoides spp. in a dechlorinating bioreactor by a combination of fluorescent in situ hybridisation (FISH) and kinetic analysis . Appl. Microbiol. Biotechnol. , 64 : 206 – 212 .
   PubMed Web of Science ®Google Scholar
• Bach , W. and Edwards , K. J. 2003 . Iron and sulfide oxidation within the basaltic ocean crust: Implications for chemolithoautotrophic microbial biomass production . Geochim. Cosmochim. Acta , 67 : 3871 – 3887 .
   Web of Science ®Google Scholar
• Balkwill , D. L. , Leach , F. R. , Wilson , J. T. , McNabb , J. F. and White , D. C. 1988 . Equivalence of microbial biomass measures based on membrane lipid and cell-wall components, adenosine-triphosphate, and direct counts in subsurface aquifer sediments . Microb. Ecol. , 16 : 73 – 84 .
   PubMed Web of Science ®Google Scholar
• Balsiger , C. 2004 . Fate of Volatile Fluorinated Compounds in the Subsurface , Lausannne : Faculté Environment Naturel, Acrchitectural et Construit, EPFL Lausanne .
   Google Scholar
• Bekins , B. A. , Godsy , E. M. and Warren , E. 1999 . Distribution of microbial physiologic types in an aquifer contaminated by crude oil . Microb. Ecol. , 37 : 263 – 275 .
   PubMed Web of Science ®Google Scholar
• Bjerrum , L. , Kjaer , T. and Ramsing , N. B. 2002 . Enumerating ammonia-oxidizing bacteria in environmental samples using competitive PCR . J. Microbiol. Methods , 51 : 227 – 239 .
   PubMed Web of Science ®Google Scholar
• Bolliger , C. , Höhener , P. , Hunkeler , D. , Häberli , K. and Zeyer , J. 1999 . Intrinsic bioremediation of a petroleum hydrocarbon-contaminated aquifer and assessment of mineralization based on stable carbon isotopes . Biodegradation , 10 : 201 – 217 .
   PubMed Web of Science ®Google Scholar
• Bunge , M. , Kleikemper , J. , Miniaci , C. , Duc , L. , Muusse , M. , Hause , G. and Zeyer , J. 2007 . Benzoate-driven dehalogenation of chlorinated ethenes in microbial cultures from a contaminated aquifer . Appl. Microbiol. Biotechnol. , 76 : 1447 – 1456 .
   PubMed Web of Science ®Google Scholar
• Bürgmann , H. , Pesaro , M. , Widmer , F. and Zeyer , J. 2001 . A strategy for optimizing quality and quantity of DNA extracted from soil . J. Microbiol. Methods , 45 : 7 – 20 .
   PubMed Web of Science ®Google Scholar
• Cole , J. R. , Chai , B. , Marsh , T. L. , Farris , R. J. , Wang , Q. , Kulam , S. A. , Chandra , S. , McGarrell , D. M. , Schmidt , T. M. , Garrity , G. M. and Tiedje , J. M. 2003 . The Ribosomal Database Project (RDP-II): Previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy . Nucleic Acids Res. , 31 : 442 – 423 .
   PubMed Web of Science ®Google Scholar
• Conrad , R. , Mayer , H. P. and Wust , M. 1989 . Temporal change of gas metabolism by hydrogen-syntrophic methanogenic bacterial associations in anoxic paddy soil . FEMS Microbiol. Ecol. , 62 : 265 – 273 .
   Web of Science ®Google Scholar
• Cupples , A. M. 2008 . Real-time PCR quantification of Dehalococcoides populations: Methods and applications . J. Microbiol. Methods , 72 : 1 – 11 .
   PubMed Web of Science ®Google Scholar
• Cupples , A. M. , Spormann , A. M. and McCarty , P. L. 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 .
   PubMed Web of Science ®Google Scholar
• Cupples , A. M. , Spormann , A. M. and McCarty , P. L. 2004 . Vinyl chloride and cis-dichloroethene dechlorination kinetics and microorganism growth under substrate limiting conditions . Environ. Sci. Technol. , 38 : 1102 – 1107 .
   PubMed Web of Science ®Google Scholar
• Dolfing , J. 2003 . “ Thermodynamic considerations for dehalogenation ” . In Dehalogenation—Microbial Processes and Environmental Applications , Edited by: Häggblom , M. M. and Bossert , I. D. 89 – 114 . Boston/Dordrecht/London : Kluwer Academic Publishers .
   Google Scholar
• Dolfing , J. and Janssen , D. B. 1994 . Estimates of Gibbs free energies of formation of chlorinated aliphatic compounds . Biodegradation , 5 : 21 – 28 .
   Google Scholar
• Duhamel , M. , Mo , K. and Edwards , E. A. 2004 . Characterization of a highly enriched Dehalococcoides-contaning culture that grows on vinyl chloride and trichloroethene . Appl. Environ. Microbiol. , 70 : 5538 – 5545 .
   PubMed Web of Science ®Google Scholar
• Fazi , S. , Aulenta , F. , Majone , M. and Rossetti , S. 2008 . Improved quantification of Dehalococcoides species by fluorescence in situ hybridization and catalyzed reporter deposition . Syst. Appl. Microbiol. , 31 : 62 – 67 .
   PubMed Web of Science ®Google Scholar
• Field , J. A. , Stams , A. J. M. , Kato , M. and Schraa , G. 1995 . Enhanced biodegradation of aromatic pollutants in cocultures of anaerobic and aerobic bacterial consortia . Antonie van Leeuwenhoek , 67 : 47 – 77 .
   PubMed Web of Science ®Google Scholar
• Förster , E. 1994 . An improved general method to generate internal standards for competitive PCR . Biotechniques , 16 : 18 – 20 .
   PubMed Web of Science ®Google Scholar
• Hall , T. A. 1999 . BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT . Nucleic Acids Symp. Ser. , 41 : 95 – 98 .
   Google Scholar
• He , J. Z. , Ritalahti , K. M. , Yang , K. L. , Koenigsberg , S. S. and Löffler , F. E. 2003 . Detoxification of vinyl chloride to ethene coupled to growth of an anaerobic bacterium . Nature , 424 : 62 – 65 .
   PubMed Web of Science ®Google Scholar
• Heijnen , J. J. and Vandijken , J. P. 1992 . In search of a thermodynamic description of biomass yields for the chemotropic growth of microorganisms . Biotechnol. Bioeng. , 39 : 833 – 858 .
   PubMed Web of Science ®Google Scholar
• Hendrickson , E. R. , Payne , J. A. , Young , R. M. , Starr , M. G. , Perry , M. P. , Fahnestock , S. , Ellis , D. E. and Ebersole , R. C. 2002 . Molecular analysis of Dehalococcoides 16S ribosomal DNA from chloroethene-contaminated sites throughout North America and Europe . Appl. Environ. Microbiol. , 68 : 485 – 495 .
   PubMed Web of Science ®Google Scholar
• Hunkeler , D. , Höhener , P. , Bernasconi , S. and Zeyer , J. 1999 . Engineered in situ bioremediation of a petroleum hydrocarbon-contaminated aquifer: Assessment of mineralization based on alkalinity, inorganic carbon and stable carbon isotope balances . J. Contam. Hydrol. , 37 : 201 – 223 .
   Web of Science ®Google Scholar
• Jakobsen , R. , Albrechtsen , H. J. , Rasmussen , M. , Bay , H. , Bjerg , P. L. and Christensen , T. H. 1998 . H2 concentrations in a landfill leachate plume (Grindsted, Denmark): In situ energetics of terminal electron acceptor processes . Environ. Sci. Technol. , 32 : 2142 – 2148 .
   Web of Science ®Google Scholar
• Jakobsen , R. and Postma , D. 1999 . Redox zoning, rates of sulfate reduction and interactions with Fe-reduction and methanogenesis in a shallow sandy aquifer, R⊘m⊘, Denmark . Geochim. Cosmochim. Acta , 63 : 137 – 151 .
   Web of Science ®Google Scholar
• Johnson , R. L. and Pankow , J. F. 1992 . Dissolution of dense chlorinated solvents into groundwater .2. Source functions for pools of solvent . Environ. Sci. Technol. , 26 : 896 – 901 .
   Web of Science ®Google Scholar
• Kielhorn , J. , Melber , C. , Wahnschaffe , U. , Aitio , A. and Mangelsdorf , I. 2000 . Vinyl chloride: Still a cause for concern . Environ. Health Perspect. , 108 : 579 – 588 .
   PubMed Web of Science ®Google Scholar
• Kittelmann , S. and Friedrich , M. W. 2008 . Identification of novel perchloroethene-respiring microorganisms in anoxic river sediment by RNA-based stable isotope probing . Environ. Microbiol. , 10 : 31 – 46 .
   PubMed Web of Science ®Google Scholar
• Kleikemper , J. , Pombo , S. A. , Schroth , M. H. , Sigler , W. V. , Pesaro , M. and Zeyer , J. 2005 . Activity and diversity of methanogens in a petroleum hydrocarbon-contaminated aquifer . Appl. Environ. Microbiol. , 71 : 149 – 158 .
   PubMed Web of Science ®Google Scholar
• Kleikemper , J. , Schroth , M. H. , Sigler , W. V. , Schmucki , M. , Bernasconi , S. M. and Zeyer , J. 2002 . Activity and diversity of sulfate-reducing bacteria in a petroleum hydrocarbon-contaminated aquifer . Appl. Environ. Microbiol. , 68 : 1516 – 1523 .
   PubMed Web of Science ®Google Scholar
• Kontar , K. 2001 . Study of natural attenuation of chlorinated solvents in the aquifer of Grenchenwiti (Canton of Solothurn) [in French] , Diploma Thesis Neuchâtel : Centre d'Hydrogéologie, Université de Neuchâtel .
   Google Scholar
• Lane , D. J. 1991 . “ 16S/23S rRNA sequencing ” . In Nucleic Acid Techniques in Bacterial Systematics , Edited by: Stackebrandt , E. and Goodfellow , M. 115 – 175 . Chichester, UK : John Wiley & Sons .
   Google Scholar
• Lee , M. D. , Odom , J. M. and Buchanan , R. J. Jr. 1998 . New perspectives on microbial dehalogenation of chlorinated solvents: Insights from the field . Annu. Rev. Microbiol. , 52 : 423 – 452 .
   PubMed Web of Science ®Google Scholar
• Leloup , J. , Quillet , L. , Oger , C. , Boust , D. and Petit , F. 2004 . Molecular quantification of sulfate-reducing microorganisms (carrying dsrAB genes) by competitive PCR in estuarine sediments . FEMS Microbiol. Ecol. , 47 : 207 – 214 .
   PubMed Web of Science ®Google Scholar
• Lendvay , J. M. , Löffler , F. E. , Dollhopf , M. , Aiello , M. R. , Daniels , G. , Fathepure , B. Z. , Gebhard , M. , Heine , R. , Helton , R. , Shi , J. , Krajmalnik-Brown , R. , Major , C. L. , Barcelona , M. J. , Petrovskis , E. , Hickey , R. , Tiedje , J. M. and Adriaens , P. 2003 . Bioreactive barriers: A comparison of bioaugmentation and biostimulation for chlorinated solvent remediation . Environ. Sci. Technol. , 37 : 1422 – 1431 .
   Web of Science ®Google Scholar
• Löffler , F. E. , Cole , J. R. , Ritalahti , K. M. and Tiedje , J. M. 2003 . “ Diversity of dechlorinating bacteria ” . In Dehalogenation: Microbial Processes and Environmental Applications , Edited by: Häggblom , M. M. and Bossert , I. D. 53 – 87 . Boston : Kluwer .
   Google Scholar
• Löffler , F. E. , Sun , Q. , Li , J. and Tiedje , J. M. 2000 . 16S rRNA gene-based detection of tetrachloroethene-dechlorinating Desulfuromonas Dehalococcoides species . Appl. Environ. Microbiol. , 66 : 1369 – 1374 .
   PubMed Web of Science ®Google Scholar
• Löffler , F. E. , Tiedje , J. M. and Sanford , R. A. 1999 . Fraction of electrons consumed in electron acceptor reduction and hydrogen thresholds as indicators of halorespiratory physiology . Appl. Environ. Microbiol. , 65 : 4049 – 4056 .
   PubMed Web of Science ®Google Scholar
• Lowe , M. , Madsen , E. L. , Schindler , K. , Smith , C. , Emrich , S. , Robb , F. and Halden , R. U. 2002 . Geochemistry and microbial diversity of a trichloroethene-contaminated Superfund site undergoing intrinsic in situ reductive dechlorination . FEMS Microbiol. Ecol. , 40 : 123 – 134 .
   PubMed Web of Science ®Google Scholar
• Lu , X. , Wilson , J. T. and Kampbell , D. H. 2006 . Relationship between Dehalococcoides DNA in ground water and rates of reductive dechlorination at field scale . Water Res. , 40 : 3131 – 3140 .
   PubMed Web of Science ®Google Scholar
• Lu , X. X. , Tao , S. , Bosma , T. and Gerritse , J. 2001 . Characteristic hydrogen concentrations for various redox processes in batch study . J. Environ. Sci. Health A Toxic/Hazard. Subst. Environ. Eng. , 36 : 1725 – 1734 .
   Web of Science ®Google Scholar
• Lynch , J. M. 1990 . Longevity of bacteria—considerations in environmental release . Curr. Microbiol. , 20 : 387 – 389 .
   Web of Science ®Google Scholar
• Major , D. W. , McMaster , M. L. , Cox , E. E. , Edwards , E. A. , Dworatzek , S. M. , Hendrickson , E. R. , Starr , M. G. , Payne , J. A. and Buonamici , L. W. 2002 . Field demonstration of successful bioaugmentation to achieve dechlorination of tetrachloroethene to ethene . Environ. Sci. Technol. , 36 : 5106 – 5116 .
   PubMed Web of Science ®Google Scholar
• Maymó-Gatell , X. , Chien , Y. T. , Gossett , J. M. and Zinder , S. H. 1997 . Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene . Science , 276 : 1568 – 1571 .
   PubMed Web of Science ®Google Scholar
• Maymó-Gatell , X. , Nijenhuis , I. and Zinder , S. H. 2001 . Reductive dechlorination of cis-1,2-dichloroethene and vinyl chloride by “Dehalococcoides ethenogenes.” . Environ. Sci. Technol. , 35 : 516 – 521 .
   PubMed Web of Science ®Google Scholar
• McCarty , P. L. 1997 . Microbiology—breathing with chlorinated solvents . Science , 276 : 1521 – 1522 .
   PubMed Web of Science ®Google Scholar
• Muyzer , G. , Brinkhoff , T. , Nübel , U. , Santegoeds , C. , Schäfer , H. and Wawer , C. 1997 . “ Denaturing gradient gel electrophoresis (DGGE) in microbial ecology ” . In Molecular Microbial Ecology Manual , 1 – 27 . Netherlands : Kluwer Academic Publishers .
   Google Scholar
• National Research Council . 1993 . In Situ Bioremediation—When Does It Work? , Washington, DC : National Academy Press .
   Google Scholar
• Norland , S. , Heldal , M. and Tumyr , O. 1987 . On the relation between dry-matter and volume of bacteria . Microb. Ecol. , 13 : 95 – 101 .
   PubMed Web of Science ®Google Scholar
• Nübel , U. , Engelen , B. , Felske , A. , Snaidr , J. , Wieshuber , A. , Amann , R. I. , Ludwig , W. and Backhaus , H. 1996 . Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis . J. Bacteriol. , 178 : 5636 – 5643 .
   PubMed Web of Science ®Google Scholar
• Pernthaler , A. , Pernthaler , J. and Amann , R. I. 2004 . “ Sensitive multi-color fluorescence in situ hybridization for the identification of environmental microorganisms ” . In Molecular Microbial Ecology Manual , Edited by: Kowalchuk , G. A. , d. Bruijn , F. J. , Head , I. M. , Akkermans , A. D. and v. Elsas , J. D. 711 – 726 . Amsterdam : Kluwer Academic Publishers .
   Google Scholar
• Qiagen . 1999 . Isopropanol precipitation of DNA . Qiagen News (3) , : 21 – 23 .
   Google Scholar
• Rahm , B. , Chauhan , S. , Holmes , V. , Macbeth , T. , Sorenson , K. Jr. and Alvarez-Cohen , L. 2006 . Molecular characterization of microbial populations at two sites with differing reductive dechlorination abilities . Biodegradation , 17 : 523 – 534 .
   PubMed Web of Science ®Google Scholar
• Reed , D. W. , Fujita , Y. , Delwiche , M. E. , Blackwelder , D. B. , Sheridan , P. P. , Uchida , T. and Colwell , F. S. 2002 . Microbial communities from methane hydrate-bearing deep marine sediments in a forearc basin . Appl. Environ. Microbiol. , 68 : 3759 – 3770 .
   PubMed Web of Science ®Google Scholar
• Ritalahti , K. M. , Amos , B. K. , Sung , Y. , Wu , Q. , Koenigsberg , S. S. and Löffler , F. E. 2006 . Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains . Appl. Environ. Microbiol. , 72 : 2765 – 2774 .
   PubMed Web of Science ®Google Scholar
• Ruder , A. M. , Ward , E. M. and Brown , D. P. 2001 . Mortality in dry-cleaning workers: An update . Am. J. Ind. Med. , 39 : 121 – 132 .
   PubMed Web of Science ®Google Scholar
• Sahm , K. , MacGregor , B. J. , J⊘rgensen , B. B. and Stahl , D. A. 1999 . Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slot-blot hybridization in a coastal marine sediment . Environ. Microbiol. , 1 : 65 – 74 .
   PubMed Web of Science ®Google Scholar
• Smidt , H. and de Vos , W. M. 2004 . Anaerobic microbial dehalogenation . Annu. Rev. Microbiol. , 58 : 43 – 73 .
   PubMed Web of Science ®Google Scholar
• Smits , T. H. M. , Devenoges , C. , Szynalski , K. , Maillard , J. and Holliger , C. 2004 . Development of a real-time PCR method for quantification of the three genera Dehalobacter Dehalococcoides Desulfitobacterium in microbial communities . J. Microbiol. Meth. , 57 : 369 – 378 .
   PubMed Web of Science ®Google Scholar
• Steiner , O. 1999 . Flow- and transport modelling of a contaminated aquifer in Grenchen, Canton of Solothurn [in German] , Diploma thesis Zurich : Institut für Hydromechanik und Wasserwirtschaft, Swiss Federal Institute of Technology .
   Google Scholar
• Stumm , W. and Morgan , J. J. 1981 . Aquatic Chemistry—An Introduction Emphasizing Chemical Equilibria in Natural Waters, , 2nd ed , New York : Wiley-Interscience .
   Google Scholar
• Takezaki , N. , Rzhetsky , A. and Nei , M. 1995 . Phylogenetic test of the molecular clock and linearized trees . Mol. Biol. Evol. , 12 : 823 – 833 .
   PubMed Web of Science ®Google Scholar
• Tamura , K. , Dudley , J. , Nei , M. and Kumar , S. 2007 . MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0 . Mol. Biol. Evol. , 24 : 1596 – 1599 .
   PubMed Web of Science ®Google Scholar
• Theron , J. and Cloete , T. E. 2000 . Molecular techniques for determining microbial diversity and community structure in natural environments . Crit. Rev. Microbiol. , 26 : 37 – 57 .
   PubMed Web of Science ®Google Scholar
• Thompson , J. D. , Higgins , D. G. and Gibson , T. J. 1994 . CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice . Nucleic Acids Res. , 22 : 4673 – 4680 .
   PubMed Web of Science ®Google Scholar
• Wiedemeier , T. H. , Rifai , H. S. , Newell , C. J. and Wilson , J. T. 1999 . Natural Attenuation of Fuels and Chlorinated Solvents in the Subsurface , New York : John Wiley & Sons .
   Google Scholar
• Yang , Y. , Pesaro , M. , Sigler , W. and Zeyer , J. 2005 . Identification of microorganisms involved in reductive dehalogenation of chlorinated ethenes in an anaerobic microbial community . Water Res. , 39 : 3954 – 3966 .
   PubMed Web of Science ®Google Scholar
• Yang , Y. R. and McCarty , P. L. 1998 . Competition for hydrogen within a chlorinated solvent dehalogenating anaerobic mixed culture . Environ. Sci. Technol. , 32 : 3591 – 3597 .
   Web of Science ®Google Scholar
• Yang , Y. R. and Zeyer , J. 2003 . Specific detection of Dehalococcoides species by fluorescence in situ hybridization with 16S rRNA-targeted oligonucleotide probes . Appl. Environ. Microbiol. , 69 : 2879 – 2883 .
   PubMed Web of Science ®Google Scholar
• Zarda , B. , Hahn , D. , Chatzinotas , A. , Schönhuber , W. , Neef , A. , Amann , R. I. and Zeyer , J. 1997 . Analysis of bacterial community structure in bulk soil by in situ hybridization . Arch. Microbiol. , 168 : 185 – 192 .
   Web of Science ®Google Scholar
• Zimmermann , K. and Mannhalter , J. W. 1996 . Technical aspects of quantitative competitive PCR . Biotechniques , 21 : 268 – 272 . 274 – 279 .
   PubMed Web of Science ®Google Scholar