Development of a real-time PCR method for quantification of the three genera Dehalobacter, Dehalococcoides, and Desulfitobacterium in microbial communities

Journal of Microbiological Methods

Volumn 57, Issue 3, 2004, Pages 369-378

  Smits, Theo H M ^a   Devenoges, Christiane ^a   Szynalski, Katia ^a   Maillard, Julien ^a   Holliger, Christof ^a  

^a EPFL   (Switzerland)

Author keywords

Microbial communities; Population abudance; Real time PCR

Indexed keywords

ACCURACY; ARTICLE; BACTERIAL GENE; BACTERIUM CULTURE; CONTROLLED STUDY; DEHALOBACTER; DEHALOCOCCOIDES; DESULFITOBACTERIUM; DNA DETERMINATION; EUBACTERIUM; GENE AMPLIFICATION; GENE IDENTIFICATION; MICROFLORA; NONHUMAN; PRIORITY JOURNAL; PROCESS DEVELOPMENT; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SAMPLE;

BACTERIA, ANAEROBIC; BASE SEQUENCE; CHLOROFLEXI; DESULFITOBACTERIUM; DNA, BACTERIAL; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS); DEHALOBACTER; DEHALOCOCCOIDES; DESULFITOBACTERIUM;

EID: 2342555069     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2004.02.003     Document Type: Article

References (46)

1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410
2. Baker G.C., Smith J.J., Cowan D.A. Review and re-analysis of domain-specific 16S primers. J. Microbiol. Methods. 55:2003;541-555
3. Bauer-Kreisel P., Eisenbeis M., Scholz-Muramatsu H. Quantification of Dehalospirillum multivorans in mixed-culture biofilms with an enzyme-linked immunosorbent assay. Appl. Environ. Microbiol. 62:1996;3050-3052
4. Becker S., Böger P., Oehlmann R., Ernst A. PCR bias in ecological analysis: a case study for quantitative Taq nuclease assays in analyses of microbial communities. Appl. Environ. Microbiol. 66:2000;4945-4953
5. Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. The complete genome sequence of Escherichia coli K-12. Science. 277:1997;1453-1474
6. Bouchard B., Beaudet R., Villemur R., McSween G., Lepine F., Bisaillon J.G. Isolation and characterization of Desulfitobacterium frappieri sp. nov., an anaerobic bacterium which reductively dechlorinates pentachlorophenol to 3-chlorophenol. Int. J. Syst. Bacteriol. 46:1996;1010-1015
7. Bradley P.M., Chapelle F.H. Microbial mineralization of VC and DCE under different terminal electron accepting conditions. Anaerobe. 4:1998;81-87
8. Bustin S.A. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J. Mol. Endocrinol. 25:2000;169-193
9. Bustin S.A. Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J. Mol. Endocrinol. 29:2002;23-39
10. Cupples A.M., Spormann A.M., McCarty P.L. Growth of a Dehalococcoides-like microorganism on vinyl chloride and cis-dichloroethene as electron acceptors as determined by competitive PCR. Appl. Environ. Microbiol. 69:2003;953-959
11. Dojka M.A., Hugenholtz P., Haack S.K., Pace N.R. Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64:1998;3869-3877
12. El Fantroussi S., Mahillon J., Naveau H., Agathos S.N. Introduction of anaerobic dechlorinating bacteria into soil slurry microcosms and nested-PCR monitoring. Appl. Environ. Microbiol. 63:1997;806-811
13. Finneran K.T., Forbush H.M., Gaw VanPraagh C.V., Lovley D.R. Desulfitobacterium metallireducens sp. nov., an anerobic bacterium that couples growth to the reduction of metals and humic acids as well as chlorinated compounds. Int. J. Syst. Evol. Microbiol. 52:2002;1929-1935
14. Gerritse J., Drzyzga O., Kloetstra G., Keijmel M., Wiersum L.P., Hutson R., Collins M.D., Gottschal J.C. Influence of different electron donors and acceptors on dehalorespiration of tetrachloroethene by Desulfitobacterium frappieri TCE1. Appl. Environ. Microbiol. 65:1999;5212-5221
15. Ginzinger D.G. Gene quantification using real-time quantitative PCR: an emerging technology hits the mainstream. Exp. Hematol. 30:2002;503-512
16. Harms G., Layton A.C., Dionisi H.M., Gregory I.R., Garrett V.M., Hawkins S.A., Robinson K.G., Sayler G.S. Real-Time PCR quantification of nitrifying bacteria in a municipal wastewater treatment plant. Environ. Sci. Technol. 37:2003;343-351
17. He J., Ritalahti K.M., Yang K.-L., Koenigsberg S.S., Löffler F.E. Detoxification of vinyl chloride to ethene coupled to growth of an anaerobic bacterium. Nature. 424:2003;62-65
18. Hermansson A., Lindgren P.-E. Quantification of ammonia-oxidizing bacteria in arable soil by real-time PCR. Appl. Environ. Microbiol. 67:2001;972-976
19. Holliger C., Hahn D., Harmsen H., Ludwig W., Schumacher W., Tindall B., Vazquez F., Weiss N., Zehnder A.J.B. Dehalobacter restrictus gen. nov. and sp. nov., a strictly anaerobic bacterium that reductively dechlorinates tetra- and trichloroethene in an anaerobic respiration. Arch. Microbiol. 1998;313-321
20. Holliger C., Wohlfarth G., Diekert G. Reductive dechlorination in the energy metabolism of anaerobic bacteria. FEMS Microbiol. Rev. 22:1999;383-398
21. Innis M.A., Gelfand D.H., Sninsky J.J., White T.J. PCR Protocols. A Guide to Methods and Applications. 1990;Academic Press, San Diego
22. Klappenbach J.A., Sayman P.R., Cole J.R., Schmidt T.M. rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res. 29:2001;181-184
23. Lane D.J. 16S/23S rRNA sequencing. Stackebrandt E., Goodfellow M. Nucleic Acid Techniques in Bacterial Systematics. 1991;115-175 Wiley, New York, NY
24. Lanthier M., Villemur R., Lépine F., Bisaillon J.-G., Beaudet R. Geographic distribution of Desulfitobacterium frappieri PCP-1 and Desulfitobacterium spp. in soils from the province of Quebec, Canada. FEMS Microbiol. Ecol. 36:2001;185-191
25. 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. Jr., Barcelona M.J., Petrovskis E., Hickey R., Tiedje J.M., Adriaens P. Bioreactive barriers: a comparison of bioaugmentation and biostimulation for chlorinated solvent remediation. Environ. Sci. Technol. 37:2003;1422-1431
26. Lévesque M.-J., la Boissière S., Thomas J.-C., Beaudet R., Villemur R. Rapid method for detecting Desulfitobacterium frappieri strain PCP-1 in soil by the polymerase chain reaction. Appl. Microbiol. Biotechnol. 47:1997;719-725
27. Löffler F.E., Sun Q., Li J., Tiedje J.M. 16S rRNA gene-based detection of tetrachloroethene-dechlorinating Desulfuromonas and Dehalococcoides species. Appl. Environ. Microbiol. 66:2000;1369-1374
28. Luijten M.L.G.C., de Weert J., Smidt H., Boschker H.T.S., de Vos W.M., Schraa G., Stams A.J.M. Description of Sulfurospirillum halorespirans sp. nov., an anaerobic, tetrachloroethene-respiring bacterium, and transfer of Dehalospirillum multivorans to the genus Sulfurospirillum as Sulfurospirillum multivorans comb. nov. Int. J. Syst. Evol. Microbiol. 53:2003;787-793
29. Mackay I.M., Arden K.E., Nitsche A. Real-time PCR in virology. Nucleic Acids Res. 30:2002;1292-1305
30. Maidak B.L., Cole J.R., Parker C.T. Jr., Garrity G.M., Larsen N., Li B., Lilburn T.G., McGCaughey M.J., Olsen G.J., Overbeek R., Pramanik S., Schmidt T.M., Tiedje J.M., Woese C.R. A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27:1999;171-173
31. Maillard J., Schumacher W., Vazquez F., Regeard C., Hagen W.R., Holliger C. Characterization of the corrinoid iron-sulfur protein tetrachloroethene reductive dehalogenase of Dehalobacter restrictus. Appl. Environ. Microbiol. 69:2003;4628-4638
32. Maymó-Gatell X., Chien Y.-T., Gossett J.M., Zinder S.H. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science. 276:1997;1568-1571
33. Maymó-Gatell X., Anguish T., Zinder S.H. Reductive dechlorination of chlorinated ethenes and 1, 2-dichloroethane by "Dehalococcoides ethenogenes" 195. Appl. Environ. Microbiol. 65:1999;3108-3113
34. Muyzer G., de Waal E.C., Uitterlinden A.G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59:1993;695-700
35. Nadkarni M.A., Martin F.E., Jacques N.A., Hunter N. Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primer set. Microbiology. 148:2002;257-266
36. Pfaffl M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29:2001;e45
37. Sambrook J., Fritsch E.F., Maniatis T. Molecular Cloning: A Laboratory Manual. 2nd ed. 1989;Cold Spring Harbor Laboratory Press, New York
38. Scholz-Muramatsu H., Neumann A., Messmer M., Moore E., Diekert G. Isolation and characterization of Dehalospirillum multivorans gen. nov. sp. nov., a tetrachloroethene-utilizing, strictly anaerobic bacterium. Arch. Microbiol. 1995;48-56
39. Stults J.R., Snoeyenbos-West O., Methe B., Lovley D.R., Chandler D.P. Application of the 5′ fluorogenic exonuclease assay (TaqMan) for quantitative ribosomal DNA and rRNA analysis in sediments. Appl. Environ. Microbiol. 67:2001;2781-2789
40. Suyama A., Iwakiri R., Kai K., Tokunaga T., Sera N., Furukawa K. Isolation and characterization of Desulfitobacterium sp. Y51 capable of efficient dehalogenation of tetrachloroethene and polychloroethanes. Biosci. Biotechnol. Biochem. 65:2001;1474-1481
41. Suzuki M.T., Taylor L.T., DeLong E.F. Quantitative analysis of small-subunit rRNA genes in mixed microbial population via 5′-nuclease assays. Appl. Environ. Microbiol. 66:2000;4605-4614
42. Tourova T.P. Copy number of ribosomal operons in prokaryotes and its effect on phylogenetic analysis. Microbiology. 72:2003;437-452
43. von Wintzingerode F., Göbel U.B., Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:1997;213-229
44. von Wintzingerode F., Selent B., Hegemann W., Göbel U.B. Phylogenetic analysis of an anaerobic, trichlorobenzene-transforming microbial consortium. Appl. Environ. Microbiol. 65:1999;283-286
45. Wild A., Hermann R., Leisinger T. Isolation of an anaerobic bacterium which reductively dechlorinates tetrachloroethene and trichloroethene. Biodegradation. 7:1996;507-511
46. Yang Y., Zeyer J. Specific detection of Dehalococcoides species by fluorescence in situ hybridization with 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 69:2003;2879-2883