Combination of Competitive Quantitative PCR and Constant- Denaturant Capillary Electrophoresis for High-Resolution Detection and Enumeration of Microbial Cells

Applied and Environmental Microbiology

Volumn 67, Issue 9, 2001, Pages 3897-3903

  Lim, Eelin L ^a,c   Tomita, Aoy V ^a   Thilly, William G ^a   Polz, Martin F ^a,b  

^a Massachusetts Institute of Technology Cambridge   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c Temple University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FRESH WATER; PRIMER DNA; PROTOZOAL DNA;

ANIMAL; ARTICLE; CAPILLARY ELECTROPHORESIS; EVALUATION; FLAGELLATE; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METHODOLOGY; PARASITOLOGY; POLYMERASE CHAIN REACTION;

ANIMALS; DNA PRIMERS; DNA, PROTOZOAN; ELECTROPHORESIS, CAPILLARY; FRESH WATER; IN SITU HYBRIDIZATION, FLUORESCENCE; MASTIGOPHORA; POLYMERASE CHAIN REACTION;

EID: 0035462374     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.67.9.3897-3903.2001     Document Type: Article

References (29)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Amann, R. I., W. Ludwig, and K.-H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
3. Becker, S., P. Böger, R. Oehlmann, and A. Ernst. 2000. PCR bias in ecological analysis: a case study for quantitative Taq nuclease assays in analyses of microbial communities. Appl. Environ Microbiol. 66:4945-4953.
4. Becker-André, M., and K. Hahlbrock. 1989. Absolute mRNA quantitation using the polymerase chain reaction (PCR): a novel approach by a PCR aided transcript titration assay (PATTY). Nucleic Acids Res. 17:9437-9446.
5. Chandler, D. P. 1998. Redefining relativity: quantitative PCR at low template concentrations for industrial and environmental microbiology. J. Ind. Microbiol. Biotechnol. 21:128-140.
6. Dahle, A. B., and M. Laake. 1982. Diversity dynamics of marine bacteria studied by immunofluorescent staining on membrane filters. Appl. Environ. Microbiol. 43:169-176.
7. Desjardin, L. E., Y. Chen, M. D. Perkins, L. Teixeira, M. D. Cave, and K. D. Eisenach. 1998. Comparison of the ABI 7700 system (TaqMan) and competitive PCR for quantification of IS6110 DNA in sputum during treatment of tuberculosis. J. Clin. Microbiol. 36:1964-1968.
8. Giovannoni, S. J., E. F. DeLong, G. J. Olsen, and N. R. Pace. 1988. Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells. J. Bacteriol. 170:720-726.
9. Head, I. M., J. R. Saunders, and R. W. Pickup. 1998. Microbial evolution, diversity and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb. Ecol. 35:1-21.
10. Johnsen, K., Ø. Enger, C. S. Jacobsen, L. Thirup, and V. Torsvik. 1999. Quantitative selective PCR of16S ribosomal DNA correlates well with selective agar plating in describing population dynamics of indigenous Pseudomonas spp. in soil hot spots. Appl. Environ. Microbiol. 65:1786-1789.
11. Khrapko, K., J. S. Hanekamp, W. G. Thilly, A. Belenkii, F. Foret, and B. L. Karger. 1994. Constant denaturant capillary electrophoresis (CDCE): a high resolution appraoch to mutational analysis. Nucleic Acids Res. 22:364-369.
12. Laurie, A. D., and G. Lloyd-Jones. 2000. Quantification of phnAc and nahAc in contaminated New Zealand soils by competitive PCR. Appl. Environ. Microbiol. 66:1814-18117.
13. Lee, S.-Y., J. Bollinger, D. Bezdicek, and A. Ogram. 1996. Estimation of the abundance of an uncultivated soil bacterial strain by a competitive quantitative PCR method. Appl. Environ. Microbiol. 62:3787-3793.
14. Leipe, D. D., P. O. Wainright, J. H. Gunderson, D. Porter, D. J. Patterson, F. Valois, S. Himmerich, and M. L. Sogin. 1994. The stramenopiles from a molecular perspective: 16S-like rRNA sequences from Labyrinthuloides minuta and Cafeteria roenbergensis. Phycology 33:369-377.
15. Leser, T. D., M. Boye, and N. B. Hendriksen. 1995. Survival and activity of Pseudomonas sp. strain B13(FRI) in a marine microcosm determined by quantitative PCR and an rRNA-targeting probe and its effect on the indigenous bacterioplankton. Appl. Environ. Microbiol. 61:1201-1207.
16. Lim, E. L., L. A. Amaral, D. A. Caron, and E. F. DeLong. 1993. Application of rRNA-based probes for observing marine nanoplanktonic protists. Appl. Environ. Microbiol. 59:1647-1655.
17. Lim, E. L., D. A. Caron, and E. K. DeLong. 1996. Development and held application of a quantitative method for examining natural assemblages of protists with oligonucleotide probes. Appl. Environ. Microbiol. 62:1416-1423.
18. Lim, E. L., M. R. Dennett, and D. A. Caron. 1999. The ecology of Paraphysomonas imperforata based on studies employing oligonucleotide probe identification in coastal water samples and enrichment cultures. Limnol. Oceanogr. 44:37-51.
19. Lim, E. L., M. R. Dennett, and D. A. Caron. 2001. Identification of heterotrophic nanoflagellates by restriction fragment length polymorphism analysis of small subunit ribosomal DNA. J. Eukaryot. Microbiol. 48:247-257.
20. Maidak, B. L., J. R. Cole, C. T. J. Parker, G. M. Garrity, N. Larsen, B. Li, T. G. Lilburn, M. J. McCaughey, G. J. Olsen, R. Overbeek, S. Pramanik, T. M. Schmidt, J. M. Tiedje, and C. R. Woese. 1999. A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27:171-173.
21. 1-denitrifying bacteria in environmental marine samples. Appl. Environ. Microbiol. 66:1564-1571.
22. Möller, A., and J. K. Jansson. 1997. Quantification of genetically tagged cyanobacteria in Baltic Sea sediment by competitive PCR. Biotechniques 22:512-518.
23. Porter, K. G., and Y. S. Feig. 1980. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25:943-948.
24. Raeymaekers, L. 1993. Quantitative PCR: thoeretical considerations with practical implications. Anal. Biochem. 214:582-585.
25. Suzuki, M. T., L. T. Taylor, and E. F. DeLong. 2000. Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5′-nuclease assays. Appl. Environ. Microbiol. 66:4605-4614.
26. Tay, T.-L., H. Hemond, L. Krumholz, C. M. Cavanaugh, and M. F. Polz. 2001. Population dynamics of two toluene degrading species in a contaminated stream assessed by quantitative PCR. Microb. Ecol. 41:124-131.
27. Tuomi, P., T. Torsvik, M. Heldal, and G. Bratbak. 1997. Bacterial population dynamics in a meromictic lake. Appl. Environ. Microbiol. 63:2181-2188.
28. Wilson, I. G. 1997. Inhibition and facilitation of nucleic acid amplification. Appl. Environ. Microbiol. 63:3741-3751.
29. Zachar, V., R. A. Thomas, and A. S. Goustin. 1993. Absolute quantitation of target DNA: a simple competitive PCR for efficient analysis of multiple samples. Nucleic Acids Res. 21:2017-2018.