Improved fluorescent in situ hybridization method for detection of bacteria from activated sludge and river water by using DNA molecular beacons and flow cytometry

Applied and Environmental Microbiology

Volumn 73, Issue 6, 2007, Pages 2020-2023

  Lenaerts, Jeremy ^a   Lappin Scott, Hilary M ^b   Porter, Jonathan ^c  

^a Denmark House   (United Kingdom)

^b UNIVERSITY OF EXETER   (United Kingdom)

^c Starcross Laboratory   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATED SLUDGE PROCESS; CELL CULTURE; DNA; FLOW CYTOMETRY; MICROBIOLOGY; RIVERS; SIGNAL TO NOISE RATIO;

CELL SORTING; DNA PROBES; PEPTIDE NUCLEIC ACID (PNA); PSEUDOMONAS PUTIDA;

BACTERIA;

PEPTIDE NUCLEIC ACID; RIVER WATER;

ACTIVATED SLUDGE; BACTERIUM; DETECTION METHOD; DNA; FLOW CYTOMETRY; RIVER WATER; SIGNAL-TO-NOISE RATIO;

ACTIVATED SLUDGE; ANALYTIC METHOD; ARTICLE; BACTERIAL GROWTH; BACTERIUM CULTURE; BACTERIUM DETECTION; CELL SELECTION; CONTROLLED STUDY; COST; DNA DETERMINATION; DNA PROBE; ECOLOGY; ESCHERICHIA COLI; FLOW CYTOMETRY; FLUORESCENCE IN SITU HYBRIDIZATION; INTERMETHOD COMPARISON; LABORATORY; NONHUMAN; PSEUDOMONAS PUTIDA; SENSITIVITY AND SPECIFICITY; SIGNAL NOISE RATIO; TARGET CELL; WATER SAMPLING;

BACTERIOLOGICAL TECHNIQUES; DNA, BACTERIAL; FLOW CYTOMETRY; IN SITU HYBRIDIZATION, FLUORESCENCE; PSEUDOMONAS PUTIDA; RIVERS; SENSITIVITY AND SPECIFICITY; SEWAGE; WATER MICROBIOLOGY;

PSEUDOMONAS PUTIDA;

EID: 33947371287     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.01718-06     Document Type: Article

References (20)

1. Amann, R. I. 1995. Fluorescently labeled, rRNA-targeted oligonucleotide probes in the study of microbial ecology. Mol. Ecol. 4:543-553.
2. Amann, R. I., B. J. Binder, R. J. Olson, S. W. Chisholm, R. Devereux, and D. A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
3. Amann, R. I., L. Krumholz, and D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic and environmental studies in microbiology. J. Bacteriol. 172:762-770.
4. Braunhowland, E. B., P. A. Vescio, and S. A. Nierzwickibauer. 1993. Use of a simplified cell blot technique and 16S rRNA-directed probes for identification of common environmental isolates. Appl. Environ. Microbiol. 59:3219-3224.
5. Broude, N. E. 2002. Stem-loop oligonucleotides: a robust tool for molecular biology and biotechnology. Trends Biotechnol. 20:249-256.
6. DeLong, E. F., L. T. Taylor, T. L. Marsh, and C. M. Preston. 1999. Visualization and enumeration of marine planktonic archaea and bacteria by using polyribonucleotide probes and fluorescent in situ hybridization. Appl. Environ. Microbiol. 65:5554-5563.
7. DeLong, E. F., G. S. Wickham, and N. R. Pace. 1989. Phylogenetic stains: rRNA-based probes for the identification of single cells. Science 243:1360-1363.
8. Forster, S., J. R. Snape, H. M. Lappin-Scott, and J. Porter. 2002. Simultaneous fluorescent Gram staining and activity assessment of activated sludge bacteria. Appl. Environ. Microbiol. 68:4772-4779.
9. Glockner, F. O., B. M. Fuchs, and R. Amann. 1999. Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl. Environ. Microbiol. 65:3721-3726.
10. MacDonald, R., and V. S. Brozel. 2000. Community analysis of bacterial biofilms in a simulated recirculating cooling-water system by fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes. Water Res. 34:2439-2446.
11. Monroe, W. T., and F. R. Haselton. 2003. Molecular beacon sequence design algorithm. BioTechniques 34:68-73.
12. Schonhuber, W., B. Fuchs, S. Juretschko, and R. Amann. 1997. Improved sensitivity of whole-cell hybridization by the combination of horseradish peroxidase-labeled oligonucleotides and tyramide signal amplification. Appl. Environ. Microbiol. 63:3268-3273.
13. Sekar, R., B. M. Fuchs, R. Amann, and J. Pernthaler. 2004. Flow sorting of marine bacterioplankton after fluorescence in situ hybridization. Appl. Environ. Microbiol. 70:6210-6219.
14. Tyagi, S., and F. R. Kramer. 1996. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14:303-308.
15. Valeur, N., P. Engel, N. Carbajal, E. Connolly, and K. Ladefoged. 2004. Colonization and immunomodulation by Lactobacillus reuteri ATCC 55730 in the human gastrointestinal tract. Appl. Environ. Microbiol. 70:1176-1181.
16. Wallner, G., R. Amann, and W. Beisker. 1993. Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14:136-143.
17. Wallner, G., R. Erhart, and R. Amann. 1995. Flow cytometric analysis of activated sludge with rRNA-targeted probes. Appl. Environ. Microbiol. 61:1859-1866.
18. Widmer, F., R. J. Seidler, P. M. Gillevet, L. S. Watrud, and G. D. Di Giovanni. 1998. A highly selective PCR protocol for detecting 16S rRNA genes of the genus Pseudomonas (sensu stricto) in environmental samples. Appl. Environ. Microbiol. 64:2545-2553.
19. Winstanley, C., J. P. Carter, M. Seasman, J. A. W. Morgan, R. W. Pickup, and J. R. Saunders. 1993. A comparison of the survival of stable and unstable chromosomally located xylE marker cassettes as an indicator of cell division within populations of Pseudomonas putida released into lake water and soil. Microb. Releases 2:97-107.
20. Xi, C. W., M. Balberg, S. A. Boppart, and L. Raskin. 2003. Use of DNA and peptide nucleic acid molecular beacons for detection and quantification of rRNA in solution and in whole cells. Appl. Environ. Microbiol. 69:5673-5678.