Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes

Current Opinion in Microbiology

Volumn 6, Issue 3, 2003, Pages 302-309

  Wagner, Michael ^a   Hornt, Matthias ^a   Daims, Holger ^a  

^a UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PEPTIDE NUCLEIC ACID; POLYRIBONUCLEOTIDE; RIBOSOME RNA;

BIOFILM; CONFOCAL LASER MICROSCOPY; DNA BINDING; DNA PROBE; ECOLOGY; ECOPHYSIOLOGY; ESCHERICHIA COLI; FLUORESCENCE IN SITU HYBRIDIZATION; GENE LIBRARY; GENE SEQUENCE; METHODOLOGY; MICROBIAL ACTIVITY; MICROBIAL BIOMASS; MICROFLORA; MICROORGANISM; NONHUMAN; OPERON; PHYLOGENY; PHYSIOLOGY; POLYMERASE CHAIN REACTION; PROKARYOTE; REVIEW; RIBOSOME; RNA GENE; RNA PROBE; SIGNAL TRANSDUCTION; SPECIES COMPARISON;

ESCHERICHIA COLI; PROKARYOTA;

EID: 0038265129     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1369-5274(03)00054-7     Document Type: Review

References (49)

1. DeLong EF, Wickham GS, Pace NR: Phylogenetic stains: ribosomal RNA based probes for the identification of single cells. Science 1989, 243:1360-1363.
2. Amann R, Fuchs BM, Behrens S: The identification of microorganisms by fluorescence in situ hybridisation. Curr Opin Biotechnol 2001, 12:231-236.
3. Moter A, Göbel UB: Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. J Microbiol Methods 2000, 41:85-112.
4. Loy A, Horn M, Wagner M: probeBase: an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res 2003, 31:514-516. Description of the most comprehensive database for published rRNA-targeted oligonucleotide probes accessible via the World Wide Web, URL: http://www.probebase.net.
5. Daims H, Nielsen JL, Nielsen PH, Schleifer KH, Wagner M: In situ characterization of Nitrospira-like nitrite-oxidizing bacteria active in wastewater treatment plants. Appl Environ Microbiol 2001, 67:5273-5284. Encompassing phylogenetic and ecophysiological analysis of Nitrospira-like nitrite-oxidising bacteria in wastewater treatment plants. By combination of FISH and microautoradiography, substrate uptake patterns under different environmental conditions were investigated. The three-dimensional reconstruction of Nitrospira microcolonies showed that these structures contain multiple branched water-permeable channels.
6. Amann RI, Ludwig W, Schleifer K-H: Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995, 59:143-169.
7. Wagner M, Rath G, Amann R, Koops H-P, Schleifer K-H: In situ identification of ammonia-oxidizing bacteria. Syst Appl Microbiol 1995, 18:251-264.
8. Morgenroth E, Obermayer A, Arnold E, Brühl A, Wagner M, Wilderer PA: Effect of long-term idle periods on the performance of sequencing batch reactors. Water Sci Technol 2000, 41:105-113.
9. Oda Y, Slagman S-J, Meijer WG, Forney LJ, Gottschal JC: Influence of growth rate and starvation on fluorescence in situ hybridization of Rhodopseudomonas palustris. FEMS Microbiol Ecol 2000, 32:205-213.
10. Ashelford KE, Weightman AJ, Fry JC: PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res 2002, 30:3481-3489.
11. Pozhitkov AE, Tautz D: An algorithm and program for finding sequence specific oligonucleotide probes for species identification. BMC Bioinformatics 2002, 3:9. The only probe design algorithm, which considers single nucleotide outloops. However, whether these outloops are actually relevant for FISH experiments remains to be investigated.
12. Ludwig W, Strunk O, Westram R, Richter L, Meier H, Yadhukumar A, Buchner A, Lai T, Steppi S, Jobb G et al.: ARB: a software environment for sequence data. Nucleic Acids Res 2003, in press. The eagerly awaited publication describing the most comprehensive software package for phylogeny inference and probe design. Program available at the World Wide Web URL: http://www.arb-home.de
13. Fuchs BM, Wallner G, Beisker W, Schwippl I, Ludwig W, Amann R: Flow cytometric analysis of the in situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probes. Appl Environ Microbiol 1998, 64:4973-4982.
14. Fuchs BM, Syutsubo K, Ludwig W, Amann R: In situ accessibility of Escherichia coli 23S rRNA to fluorescently labeled oligonucleotide probes. Appl Environ Microbiol 2001, 67:961-968.
15. Fuchs BM, Glöckner FO, Wulf J, Amann R: Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes. Appl Environ Microbiol 2000, 66:3603-3607.
16. Perry-O'Keefe H, Rigby S, Oliveira K, Sorensen D, Stender H, Coull J, Hyldig-Nielsen JJ: Identification of indicator microorganisms using a standardized PNA FISH method. J Microbiol Methods 2001, 47:281-292.
17. Stender H, Lund K, Petersen KH, Rasmussen OF, Hongmanee P, Miorner H, Godtfredsen SE: Fluorescence in situ hybridization assay using peptide nucleic acid probes for differentiation between tuberculous and nontuberculous mycobacterium species in smears of mycobacterium cultures. J Clin Microbiol 1999, 37:2760-2765.
18. Worden AZ, Chisholm SW, Binder BJ: In situ hybridization of Prochlorococcus and Synechococcus spp. (marine cyanobacteria) with rRNA-targeted peptide nucleic acid probes. Appl Environ Microbiol 2000, 66:284-289.
19. Oliveira K, Procop GW, Wilson D, Coull J, Stender H: Rapid identification of Staphylococcus aureus directly from blood cultures by fluorescence in situ hybridization with peptide nucleic acid probes. J Clin Microbiol 2002, 40:247-251.
20. Marras SAE, Kramer FR, Tyagi S: Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res 2002, 30:e122. A very detailed study investigating, among other aspects, the effect of nucleotide quenching on different fluorophores. Interestingly, fluorescein is significantly quenched by guanosine and adenosine whereas the fluorescence of Cy3 is increased after close contact to all nucleotides.
21. Torimura M, Kurata S, Yamada K, Yokomaku T, Kamagata Y, Kanagawa T, Kurane R: Fluorescence-quenching phenomenon by photo-induced electron transfer between a fluorescent dye and a nucleotide base. Anal Sci 2001, 17:155-160.
22. Sando S, Kool ET: Imaging of RNA in bacteria with self-ligating quenched probes. J Am Chem Soc 2002, 124:9686-9687. This paper presents an exciting new class of probes for the FISH-based identification of prokaryotes. The so-called 'quenched autoligation' (QUAL) probe-pairs allow in situ hybridisation without washing steps and avoid background fluorescence caused by unspecific probe binding. However, applicability of this new method for complex samples has not yet been demonstrated.
23. Molenaar C, Marras SA, Slats JC, Truffert JC, Lemaitre M, Raap AK, Dirks RW, Tanke HJ: Linear 2′ O-Methyl RNA probes for the visualization of RNA in living cells. Nucleic Acids Res 2001, 29:E89.
24. Fang X, Li JJ, Tan W: Using molecular beacons to probe molecular interactions between lactate dehydrogenase and single-stranded DNA. Anal Chem 2000, 72:3280-3285.
25. DeLong EF, Taylor LT, Marsh TL, Preston CM: Visualization and enumeration of marine planktonic archaea and bacteria by using polyribonucleotide probes and fluorescence in situ hybridization. Appl Environ Microbiol 1999, 65:5554-5563.
26. Karner MB, DeLong EF, Karl DM: Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 2001, 409:507-510.
27. Trebesius KH, Amann R, Ludwig W, Mühlegger K, Schleifer K-H: Identification of whole fixed bacterial cells with nonradioactive rRNA-targeted transcript probes. Appl Envion Microbiol 1994, 60:3228-3235.
28. Zimmermann J, Ludwig W, Schleifer K-H: DNA polynucleotide probes generated from representatives of the genus Acinetobacter and their application in fluorescence in situ hybridization of environmental samples. Syst Appl Microbiol 2001, 24:238-244.
29. Pernthaler A, Preston CM, Pernthaler J, DeLong EF, Amann R: Comparison of fluorescently labeled oligonucleotide and polynucleotide probes for the detection of pelagic marine bacteria and archaea. Appl Environ Microbiol 2002, 68:661-667. A thorough comparison on the suitability of oligonucleotide and polynucleotide probes for microbial community analysis in marine systems. This study shows that in these systems a significantly higher fraction of the total prokaryotic cells can be detected using polynucleotide probes.
30. Schönhuber W, Fuchs B, Juretschko S, Amann R: Improved sensitivity of whole-cell hybridization by the combination of horseradish peroxidase-labeled oligonucleotides and tyramide signal amplification. Appl Environ Microbiol 1997, 63:3268-3273.
31. Pernthaler A, Pernthaler J, Amann R: Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 2002, 68:3094-3101. This paper describes effective modifications of the CARD-FISH method that dramatically increase the suitability of this technique in oligotrophic environments.
32. Schmid M, Twachtmann U, Klein M, Strous M, Juretschko S, Jetten M, Metzger JW, Schleifer K-H, Wagner M: Molecular evidence for a genus-level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation. Syst Appl Microbiol 2000, 23:93-106.
33. Daims H, Ramsing NB, Schleifer K-H, Wagner M: Cultivation-independent, semiautomatic determination of absolute bacterial cell numbers in environmental samples by fluorescence in situ hybridization. Appl Environ Microbiol 2001, 67:5810-5818. A semi-automatic quantification approach for probe-labelled cells in biofilms is presented. Escherichia coli cells were used as the internal standard to determine absolute numbers of ammonia-oxidising bacteria in activated sludge by FISH combined with confocal laser scanning microscopy and digital image analysis.
34. Kuehn M, Hausner M, Bungartz H-J, Wagner M, Wilderer PA, Wuertz S: Automated confocal laser scanning microscopy and semiautomated image processing for analysis of biofilms. Appl Environ Microbiol 1998, 64:4115-4127.
35. Daims H, Brühl A, Amann R, Schleifer K-H, Wagner M: The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 1999, 22:434-444.
36. Schramm A, Fuchs BM, Nielsen JL, Tonolla M, Stahl DA: Fluorescence in situ hybridization of 16S rRNA gene clones (Clone-FISH) for probe validation and screening of clone libraries. Environ Microbiol 2002, 4:713-720. In our opinion, this is the most exciting FISH development during the past year. This novel approach allows for the first time to evaluate probes for yet not cultured prokaryotes, and even more important, it provides the basis for flow cytometric sorting of 16S rRNA gene clones with defined probe-target sites.
37. Chauhan AK, Apirion D: The gene for a small stable RNA (10Sa RNA) of Escherichia coli. Mol Microbiol 1989, 3:1481-1485.
38. Schönhuber W, Le Bourhis G, Tremblay J, Amann R, Kulakauskas S: Utilization of tmRNA sequences for bacterial identification. BMC Microbiol 2001, 1:20.
39. Oerther DB, Pernthaler J, Schramm A, Amann R, Raskin L: Monitoring precursor 16S rRNAs of Acinetobacter spp. in activated sludge wastewater treatment systems. Appl Environ Microbiol 2000, 66:2154-2165.
40. Schmid M, Schmitz-Esser S, Jetten M, Wagner M: 16S-23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium-oxidizing bacteria: implications for phylogeny and in situ detection. Environ Microbiol 2001, 3:450-459.
41. Pernthaler A, Pernthaler J, Schattenhofer M, Amann R: Identification of DNA-synthesizing bacterial cells in coastal North Sea plankton. Appl Environ Microbiol 2002, 68:5728-5736.
42. Lee N, Nielsen PH, Andreasen KH, Juretschko S, Nielsen JL, Schleifer K-H, Wagner M: Combination of fluorescence in situ hybridization and microautoradiography - a new tool for structure-function analyses in microbial ecology. Appl Environ Microbiol 1999, 65:1289-1297.
43. Nielsen JL, Aquino de Muro M, Nielsen PH: Evaluation of the redox dye 5-cyano-2,3-tolyl-tetrazolium chloride for activity studies by simultaneous use of microautoradiography and fluorescence in situ hybridization. Appl Environ Microbiol 2003, 69:641-643.
44. Wagner M, Loy A: Bacterial community composition and function in sewage treatment systems. Curr Opin Biotechnol 2002, 13:218-227.
45. Ito T, Nielsen JL, Okabe S, Watanabe Y, Nielsen PH: Phylogenetic identification and substrate uptake patterns of sulfate-reducing bacteria inhabiting an oxic-anoxic sewer biofilm determined by combining microautoradiography and fluorescence in situ hybridization. Appl Environ Microbiol 2002, 68:356-364.
46. Nielsen JL, Juretschko S, Wagner M, Nielsen PH: Abundance and phylogenetic affiliation of iron reducers in activated sludge as assessed by fluorescence in situ hybridization and microautoradiography. Appl Environ Microbiol 2002, 68:4629-4636. This study shows that by careful selection of the labelled substrate, incubation conditions and inhibitors makes it possible to target defined physiological groups of bacteria in environmental samples by FISH and microautoradiography.
47. Cottrell MT, Kirchmann DL: Contribution of major bacterial groups to bacterial biomass production (thymidine and leucine incorporation) in the Delaware estuary. Limnol Oceanogr 2003, 48:168-178.
48. Nielsen JL, Christensen D, Kloppenborg M, Nielsen PH: Quantification of cell-specific substrate uptake by probe-defined bacteria under in situ conditions by microautoradiography and fluorescence in situ hybridization. Environ Microbiol 2003, 5:202-211.
49. Behrens S, Rühland C, Inácio J, Huber H, Fonseca Á, Spencer-Martins I, Fuchs BM, Amann R: In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes. Appl Environ Microbiol 2003, 69:1748-1758.