Evaluation of tyramide solutions for an improved detection and enumeration of single microbial cells in soil by CARD-FISH

Journal of Microbiological Methods

Volumn 91, Issue 3, 2012, Pages 399-405

  Schmidt, Hannes ^a   Eickhorst, Thilo ^a   Tippkötter, Rolf ^a  

^a UNIVERSITY OF BREMEN   (Germany)

Author keywords

CARD FISH; Catalyzed reporter deposition; FISH; Fluorescence in situ hybridization; Soil microorganisms; Tyramide signal amplification

Indexed keywords

BACTERIA (MICROORGANISMS); PROKARYOTA;

ARCHAEON; ARTICLE; BACTERIUM; EVALUATION; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; INSTRUMENTATION; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; SINGLE CELL ANALYSIS;

ARCHAEA; BACTERIA; IN SITU HYBRIDIZATION, FLUORESCENCE; SINGLE-CELL ANALYSIS; SOIL MICROBIOLOGY;

EID: 84868236665     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2012.09.021     Document Type: Article

References (43)

1. Adams J.C. Biotin amplification of biotin and horseradish peroxidase signals in histochemical stains. J. Histochem. Cytochem. 1992, 40:1457-1463.
2. Amann R., Fuchs B.M. Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat. Rev. Microbiol. 2008, 6:339-348.
3. Amann R.I., Krumholz L., Stahl D.A. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 1990, 172:762-770.
4. Amann R.I., Binder B.J., Olson R.J., Chisholm S.W., Devereux R., Stahl D.A. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 1990, 56:1919-1925.
5. Amann R.I., Ludwig W., Schleifer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 1995, 59:143-169.
6. Assmus B., Hutzler P., Kirchhof G., Amann R., Lawrence J.R., Hartmann A. In situ localization of Azospirillum brasilense in the rhizosphere of wheat with fluorescently labeled, rRNA-targeted oligonucleotide probes and scanning confocal laser microscopy. Appl. Environ. Microbiol. 1995, 61:1013-1019.
7. Barra Caracciolo A., Grenni P., Ciccoli R., Di Landa G., Cremisini C. Simazine biodegradation in soil: analysis of bacterial community structure by in situ hybridization. Pest Manag. Sci. 2005, 61:863-869.
8. Bobrow M.N., Harris T.D., Shaughnessy K.J., Litt G.J. Catalyzed reporter deposition, a novel method of signal amplification. Application to immunoassays. J. Immunol. Methods 1989, 125:279-285.
9. Bobrow M.N., Shaughnessy k.J., Litt G.J. Catalyzed reporter deposition, a novel method of signal amplification. II. Application to membrane immunoassays. J. Immunol. Methods 1991, 137:103-112.
10. Bobrow, M.N., Adler, K.E., Roth, K.A., 2003. Enhanced catalyzed reporter deposition. U.S. Pat. US 6,593,100 B2.
11. Cai P., Huang Q., Zhang X., Chen H. Adsorption of DNA on clay minerals and various colloidal particles from an alfisol. Soil Biol. Biochem. 2006, 38:471-476.
12. Cavalca L., Zanchi R., Corsini A., Colombo M., Romagnoli C., Canzi E., et al. Arsenic-resistant bacteria associated with roots of the wild Cirsium arvense (L.) plant from an arsenic polluted soil, and screening of potential plant growth-promoting characteristics. Syst. Appl. Microbiol. 2010, 33:154-164.
13. Christensen H., Hansen M., Sørensen J. Counting and size classification of active soil bacteria by fluorescence in situ hybridization with an rRNA oligonucleotide probe. Appl. Environ. Microbiol. 1999, 65:1753-1761.
14. Chu C.P., Tsai D.G., Lee D.J., Tay J.H. Size-dependent anaerobic digestion rates of flocculated activated sludge: role of intrafloc mass transfer resistance. J. Environ. Manag. 2005, 76:239-244.
15. 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.
16. DeLong E.F., Wickham G.S., Norman R.P. Phylogenetc stains: ribosomal RNA-based probes for the identification of single cells. Science 1989, 243:1360-1363.
17. Eickhorst T., Tippkötter R. Improved detection of soil microorganisms using fluorescence in situ hybridization (FISH) and catalyzed reporter deposition (CARD-FISH). Soil Biol. Biochem. 2008, 40:1883-1891.
18. Ferrari B.C., Tujula N., Stoner K., Kjelleberg S. Catalyzed reporter deposition-fluorescence in situ hybridization allows for enrichment-independent detection of microcolony-forming soil bacteria. Appl. Environ. Microbiol. 2006, 72:918-922.
19. Gredner B., Tippkötter R. Effect of rice straw application on hydrolytic enzyme activities in Chinese paddy soils. Proceedings of the 19th World Congress of Soil Science. Brisbane, Australia 2010, 13-16. R.J. Gilkes, N. Prakongkep (Eds.).
20. Hahn D., Amann R.I., Ludwig W., Akkermans A.D.L., Schleifer K.H. Detection of micro-organisms in soil after in situ hybridization with rRNA-targeted, fluorescently labelled oligonucleotides. J. Gen. Microbiol. 1992, 138:879-887.
21. Hopman A.H.N., Ramaekers F.C.S., Speel E.J.M. Rapid synthesis of biotin-, digoxigenin-, trinitrophenyl-, and fluorochrome-labeled tyramides and their application for in situ hybridization using CARD amplification. J. Histochem. Cytochem. 1998, 46:771-777.
22. Ishii K., Mußmann M., MacGregor B., Amann R. An improved fluorescence in situ hybridization protocol for the identification of bacteria and archaea in marine sediments. FEMS Microbiol. Ecol. 2004, 50:203-212.
23. Kallistova A.Y., Kevbrina M.V., Nekrasova V.K., Shnyrev N.A., Einola J.K.M., Kulomaa M.S., et al. Enumeration of methanotrophic bacteria in the cover soil of an aged municipal landfill. Microb. Ecol. 2007, 54:637-645.
24. Kobabe S., Wagner D., Pfeiffer E.M. Characterisation of microbial community composition of a Siberian tundra soil by fluorescence in situ hybridisation. FEMS Microbiol. Ecol. 2004, 50:13-23.
25. MacGregor B.J., Toze S., Alm E.W., Sharp R., Ziemer C.J., Stahl D.A. Distribution and abundance of gram-positive bacteria in the environment: development of a group-specific probe. J. Microbiol. Methods 2001, 44:193-203.
26. Marras S.A.E., Kramer F.R., Tyagi S. Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res. 2002, 30:1-8.
27. Mobarry B.K., Wagner M., Urbain V., Rittmann B.E., Stahl D.A. Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria. Appl. Environ. Microbiol. 1996, 62:2156-2162.
28. Pernthaler A., Amann R. Simultaneous fluorescence in situ hybridization of mRNA and rRNA in environmental bacteria. Appl. Environ. Microbiol. 2004, 70:5426-5433.
29. Pernthaler J., Glöckner F.O., Schönhuber W., Amann R. Fluorescence in situ hybridization with rRNA-targeted oligonucleotide probes. Methods in Microbiology 2001, vol. 30:207-226. Academic Press, San Diego.
30. Pernthaler A., Preston C.M., Pernthaler J., DeLong E.F., 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.
31. Pernthaler A., Pernthaler J., Amann R. Sensitive multi-color flourescence in situ hybridization for the identification of environmental microorganisms. Molecular Microbial Ecology Manual 2004, 711-726. Kluwer Academic. 2nd ed. G.A. Kowalchuk, F.J. de Bruijn, I.M. Head, A.D. Akkermans, J.D. van Elsas (Eds.).
32. Pietramellara G., Franchi M., Gallori E., Nannipieri P. Effect of molecular characteristics of DNA on its adsorption and binding on homoionic montmorillonite and kaolinite. Biol. Fertil. Soils 2001, 33:402-409.
33. Schmidt H., Eickhorst T., Tippkötter R. Monitoring of root growth and redox conditions in paddy soil rhizotrons by redox electrodes and image analysis. Plant Soil 2011, 341:221-232.
34. Schramm A., Larsen L.H., Revsbech N.P., Ramsing N.B., Amann R., Schleifer K.H. Structure and function of a nitrifying biofilm as determined by in situ hybridization and the use of microelectrodes. Appl. Environ. Microbiol. 1996, 62:4641-4647.
35. Shiraishi F., Zippel B., Neu T.R., Arp G. In situ detection of bacteria in calcified biofilms using FISH and CARD-FISH. J. Microbiol. Methods 2008, 75:103-108.
36. Speel E.J.M., Hopman A.H.N., Komminoth P. Amplification methods to increase the sensitivity of in situ hybridization: play CARD(s). J. Histochem. Cytochem. 1999, 47:281-288.
37. Stahl D.A., Amann R.I. Development and application of nucleic acid probes. Nucleic Acid Techniques in Bacterial Systematics 1991, 205-248. John Wiley & Sons, Chichester. E. Stackebrandt, M. Goodfellow (Eds.).
38. Tujula N.A., Holmstrom C., Mußmann M., Amann R., Kjelleberg S., Crocetti G.R. A CARD-FISH protocol for the identification and enumeration of epiphytic bacteria on marine algae. J. Microbiol. Methods 2006, 65:604-607.
39. Van Gijlswijk R.P.M., Zijlmans H.J.M.A.A., Wiegant J., Bobrow M.N., Erickson T.J., Adler K.E., et al. Fluorochrome-labeled tyramides: use in immunocytochemistry and fluorescence in situ hybridization. J. Histochem. Cytochem. 1997, 45:375-382.
40. Wagner M., Erhart R., Manz W., Amann R., Lemmer H., Wedi D., et al. Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated sludge. Appl. Environ. Microbiol. 1994, 60:792-800.
41. Wagner M., Horn M., Daims H. Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. Curr. Opin. Microbiol. 2003, 6:302-309.
42. Wallner G., Amann R., Beisker W. Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 1993, 14:136-143.
43. Watt M., Hugenholtz P., White R., Vinall K. Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH). Environ. Microbiol. 2006, 8:871-884.