Design and application of two oligonucleotide probes for the identification of Geodermatophilaceae strains using flourescence in situ hybridization (FISH)

Environmental Microbiology

Volumn 6, Issue 7, 2004, Pages 678-685

  Urzì, Clara ^a   La Cono, Violetta ^a   Stackebrandt, Erko ^b  

^a UNIVERSITY OF MESSINA   (Italy)

^b LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RNA 16S;

ACTINOMYCETALES; ARTICLE; FLUORESCENCE IN SITU HYBRIDIZATION; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; OLIGONUCLEOTIDE PROBE; SENSITIVITY AND SPECIFICITY;

ACTINOMYCETALES; ENVIRONMENTAL MICROBIOLOGY; IN SITU HYBRIDIZATION, FLUORESCENCE; OLIGONUCLEOTIDE PROBES; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY;

ACTINOBACTERIA (CLASS); BACTERIA (MICROORGANISMS); BLASTOCOCCUS; GEODERMATOPHILACEAE; GEODERMATOPHILUS; MODESTOBACTER; UNCULTURED ACTINOMYCETE;

EID: 3042701609     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2004.00619.x     Document Type: Article

References (26)

1. Ahrens, R., and Moll, G. (1970) Ein neues knospendes Bakterium aus der Ostsee. Arch Microbiol 70: 243-265.
2. Alm, E.W., Oerther, D.B., Larsen, N., Stahl, D.A., and Raskin, L. (1996) The oligonucleotide probe database. Appl Environ Microbiol 62: 3557-3559.
3. Amann, R.I., Krumholz, L., and Stahl, D. (1990) Fluorescent- oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bacteriol 172: 762-770.
4. Amann, R.I., Ludwig, W., and Schleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59: 143-169.
5. Amann, R., Fuchs, B.M., and Behrens, S. (2001) The identification of microorganisms by fluorescence in situ hybridisation. Curr Opin Microbiol 12: 231-236.
6. Brosius, J., Dull, T.J., Sleeter, D.D., and Noller, H.F. (1981) Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148: 107-127.
7. Cole, J.R., Chai, B., Marsh, T.L., Farris, R.J., Wang, Q., Kulam, S.A., et al. (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31: 442-443.
8. Gurtner, C., Heyrman, J., Piñar, G., Lubitz, W., Swings, J., and Rölleke, S. (2000) Comparative analyses of the bacterial diversity on two different biodeteriorated wall opainting by DGGE and 16S rDNA sequence analysis. Int Biodeterior Biodegrad 46: 229-239.
9. Hahn, D., Amann, R., and Zeyer, J. (1993) Whole-cell hybridization of Frankia strains with fluorescence or digoxigenin-labeled, 16S rRNA-targeted oligonucleotide probes. Appl Environ Microbiol 59: 1709-1716.
10. La Cono, V., and Urzì, C. (2003) Fluorescent in situ hybridization applied on samples taken with adhesive tape strips. J Microbiol Meth 55: 65-71.
11. Liu, J.R., and Seviour, R.J. (2001) Design and application of oligonucleotide probes for fluorescent in situ identification of the filamentous bacterial morphotype Nostocoida limicola in activated sludge. Environ Microbiol 3: 551-560.
12. Luedemann, G.M. (1968) Geodermatophilus, a new genus of the Dermatophilaceae (Actinomycetales). J Bacteriol 96: 1848-1858.
13. Maidak, B., Cole, J., Lilburn, T., Parker, C., Saxman, P., Farris, R., et al. (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res 29: 171-173.
14. Manz, W., Amann, R., Ludwig, W., and Wagner, M. and Schleifer, K.-H. (1992) Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria: problems and solutions. Syst Appl Microbiol 15: 593-600.
15. Mevs, U., Stackebrandt, E., Schumann, P., Gallikowski, C.A., and Hirsch, P. (2000) Modestobacter multiseptatus gen nov., sp. nov., a budding actinomycete from soils of the Asgard Range (Transantarctic Mountains). Int J Syst Evol Microbiol 50: 337-346.
16. Piñar, G., Saiz-Jimenez, C., Schabereiter-Gurtner, C., Blanco-Varela, M.T., Lubitz, W., and Rölleke, S. (2001) Archaeal communities in two disparate deteriorated ancient wall painting: detection, identification and temporal monitoring by denaturating gradient gel electrophoresis. FEMS Microbiol Ecol 37: 45-54.
17. Roller, A., Ludwig, W., and Schleifer, K.H. (1992) Gram-positive bacteria with a high DNA G+C content are characterized by a common insertion within their 23S rRNA genes. J Gen Microbiol 138: 1167-1175.
18. Stackebrandt, E., Witt, D., Kemmerling, C., Kroppenstedt, R.M., and Liesack, W. (1991) Designation of Streptomycete 16S and 23S rRNA-based target regions for oligonucleotide probes. Appl Environ Microbiol 57: 1468-1477.
19. Stackebrandt, E., Rainey, F.A., and Ward-Rainey, N.L. (1997) Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47: 479-491.
20. Urzì, C., and Albertano, P. (2001) Studying phototrophic and heterotrophic microbial communities on stone monuments. In Methods in Enzymology. Doyle, R.J. (ed.). San Diego: Academic Press, Vol. 336, pp. 340-355.
21. Urzì, C., and Realini, M. (1998) Colour changes of Noto's Calcareous Sandstone as related with its colonization by microorganisms, Int Biodeterior Biodegrad 42: 45-54.
22. Urzì, C., Salamone, P., Schumann, P., and Stackebrandt, E. (2000) Marmoricola aurantiacus gen. nov., sp. nov., a coccoid member of the family Nocardioidaceae isolated from a marble statue. Int J Syst Evol Microbiol 50: 529-536.
23. Urzì, C., Brusetti, L., Salamone, P., Sorlini, C., Stackebrandt, E., and Daffonchio, D. (2001) Biodiversity of Geodermatophilaceae isolated from altered stones in the Mediterranean basin. Environ Microbiol 3: 471-479.
24. Urzì, C., La Cono, V., De Leo, F., and Donato, P. (2003) Fluorescent in situ hybridization (FISH) to study biodeterioration. In Molecular Biology and Cultural Heritage. Saiz-Jimenez, C. (ed.). Lisse, the Netherlands: Balkema Publishers, pp. 55-60.
25. Urzì, C., Salamone, P., Schumann, P., Ronde, M., and Stackebrandt, E. (2004) Blastococcus saxobsidens sp. nov., isolated from marble and calcareous sandstone in quarries and archeological sites in the Mediterranean Basin, and emended description of the genus Blastococcus Ahrens and Moll 1970 and Blastococcus aggregatus Ahrens and Moll 1970. Int J Syst Evol Microbiol 54: 253-259.
26. Weller, R., Glockner, F.O., and Amann, R. (2000) 16S rRNA-targeted oligonucleotide probes for the in situ detection of members of the phylum Cytophaga-Flavobacterium-Bacterioides. System Appl Microbiol 23: 107-114.