Evaluation of a 23S rRNA insertion as target for the analysis of uncultured Frankia populations in root nodules of alders by whole cell hybridization

Systematic and Applied Microbiology

Volumn 20, Issue 1, 1997, Pages 124-132

  Zepp, Kornelia ^a   Hahn, Dittmar ^a   Zeyer, Josef ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

Alnus; Fluorescent oligonucleotide probes; Frankia; In situ hybridization; In vitro transcript probes; Ribosomal RNA

Indexed keywords

DIGOXIGENIN; FLUORESCENT DYE; LYSOZYME; RIBOSOME RNA; RNA 23S;

ACTINOBACTERIA; ARTICLE; BACTERIAL SPORE; CELL HYBRIDIZATION; FRANKIA; MEMBRANE VESICLE; NONHUMAN; OLIGONUCLEOTIDE PROBE; PLANT ROOT; PRIORITY JOURNAL;

ACTINOBACTERIA (CLASS); ALNUS; ALNUS GLUTINOSA; ALNUS INCANA; ALNUS NEPALENSIS; ALNUS VIRIDIS; BACTERIA (MICROORGANISMS); FRANKIA;

EID: 0031055194     PISSN: 07232020     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0723-2020(97)80056-2     Document Type: Article

References (41)

1. AMANN, R. I., BINDER, B. J., OLSEN, 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. 56, 1919-1925 (1990).
2. AMANN, R. I., LUDWIG, W., SCHLEIFER, K.-H.: Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143-169 (1995).
3. BAKER, D.: Methods for the isolation, culture and characterization of the Frankiaceae: soil actinomycetes and symbionts of actinorhizal plants. pp. 213-236. In: Isolation of biotechnological organisms from nature (LABEDA, H. D., ed.), MacGraw Hill Inc., New York, USA (1990).
4. BAKER, D., KIDD, G. H., TORREY, J. G.: Separation of actinomycete nodule endophytes from crushed nodule suspensions by Sephadex fractionation. Bot. Gaz. 140 (SUPPL.), S49-S51 (1979A).
5. Baker, D., O'Keefe, D.: A modified sucrose fractionation procedure for the isolation of frankiae from actinorhizal root nodules and soil samples. Plant Soil 78, 23-28 (1984).
6. BAKER, D., TORREY, J. G., KIDD, G. H.: Isolation by sucrose-density fractionation and cultivation in vitro of actinomycetes from nitrogen-fixing root nodules. Nature 281, 76-78 (1979b).
7. BAKER D. D.: Opportunities for autecological studies of Frankia, a symbiotic actinomycete. pp. 271-276. In: Biology of actinomycetes '88 (OKAMI, Y., BEPPU, T., OGAWARA, H., eds.), Japan Scientific Societies Press, Tokio, Japan (1988).
8. BENSON, D. R.: Isolation of Frankia strains from alder actinorhizal root nodules. Appl. Environ. Microbiol. 44, 461-465 (1982).
9. BERRY, A., TORREY, J. G.: Isolation and characterization in vivo and in vitro of an actinomycetous endophyte from Alnus rubra Bong. pp. 69-83. In: Symbiotic nitrogen fixation in the management of temperate forests (GORDON, J. C., WHEELER, C. T., PERRY, D. A., eds.), Oregon State University, Corvallis, Oregon, USA (1979).
10. BOND, G.: Taxonomy and distribution of non-legume nitrogen-fixing systems. pp. 55-87. In: Biological nitrogen fixation in forest ecosystems: foundations and applications (GORDON, J. C., WHEELER, C. T., eds.), Nijhoff/Junk Publishers, The Hague, The Netherlands (1983).
11. CALLAHAM, D., DEL TREDICI, P., TORREY, J. G.: Isolation and cultivation in vitro of the actinomycete causing root nodulation in Comptonia. Science 199, 899-902 (1978).
12. FARRELLY, V., RAINEY, F., STACKEBRANDT, E.: Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61, 2798-2801 (1995).
13. FISCHER, K., HAHN, D., HÖHNERLAGE, W., SCHÖNHOLZER, F., ZEYER, J.: In situ detection of spores and vegetative cells of Bacillus megaterium in soil by whole cell hybridization. System. Appl. Microbiol. 18, 265-273 (1995).
14. HAHN, D., AMANN, R. I., ZEYER, J.: Detection of mRNA in Streptomyces cells by whole-cell hybridization with digoxigenin-labeled probes. Appl. Environ. Microbiol. 59, 2753-2757 (1993a).
15. HAHN, D., AMANN, R. I., ZEYER, J.: Whole-cell hybridization of Frankia strains with fluorescence-or digoxigenin-labeled, 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 59, 1709-1716 (1993b).
16. HAHN D., DORSCH, M., STACKEBRAND, E., AKKERMANS, A. D. L.: Synthetic oligonucleotide probes for identification of Frankia strains. Plant Soil 118, 211-219 (1989)
17. HÖNERLAGE W., HAHN, D., ZEPP, K., ZEYER, J., NORMAND, P.: A hypervariable 23S rRNA region provides a discriminating target for specific characterization of uncultured and cultured Frankia. System. Appl. Microbiol. 17, 433-443 (1994).
18. HÖNERLAGE, W., HAHN, D., ZEYER, J.: Detection of mRNA of nprM in Bacillus megaterium ATCC 14581 grown in soil by whole cell hybridization. Arch. Microbiol. 163, 235-241
19. KOPCZYNSKI, E. D., BATESON, M. M., WARD, D. M.: Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl. Environ. Microbiol. 60, 746-748 (1994).
20. LI, P., MEDON, P. P., SKINGLE, D. C., LANSER, J. A., SYMONS, R. H.: Enzyme-linked synthetic oligonucleotide probes: non-radioactive detection of enterotoxigenic Escherichia coli in faecal specimens. Nucleic Acids Res. 15, 5275-5287 (1987).
21. LI, S. X., HARRIS, C. P., LEONG, S. A.: Comparison of fluorescence in situ hybridization and primed in situ labeling methods for detection of single-copy genes in the fungus Ustilago maydis. Exp. Mycol. 17, 301-308 (1993).
22. LIESACK, W., WEYLAND, H., STACKEBRAND, E.: Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. Microb. Ecol. 21, 191-198 (1991).
23. MANZ, W., AMANN, R., LUDWIG, W., WAGNER, M., SCHLEIFER, K.-H.: Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria: Problems and solutions. System. Appl. Microbiol. 15, 593-600 (1992).
24. MEESTERS, T. M.: Localization of nitrogenase in vesicles of Frankia sp. Cc1.17 by immunogoldlabelling on ultrathin cryosections. Arch. Microbiol. 145, 327-331 (1987).
25. MEESTERS, T. M., VAN VLIET, W. M., AKKERMANS, A. D. L.: Nitrogenase is restricted to the vesicles in Frankia strain EAN1pec. Physiol. Plant. 70, 267-271 (1987).
26. MUJUMDAR, R. B., ERNST, L. A., MUJUMDAR, S. R., WAGGONER, A. S.: Cyanine dye labeling reagents containing isothiocyanate groups. Cytometry 10, 11-19 (1989).
27. NAZARET, S., COURNOYER, B., NORMAND, P., SIMONET, P.: Phylogenetic relationships among Frankia genomic species determined by use of amplified 16S rRNA sequences. J. Bacteriol. 173, 4072-4078 (1991).
28. NICHOLSON, W. L., SETLOW, P.: Sporulation, germination and outgrowth. pp. 391-450. In: Molecular biological methods for Bacillus (HARWOOD, C. R., CUTTING, S. M., eds.), John Wiley & Sons, Chichester, UK (1990).
29. OUIROS, L. M., PARRA, F., HARDISSON, C., SALAS, J. A.: Structural and functional analysis of ribosomal subunits from vegetative mycelium and spores of Streptomyces antibiotics. J. Gen. Microbiol. 135, 1661-1670 (1989).
30. RAINEY, F. A., WARD, N., SLY, L. I., STACKEBRANDT, E.: Dependence on the taxon composition of clone libraries for PCR amplified, naturally occurring 16S rDNA, on the primer pair and the cloning system used. Experientia 50, 796-797 (1994).
31. ROLLER, C., LUDWIG, W., SCHLEIFER, K.-H.: 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 (1992).
32. ROLLER, C., WAGNER, M., AMANN, R., LUDWIG, W., SCHLEIFER, K.-H.: In situ probing of Gram-positive bacteria with a high DNA G+C content using 23S rRNA-target oligonucleotides. Microbiology 140, 2849-2858 (1994).
33. ROSBROOK, P. A., BURGGRAAF, A. J. P., REDDELL, P.: A comparison of two methods and different media for isolating Frankia from Casuarina root nodules. Plant Soil 120, 187-193 81989).
34. SCHWINTZER, C. R., TJEPKEMA, J. D.: The biology of Frankia and actinorhizal plants. Academic Press, Inc., San Diego, USA (1990).
35. SETLOW, P.: Mechanisms which contribute to the long-term survival of spores of Bacillus species. J. Appl. Bacteriol. 76, S49-S60 (1994).
36. SIMONET, P., BOSCO, M., CHAPELON, C., MOLROUD, A., NORMAND, P.: Molecular characterization of Frankia microsymbionts from spore-positive and spore-negative nodules in a natural alder stand. Appl. Environ. Microbiol. 60, 1335-1341 (1994).
37. ST-LAURENT, L., LALONDE, M.: Isolation and characterization of Frankia strains isolated from Myrica gale. Can. J. Bot. 65, 1356-1363 (1987).
38. TREBESIUS, K., AMANN, R., LUDWIG, W., MUHLEGGER, K., SCHLEIFER, K., H.: Identification of whole fixed bacterial cells with nonradioactive 23S rRNA-target polynucleotide probes. Appl. Environ. Microbiol. 60, 3228-3235 (1994).
39. VAN DIJK, C., SLUIMER, A., WEBER, A.: Host range differentiation of spore (+) and spore (-) strain types of Frankia in stands of Alnus glutinosa and Alnus incana in Finland. Physiol. Plant. 72, 349-358 (1988).
40. WALLACE, R. B., SHAFFER, J., MURPHY, R. F., BONNER, J., HIROSE, T., ITAKURA, K.: Hybridization of synthetic oligodeoxynucleotides to ΦX174 DNA: The effect of single base pair mismatch. Nucl. Acids. Res. 6, 3543-3557 (1979).
41. ZARDA, B., AMANN, R., WALLNER, G., SCHLEIFER, K.-H.: Identification of single bacterial cells using digoxigenin-labelled, rRNA-targeted oligonucleotides. J. Gen. Microbiol. 137, 2823-2830 (1991).