Development of an oligonucleotide probe for Aureobasidium pullulans based on the small-subunit rRNA gene

Applied and Environmental Microbiology

Volumn 62, Issue 5, 1996, Pages 1514-1518

  Li, Shuxian ^a   Cullen, Daniel ^a   Hjort, Mary ^a   Spear, Russell ^a   Andrews, John H ^a,b  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b FOREST PRODUCTS LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA; RIBOSOME RNA;

ARTICLE; AUREOBASIDIUM PULLULANS; CONSENSUS SEQUENCE; DNA RNA HYBRIDIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; RIBOSOME SUBUNIT;

EID: 0029885762     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.62.5.1514-1518.1996     Document Type: Article

References (52)

1. 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.
2. 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.
3. Amann, R. I., J. Stromley, R. Devereux, R. Key, and D. A. Stahl. 1992. Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms. Appl. Environ. Microbiol. 58:614-623.
4. Andrews, J. H., R. F. Harris, R. N. Spear, G. W. Lau, and E. V. Nordheim. 1994. Morphogenesis and adhesion of Aureobasidium pullulans. Can. J. Microbiol. 40:6-17.
5. Andrews, J. H., and S. S. Hirano (ed.). 1991. Microbial ecology of leaves. Springer-Verlag, New York.
6. Andrews, J. H., and C. M. Kenerley. 1978. The effects of a pesticide program on non-target epiphytic microbial populations of apple leaves. Can. J. Microbiol. 24:1058-1072.
7. Assmus, B., P. Hutzler, G. Kirchhof, R. Amann, J. R. Lawrence, and A. Hartmann. 1995. In situ location of Azospirillum brasilense in the rhizosphere of wheat with fluorescently labeled, rRNA-targeted oligonucleotide probes and scanning confocal laser microscopy. Appl. Environ. Microbiol. 61:1013-1019.
8. Atlas, R. M., G. Sayler, R. S. Burlage, and A. K. Bej. 1992. Molecular approaches for environmental monitoring of microorganisms. BioTechniques 12:706-717.
9. Aufauvre-Brown, A., C. M. Tang, and D. W. Holden. 1993. Detection of gene-disruption events in Aspergillus transformants by polymerase chain reaction direct from conidiospores. Curr. Genet. 24:177-178.
10. Bashi, E., and N. J. Fokkema. 1977. Environmental factors limiting growth of Sporobolomyces roseus, an antagonist of Cochliobolus sativus, on wheat leaves. Trans. Br. Mycol. Soc. 68:17-25.
11. Berbee, M. L., and J. W. Taylor. 1992. 18S ribosomal RNA gene sequence characters place the human pathogen Sporothrix schenckii in the genus Ophiostoma. Exp. Mycol. 16:87-91.
12. Berbee, M. L., and J. W. Taylor. 1992. Dating the evolutionary radiations of the true fungi. Can. J. Bot. 71:1114-1127.
13. Bertin, B., O. Broux and M. Y. Hoegaerden. 1990. Flow cytometric detection of yeast by in situ hybridization with a fluorescent ribosomal RNA probe. J. Microbiol. Methods 12:1-12.
14. Bourque, S. N., J. R. Valero, M. C. Lavoie, and R. C. Levesque. 1995 Comparative analysis of the 16S to 23S ribosomal intergenic spacer sequences of Bacillus thuringiensis strains and subspecies and closely related species. Appl. Environ. Microbiol. 61:1623-1626.
15. Bowman, B. 1993. A model PCR/probe system for the identification of fungal pathogens, p. 423-430. In D. H. Persing, T. F. Smith, F. C. Tenover, and T. J. White (ed.), Diagnostic medical microbiology: principles and applications. American Society for Microbiology, Washington, D.C.
16. Bruns, T. D., R. Vilgalys, S. M. Barns, D. Gonzalez, D. S. Hibbett, D. J. Lane, L. Simon, S. Stickel, T. M. Szaro, W. G. Weisburg, and M. L. Sogin. 1992. Evolutionary relationships within the fungi: analyses of nuclear small subunit rRNA sequences. Mol. Phylogenet. Evol. 1:231-241.
17. Burge, H. A., M. L. Muilenberg, and J. A. Chapman. 1991. Crop plants as a source of fungus spores of medical importance, p. 222-236. In J. H. Andrews and S. S. Hirano (ed.), Microbial ecology of leaves. Springer-Verlag, New York.
18. Cooke, W. B. 1959. An ecological life history of Aureobasidium pullulans (de Bary) Arnaud. Mycopathol. Mycol. Appl. 21:225-271.
19. De Hoog, G. S., and N. A. Yurlova. 1994. Conidiogenesis, nutritional physiology and taxonomy of Aureobasidium and Hormonema. Antonie Leeuwenhoek J. Microbiol. Serol. 365:341-395.
20. DeLong, E. F., G. S. Wickham, and N. R. Pace. 1989. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360-1363.
21. Dichristina, T. J., and E. F. DeLong. 1993. Design and application of rRNA-targeted oligonucleotide probes for the dissimilatory iron-and manganese-reducing bacterium Shewanella putrefaciens. Appl. Environ. Microbiol. 59:51-56.
22. Domsch, K. H., W. Gams, and T. Anderson. 1980. Compendium of soil fungi. Academic Press, London.
23. Donegan, K., C. Matyac, R. Seider, and A. Porteous. 1991. Evaluation of methods for sampling, recovery, and enumeration of bacteria applied to the phylloplane. Appl. Environ. Microbiol. 57:4152-4160.
24. Drahos, D. J. 1991. Methods for detection, identification, and enumeration of microbes, p. 135-157. In J. H. Andrews and S. S. Hirano (ed.), Microbial ecology of leaves. Springer-Verlag, New York.
25. Fell, J. W. 1995. rDNA targeted oligonucleotide primers for the identification of pathogenic yeasts in a polymerase chain reaction. J. Indust. Microbiol. 14:475-477.
26. Giovannoni, S. J., E. F. DeLong, G. J. Olsen, and N. R. Pace. 1988. Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells. J. Bacteriol. 170:720-726.
27. Hermanides-Nijhof, E.J. 1977. Aureobasidium and allied genera, p. 141-177. In G. S. De Hoog and E. J. Hermanides-Nijhof (ed.), The black yeasts and allied hyphomycetes. Elsevier, Amsterdam.
28. Hicks, R., R. I. Amann, and D. A. Stahl. 1992. Dual staining of natural bacterioplankton with 4′,6-diamidino-2-phenylindole and fluorescent oligonucleotide probes targeting kingdom-level 16S rRNA sequences. Appl. Environ. Microbiol. 58:2158-2163.
29. Higgins, D. G., and P. M. Sharp. 1989. Fast and sensitive multiple sequence alignments on a microcomputer. Comput. Appl. Biosci. 5:151-153.
30. Holben, W. E., and J. M. Tiedje. 1988. Applications of nucleic acid hybridization in microbial ecology. Ecology 69:561-568.
31. Ikuta, S., K. Takagi, R. B. Wallace, and K. Itakura. 1987. Dissociation kinetics of 19 base paired oligonucleotide-DNA duplexes containing different single mismatched base pairs. Nucleic Acids Res. 15:797-811.
32. Illingworth, C. A., J. H. Andrews, C. Bibeau, and M. L. Sogin. 1991. Phylogenetic placement of Athelia bombacina, Aureobasidium pullulans, and Colletotrichum gloeosporioides inferred from sequence comparisons of small-subunit ribosomal RNAs. Exp. Mycol. 15:65-75.
33. Kreger-van Rij, N. J. W. 1984. The yeasts, 3rd ed. Elsevier, Amsterdam.
34. Lachke, A. H., and V. B. Rale. 1995. Trends in microbial production and its novel applications in the food industry, p. 589-604. In Y. H. Hui and G. G. Khachatourians (ed.), Food biotechnology microorganisms. VCH, New York.
35. Leitch, A. R., T. Schwarzacher, D. Jackson, and I. J. Leiteh. 1994. In situ hybridization: a practical guide. Bios Scientific Publishers, Oxford.
36. Li, S., C. P. Harris, and S. A. Leong. 1993. 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.
37. Li, S., R. Spear, and J. H. Andrews. 1994. Detection and quantification of fungal cells on leaves by in situ hybridization based on 18S rRNA-targeted fluorescent oligonucleotide probes, p. 125. In Abstracts of the Fifth International Mycological Congress. Mycological Society of America, Lawrence, Kans.
38. 37a. Li, S., et al. Unpublished data.
39. McSweeney, C. S., R. I. Mackie, A. A. Odenyo, and D. A. Stahl. 1993. Development of an oligonucleotide probe targeting 16S rRNA and its application for detection and quantification of the ruminal bacterium Synergistes jonesii in a mixed-population chemostat. Appl. Environ. Microbiol. 59:1607-1612.
40. Meinkoth, J., and G. Wahl. 1984. Hybridization of nucleic acids immobilized on solid supports. Anal. Biochem. 138:267-284.
41. Odenyo, A. A., R. I. Mackie, D. A. Stahl, and B. A. White. 1994. The use of 16S rRNA-targeted oligonucleotide probes to study competition between ruminal fibrolytic bacteria: development of probes for Ruminococcus species and evidence for bacteriocin production. Appl. Environ. Microbiol. 60:3688-3696.
42. Pace, N. R., D. A. Stahl, D. J. Lane, and O. J. Olsen. 1985. Analyzing natural microbial populations by rRNA sequences. ASM News 51:4-12.
43. Parkinson, D., and D. C. Coleman. 1991. Microbial communities: activity and biomass. Agric. Ecosys. Environ. 34:3-33.
44. Reysenbach, A.-L., L. J. Giver, G. S. Wickham, and N. R. Pace. 1992. Differential amplification of rRNA genes by polymerase chain reaction. Appl. Environ. Microbiol. 58:3417-3418.
45. Sanger, F., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463-5467.
46. Sayler, G. S., and A. C. Layton. 1990. Environmental application of nucleic acid hybridization. Annu. Rev. Microbiol. 44:625-648.
47. Smith, C. S., T. Chand, R. F. Harris, and J. H. Andrews. 1989. Colonization of a submersed aquatic plant, Eurasian water milfoil (Myriophyllum spicatum), by fungi under controlled conditions. Appl. Environ. Microbiol. 55:2326-2332.
48. Steven, B., S. Lee, and J. W. Taylor. 1990. Isolation of DNA from fungal mycelia and single spores, p. 282-287. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, and T. J. White (ed.), PCR protocols: a guide to methods and applications. Academic Press, San Diego, Calif.
49. Török, T., and A. D. King, Jr. 1991. Comparative study on the identification of food-borne yeasts. Appl. Environ. Microbiol. 57:1207-1212.
50. Wallace, B. R., and C. G. Miyada. 1987. Oligonucleotide probes for the screening of recombinant DNA libraries. Methods Enzymol. 152:432-442.
51. White, T. J., T. Bruns, S. Lee, and J. Taylor. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, p. 315-322. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, and T. J. White (ed.), PCR protocols: a guide to methods and applications. Academic Press, San Diego, Calif.
52. Yan, Z. H., S. O. Rogers, and C. J. K. Wang. 1995. Assessment of Phialophora species based on ribosomal DNA internal transcribed spacers and morphology. Mycologia 87:72-83.