Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients

Applied and Environmental Microbiology

Volumn 63, Issue 8, 1997, Pages 3233-3241

  Heuer, Holger ^a   Krsek, Martin ^b   Baker, Paul ^b   Smalla, Kornelia ^a   Wellington, Elizabeth M H ^b  

^a INSTITUTE FOR EPIDEMIOLOGY AND PATHOGEN DIAGNOSTICS   (Germany)

^b UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA; BACTERIAL COMMUNITY; GEL ELECTROPHORESIS; MICROBIAL COMMUNITY;

ACTINOBACTERIA; ARTICLE; DNA DETERMINATION; GENE AMPLIFICATION; GENE SEQUENCE; NONHUMAN; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS;

ACTINOBACTERIA (CLASS); ACTINOMYCETES; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; SOLANUM TUBEROSUM; UNCULTURED ACTINOMYCETE;

EID: 0030739128     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.63.8.3233-3241.1997     Document Type: Article

References (60)

1. Brosius, J., T. J. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organisation and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148:107-127.
2. Bull, A. T., M. Goodfellow, and J. H. Slater. 1992. Biodiversity as a source of innovation in biotechnology. Annu. Rev. Microbiol. 46:219-252.
3. Chien, A., D. B. Edgar, and J. M. Trela. 1976. Deoxyribonucleic acid polymerase from the extreme thermophile Thermus aquaticus. J. Bacteriol. 127; 1550-1557.
4. Chou, Q., M. Russel, D. Birch, J. Raymond, and W. Bloch. 1992. Prevention of pre-PCR mis-priming and primer dimerization improves low-copy-number amplifications. Nucleic Acids Res. 20:1717-1723.
5. Crawford, D. L. 1988. Biodegradation of agricultural and urban wastes, p. 433-139. In M. Goodfellow, S. T. Williams, and M. Mordarski (ed.), Actinomycetes in biotechnology. Academic Press, Ltd., London, United Kingdom.
6. Crawford, D. L., J. M. Lynch, J. M. Whipps, and M. A. Ousley. 1993. Isolation and characterization of actinomycete antagonists of a fungal root pathogen. Appl. Environ. Microbiol. 59:3899-3905.
7. Cresswell, N., P. R. Herron, V. A. Saunders, and E. M. H. Wellington. 1992. The fate of introduced streptomycetes, plasmid and phage populations in a dynamic soil system. J. Gen. Microbiol. 138:659-666.
8. Crombach, W. H. J. 1972. DNA base composition of soil arthrobacters and other coryneforms from cheese and sea fish. Antonie Leeuwenhoek 29:105-120.
9. Düring, K., P. Porsch. M. Fladung, and H. Lörz. 1993. Transgenic potato plants resistant to the phytopathogenic bacterium Erwinia carotovora. Plant J. 3:587-598.
10. Elliott-Juhnke, M., D. E. Mathre, and D. C. Sands. 1987. Identification and characterization of rhizosphere-competent bacteria of wheat. Appl. Environ. Microbiol. 53:2793-2799.
11. Embley, T. M., and E. Stackebrandt. 1994. The molecular phylogeny and systematics of the actinomycetes. Annu. Rev. Microbiol. 48:257-289.
12. Felske, A., B. Engelen, U. Nübel, and H. Backhaus. 1996. Direct ribosome isolation from soil to extract bacterial rRNA for community analysis. Appl. Environ. Microbiol. 62:4162-4167.
13. Giovannoni, S. J., T. B. Britschgi, C. L. Moyer, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60-63.
14. Goodfellow, M., S. T. Williams, and M. Mordarski (ed.). 1988. Actinomycetes in biotechnology. Academic Press Ltd., London, United Kingdom.
15. Herron, P. R., and E. M. H. Wellington. 1990. New methods for extraction of streptomycete spores from soil and application to the study of lysogeny in sterile amended and nonsterile soil. Appl. Environ. Microbiol. 56:1406-1412.
16. Heuer, H., K. Hartung, B. Engelen, and K. Smalla. 1995. Studies on microbial communities associated with potato plants by BIOLOG and TGGE patterns. Meded. Fac. Landbouwwet Univ. Gent 60/4b:2639-2645.
17. Heuer, H., and K. Smalla. 1997. Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) for studying soil microbial communities, p. 353-373. In J. D. van Elsas, E. M. H. Wellington, and J. T. Trevors (ed.), Modern soil microbiology. Marcel Dekker, Inc., New York, N.Y.
18. Hopwood, D. A., M. J. Bibb, K. F. Chater, T. Kieser, C. J. Bruton, H. M. Kieser, D. J. Lydiate, C. P. Smith, J. M. Ward, and H. Schrempf. 1985. Genetic manipulation of streptomyces - a laboratory manual. The John Innes Foundation, Norwich, United Kingdom.
19. Kane, M. D., L. K. Poulsen, and D. A. Stahl. 1993. Monitoring the enrichment and isolation of sulfate-reducing bacteria by using oligonucleotide hybridization probes designed for environmentally derived 16S rRNA sequences. Appl. Environ. Microbiol. 59:682-686.
20. Krsek, M., and P. Baker. Unpublished data.
21. Kwok, S., S.-Y. Chang, J. J. Sninsky, and A. Wang. 1994. A guide to the design and use of mismatched and degenerate primers. PCR Methods Appl. 3:S39-S47.
22. Kwok, S., D. E. Kellogg, N. McKinney, D. Spasic, L. Goda, C. Levenson, and J. J. Sninsky. 1990. Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucleic Acids Res. 18:999-1005.
23. Liu, D., N. A. Anderson, and L. K. Kinkel. 1996. Selection and characterization of strains of Streptomyces suppressive to the potato scab pathogen. Can. J. Microbiol. 42:487-502.
24. Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1997. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25:109-110.
25. McCarthy, A. J. 1987. Lignocellulose-degrading actinomycetes. FEMS Microbiol. Rev. 46:145-163.
26. Muyzer, G., E. C. de Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microhiol. 59:695-700.
27. Muyzer, G., and N. B. Ramsing. 1996. Molecular methods to study the organization of microbial communities. Water Sci. Technol. 32:1-9.
28. Muyzer, G., A. Teske, C. O. Wirsen, and H. W. Jannasch. 1995. Phylogenetic relationship of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch. Microbiol. 164:165-172.
29. Myers, R. M., S. G. Fischer, L. S. Lerman, and T. Maniatis. 1985. Nearly all single base substitutions in DNA fragments joint to a GC-clamp can be detected by denaturing gradient gel electrophoresis. Nucleic Acids Res. 13:3131-3145.
30. Neefs, J.-M., Y. Van de Peer, L. Hendriks, and R. De Wachter. 1990. Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 18:2237-2242.
31. Niner, B. N., J. P. Brandt, M. Villegas, C. R. Marshall, A. M. Hirsch, and M. Valdés. 1996. Analysis of partial sequences of genes coding for 16S rRNA of actinomycetes isolated from Casuarina equisetifolia nodules in Mexico. Appl. Environ. Microbiol. 62:3034-3036.
32. Nübel, U., B. Engelen, A. Felske, J. Snaidr, A. Wieshuber, R. I. Amann, W. Ludwig, and H. Backhaus. 1996. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J. Bacteriol. 178:5636-5643.
33. Relman, D. A., M. D. Thomas, T. M. Schmidt, P. Richard, M. D. MacDermott, and S. Falkow. 1992. Identification of the uncultured bacillus of Whipple's disease. N. Engl. J. Med. 327:293-301.
34. Reyes, F. L., W. Ritter, and L. Raskin. 1997. Group-specific small-subunit rRNA hybridization probes to characterize filamentous foaming in activated sludge systems. Appl. Environ. Microbiol. 63:1107-1117.
35. 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.
36. Rheims, H., C. Spröer, F. A. Rainey, and E. Stackebrandt. 1996. Molecular biological evidence for the occurrence of uncultured members of the actinomycete line of descent in different environments and geographical locations. Microbiology 142:2863-2870.
37. Riesner, D., G. Steger, R. Zimmat, R. A. Owens, M. Wagenhöfer, W. Hillen, S. Vollbach, and K. Henco. 1989. Temperature-gradient gel electrophoresis of nucleic acids: analysis of conformational transitions, sequence variations, and protein-nucleic acid interactions. Electrophoresis 10:377-389.
38. Romanowski, G., M. G. Lorenz, and W. Wackernagel. 1993. Use of polymerase chain reaction and electroporation of Escherichia coli to monitor the persistence of extracellular plasmid DNA introduced into natural soils. Appl. Environ. Microbiol. 59:3438-3446.
39. Rothrock, C. S., and D. Gottlieb. 1984. Role of antibiosis of Streptomyces hygroscopicus var. geldanus to Rhizoctonia solam in soil. Can. J. Microbiol. 30:1440-1447.
40. Rychlik, W., and R. E. Rhoads. 1989. A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Res. 17:8543-8551.
41. Rychlik, W., W. J. Spencer, and R. E. Rhoads. 1990. Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acids Res. 18:6409-6412.
42. Saiki, R. K., D. H. Gelfand, S. Stoffel, S. J. Scharf, R. Higuchi, G. T. Horn, K. B. Mullis, and H. A. Erlich. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487-491.
43. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
44. Sheffield, V. C., R. D. Cox, L. S. Lerman, and R. M. Myers. 1989. Attachment of a 40-base-pair G+C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc. Natl. Acad. Sci. USA 86:232-236.
45. Smalla, K., N. Cresswell, L. C. Mendoca-Hagler, A. Wolters, and J. D. van Elsas. 1993. Rapid DNA extraction protocol from soil for polymerase chain reaction-mediated amplification. J. Appl. Bacteriol. 74:78-85.
46. Sommer, R., and D. Tautz. 1989. Minimal homology requirements for PCR primers. Nucleic Acids Res. 17:6749.
47. Stackebrandt, E., F. A. Rainey, and N. L. Ward-Rainey. 1997. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int. J. Syst. Bacteriol. 47:479-491.
48. Stackebrandt, E., D. Witt, C. Kemmerling, R. Kroppenstedt, and W. Liesack. 1991. Designation of streptomycete 16S and 23S rRNA-based target regions for oligonucleotide probes. Appl. Environ. Microbiol. 57:1468-1477.
49. Steger, G. 1994. Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction. Nucleic Acids Res. 22:2760-2768.
50. Suzuki, M. T., and S. J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:625-630.
51. Takeuchi, T., H. Sawada, F. Tanaka, and I. Matsuda. 1996. Phylogenetic analysis of Streptomyces spp. causing potato scab based on 16S rRNA sequences. Int. J. Syst. Bacteriol. 46:476-479.
52. Teske, A., P. Sigalevich, Y. Cohen, and G. Muyzer. 1996. Molecular identification of bacteria from coculture by denaturing gradient gel electrophoresis of 16S ribosomal DNA fragments as a tool for isolation in pure cultures. Appl. Environ. Microbiol. 62:4210-4215.
53. Torsvik, V., J. Goksøyr, and F. L. Daae. 1990. High diversity in DNA of soil bacteria. Appl. Environ. Microbiol. 56:782-787.
54. Wagner, M., R. Amann, H. Lemmer, and K.-H. Schleifer. 1993. Probing activated sludge with proteobacteria-specific oligonucleotides: inadequacy of culture-dependent methods for describing microbial community structure. Appl. Environ. Microbiol. 59:1520-1525.
55. Ward, D. M., R. Weller, and M. M. Bateson. 1990. 16S rRNA sequences reveal uncultured inhabitants of a well studied thermal community. FEMS Microbiol. Rev. 6:105-115.
56. Weissburg, W. G., S. M. Barns, D. A. Pelletier, and D. J. Lane. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173:697-703.
57. Wellington, E. M. H., N. Cresswell, and V. A. Saunders. 1990. Growth and survival of streptomycete inoculants and the extent of plasmid transfer in sterile and nonsterile soil. Appl. Environ. Microbiol. 56:1413-1419.
58. Williams, S. T., S. Lanning, and E. M. H. Wellington. 1984. Ecology of actinomycetes, p. 481-528. In M. Goodfellow, M. Mordarski, and S. T. Williams (ed.), The biology of the actinomycetes. Academic Press Ltd., London, United Kingdom.
59. Wilson, K. 1987. Preparation of genomic DNA from bacteria, p. 2.10-2.12. In F. M. Ausubel, R. Bent, R. E. Kingston et al. (ed.), Current protocols in molecular biology. J. Wiley & Sons, New York, N.Y.
60. Winker, S., and C. R. Woese. 1991. A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics. Syst. Appl. Microbiol. 14:305-310.