Utility of internally transcribed 16S-23S rDNA spacer regions for the definition of Pseudomonas stutzeri genomovars and other Pseudomonas species

International Journal of Systematic and Evolutionary Microbiology

Volumn 50, Issue 4, 2000, Pages 1629-1639

  Guasp, Caterina ^a   Moore, Edward R B ^b   Lalucat, Jorge ^a   Bennasar, Antonio ^b  

^a INSTITUTO MEDITERRÁNEO DE ESTUDIOS AVANZADOS   (Spain)

^b HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

Author keywords

16S rRNA gene sequencing; 16S 23S internally transcribed spacer region; DNA DNA hybridization; Genomovar; RFLP fingerprinting

Indexed keywords

ALANINE TRANSFER RNA; ISOLEUCINE TRANSFER RNA; RIBOSOME DNA; RNA 16S; RNA 23S; SPACER DNA;

ANALYTIC METHOD; ARTICLE; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; DNA DETERMINATION; DNA DNA HYBRIDIZATION; GENOTYPE; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PHYLOGENY; PRIORITY JOURNAL; PSEUDOMONAS; PSEUDOMONAS STUTZERI; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENTIATION; STRAIN DIFFERENCE;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; PSEUDOMONAS; PSEUDOMONAS STUTZERI;

EID: 0033867757     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/00207713-50-4-1629     Document Type: Article

References (58)

1. Abraham, W.-R., Strömpl, C., Meyer, H. & 8 other authors (1999). Phylogeny and polyphasic taxonomy of Caulobacter species. Proposal of Maricaulis gen. nov. with Maricaulis maris (Poindexter) comb. nov. as the type species, and emended description of the genera Brevundimonas and Caulobacter. Int J Syst Bacteriol 49, 1053-1073.
2. Ash, C., Farrow, J. A. E., Wallbanks, S. & Collins, M. D. (1991). Phylogenetic heterogeneity of the genus Bacillus revealed by comparative analysis of small-subunit-ribosomal RNA sequences. Lett Appl Microbiol 13, 202-206.
3. Barry, T., Colleran, G., Glennon, M., Dunican, L. K. & Gannon, F. (1991). The 16S/23S ribosomal spacer region as a target for DNA probes to identify eubacteria. PCR Methods Appl 1, 51-56 (erratum 1, 149).
4. Bennasar, A., Rosselló-Mora, R., Lalucat, J. & Moore, E. R. B. (1996). 16S rRNA gene sequence analysis relative to genomovars of Pseudomonas stutzeri and proposal of Pseudomonas balearica sp. nov. Int J Syst Bacteriol 46, 250-255.
5. Bennasar, A., Guasp, C. & Lalucat, J. (1998a). Molecular methods for the detection and identification of Pseudomonas stutzeri in pure culture and environmental samples. Microb Ecol 35, 22-33.
6. Bennasar, A., Guasp, C., Tesar, M. & Lalucat, J. (1998b). Genetic relationships among Pseudomonas stutzeri strains based on molecular typing methods. J Appl Microbiol 85, 643-656.
7. Berg, K. L., Squires, C. & Squires, C. L. (1989). Ribosomal RNA operon anti-termination. Function of leader and spacer region box B-box A sequences and their conservation in diverse microorganisms. J Mol Biol 209, 345-348.
8. Brosius, J., Palmer, M. L., Kennedy, P. J. & Noller, H. F. (1978). Complete nucleotide sequence of a 16S ribosomal RNA gene from Excherichia coli. Proc Natl Acad Sci USA 75, 4801-4805.
9. Brosius, J., Dull, T. J. & Noller, H. F. (1980). Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci USA 77, 201-204.
10. Carlson, C. A., Pierson, L. S., Rosen, J. J. & Ingraham, J. L. (1983). Pseudomonas stutzeri and related species undergo natural transformation. J Bacteriol 153, 93-99.
11. Felsenstein, J. (1989). PHYLIP - phylogeny inference package (version 3.2). Cladistics 5, 164-166.
12. Fox, G. E., Wisotzkey, J. D. & Jurtshuk, P., Jr (1992). How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42, 166-170.
13. Fuller, W. & Hodgson, A. (1967). Conformation of the anticodon loop in the tRNA. Nature 215, 817-821.
14. García-Martínez, J., Martínez-Murcia, A., Anton, A. I. & Rodríguez-Valera, F. (1996). Comparison of the small 16S to 23S intergenic spacer region (ISR) of the rRNA operons of some Escherichia coli strains of the ECOR collection and E. coli K-12. J Bacteriol 178, 6374-6377.
15. Ginard, M., Lalucat, J., Tümmler, B. & Römling, U. (1997). Genome organization of Pseudomonas stutzeri and resulting taxonomic and evolutionary considerations. Int J Syst Bacteriol 47, 132-143.
16. Guasp, C. M. (1999). Métodos moleculares de estudio de las poblaciones de Pseudomonas stutzeri. Doctoral Thesis, Universitat Illes Balears, Palma de Mallorca, Spain.
17. Gürtler, V. & Stanisich, V. A. (1996). New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142, 3-16.
18. Gutell, R. R., Larsen, N. & Woese, C. R. (1994). Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol Rev 58, 10-26.
19. Hauben, L., Vauterin, L., Swings, J. & Moore, E. R. B. (1997). Comparison of 16S ribosomal DNA sequences of all Xanthomonas species. Int J Syst Bacteriol 47, 328-335.
20. Hauben, L., Moore, E. R. B., Vauterin, L., Steenackers, M., Mergaert, J., Verdonck, L. & Swings, J. (1998). Phylogenetic position of phytopathogens within the Enterobacteriaceae. Syst Appl Microbiol 21, 384-397.
21. Holmes, B. (1986). Identification and distribution of Pseudomonas stutzeri in clinical material. J Appl Bacteriol 60, 401-411.
22. Jensen, M. A., Webster, J. A. & Strauss, N. (1993). Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl Environ Microbiol 59, 945-952.
23. Johnson, J. L. (1973). Use of nucleic acid homologies in the taxonomy of anaerobic bacteria. Int J Syst Bacteriol 23, 308-315.
24. Johnson, J. L. (1984). Nucleic acids in bacterial classification. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 8-11. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
25. Johnson, J. L. & Palleroni, N. J. (1989). Deoxyribonucleic acid similarities among Pseudomonas species. Int J Syst Bacteriol 39, 230-235.
26. Jukes, T. H. & Cantor, C. R. (1969). Evolution of protein molecules. In Mammalian Protein Metabolism, pp. 21-132. Edited by H. N. Munro. New York: Academic Press.
27. Kerkhof, L. (1997). A ribosomal RNA operon from Pseudomonas stutzeri ZoBell. Gene 192, 241-243.
28. Lane, D. J., Pace, B., Olsen, G. J., Stahl, D. A., Sogin, M. L. & Pace, N. R. (1985). Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci USA 82, 6955-6959.
29. Leblond-Bourget, N., Philippe, H., Mangin, I. & Decaris, B. (1996). 16S rRNA and 16S to 23S internal transcribed spacer sequence analyses reveal inter- and intraspecific Bifidobacterium phylogeny. Int J Syst Bacteriol 46, 102-111.
30. Lorenz, M. G. & Wackernagel, W. (1994). Bacterial gene transfer by natural genetic transformation in the environment. Microbiol Rev 58, 563-602.
31. Manceau, C. & Horvais, A. (1997). Assessment of genetic diversity among strains of Pseudomonas syringae by PCR-restriction fragment length polymorphism analysis of rRNA operons with special emphasis on P. svringae pv. tomato. Appl Environ Microbiol 63, 498-505.
32. Marmur, J. (1961). A procedure for the isolation of DNA from microorganisms. J Mol Biol 3, 208-218.
33. Martinez-Murcia, A. J., Benlloch, S. & Collins, M. D. (1992). Phylogenetic interrelationships of members of the general Aeromonas and Plesiomonas as determined by 16S ribosomal DNA sequencing: lack of congruence with results of DNA-DNA hybridizations. Int J Syst Bacteriol 42, 412-421.
34. Mendoza, M., Meugnier, H., Bes, M., Etienne, J. & Freney, J. (1998). Identification of Staphylococcus species by 16S-23S rDNA intergenic spacer PCR analysis. Int J Syst Bacteriol 48, I049-1055.
35. Moore, E. R. B., Mau, M., Arnscheidt, A., Böttger, E., Hutson, R. A., Collins, M. D., Van de Peer, Y., De Wachter, R. & Timmis, K.N. (1996). The determination and comparison of the 16S rRNA gene sequences of species of the genus Pseudomonas (sensu stricto) and estimation of the natural intrageneric relationships. Syst Appl Microbiol 19, 478-492.
36. Moore, E., Arnscheidt, A., Krüger, A., Strömple, C. & Mau, M. (1999). Simplified protocols for the preparation of genomic DNA from bacterial cultures. In Molecular Microbial Ecology Manual, 1.6.1, pp. 1-15. Edited by A. D. L. Akkermans, J. D. van Elsas & F. J. de Bruijn. Dordrecht, The Netherlands: Kluwer Academic Press.
37. Obradors, N. & Aguilar, J. (1991). Efficient biodegradation of high-molecular-weight polyethylene glycols by pure cultures of Pseudomonas stutzeri. Appl Environ Microbiol 57, 2383-2388.
38. Palleroni, N. J. (1984). Genus I Pseudomonas. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 141-199. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
39. Palleroni, N. J., Doudoroff, M., Stanier, R. Y., Solanes, R. E. & Mandel, M. (1970). Taxonomy of the aerobic pseudomonads: the properties of the Pseudomonas stutzeri group. J Gen Microbiol 60, 215-231.
40. Pérez-Luz, S., Rodríguez-Valera, F., Lan, R. & Reeves, P. R. (1998). Variation of the ribosomal operon 16S-23S gene spacer region in representatives of Salmonella enterica subspecies. J Bacteriol 180, 2144-2151.
41. Rambaut, A. (1996). Se-Al: sequence alignment editor. Version 1.0 alpha 1. Department of Zoology. University of Oxford, South Parks Road, Oxford OX1 4JD, UK.
42. Riffard, S., Lo Presti, F., Normand, P., Forey, F., Reyrolle, M., Etienne, J. & Vandenesh, F. (1998). Species identification of Legionella via intergenic 16S-23S ribosomal spacer PCR analysis. Int J Syst Bacteriol 48, 723-730.
43. Rosselló, R., García-Valdés, E., Lalucat, J. & Ursing, J. (1991). Genotypic and phenotypic diversity of Pseudomonas stutzeri. Syst Appl Microbiol 14, 150-157.
44. Rosselló-Mora, R. A., Lalucat, J., Dott, W. & Kämpfer, P. (1994). Biochemical and chemotaxonomic characterization of Pseudomonas stutzeri genomovars. J Appl Bacteriol 76, 226-233.
45. Rosselló-Mora, R. A., Lalucat, J., Timmis, K. N. & Moore, E. R. B. (1996). Strain JM300 represents a new genomovar within Pseudomonas stuzeri. Syst Appl Microbiol 19, 596-599.
46. Shine, J. & Dalgarno, L. (1974). The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci USA 71, 1342-1346.
47. Sikorski, J., Graupner, S., Lorenz, M. G. & Wackernagel, W. (1998). Natural genetic transformation of Psuedomonas stutzeri in a non-sterile soil. Microbiology 144, 569-576.
48. Sprinzl, M., Horn, C., Brown, M., Ioudovitch, A. & Steinberg, S. (1998). Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 26, 148-153.
49. Srivastava, A. K. & Schlessinger, D. (1990). Mechanism and regulation of bacterial ribosomal RNA processing. Annu Rev Microbiol 44, 105-129.
50. Stanier, R. Y., Palleroni, N. J. & Doudoroff, M. (1966). The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 43, 159-271.
51. Stewart, G. J. & Sinigalliano, C. D. (1991). Exchange of chromosomal markers by natural transformation between the soil isolate. Pseudomonas stutzeri JM300, and the marine isolate Pseudomonas stutzeri strain ZoBell. Antonie Leeuwenhoek 59, 19-25.
52. Thompson, J. D., Higgins, D. G. & Gibson, T. G. (1994). CLUSTAL w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
53. Tyrrell, G. J., Bethune, R. N., Willey, B. & Low, D. E. (1997). Species identification of enterococci via intergenic ribosomal PCR. J Clin Microbiol 35, 1054-1060.
54. Vaneechoutte, M., Boerlin, P., Tichy, H.-V., Bannerman, E., Jäger, B. & Bille, J. (1998). Comparison of PCR-based DNA finger-printing techniques for the identification of Listeria species and their use for atypical Listeria isolates. Int J Syst Bacteriol 48, 127-139.
55. Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors (1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463-464.
56. Yoon, J.-H., Lee, S.-T. & Park, Y.-H. (1998). Genetic analyses of the genus Nocardioides and related taxa based on 16S 23S rDNA internally transcribed spacer sequences. Int J Syst Bacteriol 48, 641-650.
57. Ziemke, F., Höfle, M. G., Lalucat, J. & Rossello-Mora, R. (1998). Reclassification of Shewanell putrefaciens Owen's genomic group II as Shewanella baltica sp. nov. Int J Syst Bacteriol 48, 179-186.
58. Zumft, W. G. (1992). The denitrifying prokaryotes. In The Prokaryotes, pp. 554-582. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. Berlin: Springer.