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

Systematic and Applied Microbiology

Volumn 19, Issue 4, 1996, Pages 478-492

  Moore, Edward R B ^a   Mau, Margit ^a   Arnscheidt, Angelika ^a   Böttger, Erik C ^b   Hutson, Roger A ^c   Collins, Matthew D ^c   Van De Peer, Yves ^d   De Wachter, Rupert ^d   Timmis, Kenneth N ^a  

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^b HANNOVER MEDICAL SCHOOL   (Germany)

^c INSTITUTE OF FOOD RESEARCH   (United Kingdom)

^d UNIVERSITY OF ANTWERP   (Belgium)

Author keywords

16S rRNA genes; Gene sequences; Hypervariable sequence regions; Intrageneric relationships; Phylogeny; Pseudomonas (sensu stricto); Sequence signatures

Indexed keywords

PSEUDOMONAS; UNIDENTIFIED AGENTS;

RNA 16S;

ARTICLE; BACTERIAL GENE; BACTERIUM IDENTIFICATION; GENE SEQUENCE; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PSEUDOMONAS;

EID: 0030459930     PISSN: 07232020     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0723-2020(96)80021-X     Document Type: Article

References (65)

1. Amann, R., Ludwig, W., Schleifer, K.-H.: Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143-169 (1995)
2. Amann, R., Ludwig, W., Schulze, R., Spring, S., Moore, E., Schleifer, K.-H.: rRNA-targeted oligonucleotide probes for the identification of genuine and former pseudomonads. System. Appl. Microbiol., this issue (1996)
3. Ambler, R.: The evolutionary stability of cytochrome c-551 in Pseudomonas aeruginosa and Pseudomonas fluorescens biotype c. Biochem. J. 137, 3-14 (1974)
4. Bennasar, A., Rosselló-Mora, R., Lalucat, J., Moore, E. R. B.: 16S rRNA gene sequence analysis relative to genomovars of Pseudomonas stutzen and proposal of Pseudomonas balearica sp. nov. Int. J. Syst. Bacteriol. 46, 200-205 (1996)
5. Brosch, R., Lefevre, M., Grimont, F., Grimont, P. A. D.: Taxonomic diversity of pseudomonads revealed by computer-interpretation of ribotyping data. System. Appl. Microbiol., this issue (1996)
6. Collins, M. D., Jones, D.: Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol. Rev. 45, 316-354 (1981)
7. Delaporte, B., Raynaud, M., Daste, M. P.: Une bactérie du sol capable d'utiliser; comme source de carbone, la fraction fixe de certaines oléorésines, Pseudomonas resinovorans n. sp. C.R. Hebd. Séances Acad. Sci. Paris. 252, 1073-1075 (1961)
8. De Vos, P., De Ley, J.: Intra- and inter generic similarities of Pseudomonas and Xanthomonas ribosomal ribonucleic acid cistrons. Int. J. Syst. Bacteriol. 33, 487-509 (1983)
9. De Vos, P., Goor, N., Gillis, M., De Ley, J.: Ribosomal ribonucleic acid cistron similarities of phytophatogenic Pseudomonas spcies. Int. J. Syst. Bacteriol. 35, 169-184 (1985)
10. De Vos, P., Landschoot, A. V., Segers, P., Tytgat, R., Gillis, M., Bauwens, M., Rossau, R., Goor, M., Pot, B., Kersters, K., Lizzaraga, P., De Ley, J.: Genotypic relationships and taxonomic localization of unclassified Pseudomonas and Pseudomonas-like strains by deoxy-ribonucleic acid:ribosomal ribonucleic acid hybridizations. Int. J. Syst. Bacteriol. 39, 35-49 (1989)
11. Douderoff, M., Palleroni, N. J.: Genus I. Pseudomonas Migula 1894, 237, pp. 217-243. In: Bergey's Manual of Determinative Bacteriology (R. E. Buchanan, N. E. Gibbons, eds.) 8th ed., Baltimore, Williams & Wilkins 1974
12. Edwards, U., Rogall, T., Blöcker, H., Emde, M., Böttger, E. C.: Isolation and direct nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucl. Acids Res. 17, 7843-7853 (1989)
13. Felsenstein, J.: Confidence limits on phytogenies: an approach using the bootstrap. Evolution 39, 783-791 (1985)
14. Gibson, J., Stackebrandt, E., Zahlen, L. B., Gupta, R., Woese, C. R.: A phylogenetic analysis of the purple photosynthetic bacteria. Curr. Microbiol. 3, 59-64 (1979)
15. Green, S. K., Schroth, M. N., Cho, J. J., Kominos, S. D., Vitanza-Jack, V. B.: Agricultural plants and soil as a possible reservoir for Pseudomonas aeruginosa. Appl. Microbiol. 28, 987-991 (1974)
16. Gutell, R. R., Weiser, B., Woese, C. R., Noller, H. F.: Comparative anatomy of 16S-like ribosomal RNA. Progr. Nucl. Acid Res. Molec. Biol. 32, 155-216 (1985)
17. Hauben, L., Vauterin, L., Swings, J., Moore, E. R. B.: 16S ribosomal DNA sequence comparison of all Xanthomonas species. Int. J. Syst. Bacteriol. (submitted)
18. Hildebrand, D. C., Palleroni, N. J., Hendson, M., Toth, J., Johnson, J. L.: Pseudomonas flavescens sp. nov., isolated from walnut blight cankers. Int. J. Syst. Bacteriol. 44, 410-415 (1994)
19. Hutson, R. A., Thompson, D. E., Collins, M. D.: Genetic interrelationships of saccharolytic Chlostridium botulinum types B, E and F and related clostridia as revealed by small-subunit rRNA gene sequences. FEMS Microbiol. Lett. 108, 103-110 (1993)
20. Jaeger, J. A., Turner, D. H., Zuker, M.: Predicting optimal and suboprimal secondary structure for RNA. Meth. Enzymol. 183, 281-306 (1990)
21. Johnson, J. L., Palleroni, N. J.: Deoxyribonucleic acid similarities among Pseudomonas species. Int. J. Syst. Bacteriol. 39, 230-235 (1989)
22. Jukes, T. H., Cantor, C. R.: Evolution of protein molecules, pp. 21-132. In: Mammalian protein metabolism (H. N. Munro, ed.) New York, Academic Press 1969
23. Karlson, U., Dwyer, D. F., Hooper, S. W., Moore, E. R. B., Timmis, K. N., Eltis, L. D.: Two independently regulated cytochromes P-450 in Rhodococcus rhodochrous strain that degrades 2-ethoxyphenol and 4-methoxybenzoate. J. Bact. 175, 1467-1474 (1993)
24. Kersters, K., Ludwig, W., Vancanneyt, M., De Vos, P., Gillis, M., Schleifer, K.-H.: Recent changes in the classification of the pseudomonads: an overview. Syst. Appl. Microbiol. this issue (1996)
25. Lane, D. J.: 16S/23S sequencing, pp. 115-175. In: Nucleic Acid Techniques in Bacterial Systematics (E. Stackebrandt, M. Goodfellow, eds.) Chichester, John Wiley 1991
26. Lelliott, R. A., Billing, E., Hayward, A. C.: A determinative scheme for the fluorescent plant pathogenic pseudomonads. J. Appl. Bact. 29, 470-489 (1966)
27. Lysenko, O.: Pseudomonas - an attempt at a general classification. J. Gen. Microbiol. 25, 379-408 (1961)
28. Maidak, B. J., Olson, G. J., Larsen, N., Overbeek, R., McCaughey, M. J., Woese, C. R.: The ribosomal RNA database project (RDP). Nucl. Acids Res. 24, 82-85 (1996)
29. Mandel, M.: Deoxyribonucleic acid base composition in the genus Pseudomonas. J. Gen. Microbiol. 43, 273-292 (1966)
30. Moore, E. R. B., Krüger, A. S., Hauben, L., Seal, S. E., De Baere, R., De Wachter, R., Timmis, K. N., Swings, J.: 16S rRNA gene sequence analyses and inter- and intra-specific relationships of Xanthomonas species and Stenotrophomonas maltophilia. FEMS Microbiol. Lett. (submitted)
31. Mullis, K. B., Faloona, F.: Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol. 155, 335-350 (1987)
32. Neefs, J.-M., Van de Peer, Y., Hendriks, L., De Wachter, R.: Compilation of small ribosomal subunit RNA sequences. Nucl. Acids. Res. 18, 2237-2330 (1990)
33. Palleroni, N. J.: Genus I. Pseudomonas Migula 1894, 237, pp. 141-199. In: Bergey's Manual of Systematic Bacteriology, vol. 1 (N. J. Krieg, J. G. Holt, eds.) Baltimore, Williams & Wilkins 1984
34. Palleroni, N. J.: Human and animal-pathogenic pseudomonads, pp. 3086-3103. In: The Prokaryotes, A Handbook on the Biology of Bacteria, Ecophysiology, Isolation, Identification and Applications, 2nd ed., vol. III, (A. Balows, H. G. Trüper, M. Dworkin, W. Harder and K. H. Schleifer, eds.) New York, Springer 1992.
35. Palleroni, N. J., Ballard, R. W., Ralston, E., Doudoroff, M.: Deoxyribo-nucleic acid homologies among some Pseudomonas species. J. Bacteriol. 110, 1-11 (1972)
36. Palleroni, N. J., Doudoroff, M., Stanier, R. Y., Solanes, R. E., Mandel, M.: Taxonomy of the aerobic pseudomonads: the properties of the Pseudomonas stutzeri group. J. Gen. Microbiol. 60, 215-231 (1970)
37. Palleroni, N. J., Kunisawa, R., Contopoulou, R., Doudoroff, M.: Nucleic acid homologies in the genus Pseudomonas. Int. J. Syst. Bacteriol. 23, 333-339 (1973)
38. Psallidas, P. G., Panagopoulos, C. G.: A new bacteriosis of almond caused by Pseudomonas amygdali sp. nov. Ann. Inst. Phytopathol. Benaki. 11, 94-108 (1975)
39. Rhodes, M. E.: The characterization of Pseudomonas fluorescens. J. Gen. Microbiol. 21, 221-263 (1959)
40. Rodriguez-Tome, P., Stoehr, P. J., Cameron, G. N., Flores, T. P.: The European Bio-informatics Institute (EBI) databases. Nucl. Acids Res. 24, 6-12 (1996)
41. Rosselló, R., Garcia-Valdes, E., Lalucat, J., Ursing, J.: Genotypic and phenotypic diversity of Pseudomonas stutzeri. System. Appl. Microbiol. 14, 150-157 (1991)
42. Rosselló-Mora, R., Lalucat, J., Moore, E. R. B.: JM300 represents a new genomovar within Pseudomonas stutzeri. System. Appl. Microbiol. this issue (1996)
43. Saitou, N., Nei, M.: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425 (1987)
44. Sands, D. C., Schroth, M. N., Hildebrand, D. C.: Taxonomy of phyto-pathogenic pseudomonads. J. Bacteriol. 101, 9-23 (1970)
45. Schaad, N. W., Sowell, G., Goth, R. W., Colwell, R. R., Webb, R. E.: Pseudomonas pseudoalcaligenes subsp. citrulli subsp. nov. Int. J. Syst. Bacteriol. 28, 117-125 (1978)
46. Schroth, M., Hildebrand, D. C., Panopoulos, N.: Phytopathogenic pseudomonads and related plant-associated pseudomonads, pp. 3104-3131. In: The Prokaryotes, a Handbook on the Biology of Bacteria, Ecophysiology, Isolation, Identification and Applications, 2nd ed., vol. III, (A. Balows, H. G. Trüper, M. Dworkin, W. Harder and K. H. Schleifer, eds.) New York, Springer 1992
47. Sneath, P. H. A., Stevens, M., Sackin, M. J.: Numerical taxonomy of Pseudomonas based on published records of substrate utilization. Antonie Leeuwenhoek 47, 423-448 (1981)
48. Stackebrandt, E., Murray, R. G. E., Trüper, H. G.: Proteobacteria classis nov., a name for the phylogenetic taxon that includes the "purple bacteria and their relatives". Int. J. Syst. Bacteriol. 38, 321-325 (1988)
49. Swingle, D. B.: Center rot of "French endive" or wilt of chicory (Chichorium intybus L.). Phytopathology 15, 730 (1925)
50. Toschka, H. Y., Höpfl, P., Ludwig, W., Schleifer, K.-H., Ulbrich, N., Erdmann, V. A.: Complete nucleotide sequence of a 16S ribosomal RNA gene from Pseudomonas aeruginosa. Nucl. Acids Res. 16, 2348 (1988)
51. Vancanneyt, M., Torch, U., Dewettinck, D., Vaerewijck, M., Kersters, K.: Grouping of pseudomonads by SDS-PAGE of whole-cell proteins. System. Appl. Microbiol. this issue (1996a)
52. Vancanneyt, M., Witt, S., Abraham, W.-R., Kersters, K., Fredrickson, H. L.: Fatty acid content in whole-cell hydrolysates and phospholipid fractions of pseudomonads: a taxonomic evaluation. System. Appl. Microbiol. this issue (1996b)
53. Van den Berghe, A., Wassink, A., Raeyemaekers, P., De Baere, R., Huysmans, E., De Wachter, R.: Nucleotide sequence, secondary structure and evolution of the 5S ribosomal RNA from five bacterial species. Eur. J. Biochem. 149, 537-542 (1985)
54. Van de Peer, Y., De Wachter, R.: TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Applic. Biosci. 10, 569-570 (1994)
55. Van de Peer, Y., Nicolaï, S., De Rijk, P., De Wachter, R.: Database on the structure of small ribosomal subunit RNA. Nucl. Acids Res. 24, 86-91 (1996a)
56. Van de Peer, Y., Vancanneyt, M., De Wachter, R.: Compilation of pseudomonad sequences present in a database on the structure of ribosomal RNA. Syst. Appl. Microbiol. this issue (1996b)
57. Vauterin, L., Sicings, J., Kersters, K., Gillis, M., Mew, T. W., Schroth, M. N., Palleroni, N. J., Hildebrand, D. C., Stead, D. E., Civerolo, E. L., Hayward, A. C., Maraite, H., Stall, R. E., Vidaver, A. K., Bradbury, J. F.: Towards and improved taxonomy of Xanthomonas. Int. J. Syst. Bacteriol. 40, 312-316 (1990)
58. Vauterin, L., Hoste, B., Kersters, K., Swings, J.: Reclassification of Xanthomonas. Int. J. Syst. Bacteriol. 45, 472-489 (1995)
59. Wilkenson, S. G.: Studies on the cell walls of Pseudomonas species resistant to ethylene-diaminetetraacetic acid. J. Gen. Microbiol. 54, 195-213 (1968)
60. Wilson, K.: Preparation of genomic DNA from bacteria, pp. 2.4.1-2.4.2. In: Current protocols in molecular biology (F. M. Ausubel, R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, K. Struhl, eds.) New York, John Wiley 1987
61. Woese, C. R.: Bacterial evolution. Microbiol. Rev. 51, 221-271 (1987)
62. Woese, C. R., Blanz, P., Hahn, C. M.: What isn't a pseudomonad: the importance of nomenclature in bacterial classification. Syst. Appl. Microbiol. 5, 179-195 (1984)
63. Woese, C. R., Gutell, R., Gupta, R., Noller, H. F.: Detailed higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol. Rev. 47, 621-669 (1983)
64. Wong, W. C., Preece, T. F.: Identification of Pseudomonas tolaasit: the white line in agar and mushroom tissue block rapid pitting tests. J. Appl. Bact. 47, 401-407 (1979)
65. Young, J. M., Dye, D. W., Bradbury, J. F., Panagopoulos, C. G., Robbs, C. F.: A proposed nomenclature and classification for plant pathogenic bacteria. N. Z. J. Agric. Res. 21, 153-177 (1978)