Taxonomic study of bacteria isolated from Lebanese spring waters: Proposal for Pseudomonas cedrella sp. nov. and P. orientalis sp. nov.

Research in Microbiology

Volumn 150, Issue 5, 1999, Pages 303-316

  Dabboussi, Fouad ^a   Hamze, Monzer ^b   Elomari, Malika ^a   Verhille, Sophie ^a   Baida, Nader ^a   Izard, Daniel ^a   Leclerc, Henri ^a  

^a UNIV LILLE   (France)

^b LEBANESE UNIVERSITY   (Lebanon)

Author keywords

16S rRNA; DNA DNA hybridization; Pseudomonas taxonomy; Spring water

Indexed keywords

WATER;

ARTICLE; BACTERIUM ISOLATE; CONTROLLED STUDY; DNA DNA HYBRIDIZATION; GENE SEQUENCE; LEBANON; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PSEUDOMONAS; TAXONOMY; THERMOSTABILITY;

PSEUDOMONAS CEDRELLA; PSEUDOMONAS ORIENTALIS;

EID: 0032706433     PISSN: 09232508     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0923-2508(99)80056-4     Document Type: Article

References (42)

1. 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. 19:1996;501-509.
2. Beji A., Izard D., Gavini F., Leclerc H., Leseine-Delstanche M., Krembel J. A rapid chemical procedure for isolation and purification of chromosomal DNA from Gram-negative bacilli. Anal. Biochem. 161:1987;18-23.
3. Boivin-Jahns V., Bianchi A., Ruimy R., Daumas S., Christen R. Comparison of phenotypical and molecular methods for the identification of bacterial strains isolated from a deep subsurface environment. Appl. Environ. Microbiol. 61:1995;3400-3406.
4. Bowman J.P., Sly L.I., Hayward A.C., Spiegel Y., Stackebrandt E. Telluria mixta (Pseudomonas mixta Bowman Sly and Hayward1988) gen. nov., comb. nov., and Telluria chitinolytica sp. nov., soil-dwelling organisms which actively degrade polysaccharides. Int. J. Syst. Bacteriol. 43:1993;120-124.
5. Brosch R., Lefèvre M., Grimont F., Grimont P.A.D. Taxonomic diversity of pseudomonads revealed by computer-interpretation of ribotyping data. System. Appl. Microbiol. 19:1996;541-555.
6. Brosius J., Palmer M.L., Kennedy P.J., Noller H.F. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc. Natl. Acad. Sci. USA. 75:1978;4801-4805.
7. Coroler L., Elomari M., Hoste B., Gillis M., Izard D., Leclerc H. Pseudomonas rhodesiae sp. nov., a new species isolated from natural mineral waters. System. Appl. Microbiol. 19:1996;600-607.
8. Crosa J.H., Brenner D.J., Falkow S. Use of a single-strand specific nuclease for analysis of bacterial and plasmid deoxyribonucleic acid homo- and hetero-duplexes. J. Bacteriol. 115:1973;904-911.
9. Dabboussi F., Hamze M., Elomari M., Verhille S., Baida N., Izard D., Leclerc H. A numerical study of fluorescent Pseudomonas strains isolated from three Lebanese spring waters. J. Eur. Hydrol. 28:1998;311-324.
10. De Ley J. Reexamination of the association between melting point buoyant density and chemical base composition of deoxyribonucleic acid. J. Bacteriol. 101:1970;737-754.
11. De Vos P., DeLey J. Intra- and intergeneric similarities of Pseudomonas and Xanthomonas ribosomal ribonucleic acid cistrons. Int. J. Syst. Bacteriol. 33:1983;487-509.
12. De Vos P., Kersters K., Falsen E., Pot B., Gillis M., Segers P., DeLey J. Comamonas David and Park(1962) gen. nov., nom. rev. emend., and Comamonas terrigena Hugh(1962) sp. nov., nom. rev. Int. J. Syst. Bacteriol. 35:1985;443-453.
13. De Vos P., Van Landshoot A., Segers P., Tytgat R., Gillis M., Bauwens M., Rossau R., Goor M., Pot B., Kersters K., Lizzaraga P., DeLey J. Genotypic relationships and taxonomic localisation of unclassified Pseudomonas and Pseudomonas-like strains by deoxyribonucleic acid ribosomal ribonucleic acid hybridization. Int. J. Syst. Bacteriol. 39:1989;35-49.
14. Edwards U., Rogall T., Blacker H., Emde M., Bottger E. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res. 17:1989;7843-7853.
15. Elomari M., Coroler L., Hoste B., Gillis M., Izard D., Leclerc H. DNA relatedness among Pseudomonas strains isolated from natural mineral waters and proposal of Pseudomonas veronii sp. nov. Int. J. Syst. Bacteriol. 46:1996;1138-1144.
16. Elomari M., Coroler L., Verhille S., Izard D., Leclerc H. Pseudomonas monteilii sp. nov., isolated from clinical specimens. Int. J. Syst. Bacteriol. 47:1997;846-852.
17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39:1985;783-791.
18. Gould W.D., Hagedorn C., Bardinelli T.R., Zablotow R.H. New selective media for enumeration and recovery of fluorescent pseudomonads from various habitats. Appl. Environ. Microbiol. 49:1985;28-32.
19. Grimont P.A.D., Popoff M.Y., Grimont F., Coynault C., Lemelin M. Reproducibility and correlation study of three deoxyribonucleic acid hybridization procedures. Curr. Microbiol. 4:1980;325-330.
20. Grimont P.A.D., Vancanneyt M., Lefèvre M., Vandemeulebroecke K., Vauterin L., Brosch R., Kersters K., Grimont F. Ability of biolog-100 systems to reveal the taxonomic diversity of the pseudomonads. System. Appl. Microbiol. 19:1996;510-527.
21. Hoeniger J.F.M. Development of flagella by Proteus mirabilis. J. Gen. Microbiol. 40:1965;29-33.
22. Holmes B., Steigerwalt A.G., Weaver R.E., Brenner D.J. Chryseomonas luteola comb. nov. and Flavimonas oryzihabitans gen. nov., comb. nov., Pseudomonas-Like species from human clinical specimens and formely known respectively as groups Ve-1 and Ve-2. Int. J. Syst. Bacteriol. 37:1987;245-250.
23. Kersters K., Ludwig W., Vancanneyt M., DeVos P., Gillis M., Schleifer K.H. Recent changes in the classification of the pseudomonads: an overview. System. Appl. Microbiol. 19:1996;465-477.
24. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:1980;111-120.
25. Leclerc H., Guillot E. Etude de la flore bactérienne de deux sources d'eaux minérales naturelles; caractérisation par les profils de restriction des gènes codant pour les ARN ribosomaux; spécificité et stabilité biologique. Bull. Acad. Natl. M. 176:1992;1491-1504.
26. Meyer O., Stackebrandt E., Auling G. Reclassification of ubiquinone Q-10 containing carboxydotrophic bacteria: transfer of '(Pseudomonas) carboxydovorans' OM5T to Oligotropha gen. nov., as Oligotropha carboxydovorans comb. nov., transfer of '(Alcaligenes) carboxydus' DSM 1086T to Carbophilus gen. nov., as Carbophilus carboxidus comb. nov., transfer of '(Pseudomonas) compransoris' DSM 1231T to Zavarzinia gen. nov., as Zavarzinia compransoris comb. nov., and emended descriptions of the new genera. Syst. Appl. Microbiol. 16:1993;390-395.
27. Moore E.R.B., Mau M., Arnsceidt A., B?Ttger E.C., Hutson R.A., Collins M.D., Van De Peer Y., De Wachter R., Timmis K.N. 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. 19:1996;478-492.
28. Nakagawa Y., Sakane T., Yokota A. Transfer of 'Pseudomonas riboflavina' (Foster1944) a Gram-negative motile rod with long-chain 3-hydroxy fatty acids to Devosia riboflavina gen. nov., sp. nov., nom. Rev. Int. J. Syst. Bacteriol. 46:1996;16-22.
29. Palleroni N.J. Genus I. Pseudomonas Migula237AL (n. m. cons. opin. 5 jud. comm.1952, 237). Krieg N.R, Holt J.G. Bergey's Manual of Systematic Bacteriology vol. 1. 1984;141-199 The Williams and Wilkins Co., Baltimore, MD.
30. Palleroni N.J., Bradbury J.F. Stenotrophomonas a new bacterial genus for Xanthomonas maltophilia (Hugh1990) Swings et al., 1983. Int. J. Syst. Bacteriol. 43:1993;606-609.
31. Palleroni N.J., Kunisawa R., Contopoulou R., Doudoroff M. Nucleic acid homologies in the genus Pseudomonas. Int. J. Syst. Bacteriol. 23:1973;333-339.
32. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425.
33. Segers P., Vancanneyt M., Pot B., Torck U., Hoste B., Dewettinck D., Falsen E., Kersters K., DeVos P. Classification of Pseudomonas diminuta Leifson and Hugh1954 and Pseudomonas vesicularis Büsing Dall and Freytag1953 in Brevundimonas gen. nov., as Brevundimonas diminuta comb. nov. and Brevundimonas vesicularis comb. nov., respectively. Int. J. Syst. Bacteriol. 44:1994;499-510.
34. Stanier R.Y., Palleroni N.J., Doudoroff N. The aerobic pseudomonads: a taxonomic study. J. Gen. Microbiol. 43:1966;159-271.
35. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting positions-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680.
36. Urakami T., Araki H., Oyanagi H., Suzuki K.I., Komogata K. Transfer of Pseudomonas aminovorans (den Dooren de Jong1926) to Aminobacter gen. nov. as Aminobacter aminovorans comb. nov. and description of Aminobacter aganoensis sp. nov. and Aminobacter niigataensis sp. nov. Int. J. Syst. Bacteriol. 42:1992;84-92.
37. Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.L., Moore L.H., Moore W.E.C., Murray R.G.E., Stackbrandt E., Starr M.P., Trüper H.G. Report of the Ad Hoc Committee on the reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37:1987;463-464.
38. Willems A., Busse J., Goor M., Pot B., Falsen E., Jantzen E., Hoste B., Gillis M., Kersters K., Auling G., DeLey J. Hydrogenophaga a new genus of hydrogen-oxidizing bacteria that includes Hydrogenophaga flava comb. nov., (formerly Pseudomonas flava) Hydrogenophaga palleroni (formerly Pseudomonas palleroni) Hydrogenophaga pseudoflava (formerly Pseudomonas pseudoflava and 'Pseudomonas carboxydoflava') and Hydrogenophaga taeniospiralis (formerly Pseudomonas taeniospiralis). Int. J. Syst. Bacteriol. 39:1989;319-333.
39. Willems A., Falsen E., Pot B., Jantzen E., Hoste B., Vandamme P., Gillis M., Kersters K., DeLey J. Acidovorax a new genus for Pseudomonas facilis Pseudomonas delafieldii EF group 13 EF group 16 and several clinical isolates with the species Acidovorax facilis comb. nov., Acidovorax delafieldii comb. nov., and Acidovorax temperans sp. nov. Int. J. Syst. Bacteriol. 40:1990;384-398.
40. Yabuuchi E., Kosako Y., Oyaizu H., Yano I., Hotta H., Hashimoto Y., Ezaki T., Arakawa M. Proposal of Burkholderia gen. nov., and transfer of seven species of the genus Pseudomonas homology group II to the new genus with the type species Burkholderia cepacia (Palleroni and Holmes1981) comb. nov. Microbiol. Immunol. 36:1992;1251-1275.
41. Yabuuchi E., Kosako Y., Yano I., Hotta H., Nishiuchi Y. Transfer of two Burkholderia and an Alcaligenes species to Ralstonia gen. nov.: proposal of Ralstonia pickettii (Ralston Palleroni and Doudor-off1973) comb. nov., Ralstonia solanacearum (Smith 1896) comb. nov., and Ralstonia eutropha (Davis1969) comb. nov. Microbiol. Immunol. 39:1995;897-904.
42. Yabuuchi E., Yano I., Oyaizu H., Hashimoto Y., Ezaki T., Yamamoto H. Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol. Immunol. 34:1990;99-119.