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

• Published in: International journal of systematic and evolutionary microbiology Vol. 50; no. 4; pp. 1629 - 1639
• Main Authors: Guasp, C, Moore, ERB, Lalucat, J, Bennasar, A
• Format: Journal Article
• Language: English
• Published: Reading Soc General Microbiol 01-07-2000; Society for General Microbiology
• Subjects: Bacteriology; Biological and medical sciences; DNA, Bacterial - analysis; DNA, Ribosomal Spacer - analysis; Environmental Microbiology; Fundamental and applied biological sciences. Psychology; Genotype; Humans; internal transcribed spacer; Microbiology; Nucleic Acid Hybridization; Phylogeny; Polymerase Chain Reaction; Polymorphism, Restriction Fragment Length; Pseudomonas; Pseudomonas - classification; Pseudomonas - genetics; Pseudomonas stutzeri; RNA, Ribosomal, 16S - analysis; RNA, Ribosomal, 23S - analysis; Sequence Homology, Nucleic Acid; Systematics; Pseudomonadales; Taxonomy; Internal transcribed spacer region; Ribosomal DNA; Genotype; Taxonomic character; Species specificity; Phylogeny; Pseudomonas stutzeri; Restriction fragment length polymorphism; Bacteria; Pseudomonadaceae; Structural analysis
• ISSN: 1466-5026; 1466-5034
• DOI: 10.1099/00207713-50-4-1629

C Guasp, ERB Moore, J Lalucat and A Bennasar
Microbiologia, Departament de Biologia, Institut Mediterrani d'Estudis Avancats (CSIC-UIB), Palma de Mallorca, Spain
Bacteria identified and classified as Pseudomonas stutzeri, on the basis of
traditional criteria, are recognized to be markedly heterogeneous, such
that a systematic phenotypic characterization has not been correlated with
genotypic groupings (i.e. genomovars) based upon DNA--DNA similarities. The
internally transcribed 16S--23S rDNA spacer (ITS1) regions of P. stutzeri
were analysed with respect to the ability of these nucleic acid regions to
differentiate and identify the genomic groups (i.e. genomovars) of P.
stutzeri. The ITS1s of 34 strains of P. stutzeri were amplified by PCR and
the PCR product was subjected to RFLP analysis, which allowed the
differentiation and identification of the strains to their respective
genomovars. Sequence determination and analysis of ITS1s supported further
the results obtained by RFLP, i.e. nucleotide signatures were identified in
strains belonging to different genomovars. The ITS1s of all strains of P.
stutzeri contained the tandem tRNA(Ile)/tRNA(Ala) genes and did not exhibit
distinct sequence heterogeneity between different operons of a strain.
Phylogenetically informative variable sites were located, exclusively, in
non-coding regions. The results of the RFLP and sequence analysis of ITS1s
supported and correlated with the phylogenetic relationships estimated from
16S rRNA gene sequence comparisons and DNA--DNA hybridizations, offering an
alternative tool for genomovar and species differentiation.