Genotypic Relationships and Taxonomic Localization of Unclassified Pseudomonas and Pseudomonas-Like Strains by Deoxyribonucleic Acid:Ribosomal Ribonucleic Acid Hybridizations

Abstract

The deoxyribonucleic acid (DNA):ribosomal ribonucleic acid (rRNA) hybridization technique was used to reveal the relationships and taxonomic positions of an additional 83 strains belonging to 43 saprophytic or pathogenic Pseudomonus species and 29 named and unnamed Pseudomonus-like strains. The DNA:rRNA hybrids were characterized by the following two parameters: (i) the temperature at which one-half of the hybrid was eluted and (ii) the percentage of rRNA binding (the amount of rRNA bound per 100 pg of filter-fixed DNA). We also used, for a limited number of strains, numerical analysis of carbon assimilation tests to delineate the finer taxonomic relationships of organisms. Of the 83 strains examined, 78 could be definitely assigned either to an rRNA branch or to an rRNA superfamily within the Proteobucteriu. Only 25 of our strains belong in the genus Pseudomonus sensu strict0 (our PseudomonusJluorescens rRNA branch). In general, about two-thirds of the named Pseudomonas species have been misclassified and are distributed over at least seven genera all through the Proteobacteriu. These organisms need to be reclassified and generically renamed according to their phylogenetic rglationships. However, more detailed phenotypic and genotypic studies are necessary before definite nomenclatural proposals can be made. A comprehensive list of the phylogenetic affiliations of the Pseudomonus species is included.From the original creation of Pseudomonas Migula 1894 until now, this genus has been a dumping ground for incompletely described, aerobic, polarly flagellated, gram-negat h e , rodlike bacteria. In the past and even today organisms isolated from a heterogeneous variety of ecological niches were and still are classified without sufficient grounds as new Pseudomonas species. One of the reasons for this situation is the incomplete generic definition.In the United States, the Berkeley group has reported in several papers (42,43,48) on the taxonomy of the genus Pseudomonas. The several hundred strains included in the important study of these workers involved only a relatively small number of species. Their new generic definition and subdivision of Pseudomonas was reflected in Bergey 's Manual of Determinative Bacteriology, 8th ed. (20). In an important reduction in the number of Pseudomonas species, more than 90% of the clinical, phytopathological, and saprophytic pseudomonads were relegated to four addenda to the genus Pseudomonas and were thus only marginally retained in this genus (20). Most of these organisms have no clear taxonomic status because their names were not retained on the Approved Lists of Bacterial Names (38, 46) nor were they on Validation Lists 17 to 23 (24-30). In Bergey's Manual of Systematic Bacteriology , Palleroni (41) listed 62 of these species in Section V of the genus Pseudomonas, although their natural relationships with other taxa are still largely unknown.We have shown in the past (11-15, 21, 45, 51, 54, 55) that the deoxyribonucleic acid (DNA):ribosomal ribonucleic acid (rRNA) hybridization...

Transfer of Pseudomonas plantarii and Pseudomonas glumae to Burkholderia as Burkholderia spp. and Description of Burkholderia vandii sp. nov.

“…P, avenae and P. cattleyae were included in section V of the genus Pseudomonas in Bergey's Manual of Systematic Bacteriology (28). The results of rRNA-DNA hybridization experiments performed with P. avenae and P. cattleyae (9,11,55) demonstrated that these bacteria belong in the Pseudomonas acidovorans rRNA complex in rRNA superfamily I11 (11,28). In 1992, Willems et al (54) proposed the transfer of P. avenue and P. cattleyae to the new genus Acidovorax (53) as Acidovorax avenue subsp.…”

“…avenae and Acidovorax avenae subsp. cattleyae had the same chemotaxonomic characteristics and could be distinguished clearly from the genus Pseudomonas sensu strict0 (P. jluorescens rRNA branch [ll]), Burkholderia species, Comamonas species, and Hydrogenophaga species on the basis of phenotypic characteristics (10,17,28,35,38,44), ubiquinone systems, DNA base compositions, DNA-DNA homology data, and rRNA-DNA hybridization data (9,11,52,53) (Table 9). Minimal characteristics for differentiating the genera Burkholderia, Acidovorax, Comamonas, Hydrogenophaga, and Pseudomonas are shown in Table 9.…”

Phylogenetic relationships of Xylella fastidiosa strains from different hosts, based on 16S rDNA and 16S-23S intergenic spacer sequences.

“…A striking similarity of 95 % was found between the Xylella fastidiosa 16S rDNA sequence and that of Pseudomonas boreopolis, a bacterium isolated from the soil. There is, however, some uncertainty about the taxonomic position of P. boreopolis, which could be assigned to the genus Xanthomonas on the basis of DNA-rDNA hybridization (De Vos et al, 1989). The similarity levels between Xanthomonas species and Xylella fastidiosa strains ranged from 94n3 to 96n1% and the highest similarity value was found between Xanthomonas campestris and strain PE.PLS.…”

Temperature-sensitive production of azoverdin, the pyoverdin-like sid rophore of Azomonas macrocytogenes ATCC 12334

“…(Tchan & New, 1984) and the group I fluorescent Pseudomonas spp. (De Smedt et al, 1980;De Vos et al, 1989), also produces an extracellular fluorescent compound when cells are cultured under ironlimited conditions (Johnstone, 1957 ;Thompson & Skerman, 1979). Although D. B. Johnstone and co-workers first suggested similarities between the fluorescent compounds elaborated by A .…”