Nucleic Acid Homologies in the Genus Pseudomonas

Abstract

On the basis of ribosomal ribonucleic acid homologies, the genus Pseudomonas can be divided into at least five distinct groups, some of which are as distantly related t o each other as they are to Escherichia coli. One of these groups contains members of the genus Xanthomonas. The data presented support and extend the previous grouping based on deoxyribonucleic acid homologies and support the current view that the portion of the genome coding for ribosomal ribonucleic acid is more conserved in the course of evolution than the bulk of the genome.For about nine years our laboratory has been largely involved in taxonomic studies of the genus Pseudomonas. Our first approach was the phenotypic characterization of a large number of strains using mainly nutritional characters. On the basis of phenotypic resemblance, we recognized several "species groups," comprised of what we regarded as recognizable species. Below the specific rank, we further recognized a number of "biotypes," some of which had been previously described as species, and many of which may deserve specific rank (14). Deoxyribonucleic acid (DNA)-DNA hybridization experiments generally supported our conclusions based on phenotypic data but showed that some of the species and biotypes were quite heterogeneous with respect to DNA homology. It was also found that some species groups were sufficiently closely related to each other t o be united in a larger DNA homology complex. For example, the "P. fluorescens complex" was found to contain not only the "fluorescent group" but also the nonfluorescent pseudomonads that had been assigned to the "alcaligenes" and "stutzeri" groups ( 10, 14). Our studies have been reviewed recently (9).To pursue further our studies on bacterial phylogeny and speciation, we have resorted to ribosomal ribonucleic acid (rRNA)-DNA hybridizations among selected members of the various DNA homology groups, and included three species of Xanthomonas in the studies. The results are reported in the present paper. MATERIALS AND METHODSBacterial strains. The bacterial strains used in the presently described experiments are numbered as in our previous publications (1,2,4,7,8,(10)(11)(12)14). Reparation of rRNA. For the preparation of unlabeled rRNA, most strains were grown in a medium containing 0.033 M K-Na phosphate buffer, pH 6.8; (NH,), SO,, 0.1%; asparagine, 0.2%; yeast extract, 0.5%; Hutner mineral base (3), 10 ml per liter. For the growth of P. rnaltophilia, DL-sodium lactate was substituted for asparagine. P. saccharophila was grown in a medium containing 0.033 M K-Na phosphate buffer, pH 6.8; NH,Cl, 0.1%; MgSO, 07 H,O, 0.05%; ferric ammonium citrate, 0.005%; CaCl, , 0.0005%; and sodium succinate, 0.2%. For the growth of P. diminuta, the same basal medium was used as for P. saccharophila except that succinate was replaced by asparagine and the essential growth factors (1) were added. The cultures were grown at 30 C on a rotary shaker. The cells were suspended in 0.02 M tris-(hydroxymethy1)aminomethane (Tris)-hydrochloride buffer, pH 7....

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

“…In our first paper on Pseudomonas (14), we confirmed in this genus sensu Doudoroff and Palleroni (20) five different rRNA branches. These branches correspond extremely well with the Palleroni rRNA homology groups (41,43), although the latter were derived from a very small number of strains. However, we proved that these groups are genotypically too far removed from each other to be united in a single genus; furthermore, we established their exact relationship with other gram-negative genera (14).…”

“…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.…”

“…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.…”

Intraspecific Variation and Interspecific Differences in the Bacterial and Fungal Assemblages of Blue Tit (Cyanistes caeruleus) and Great Tit (Parus major) Nests

“…Because atypical strains of fluorescent Pseudomonas spp. in ribosomal Ribonucleic Acid (rRNA) similarity group 1 [43] can occasionally be confused using FAME analysis [42], identifications of these isolates were verified by growth at high (42) and low (3C) temperatures and by their ability to hydrolyse gelatin [25].…”

Towards an Improved Taxonomy of Xanthomonas

“…Because of its economic importance, this genus has been subjected to many taxonomic and determinative studies. DNA-rRNA hybridizations (4, 17) have revealed that the genus constitutes a separate rRNA branch in the gamma taxon of the Proteobacteria (sensu Stackebrandt et al [21]). In Bergey's Manual of Systematic Bacteriology, the genus is divided into the following five species (1): Xanthomonas albilineans, Xanthomonas ampelina, Xanthomonas axonopodis, Xanthomonas campestris (type species), and Xanthomonas fragariae.…”