Phylogenetic analysis and siderotyping as useful tools in the taxonomy of Pseudomonas stutzeri: description of a novel genomovar.

An examination of the results of phylogenetic analyses based on the sequences of fragments of the 16S rRNA, gyrB and rpoD genes, and the discrimination of genomovars based on siderophore diversity within the genus Pseudomonas, has added important taxonomic tools in the characterization of Pseudomonas stutzeri. Eighteen reference strains, nine newly identified hydrocarbon-degrading strains and three strains showing relevant physiological characteristics of P. stutzeri, together with the type strains of four related species, were included in the study. A novel genomovar within the species is described. A summary of the methodology used in these studies and the results of our attempts to define a solid internal subdivision of this important species within the genus Pseudomonas are presented and discussed.

Biology of Pseudomonas stutzeri.

Pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. Over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. The species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many strains have natural transformation properties, making it relevant for study of the transfer of genes in the environment; several strains are able to fix dinitrogen; and others participate in the degradation of pollutants or interact with toxic metals. This review considers the history of the discovery, nomenclatural changes, and early studies, together with the relevant biological and ecological properties, of P. stutzeri.

Hydrocarboniphaga effusa gen. nov., sp. nov., a novel member of the gamma-Proteobacteria active in alkane and aromatic hydrocarbon degradation.

Novel alkane-degrading strains of bacteria were isolated from soil contaminated with fuel oil from a leaking underground tank in New Jersey, USA. Two phenotypically similar strains (designated AP102 and AP103T) possessed 16S rRNA sequences unique among the majority of known hydrocarbon-degrading bacteria. The 16S rRNA sequences showed a moderate but distant relationship to the genus Nevskia and a substantial similarity to strains that had previously been isolated for growth on phenol (in Japan) and on toluene (in Canada) by other researchers. The hydrocarbon-degrading strains from Japan, Canada and New Jersey showed no resemblance to the typical morphology of Nevskia but did share a striking similarity among themselves in cell morphology, in the unusual appearance of colonies on various solid media and in various physiological properties. A full taxonomic analysis was performed, including DNA-DNA hybridization and nutritional screening with 117 organic compounds as sole sources of carbon and energy. The strains are active in the degradation of important environmental pollutants, and their phenotypic, physiological, metabolic and genomic properties suggest that they are members of a novel taxon in the gamma-Proteobacteria, for which the name Hydrocarboniphaga gen. nov. is proposed, with the single species Hydrocarboniphaga effusa sp. nov. The type strain is AP103T (=ATCC BAA-332T=DSM 16095T).

Prokaryote taxonomy of the 20th century and the impact of studies on the genus Pseudomonas: a personal view.

The taxonomic studies on the genus Pseudomonas performed in the Department of Bacteriology of the University of California at Berkeley played a significant rôle in the development of modern prokaryote taxonomy, which started in the 1960s. This impact was due to a revival of the method of den Dooren de Jong for the nutritional analysis of chemoorganotrophic organisms and, mostly, to the introduction of the determination of rRNA as a method of taxonomic analysis. While the introduction of the nutritional studies facilitated the characterization of Pseudomonas and other chemoorganotrophs, the applicability of the rRNA studies extended to all prokaryotes.

Siderophore typing, a powerful tool for the identification of fluorescent and nonfluorescent pseudomonads.

A total of 301 strains of fluorescent pseudomonads previously characterized by conventional phenotypic and/or genomic taxonomic methods were analyzed through siderotyping, i.e., by the isoelectrophoretic characterization of their main siderophores and pyoverdines and determination of the pyoverdine-mediated iron uptake specificity of the strains. As a general rule, strains within a well-circumscribed taxonomic group, namely the species Pseudomonas brassicacearum, Pseudomonas fuscovaginae, Pseudomonas jessenii, Pseudomonas mandelii, Pseudomonas monteilii, "Pseudomonas mosselii," "Pseudomonas palleronii," Pseudomonas rhodesiae, "Pseudomonas salomonii," Pseudomonas syringae, Pseudomonas thivervalensis, Pseudomonas tolaasii, and Pseudomonas veronii and the genomospecies FP1, FP2, and FP3 produced an identical pyoverdine which, in addition, was characteristic of the group, since it was structurally different from the pyoverdines produced by the other groups. In contrast, 28 strains belonging to the notoriously heterogeneous Pseudomonas fluorescens species were characterized by great heterogeneity at the pyoverdine level. The study of 23 partially characterized phenotypic clusters demonstrated that siderotyping is very useful in suggesting correlations between clusters and well-defined species and in detecting misclassified individual strains, as verified by DNA-DNA hybridization. The usefulness of siderotyping as a determinative tool was extended to the nonfluorescent species Pseudomonas corrugata, Pseudomonas frederiksbergensis, Pseudomonas graminis, and Pseudomonas plecoglossicida, which were seen to have an identical species-specific siderophore system and thus were easily differentiated from one another. Thus, the fast, accurate, and easy-to-perform siderotyping method compares favorably with the usual phenotypic and genomic methods presently necessary for accurate identification of pseudomonads at the species level.