Norberto J. Palleroni

The Aerobic Pseudomonads a Taxonomic Study

SUMMARY A collection of 267 strains, representing many of the principal biotypes among aerobic pseudomonads, has been subjected to detailed study, with particular emphasis on biochemical, physiological and nutritional characters. A total of 146 different organic compounds were tested for their ability to serve as sources of carbon and energy. Other characters that were studied included : production of extracellular hydrolases; nitrogen sources and growth factor requirements H-chemolithotrophy; denitrifying ability; pigment production; ability to accumulate poly-p-hydroxybutyrate as a cellular reserve material; biochemical mechanisms of aromatic ring cleavage; and nature of the aerobic electron transport system. The resultant data have revealed many hitherto unrecognized characters of taxonomic significance. As a consequence, it has become possible to recognize among the biotypes examined a limited number of species which can be readily and clearly distinguished from one another by multiple, unrelated phenotypic differences.

Nucleic Acid Homologies in the Genus Pseudomonas

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 to 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.

Stenotrophomonas, a New Bacterial Genus for Xanthomonas maltophilia (Hugh 1980) Swings et al. 1983

In consideration of the criticisms of the transfer of Pseudomonas maltophilia to the genus Xanthomonas proposed by J. Swings, P. De Vos, M. Van den Mooter, and J. De Ley (Int. J. Syst. Bacteriol. 33:409-413, 1983), a new generic name is created for this taxon. The name Stenotrophomonas is here proposed for the new genus, which includes a single species, Stenotrophomonas maltophilia. This proposal restores the genus Xanthomonas to its former definition (J. Bradbury, p. 199-210, in N. R. Krieg and J. G. Holt, ed., Bergeys Manual of Systematic Bacteriology, 1984) The arguments on which this proposal is based are presented.

Isolation and Characterization of Diverse Halobenzoate-Degrading Denitrifying Bacteria from Soils and Sediments

ABSTRACT Denitrifying bacteria capable of degrading halobenzoates were isolated from various geographical and ecological sites. The strains were isolated after initial enrichment on one of the monofluoro-, monochloro-, or monobromo-benzoate isomers with nitrate as an electron acceptor, yielding a total of 33 strains isolated from the different halobenzoate-utilizing enrichment cultures. Each isolate could grow on the selected halobenzoate with nitrate as the terminal electron acceptor. The isolates obtained on 2-fluorobenzoate could use 2-fluorobenzoate under both aerobic and denitrifying conditions, but did not degrade other halobenzoates. In contrast, the 4-fluorobenzoate isolates degraded 4-fluorobenzoate under denitrifying conditions only, but utilized 2-fluorobenzoate under both aerobic and denitrifying conditions. The strains isolated on either 3-chlorobenzoate or 3-bromobenzoate could use 3-chlorobenzoate, 3-bromobenzoate, and 2- and 4-fluorobenzoates under denitrifying conditions. The isolates were identified and classified on the basis of 16S rRNA gene sequence analysis and their cellular fatty acid profiles. They were placed in nine genera belonging to either the α-, β-, or γ-branch of theProteobacteria, namely, Acidovorax,Azoarcus, Bradyrhizobium,Ochrobactrum, Paracoccus,Pseudomonas, Mesorhizobium,Ensifer, and Thauera. These results indicate that the ability to utilize different halobenzoates under denitrifying conditions is ubiquitously distributed in theProteobacteria and that these bacteria are widely distributed in soils and sediments.

Siderophore Typing, a Powerful Tool for the Identification of Fluorescent and Nonfluorescent Pseudomonads

ABSTRACT 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.

Taxonomy of the aerobic pseudomonads: the properties of the Pseudomonas stutzeri group.

SUMMARY: Strains of Pseudomonas stutzeri and related denitrifying bacteria were compared in their phenotypic properties and mean deoxyribonucleic acid (DNA) base composition. On the basis of this comparison and of in vitro DNA hybridization experiments, it was concluded that, using practical diagnostic tests, no more than two nomenspecies can be recognized within the group. One, P. stutzeri, was extremely variable in phenotypic characteristics and in DNA base composition; we included in it the strains previously assigned to P. stanieri. The other was a new species, P. mendocina Palleroni, which was more homogeneous in phenotypic characters, and in DNA base composition and homology. The comparative properties of known denitrifying pseudomonads are tabulated.

Taxonomy of the aerobic pseudomonads: Pseudomonas cepacia, P. marginata, P. alliicola and P. caryophylli

SUMMARY: On the basis of phenotypic characterization and DNA-DNA homology studies of strains of phytopathogenic Pseudomonas species, it is concluded that P. cepacia is so similar to P. multivorans that the latter name should be regarded as a synonym. On similar grounds, P. alliicola appears to be a synonym of P. marginata. P. caryophylli is a readily distinguishable species. From the DNA-DNA hybridization studies all of these species seem to be related to each other and to the animal pathogens P. pseudomallei and P. mallei.

Introduction to the Family Pseudomonadaceae

The pseudomonads are a very large and important group of Gram-negative bacteria. Members of the group are found in substantial numbers as free-living saprophytes in soils, fresh water, marine environments, and many other natural materials, or in association with plants or animals as agents of diseases.

Pseudomonas classification : a new case history in the taxonomy of Gram-negative bacteria

Various criteria that have been used in the development of a system of classification ofPseudomonas species, as well as in the precise circumscription of the genus on phenotypic and molecular bases, are discussed.Pseudomonas taxonomy has transcended its own limits by suggesting a general strategy for the definition of taxonomic hierarchies at and above the genus level. A selection of studies on the biochemical and physiological properties of members of the genus is critically examined in relation to the current taxonomic scheme as a frame of reference.

Characterization of halobenzoate-degrading, denitrifying Azoarcus and Thauera isolates and description of Thauera chlorobenzoica sp. nov.

The taxonomic relationships of Azoarcus and Thauera isolates in the beta-subclass of the Proteobacteria capable of degrading fluoro-, chloro- or bromobenzoate under denitrifying conditions were analysed. A detailed classification of these strains was performed using a polyphasic approach, which included studies on morphology, phenotypic characterization, fatty acid analysis, 16S rRNA gene sequence analysis, 16S rRNA gene mapping (ribotyping) and DNA-DNA hybridization. The analyses of fatty acids and 16S rRNA gene sequencing differentiated strains 2FB2, 2FB6 and 4FB10 as new members of the genus Azoarcus and strains 4FB1, 4FB2, 3CB2, 3CB3 and 3BB1 as new members of the genus Thauera. DNA-DNA hybridization experiments established that strains 2FB2, 2FB6 and 4FB10 belong to the species Azoarcus tolulyticus. Strains 3CB2 and 3CB3 were assigned to the species Thauera aromatica on the basis of DNA-DNA hybridization and ribotyping experiments. Strains 4FB1, 4FB2 and 3BB1 showed close relatedness with strain 3CB-1T, previously described as T. aromatica genomovar chlorobenzoica. This group of strains is clearly differentiated from the species T. aromatica on the basis of 16S rRNA sequence analysis, DNA homology and ribotyping analysis. Strains 3CB-1T, 4FB1, 4FB2 and 3BB1 are proposed as members of the new species Thauera chlorobenzoica sp. nov., strain 3CB-1T (= ATCC 700723T) being the type strain.