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.

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.

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.

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.

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.

Isolation and characterization of diverse halobenzoate-degrading denitrifying bacteria from soils and sediments.

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.

Taxonomic implications of synthesis of poly-beta-hydroxybutyrate and other poly-beta-hydroxyalkanoates by aerobic pseudomonads.

Whereas poly-beta-hydroxybutyrate (PHB) production by Pseudomonas species is rare, synthesis of medium-chain-length poly-beta-hydroxyalkanoates (mcl-PHAs) other than PHB, has been observed in fluorescent and non-fluorescent species. Contrary to original reports, Pseudomonas corrugata and Pseudomonas ficuserectae accumulate mcl-PHAs and not PHB. The taxonomic implications of these characteristics are discussed.

Description of strain 3CB-1, a genomovar of Thauera aromatica, capable of degrading 3-chlorobenzoate coupled to nitrate reduction.

A Gram-negative bacterium, strain 3CB-1, isolated from a 3-chlorobenzoate enrichment culture inoculated with a sediment sample is capable of degrading various aromatic compounds and halogenated derivatives with nitrate as electron acceptor. Compounds capable of serving as carbon and energy sources include 3-chlorobenzoate, 3-bromobenzoate, 2-fluorobenzoate, 4-fluorobenzoate, benzoate, 3-hydroxybenzoate, 4-hydroxybenzoate, 3-aminobenzoate, protocatechuate, m-cresol and p-cresol. Oxygen, nitrate and nitrite were used as electron acceptors for growth.

Taxonomic characterization of denitrifying bacteria that degrade aromatic compounds and description of Azoarcus toluvorans sp. nov. and Azoarcus toluclasticus sp. nov.

A taxonomic characterization of twenty-one strains capable of degrading aromatic compounds under denitrifying conditions, isolated from ten different geographical locations, was performed on the basis of general morphological and physiological characteristics, cellular fatty acids, DNA base composition, small ribosomal (16S) subunit DNA sequences, whole-cell protein patterns and genomic DNA fragmentation analysis, in addition to DNA similarity estimations using hybridization methods. The collection of strains was subdivided into a number of different groups. A first group, consisting of four strains, could be assigned to the previously described species Azoarcus tolulyticus.

Identification of denitrifier strain T1 as Thauera aromatica and proposal for emendation of the genus Thauera definition.

Bacterial strain, T1, originally isolated by P.J. Evans on the basis of its capacity for toluene degradation under denitrifying conditions, has been classified as Thauera aromatica.

Nitric oxide synthase induction in lines of macrophages from different anatomical sites.

Induction of nitric oxide synthase (iNOS) and nitric oxide (NO) production have been demonstrated using three macrophage cell lines from different anatomical sites, which had been immortalized using a rapid and convenient procedure previously described. Lysis of tumor cells presumably was caused by NO accumulation in the supernatants of cultures of the three cell lines after induction with a mixture of recombinant murine interferon gamma (rMuIFNgamma) and lipopolysaccharide (LPS). Induction by these two biological response modifiers (BRM) caused lysis of tumor cells and was repressed by addition of 1 microM (final concentration) of methyl-L-arginine (MMA) to the mixture during induction of the enzyme.

Prokaryotic diversity and the importance of culturing.

Modern approaches based on the use of molecular techniques presumed to circumvent the need for culturing prokaryotes, fail to provide sufficient and reliable information for estimation of prokaryote diversity. Many properties that make these organisms important members of the living world are amenable to observation only through the study of living cultures. Since current culture techniques do not always satisfy the need of providing a balanced picture of the microflora composition, future developments in the study of bacterial diversity should include improvements in the culture methods to approach as closely as possible the conditions of natural habitats.

Transfer of polychlorophenol-degrading Rhodococcus chlorophenolicus (Apajalahti et al. 1986) to the genus Mycobacterium as Mycobacterium chlorophenolicum comb. nov.

Three independently isolated polychlorophenol-degrading strains of bacteria were characterized on the basis of chemotaxonomic and nutritional characteristics. Previously, these strains were assigned to the species Rhodococcus chlorophenolicus, which was described on the basis of the properties of one of the strains, strain PCP-I(T) (T = type strain) (J. H.

Pseudomonas flavescens sp. nov., isolated from walnut blight cankers.

Two pseudomonad strains that produce a yellow cellular pigment, in addition to a diffusible fluorescent pigment on Kings medium B, were isolated from cankers on walnut trees. Biochemical properties, such as a positive oxidase reaction, a negative arginine dihydrolase reaction, and the production of a fluorescent pigment, in addition to the results of an extensive nutritional characterization study and DNA-DNA hybridization experiments, indicated that these strains belong to a new Pseudomonas rRNA group I species. This conclusion was supported by the results of a determination of the sequence of the PCR-amplified 16S rRNA gene and a comparison with the 16S rRNA genes of other bacterial species.

Genome and fatty acid analysis of Pseudomonas stutzeri.

A genome and fatty acid analysis of 16 Pseudomonas stutzeri reference strains having DNA compositions ranging from 62.2 to 65.5 mol% G+C was performed by pulsed-field gel electrophoresis of XbaI and SpeI macrorestriction fragments and gas chromatography of total cellular fatty acids.

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.

Three novel polyether antibiotics X-14889A, C, and D from a streptomycete. Taxonomy of the producing organism, fermentation production and biological properties of the antibiotics.

Antibiotic X-14889A, C, and D are novel polyether antibiotics related to lysocellin and antibiotic X-14873A. They are produced by a streptomycete isolated from a soil of Wisconsin. The antibiotic X-14889C is active against Gram-positive bacteria and exhibits ionophore property.

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 of Pseudomonas 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.

Quantification of denitrification by strain T1 during anaerobic degradation of toluene.

Strain T1 is a denitrifying bacterium that is capable of toluene degradation under anaerobic conditions. During anaerobic growth on toluene, the specific growth rate of strain T1 was 0.14 h-1.

Novel polyether antibiotics X-14873A, G and H produced by a Streptomyces: taxonomy of the producing culture, fermentation, biological and ionophorous properties of the antibiotics.

Novel polyether antibiotics X-14873A, X-14873G, and X-14873H are produced by the fermentation of Streptomyces sp. X-14873 (ATCC 31679). This report presents taxonomic studies and fermentation conditions for the antibiotic producing culture.

Pseudomonas fluorescens biovar V: its resolution into distinct component groups and the relationship of these groups to other P. fluorescens biovars, to P. putida, and to psychrotrophic pseudomonads associated with food spoilage.

A numerical taxonomic analysis was performed to evaluate the appropriateness of a single biovar designation (biovar V) for all Pseudomonas fluorescens isolates negative for denitrification, levan production and phenazine pigmentation and to determine the relationship of biovar V strains to other taxa within the same Pseudomonas RNA homology group. Seventy-two strains assigned to P. fluorescens biovar V and four strains of P.

Microbial 7alpha-hydroxylation of 3-ketobisnorcholenol.

The transformation of 22-hydroxy-23,24-bisnorchol-4-en-3-one to 7alpha-22-dihydroxy-23,24-bisnorchol-4-en-3-one by Botryodiploida theobromae, Lasiodiplodia theobromae, and various Botryosphaeria strains is described. Factors affecting the reaction were incubation temperature, sonication of the substrate, and addition of 2,2'-dipyridyl, extra carbohydrate, and Amberlite XAD-7. The enzyme responsible for the reaction appeared to be very specific and was not characteristic of all members of the genera listed above.

Microbial products. VIII. Azinothricin, a novel hexadepsipeptide antibiotic.

Azinothricin was isolated from the culture filtrate of Streptomyces sp. X-14950 in crystalline form. It represents a new type of hexadepsipeptide antibiotic as it contains a 19-membered cyclodepsipeptide ring composed of six unusual amino acids and bearing a novel C21 side chain.