Phylogenetic analysis of the coryneform bacteria by 5S rRNA sequences.

Nucleotide sequences of 5S rRNAs from 11 coryneform bacteria were determined. These were the type strains of Corynebacterium glutamicum, Corynebacterium xerosis, Brevibacterium linens, Arthrobacter globiformis, Cellulomonas biazotea, Aureobacterium testaceum, Curtobacterium citreum, Pimelobacter simplex, and Caseobacter polymorphus and representative strains of "Corynebacterium aquaticum" and Corynebacterium xerosis. A phylogenetic tree constructed from the sequences of these bacteria and published sequences indicated that the coryneform bacteria consist of a distinct eubacterial branch together with Streptomyces and Micrococcus spp. These bacteria could be further divided into four subgroups.     

Isoprenoid quinones in the classification of coryneform and related bacteria.

Menaquinones were the only isoprenoid quinones found in 85 of the 95 coryneform bacteria examined. Dihydromenaquinones having nine isoprene units were the main components isolated from Corynebacterium bovis, from other glutamic acid-producing strains, and from Arthrobacter globiformis and related species. Dihydromenaquinones with eight isoprene units were found in Brevibacterium linens, the remaining Corynebacterium species and strains probably belonging to the genus Rhodococcus. Tetrahydromenaquinones with eight isoprene units were found in Arthrobacter simplex and Arthrobacter tumescens, and with nine isoprene units in Cellulomonas and Oerskovia. Kurthia and Curtobacterium were characterized by menaquinones with seven and nine isoprene units, respectively, and Microbacterium lacticum and Corynebacterium aquaticum had comparable amounts of menaquinones with 10 and 11 isoprene units. Strains received as Brevibacterium leucinophagum, Corynebacterium autotrophicum, Corynebacterium nephridii, Mycobacterium flavum, Mycoplana rubra and Protaminobacter ruber contained uniquinones as their sole isoprenoid quinones. The isoprenoid quinone data correlate well with major trends in coryneform taxonomy and are of value in the classification of coryneform and related bacteria.     

Molecular identification and differentiation of Brevibacterium species and strains

Amplified ribosomal DNA restriction enzyme analysis (ARDRA), pulsed field gel electrophoresis (PFGE) and ribotyping were used to differentiate among 24 strains of Brevibacterium linens, Brevibacterium casei and Brevibacterium epidermidis obtained from type culture collections or isolated from various smear ripened cheeses. ARDRA was applied to the 16S rDNA. B. linens was shown to be a quite heterogenic group with 2 to at least 4 copies of rrn operons per strain with aberrant nucleotide sequences. AccI gave genus specific restriction patterns and was used to separate Brevibacterium from Corynebacterium species. The expected species specificity of TaqI applied to B. linens type culture strains, but not to all strains isolated from cheese. By AvaI restriction, B. casei and B. linens were differentiated from B. epidermidis and the orange pigmented Arthrobacter casei, a new species of coryneform bacteria; by XmnI restriction, B. linens and B. epidermidis were differentiated from B. casei. One of 4 B. linens genotypes could not be distinguished from B. casei by this method. Here, the typical orange B. linens pigments were used for classification, which was confirmed by partial sequencing of the 16S rDNA.     

Arthrobacter siderocapsulatus isolated from lake water]

Two microbial strains have been isolated from lake water. The strains oxidize ferrous compounds and manganese. By the structure of microcolonies and the character of deposited oxides of these metals, the strains are identical to the genus Siderocapsa. However, according to their growth cycle and some morpho-physiological characteristics, they were included into the genus Arthrobacter (Corynebacteriaceae). Since these microorganisms differ, by their cultural and morpho-physiological properties, from other species of this genus, they were classed as a new species. Arthrobacter siderocapsulatus nov. sp.     

The Cell Wall Composition and Distribution of Free Mycolic Acids in Named Strains of Coryneform Bacteria and in Isolates from Various Natural Sources

The major cell wall amino acids and sugars in 177 strains of coryneform bacteria were determined using a 'rapid'method. Representatives were examined for free mycolic acids and the oxygen requirements of all strains were determined. Included were named strains, most of which were labelled Arthrobacter, Brevibacterium, Cellulomonas, Corynebacterium or Microbacterium , and a similar number of unnamed isolates from various natural sources. Strains which contained meso -diaminopimelic acid (DAP) were divided into four groups according to their oxygen requirements, the wall sugars and the occurrence and nature of free mycolic acids. Group 1 strains were mainly facultatively anaerobic and contained arabinose and mycolic acids of the Corynebacterium type. They were considered to be members of Corynebacterium sensu stricto and included Cor. diphtheriae and related animal parasites, Microbact. flavum , and Cor. glutamicum and similar species. Group 2 strains were aerobic, contained arabinose and mycolic acids of the 'rhodochrous'type and were considered members of the ' rhodochrous 'complex. Group 3 strains were aerobic, contained ribose and no mycolic acids. Most were Br. linens strains from cheese but a few, possibly related strains, were from other habitats. Group 4 strains were aerobic and contained neither a pentose sugar nor mycolic acids and were of unknown taxonomic status. Most remaining strains contained lysine or ornithine in the wall and smaller numbers contained L-DAP or diaminobutyric acid; none contained mycolic acids. The chemotaxonomic data are discussed in relation to recent numerical taxonomic studies of coryneform bacteria.     

The Bacteria in an Antarctic Peat

S ummary : Of a total of 119 strains of bacteria from 3 depths in an acid peat on Signy Island, S. Orkney, 52% belonged to the genus Brevibacterium. Twelve other genera were recorded of which numerically the most important were Arthrobacter, Cellulomonas, Kurthia and Micrococcus. 62% of the collection were psychrophilic, but only 4 strains were obligate psychrophiles. No pattern could be established for the various genera from different depths. The fine structure of an obligately psychrophilic pleomorphic rod from the peat is illustrated and discussed.     

Arthrobacter subterraneus sp. nov., isolated from deep subsurface water of the South Coast of Korea

Strain CH7T, a pale yellow-pigmented bacterium and new isolate from deep subsurface water of the South Coast of Korea, was subjected to a polyphasic taxonomic study. CH7T grew between 5 and 37 degrees C, pH 5.3-10.5, and tolerated up to 13% NaCl. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain CH7T was associated with the genus Arthrobacter and phylogenetically closely related to the type strains Arthrobacter tumbae (99.4%) and Arthrobacter parietis (99.1%). However, DNA-DNA hybridization experiments revealed 2.1% and 12% between strain CH7T and Arthrobacter tumbae and Arthrobacter parietis, respectively. Thus, the phenotypic and phylogenetic differences suggested that CH7T should be placed in the genus Arthrobacter as a novel species, for which the name Arthrobacter subterraneus sp. nov. is proposed. In addition, the type strain for the new species is CH7T (=KCTC 9997T=DSM 17585T).     

Isolation and Characterization of Cellulolytic Bacteria from Activated Sludge

Cellulolytic aerobic bacteria were isolated from activated sludge systems. Of the media tested for enumeration, only filter paper media gave reliable counts. Five isolates were studied further for characterization. It was found that one strain (DK) belonged to the genus Cellulomonas. The other four strains expressed similarity to the genus Pseudomonas. The different characteristics that were studied, however, do not permit them to be identified with any recognized species. Based on certain characters we believe that they are alcaligenes-like pseudomonads.     

Peptidoglycantyp und Zusammensetzung der Zellwandpolysaccharide vonCellulomonas cartalyticum und einigen coryneformen Organismen

Cellulomonas cartalyticum was found to contain a peptidoglycan type different from that of the other species ofCellulomonas. The diamino acid is lysine instead of ornithine and the interpeptide bridge consists ofd-Asp-d-Ser. The same peptidoglycan type occurs inCorynebacterium manihot, Brevibacterium liticum andArthrobacter luteus. These non cellulolytic organisms are most likely not closely related withCellulomonas cartalyticum, as indicated by the very different G+C content of their DNA, although they formed a narrow cluster includingC. cartalyticum when numeric taxonomical methods were applied.

     

Numerical classification of some Rhodococci, Corynebacteria and related organisms

Nineteen strains of Corynebacterium sensu stricto, 23 received as Corynebacterium equi or Rhodococcus equi, marker cultures of Arthrobacter, Brevibacterium, Bacterionema matruchotii, Cellulomonas flavigena, Kurthia zopfii, Listeria denitrificans, Microbacterium lacticum, Rhodococcus rubropertinctus and 88 representatives of Mycobacterium, Nocardia, Rhodococcus and the 'aurantiaca' taxon were the subject of numerical phenetic analyses using 92 characters. The data were examined using the simple matching (SSM) and Jaccard (SJ) coefficients and clustering was achieved using the average linkage algorithm. With a single exception, strains containing meso-diaminopimelic acid, arabinose, galactose and mycolic acids were recovered in five aggregate clusters corresponding to Corynebacterium sensu stricto, Mycobacterium, Nocardia, Rhodococcus and the 'aurantiaca' taxon. Most of the Corynebacterium (Rhodococcus) equi strains formed a good taxospecies which included the type strain of Corynebacterium hoagii. The numerical data, and the results of earlier chemical and genetical studies, also provide sufficient evidence for the transfer of Bacterionema matruchotii to Corynebacterium sensu stricto as Corynebacterium matruchotii comb.nov. and for the recognition of Rhodococcus globerulus sp.nov. for some strains previously classified as Rhodococcus rubropertinctus (Hefferan) Goodfellow & Alderson. The classification of the remaining marker strains correlates well with other major developments in coryneform taxonomy.     

Reclassification of two strains of Arthrobacter oxydans and proposal of Arthrobacter nicotinovorans sp. nov.

Arthrobacter oxydans DSM 419 and DSM 420 have chemical and microbiological properties that are consistent with assignment to the genus Arthrobacter. Both organisms have the lysine-alanine-threonine-alanine peptidoglycan type. DNA-DNA pairing studies indicated that A. oxydans DSM 419 should be reclassified as Arthrobacter ureafaciens and that A. oxydans DSM 420T forms the nucleus of a distinct genomic species. We propose that A. oxydans DSM 420 should be reclassified as Arthrobacter nicotinovorans sp. nov. The type strain is strain DSM 420.     

Phylogenetic Relationships of Species of the Genus Kluyveromyces van der Walt (Saccharomycetaceae) Deduced from the Partial Sequences of 18S and 26S Ribosomal RNAs

In order to clarify the phylogenetic relationships of the species classified in the genus Kluyveromyces (Saccharomycetaceae), three partial base sequences of 18S and 26S rRNAs of eighteen strains were determined. The regions determined of the strains corresponded to positions 1451 through 1618 (168 bases) of 18S rRNA and to positions 1611 through 1835 (225 bases) and 493 through 622 (130 bases) of a strain (IFO 2376) of Saccharomyces cerevisiae. The analyses of the partial base sequences suggested that the genus Kluyveromyces is phylogenetically heterogeneous, ranging from the strains that are quite close to the strain of S. cerevisiae to the strains that are distinct enough to be classified in genera separate from the genus Saccharomyces. From our sequence data, we concluded that the extent of the genus Kluyveromyces should be restricted to only one species, K. polysporus, the type species of the genus. Kluyveromyces phaffii was also distinct enough to deserve another genus. Kluyveromyces cellobiovorus was not close to any of the strains of Kluyveromyces species examined, and should be excluded from the genus. Most of the strains of the species examined were fairly close to the strain of S. cerevisiae.     

Three new species of brevibacteria--Brevibacterium antiquum sp. nov., Brevibacterium aurantiacum sp. nov. and Brevibacterium permense sp. nov

This work deals with the taxonomic study of 12 orange-pigmented bacteria isolated from permafrost sediments, rice plots, and soils contaminated with wastes from the chemical and salt industries, which were assigned to the genus Brevibacterium on the basis of phenotypic characteristics, as well as of some strains described previously as Brevibacterium linens. The study revealed three genomic species, whose members and the type strains of the closest species of Brevibacterium had DNA similarity levels between 24 and 59%. The strains of the genomic species differed from each other and from the known species of Brevibacterium in some physiological and biochemical characteristics, as well as in the sugar and polyol composition of their teichoic acids. The 16S rDNA sequence analysis confirmed the assignment of the environmental isolates to the genus Brevibacterium and showed the phylogenetic distinction of the three genomic species. The results obtained in this study allow three new Brevibacterium species to be described: Brevibacterium antiquum (type strain VKM Ac-2118T = UCM Ac-411T), Brevibacterium aurantiacum (type strain VKM Ac-2111T = NCDO 739T = ATCC 9175T), and Brevibacterium permense (type strain VKM Ac-2280T = UCM Ac-413T).     

Growth stimulation of Brevibacterium sp. by siderophores

AIMS: To assess which types of siderophores are typically produced by Brevibacterium and how siderophore production and utilization traits are distributed within this genus. METHODS AND RESULTS: During co-cultivation experiments it was found that growth of B. linens Br5 was stimulated by B. linens NIZO B1410 by two orders of magnitude. The stimulation was caused by the production of hydroxamate siderophores by B. linens NIZO B1410 that enabled the siderophore-auxotrophic strain Br5 to grow faster under the applied iron-limited growth conditions. Different patterns of siderophore production and utilization were observed within the genus Brevibacterium. These patterns did not reflect the phylogenetic relations within the group as determined by partial 16S rDNA sequencing. Most Brevibacterium strains were found to utilize hydroxamate siderophores. CONCLUSIONS: Brevibacteria can produce and utilize siderophores although certain strains within this genus are siderophore-auxotrophic. SIGNIFICANCE AND IMPACT OF THE STUDY: It is reported for the first time that brevibacteria produce and utilize siderophores. This knowledge can be utilized to stimulate growth of auxotrophic strains under certain conditions. Enhancing the growth rate of Brevibacterium is of importance for the application of this species, for example, for cheese manufacturing or for industrial production of enzymes or metabolites.     

Differentiation of Coll plasmids by ability to cause abortive infection of bacteriophages BF23 and T5

Eight strains, comprising all recognized species of Cellulomonas , were subjected to 51 different biochemical tests on four occasions. For 32 of these tests, a mixture of positive and negative results was obtained and from these data as few as six commonly used biochemical tests (glucose, indole, lactose, ONPG, nitrate and lysine) permit separation of the species of the genus Cellulomonas . A tentative simplified schema or dichotomous key is proposed.     

Proposal of Corynebacterium propinquum sp. nov. for Corynebacterium group ANF-3 strains

Abstract Chemotaxonomic and genomic studies were performed on seven Corynebacterium group ANF-3 strains isolated from human sources. All these strains possess cell wall component type IV ( meso -diaminopimelic acid, arabinose and galactose), corynemycolic acids and a G+C content of DNA of 57 to 59 mol%. These results confirm that they can be placed in the genus Corynebacterium . Six of these strains were found to constitute a tight hybridization group distinct from named Corynebacterium species or related organisms. This genomic group constitutes a new species which can be identified within the genus Corynebacterium by ribotyping or phenotypic tests and for which the name Corynebacterium propinquum is proposed. The type strain is strain B 77159 (= Collection of the Institut Pasteur CIP 103792).     

Taxonomic heterogeneity of strains comprising Gluconacetobacter hansenii

The taxonomic standing of Gluconacetobacter hansenii was clarified through phenotypic characteristics, quinones, DNA base composition, DNA relatedness, and the production of gluconic and ketogluconic acids from glucose. All strains that Gosselé et al. (Syst. Appl. Microbiol., 4, 338-368, 1983) employed in the establishment of Acetobacter hansenii (=G. hansenii) were used in this study. Phenotypic differences were shown among the strains of G. hansenii, suggesting heterogeneity within the species. The major ubiquinone was Q-10 for all strains of G. hansenii, except for strain IFO 3296, which was characterized by Q-9. This excluded IFO 3296 from the species G. hansenii and placed it in the genus Acetobacter. DNA relatedness revealed four distinct homology groups (I, II, III, and IV) among strains of the species. Group I was distinguished from the other genomic groups by a lower G1C range from 58.9 to 59.2 mol%. Groups II, III, and IV showed higher G+C contents of 60.4 to 62.2, 60.8, and 61.7 mol%, respectively. Groups I and IV produced both 2- and 5-ketogluconic acids from glucose, and Group III produced only 2-ketogluconic acid. Group II included strains that produced both 2- and 5-ketogluconic acids and strains that produced only 2-ketogluconic acid. It is clear that G. hansenii consists of genotypically heterogeneous strains comprising four homology groups (I, II, III, and IV). Since group I contains the type strain (IFO 14820(T)=LMG 1527(T)) of the species, this group is designated as the species G. hansenii.     

Description of the erythromycin-producing bacterium Arthrobacter sp. strain NRRL B-3381 as Aeromicrobium erythreum gen. nov., sp. nov

Arthrobacter sp. strain NRRL B-3381T (T = type strain) is a nonmycelial, nonsporulating actinomycete that produces the macrolide antibiotic erythromycin. This bacterium differs in many ways from the type species of the genus Arthrobacter (Arthrobacter globiformis), suggesting that a taxonomic revision is appropriate. The G + C content of strain NRRL B-3381T DNA is 71 to 73 mol%, and the peptidoglycan of this organism contains LL-diaminopimelic acid. Evolutionary distance data obtained from 16S rRNA sequences identified NRRL B-3381T as the deepest branching member of the Nocardioides group of actinomycetes. The principal long-chain fatty acids which we identified that distinguished strain NRRL B-3381T from related G + C-rich bacteria were 10-methyloctadecanoic (tuberculosteric), octadecenoic, and hexadecanoic acids. These characteristics, together with phage typing and biochemical characteristics, form the basis for our recommendation that strain NRRL B-3381 should be the type strain of a new taxon, for which we propose the name Aeromicrobium erythreum.     

Paracoccus bengalensis sp. nov., a novel sulfur-oxidizing chemolithoautotroph from the rhizospheric soil of an Indian tropical leguminous plant

Paracoccus versutus-like isolates from the rhizosphere of Clitoria ternatea, a slender leguminous herb (family--Papilionaceae), found ubiquitously in waste places and village forests of the Lower Gangetic plains of India, presented a case of graduated infraspecific variation that was capped by the identification of a new species Paracoccus bengalensis (type strain JJJ(T) = LMG 22700(T) = MTCC 7003(T)). The diverged phenetic and genetic structure of these sulfur-oxidizing chemolithoautotrophs presented a case of apparent nonconformity of 16S rRNA gene sequence similarities with results of DNA-DNA hybridization. Despite high 16S rRNA gene sequence similarity with P. versutus one of the newly isolated strains, viz., JJJ(T) was identified as a new species of Paracoccus by virtue of its explicitly low DNA-DNA hybridization (42-45%) with the type strain of the closest species P. versutus (), distinct G + C content (65.3 mol%), physiological and biochemical differences amounting to <60% phenetic similarity with strains of P. versutus as well as new isolates akin to the species. The newly described species also had a unique fatty acid profile that was distinguished by the absence of 18:1 omega9c, unique possession of Summed feature 3 (16:1omega7c & 15:0 iso 2-OH), 19:0 10 methyl, and a much higher concentration of 19:0 cycloomega8c.