- Volume 52, Issue 6, 2002

Two novel species, Rathayibacter caricis sp. nov. (type strain VKM Ac-1799T = UCM Ac-618T) and Rathayibacter festucae sp. nov. (type strain VKM Ac-1390T UCM Ac-619T), are proposed for two coryneform actinomycetes found in the phyllosphere of Carex sp. and in the leaf gall induced by the plant-parasitic nematode Anguina graminis on Festuca rubra L., respectively. The strains of the novel species are typical of the genus Rathayibacter in their chemotaxonomic characteristics and fall into the Rathayibacter 16S rDNA phylogenetic cluster. They belong to two separate genomic species and differ markedly from current validly described species of Rathayibacter at the phenotypic level. The most striking feature differentiating Rathayibacter caricis sp. nov. from other species of the genus is the presence of fucose in its cell wall and Rathayibacter festucae sp. nov. can be easily recognized among other yellow-pigmented rathayibacters because of its rose-orange-coloured colonies.

Based upon significant differences in chemotaxonomic properties, i.e., amino acid composition of peptidoglycan, fatty acids and base composition of DNA, and supported by the phylogenetic position of the 165 rDNA sequence the species Propionibacterium lymphophilum was reclassified as Propionimicrobium lymphophilum comb. nov.

Strain 853-15A(T) was enriched and isolated from uranium-contaminated aquifer sediment by its ability to grow under anaerobic conditions via the oxidation of lactate coupled to the reduction of anthraquinone-2,6-disulfonate (AQDS) to anthrahydroquinone-2,6-disulfonate (AHQDS). Lactate was oxidized incompletely to acetate and carbon dioxide according to the reaction CH3CHOHCOO(-)+ 2AQDS+H2O --> CH3COO(-)+ 2AHQDS+CO2. Additional electron donors utilized included formate, ethanol, butanol, butyrate, malate and pyruvate. Lactate also supported growth with Fe(III) citrate, Mn(IV) oxide, humic substances, elemental sulfur, 3-chloro-4-hydroxyphenylacetate, trichloroethylene or tetrachloroethylene serving as the electron acceptor. Growth was not observed with sulfate, sulfite, nitrate or fumarate as the terminal electron acceptor. The temperature optimum for growth was 30 degrees C, but growth was also observed at 20 and 37 degrees C. The pH optimum was approximately 7.0. The 16S rDNA sequence of strain 853-15A(T) suggested that it was most closely related to Desulfitobacterium dehalogenans and closely related to Desulfitobacterium chlororespirans and Desulfitobacterium frappieri. The phylogenetic and physiological properties exhibited by strain 853-15A(T) (= ATCC BAA-636(T)) place it within the genus Desulfitobacterium as the type strain of a novel species, Desulfitobacterium metallireducens sp. nov.

A polyphasic taxonomic study was performed on 16 Stenotrophomonas strains from environmental and clinical sources. A group of three plant-associated isolates were shown to be phenotypically different from the other strains. This group formed a separate physiological cluster (B1) with 42% heterogeneity to the other isolates. The defining characteristics of the new species were as follows: growth at 4 degrees C and the absence of growth at 40 degrees C; the utilization of xylose as a carbon source; lower osmolytic tolerance (< 4.5% NaCl, w/v), although the isolates can produce trehalose and glucosylglycerol as osmoprotective substances; the absence of lipase and beta-glucosidase production; and antifungal activity against plant-pathogenic fungi. The whole-cell fatty acid profile of this group was different and characterized by the main fatty acids iso-C15:0 and anteiso-C15:0. Numerical analysis of the fatty acid profiles of the strains examined supports the differentiation of the physiological B1 group. By 16S rDNA analysis, three clusters were distinguished. The three strains of the B1 group formed a separate environmental cluster (E1). They showed a mean similarity of 99.5% within the cluster, and differed from strains of a second environmental cluster (E2) by 2.2% and from the clinical cluster (C) by about 3.0%. DNA-DNA hybridization data supported the taxonomic differentiation. All results led to the proposal of a new species, Stenotrophomonas rhizophila sp. nov., with strain e-p10(T) (= DSM 14405(T) = ATCC BAA-473(T)) as the type strain.

The relationships between Bifidobacterium infantis, Bifidobacterium longum and Bifidobacterium suis were examined by means of carbohydrate fermentation, DNA-DNA hybridization, ribotyping and random amplified polymorphic DNA-PCR (RAPD-PCR). The levels of DNA-DNA hybridization among the strains of B. infantis, B. longum and B. suis used in this study were 67-81% under optimal conditions (42 degrees C) and 63-85% under stringent conditions (52 degrees C). Although the strains showed varied carbohydrate-fermentation patterns, the three species were divided into three types, namely the infantis type, the longum type and the suis type, by ribotyping and RAPD-PCR. On the basis of these results, strains of B. infantis, B. longum and B. suis were recognized as distinct groups within a single species. It is concluded that B. infantis and B. suis should be unified as B. longum, the latter species being divided into three biotypes, the infantis type, the longum type and the suis type, by molecular methods.

Farnesyl diphosphate (FPP) synthase is essential not only for phototrophic bacteria in carotenoid biosynthesis, but also for non-phototrophic bacteria in the biosynthesis of physiologically important compounds. The gene encoding FPP synthase was assessed as a molecular marker to investigate the intermingled relationship between the phototropic and non-phototropic bacteria in the alpha-Proteobacteria based on 16S rRNA analysis. The FPP synthase amino acid sequences from three phototropic bacteria, Rhodobacter sphaeroides ATCC 11167(T), Rhodobacter capsulatus ATCC 11166(T) and Rhodovulum sulfidophilum W4(T), were determined and used in conjunction with sequences of other representative members of the alpha-, gamma- and epsilon-Proteobacteria and the low-G+C Gram-positive bacteria for phylogenetic analyses by the neighbour-joining and maximum-likelihood methods. The overall topology of the FPP synthase gene tree is consistent with that of the 16S rRNA tree, producing a distinct cluster of the three phototropic bacteria. A minor discordance between the two trees was observed in the cluster of the non-phototrophic Bradyrhizobiumjaponicum USDA 110 and Mesorhizobium loti MAFF 303099; the FPP synthase genes of these two rhizobial species are highly homologous as compared with their respective 16S rRNA. The results suggest that the FPP synthase and 16S rRNA genes have the same evolutionary pattern, evolving vertically from each common ancestral gene; the FPP synthase gene, therefore, could possibly be used for further study on the molecular systematics of photosynthetic bacteria.

A novel anaerobic, thermophilic, CO-utilizing bacterium, strain 41(T), was isolated from a terrestrial hot vent on the Kamchatka Peninsula. Strain 41(T) was found to be a Gram-positive bacterium, its cells being short, straight, motile rods. Chains of three to five cells were often observed. The isolate grew only chemolithoautotrophically on CO, producing equimolar quantities of H2 and CO2 (according to the equation CO+H2O --> CO2+H2). Growth was observed in the temperature range 40-68 degrees C, with an optimum at 58 degrees C, and in the pH range 6.5-7.6, with an optimum at pH 7.0. The generation time under optimal conditions for chemolithotrophic growth was 1.1 h. The DNA G+C content was 46 +/- 1 mol%. Growth was completely inhibited by penicillin, ampicillin, streptomycin, kanamycin and neomycin. On the basis of the phenotypic and phylogenetic features, it is proposed that this isolate represents a new genus and species, Carboxydocella thermautotrophica gen. nov., sp. nov. (type strain 41(T) = DSM 12356(T) = VKM B-2282(T)).

Mainly on the basis of phylogenetic and genotypic evidence, it has been suggested previously that the species Aeromonas enteropelogenes Schubert et al. 1990 is identical to the species Aeromonas trota Carnahan et al. 1991. Probably because the description of A. enteropelogenes preceded the proposal of A. trota by only a few months, DNA-DNA hybridizations were never performed between representative strains of these two taxa. In the present study, new DNA-DNA hybridizations between the type strain of A. enteropelogenes, LMG 12646(T) (= DSM 6394(T)), and reference strains of A. trota, including its type strain LMG 12223(T)(= ATCC 49657(T)), showed a genomic relatedness of 81-99%. In addition, phenotypic characterization revealed that the two type strains exhibited identical API 20E and API 50CHE biochemical profiles and were both susceptible to ampicillin and carbenicillin. Collectively, our new DNA reassociation and phenotypic data confirm previous taxonomic data that indicate that the taxa A. enteropelogenes and A. trota are synonymous members of the same Aeromonas species. Although the species name A. enteropelogenes has nomenclatural priority, the authors would like to discourage the use of this name because the name A. trota has been cited much more frequently. The preferential use of A. trota in future publications may be the best option to avoid ambiguity in the description of ampicillinsusceptible aeromonads and to secure nomenclatural continuity in Aeromonas literature.

Pathogenic bacteria are frequently associated with mushroom sporophores exhibiting brown blotch disease symptoms. These bacteria belong mainly to Pseudomonas tolaasii or occasionally to 'Pseudomonas reactans'. Although a group of isolates originating from some Finnish mushroom farms satisfied the two characteristic criteria for diagnosis of infection with P. tolaasii (i.e. yielding a typical brown blotch symptom on Agaricus bisporus sporophores and producing a typical white line in agar when streaked towards the 'P. reactans' LMG 5329 inducing strain), results based on numerical taxonomy, siderotyping, DNA-DNA hybridizations and 16S rDNA phylogenetic analyses supported the view that these isolates constituted a novel species within the genus Pseudomonas, Pseudomonas costantinii. The type strain is PS 3a(T) (= CFBP 5705(T) = HAMBI 2444(T)).

Aerobic, endospore-forming bacteria were found in soil taken from an active fumarole on Lucifer Hill, Candlemas Island, South Sandwich archipelago. Amplified rDNA restriction analysis, SDS-PAGE, repetitive element primed-PCR (rep-PCR) and routine phenotypic tests suggested that six of the isolates represent a novel taxon, and 16S rDNA sequence comparisons support the proposal of a novel species, Bacillus luciferensis sp. nov., the type strain of which is strain LMG 18422(T) (= CIP 107105(T)).

Strains of a novel species of the rapidly growing mycobacteria, Mycobacterium holsaticum sp. nov., were isolated from various clinical specimens. The isolates grew at 22-40 degrees C, were positive for nitrate and tellurite reduction, had phosphatase, urease, nicotinamidase and pyrazinamidase activities, were resistant to isoniazid and rifampin and were susceptible to streptomycin and ethambutol. Analyses of the 165 rRNA gene and a fragment of the heat-shock protein gene hsp65 revealed unique nucleotide sequences. A phylogenetic analysis based on the comparison of the 16S rDNA sequence with that of other mycobacterial species allocated the strain to the rapidly growing mycobacteria. A conspicuous characteristic of the novel species is the similarity of the species-specific sequence of the 16S rRNA gene to the sequence of the Mycobacterium tuberculosis complex, resulting in a cross-reaction with the AccuProbe for the M. tuberculosis complex when performed with a 5 min selection step. The type strain of the novel species is strain 1406(T) ( = DSM 44478(T) = CCUG 46266(T)). Another strain of M. holsaticum sp. nov., strain 5050, which differed in the internal transcribed spacer sequence, was deposited as DSM 44479 ( = CCUG 46267).

A polycyclic aromatic hydrocarbon (PAH)-utilizing Mycobacterium strain, PYR-1(T), was isolated from petroleum-contaminated estuarine sediments and has been shown by 16S rRNA gene sequencing to be closely related to Mycobacterium aurum ATCC 23366(T) and Mycobacterium vaccae ATCC 15438(T). In this investigation, the 16S rDNA, fatty acid methyl esters, DNA-DNA hybridization, PFGE analysis of restriction-digested total genomic DNA and biochemical tests were used to determine the taxonomic relationship of strain PYR-1(T) to other closely related Mycobacterium species. The sequence of the 16S rRNA gene of strain PYR-1(T) was similar to that of Mycobacterium austroafricanum ATCC 33464(T), except for one gap at position 43. Fatty acid methyl ester analysis also showed similarity to M. austroafricanum ATCC 33464(T); however, the Euclidean distance was greater than 4.0, indicating that these strains were not identical. Dot-blot DNA-DNA hybridization of strain PYR-1(T) with M. austroafricanum indicated less than 40% relatedness. When the total chromosomal DNA of M. aurum ATCC 23366(T), M. austroafricanum ATCC 33464(T) and strain PYR-1(T) was digested with restriction enzyme Xbal and analysed by PFGE, all three organisms gave different restriction patterns. Previous studies from our laboratory have shown that the reverse-phase HPLC elution profiles of mycolic acids of strain PYR-1(T) and M. austroafricanum ATCC 33464(T) have different patterns. Based on phylogenetic analysis using 165 rRNA gene sequences, fatty acid analysis, DNA-DNA hybridization and PFGE analysis and physiological and chemotaxonomic characteristics, it is concluded that strain PYR-1(T) (= DSM 7251(T) = NRRL B-24157(T)) represents a novel species of the genus Mycobacterium, for which the name Mycobacterium vanbaalenii sp. nov. is proposed.

Pediococci are found in foods and on plants and as beer-spoilage agents. The goal of the present study was to use the DNA sequences of the first three variable regions of the 165 rRNA gene, the 16S-23S rRNA internally transcribed spacer region sequence and approximately a third of the 60 kDa heat-shock protein gene to elucidate phylogenetic groupings within the genus Pediococcus. Phylogenetic trees were created with sequence data from 31 Pediococcus and three Lactobacillus isolates. Complete 16S rRNA gene sequences from selected Pediococcus isolates were also examined. The results were interpreted in relation to the currently accepted Pediococcus species. We found that, where previously done, speciation of many Pediococcus isolates is inaccurate. Also, one grouping of seven isolates did not include any currently recognized Pediococcus species type isolate. Our phylogenetic analyses support the conclusion that these seven isolates, all of brewing spoilage origin, belong to a novel species, for which the name Pediococcus claussenii sp. nov. is proposed (type strain P06(T0 = ATCC BAA-344(T) = DSM 14800(T)). Phylogenetic analysis has therefore helped to resolve problems surrounding species identification of Pediococcus isolates.

The taxonomic status of 'Streptomyces avermitilis' strain MA-4680 was established using a polyphasic approach. Strain MA-4680 formed a distinct phyletic line in the 16S rDNA streptomycete tree, and it was evident from the almost complete 16S rDNA sequence data that it was most closely related to Streptomyces cinnabarinus, Streptomyces griseochromogenes, Streptomyces resistomycificus and Streptomyces viridochromogenes. However, strain MA-4680 was readily distinguished from the type strains of these species by using a range of phenotypic properties, notably morphological and pigmentation features. The combined genotypic and phenotypic datasets indicate that the organism forms a recognizable centre of variation within the genus Streptomyces. It is proposed that 'Streptomyces avermitilis' be formally recognized as a species of Streptomyces. The type strain is MA-4680(T) (ATCC 31267(T) = NCIMB 12804(T0 = NRRL 8165(T)).

Twenty-two isolates originating from the gut of healthy cultured turbot larvae in Norway were investigated using a polyphasic approach. Amplified fragment length polymorphism fingerprinting analysis showed that the isolates have typical patterns and form two main groups. Phylogenetic analysis revealed that the isolates belong to the gamma-Proteobacteria, with Vibrio hollisae as their closest neighbour. DNA-DNA hybridization, chemotaxonomic and phenotypic analyses further proved that these isolates represent a tight novel taxon that differs from currently described species in the family Vibrionaceae. It is proposed that these novel isolates be accommodated in a new genus, Enterovibrio gen. nov., with Enterovibrio norvegicus sp. nov. as the type species. Isolates were motile by a polar flagellum, positive for oxidase, catalase, arginine dihydrolase and beta-galactosidase, but negative for the Voges-Proskauer reaction. They produced indole, did not reduce nitrate and were resistant to the vibriostatic agent O/129. The DNA G+C content of E. norvegicus was 47.1-47.9 mol%. The type strain is E. norvegicus LMG 19839(T) (= CAIM 430(T)).

This paper reports the identification of bacterial endosymbionts inhabiting the leaf galls of Psychotria kirkii. A phylogenetic approach was used to reveal the identity of these as yet uncultivable bacterial endophytes. Based on the analysis of 16S rDNA sequences, evolutionary trees were constructed that place the endosymbiont in the genus Burkholderia. Low levels of sequence identity and rather large evolutionary distances to the closest validly named relatives indicate that these symbiotic bacteria represent a novel species. Until cultivation is successful or until more phenotypic data become available the provisional name 'Candidatus Burkholderia kirkii' sp. nov. is proposed.

Classification of strain W-50(T), which was isolated from a wastewater treatment plant, was investigated by a polyphasic approach. Cells of strain W-50(T) were Gram-negative, strictly aerobic, oxidase-positive and yellow-pigmented. Ubiquinone Q-10 was the main respiratory lipoquinone system and polar lipid fingerprints were characterized by the presence of a sphingoglycolipid, suggesting that strain W-50(T) belongs to the alpha-4 subclass of the Proteobacteria. Sequencing and comparative analyses of the 16S rRNA gene of strain W-50(T) supported its chemotaxonomic allocation as an alpha-4 proteobacterium. The most closely related established taxa were species of the genus Sphingopyxis, including Sphingopyxis macrogoltabida (97.3% similarity) and Sphingopyxis terrae (96-4% similarity), and Sphingomonas taejonensis (97.3%). These findings were supported by both the polyamine content, which consisted mainly of spermidine [12.9 micromol (g dry wt)(-1)], and the presence of 2-OH 14:0, 2-OH 15:0 and 2-OH 16:0 in the cellular fatty acid profile. DNA-DNA hybridization experiments resulted in similarity values of 31.9% between strain W-50(T) and Sphingopyxis macrogoltabida IFO 15033(T), 44.9% between strain W-50(T) and Sphingopyxis terrae IFO 15098(T) and 31.0% between strain W-50(T) and Sphingomonas taejonensis KCTC 2884(T). Based upon results obtained by detailed physiological/biochemical testing and previously published molecular evidence, strain W-50(T) was clearly distinguishable from all other Sphingopyxis species. For these reasons, the creation of a novel species, Sphingopyxis witflariensis sp. nov., is proposed; strain W-50(T) (= DSM 14551(T) = CIP 107174(T)) is the type strain.

On the basis of phenotypic data obtained on the strain Marseille-URRWFXCal2(T), isolated from the cat flea Ctenocephalides felis, the description of Rickettsia felis (Bouyer et al., 2001) is emended and Marseille-URRWFXCal2(T) is proposed as the type strain of the species. On the basis of polyphasic characterization, especially the inability to grow at temperatures higher than 32 degrees C on Vero cells that allow growth of other Rickettsia to at least 35 degrees C, it is confirmed that this agent, although different from other recognized rickettsial species, is genotypically indistinguishable from bacteria previously detected within cat fleas and provisionally named ELB. Comparison of the phenotypic characteristics previously described for R. felis and those observed for the isolate in this study indicated some differences, although concurrent analysis of the two was not possible as no extant isolates of the first isolate of R. felis exist.

A Gram-variable, aerobic, endospore-forming, rod-shaped bacterial strain, SF-20(T), which was isolated from a salt field in Korea, was subjected to a polyphasic taxonomic study. Cells of this organism were motile by means of single flagella. Strain SF-20(T) grew optimally in the presence of 4-8% NaCl. The cell wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone is MK-7. Strain SF-20(T) has a cellular fatty acid profile containing major amounts of branched fatty acids. The major fatty acids are anteiso-C15:0 and iso-C16:0. The cellular phospholipids are phosphatidylglycerol and diphosphatidylglycerol. The G+C content of the DNA is 44 mol%. Strain SF-20(T) is phylogenetically closely related to the genus Bacillus and some related genera and, particularly, formed a coherent cluster with the genera Salibacillus and Virgibacillus. The clustering fidelity between strain SF-20(T) and the cluster comprising these two genera was supported by bootstrap analysis at a confidence level of 67.2%. Strain SF-20(T) exhibited levels of 16S rDNA similarity of 93.0-94.7% to the genus Salibacillus and 94.0-94.1% to the genus Virgibacillus. On the basis of phenotypic and phylogenetic data, strain SF-20(T) should be classified in a novel genus and species, for which the name Lentibacillus salicampi gen. nov., sp. nov. is proposed. The type strain is strain SF-20(T) (= KCCM 41560(T) = JCM 11462(T)).