- Volume 54, Issue 2, 2004

The taxonomic position of an actinomycete isolated from a hypermagnesian ultramafic soil was examined using a polyphasic approach. The strain, designated SBHR OA6T, was shown to have chemical and morphological properties typical of members of the genus Nocardia. The organism was most closely associated with Nocardia asteroides using 16S rRNA gene sequence data. It showed a distinctive set of phenotypic properties that distinguished it from representatives of all species with validly published names classified in the genus Nocardia. The combined genotypic and phenotypic data show that strain SBHR OA6T (=DSM 44717T=NCIMB 13955T) merits description as the type strain of a novel Nocardia species, Nocardia neocaledoniensis sp. nov.

An unknown Gram-positive, catalase-positive, facultatively anaerobic, non-spore-forming, coccus-shaped bacterium originating from sediment was characterized using phenotypic, molecular chemical and molecular phylogenetic methods. Chemical studies revealed the presence of a cell-wall murein based on ll-diaminopimelic acid (type ll-Dpm-glycine1), a complex mixture of saturated, monounsaturated and iso- and anteiso-methyl-branched, non-hydroxylated, long-chain cellular fatty acids and tetrahydrogenated menaquinones with eight isoprene units [MK-8(H4)] as the major respiratory lipoquinone. This combination of characteristics somewhat resembled members of the suborder Micrococcineae, but did not correspond to any currently described species. Comparative 16S rRNA gene sequencing confirmed that the unidentified coccus-shaped organism is a member of the Actinobacteria and represents a hitherto-unknown subline related to, albeit different from, a number of taxa including Intrasporangium, Janibacter, Terrabacter, Terracoccus and Ornithinicoccus. Based on phenotypic and phylogenetic considerations, it is proposed that the unknown bacterium originating from lake sediment be classified as a new genus and species, Arsenicicoccus bolidensis gen. nov., sp. nov. (type strain CCUG 47306T=DSM 15745T).

Brevibacterium liquefaciens ATCC 14929T was reclassified as Corynebacterium liquefaciens by Lanéelle et al. (1980) . A further study by Stackebrandt et al. (1983) described the same strain, indicating high genomic and chemotaxonomic relatedness to Arthrobacter nicotianae; however, reclassification was not formally proposed. Because of the discrepancies between their previous work and the data of Collins & Kroppenstedt (1983) , Lanéelle and colleagues re-examined B. liquefaciens and withdrew their recommendation for the assignment of B. liquefaciens to the genus Corynebacterium ( Lanéelle et al., 1984 ). Formal reclassification of B. liquefaciens as A. nicotianae is now proposed.

A novel Bacillus isolate from raw milk and four strains from diverse origins that were identified previously as Bacillus lentus, Bacillus firmus and Bacillus circulans showed a high degree of similarity in amplified rDNA restriction analysis, SDS-PAGE and routine phenotypic tests, whilst 16S rDNA sequence comparisons and DNA relatedness data showed that this taxon was different from related Bacillus species. On the basis of these data, Bacillus galactosidilyticus sp. nov. is proposed, with the type strain LMG 17892T (=DSM 15595T=Logan B2188T=MB 800T).

Five isolates of a novel species of the yeast genus Malassezia were isolated from animals in Japan and Brazil. Phylogenetic trees based on the D1/D2 domains of the large-subunit (26S) rDNA sequences and nucleotide sequences of the internal transcribed spacer 1 region showed that the isolates were conspecific and belonged to the genus Malassezia. They were related closely to Malassezia dermatis and Malassezia sympodialis, but were clearly distinct from these two species and the other six species of Malassezia that have been reported, indicating that they should be classified as a novel species, Malassezia nana sp. nov. Morphologically and physiologically, M. nana resembles M. dermatis and M. sympodialis, but can be distinguished from these species by its inability to use Cremophor EL (Sigma) as the sole lipid source and to hydrolyse aesculin. The type strain of M. nana is NUSV 1003T (=CBS 9557T=JCM 12085T).

Characterization of strains of Xanthomonas axonopodis pv. citri by using DNA fingerprints that were generated from primers for enterobacterial repetitive intergenic consensus (ERIC) elements led to the discovery of differential sequences for a leucine-responsive regulatory protein (lrp) gene in two subgroups of strains with different host ranges on Citrus spp. DNA hybridization and PCR-based assays that used different sets of primers were designed to detect the core sequence, as well as to obtain the entire sequence of the lrp gene for several Xanthomonas species and pathovars. Higher variability was observed at the nucleotide level than at the amino acid level among the different species and pathovars, revealing selection pressure on the lrp gene, which is presumably due to an essential role of the gene in bacterial metabolism. Moderate variability in the 3′ and 5′ domains was used to study relationships among different species within the genus Xanthomonas. Species of this genus that were isolated from citrus, as well as other pathovars of X. axonopodis, showed highly similar lrp gene sequences, whereas other Xanthomonas species, especially Xanthomonas campestris, had sequences that were more dissimilar to that of X. axonopodis. Thus, the lrp gene sequence is useful to distinguish X. axonopodis pv. citri groups and promising for polyphasic taxonomic analysis of the genus Xanthomonas. Data from analysis of lrp gene sequences support the current concepts for classification of xanthomonads, which are based on other approaches.

The heterocystous cyanobacteria are currently placed in subsections IV and V, which are distinguished by cellular division in one plane (false branching) and in more than one plane (true branching), respectively. Published phylogenies of 16S rRNA gene sequence data support the monophyly of the heterocystous cyanobacteria, with members of subsection V embedded within subsection IV. It has been postulated that members of subsection V arose from within subsection IV. Therefore, phylogenetic analysis of nucleotide sequences of the nitrogen-fixation gene nifD from representatives of subsections IV and V was performed by using maximum-likelihood criteria. The heterocystous cyanobacteria are supported as being monophyletic, with the non-heterocystous cyanobacteria as their closest relative. However, neither subsection IV nor subsection V is monophyletic, with representatives of both subsections intermixed in two sister clades. Analysis of nifD does not support recognition of two distinct subsections.

The taxonomy of canine Mollicutes is described, based on phylogenetic analysis of 16S rRNA gene and 16S/23S rRNA intergenic spacer (IGS) region sequences. The nucleotide sequences of the 16S rRNA gene of two untyped mycoplasmas and the IGS region of 11 Mycoplasma species were determined and used for phylogenetic analysis. The two untyped Mycoplasma strains, HRC 689 and VJC 358, were found to be distinct from all known canine mycoplasmas and all published mycoplasma 16S rRNA gene sequences.

The RNA polymerase β-subunit genes (rpoB) of 67 Streptomyces strains, representing 57 species, five Kitasatospora strains and Micromonospora echinospora KCTC 9549 were partially sequenced using a pair of rpoB PCR primers. Among the streptomycetes, 99·7–100 % similarity within the same species and 90·2–99·3 % similarity at the interspecific level were observed by analysis of the determined rpoB sequences. The topology of the phylogenetic tree based on rpoB sequences was similar to that of 16S rDNA. The five Kitasatospora strains formed a stable monophyletic clade and a sister group to the clade comprising all Streptomyces species. Although there were several discrepancies in the details, considerable agreement was found between the results of rpoB analysis and those of numerical phenetic classification. This study demonstrates that analysis of rpoB can be used as an alternative genetic method in parallel to conventional taxonomic methods, including numerical phenetic and 16S rDNA analyses, for the phylogenetic analyses of the genera Streptomyces and Kitasatospora.