Phylogenetic analysis of the genera Rhodococcus and Nocardia and evidence for the evolutionary origin of the genus Nocardia from within the radiation of Rhodococcus species

Rainey, Frederick A.; Burghardt, Jutta; Kroppenstedt, Reiner M.; Klatte, Stefan; Stackebrandt, Erko

doi:10.1099/13500872-141-2-523

Cited by 115 publications

(67 citation statements)

References 37 publications

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“…This observation is in accordance with a report that physiological and biochemical characteristics and chemotaxonomic properties are not particularly discriminatory for mycolic acid-containing bacteria (Rainey et al, 1995a). Based on physiological and biochemical characteristics, the phylogenetic position as determined by 16S rRNA gene analysis and DNA-DNA relatedness, the name Dietzia psychralcaliphila sp.…”

Section: Discussionsupporting

confidence: 76%

Dietzia psychralcaliphila sp. nov., a novel, facultatively psychrophilic alkaliphile that grows on hydrocarbons.

Yumoto¹,

Nakamura²,

Iwata³

et al. 2002

International Journal of Systematic and Evolutionary Microbiology

150

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A novel, facultatively psychrophilic alkaliphile that grows on a chemically defined medium containing n-alkanes as the sole carbon source was isolated from a drain of a fish product-processing plant. The isolate was an aerobic, non-motile, Gram-positive bacterium. The bacterium was catalase-positive and oxidase-negative. The cell wall contained meso-diaminopimelic acid, arabinose and galactose ; the glycan moiety of the cell wall contained acetyl residues. The GMC content of the DNA was 69 6 mol %. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate was closely related to members of the genus Dietzia (96 1-96 8 % similarity). Comparisons of phenotypic and chemotaxonomic characteristics between the isolate and the two known Dietzia species showed that they were very similar. However, the isolate differed from the two known Dietzia species in growth temperature range and certain physiological characteristics. DNA-DNA hybridization revealed that the isolate had 38 4 and 49 7 % relatedness, respectively, to Dietzia maris and Dietzia natronolimnaea. On the basis of the physiological and biochemical characteristics, the phylogenetic position as determined by 16S rRNA gene analysis and DNA-DNA relatedness, it is concluded that the isolate should be designated as a novel species, for which the name Dietzia psychralcaliphila sp. nov. is proposed. The type strain is ILA-1 T (l JCM

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Section: Discussionsupporting

confidence: 76%

Dietzia psychralcaliphila sp. nov., a novel, facultatively psychrophilic alkaliphile that grows on hydrocarbons.

Yumoto¹,

Nakamura²,

Iwata³

et al. 2002

International Journal of Systematic and Evolutionary Microbiology

150

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“…Bar, 10?0 % sequence divergence. Goodfellow (1986), a result that is in accordance with an earlier study (Rainey et al, 1995).…”

supporting

confidence: 80%

“…This was not a nomenclaturally valid proposition, as cases of synonymy must be reported in the original literature. In a subsequent phylogenetic study of the genera Rhodococcus and Nocardia, Rainey et al (1995) underpinned Goodfellow's view that the type strain of N. corynebacterioides belonged to the genus Rhodococcus, and their phylogenetic data excluded the possibility that the type strain of this species should be classified as a strain of R. globerulus (96?7-96?8 % sequence similarity), but that it formed a distinct phyletic line within the 16S rRNA Rhodococcus gene tree. Therefore, the aim of the present investigation was to clarify the taxonomic status of N. corynebacterioides by using a polyphasic taxonomic approach.…”

mentioning

confidence: 99%

Reclassification of Nocardia corynebacterioides Serrano et al. 1972 (Approved Lists 1980) as Rhodococcus corynebacterioides comb. nov.

Yassin

Schaal

2005

International Journal of Systematic and Evolutionary Microbiology

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The type strain of Nocardia corynebacterioides was the subject of a polyphasic taxonomic study. The 16S rRNA gene sequence was aligned with the sequences of representatives of the genera Corynebacterium, Dietzia, Gordonia, Mycobacterium, Nocardia, Rhodococcus, Skermania, Tsukamurella and Williamsia, and phylogenetic trees were constructed by using maximum-parsimony, maximum-likelihood and neighbour-joining methods. It was evident from the phylogenetic analysis that N. corynebacterioides represents a distinct phyletic line within the genus Rhodococcus. Menaquinone analysis showed that the organism contained dihydrogenated menaquinone with eight isoprene units, MK-8(H2), as the major isoprenologue. The genealogical evidence, together with chemotaxonomic and phenotypic data from this and previous studies, indicates that N. corynebacterioides DSM 20151T (=CIP 104510T) should be reclassified in the genus Rhodococcus as Rhodococcus corynebacterioides comb. nov.

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“…The 16s rRNA sequence analysis described above could not distinguish between the following two possible relationships of kitasatosporae to streptomycetes: (i) both groups are monophyletic, and the two taxa are sister taxa; and (ii) the kitasatosporae represent a lineage that originated from within the radiation of the genus Streptomyces, in which case the genus Streptomyces would be paraphyletic. An example of the second type of relationship is the evolutionary origin of the genus Nocardia from within the radiation of Rhodococcus species (17).…”

Section: Resultsmentioning

confidence: 99%

A Proposal To Revive the Genus Kitasatospora (Omura, Takahashi, Iwai, and Tanaka 1982)

Zhang

Wang²,

Ruan³

1997

International Journal of Systematic Bacteriology

114

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We determined almost complete 16s ribosomal DNA sequences for 12 actinomycete strains which were either previously classified as Kitusutospora strains or defined as Streptomyces strains but shown to contain major amounts of meso-diaminopimelic acid in their whole-cell hydrolysates. These sequences were subjected to phylogenetic analyses together with the sequences of 34 Streptomyces species. Phylogenetic trees were reconstructed by using both neighbor-joining and maximum-parsimony methods. The Kitasatospora species always formed a stable monophyletic clade. However, the genus Kitasatospora appeared to be either a sister taxon of the genus Streptomyces or a lineage that originated from within Streptomyces species, depending on the outgroup used. Phylogenetic trees were also constructed by using the sequences of the 16s-23s rRNA gene spacers. Streptomyces and Kitasatospora species were consistently recovered as two distinct clades independent of the outgroup used. On the basis of phylogenetic, chemotaxonomic, and phenotypic evidence, we propose that the genus Kitusutospora Omura et al. 1982 should be revived.

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Phylogenetic analysis of the genera Rhodococcus and Nocardia and evidence for the evolutionary origin of the genus Nocardia from within the radiation of Rhodococcus species

Cited by 115 publications

References 37 publications

Dietzia psychralcaliphila sp. nov., a novel, facultatively psychrophilic alkaliphile that grows on hydrocarbons.

Dietzia psychralcaliphila sp. nov., a novel, facultatively psychrophilic alkaliphile that grows on hydrocarbons.

Reclassification of Nocardia corynebacterioides Serrano et al. 1972 (Approved Lists 1980) as Rhodococcus corynebacterioides comb. nov.

A Proposal To Revive the Genus Kitasatospora (Omura, Takahashi, Iwai, and Tanaka 1982)

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