Mariko Takeuchi

Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses.

Phylogenetic analyses of 16S rRNA gene sequences by distance matrix and parsimony methods indicated that the currently known species of the genus Sphingomonas can be divided into four clusters. Some chemotaxonomic and phenotypic differences were noted among these clusters. Three new genera, Sphingobium, Novosphingobium and Sphingopyxis, are proposed in addition to the genus Sphingomonas sensu stricto. The genus Sphingobium is proposed to accommodate Sphingomonas chlorophenolica, Sphingomonas herbicidovorans and Sphingomonas yanoikuyae. The genus Novosphingobium is proposed for Sphingomonas aromaticivorans, Sphingomonas capsulata, Sphingomonas rosa, Sphingomonas stygia, Sphingomonas subarctica and Sphingomonas subterranea. Sphingomonas macrogoltabidus and Sphingomonas terrae are reclassified in the genus Sphingopyxis. The type species of Sphingobium, Novosphingobium and Sphingopyxis are Sphingobium yanoikuyae, Novosphingobium capsulatum and Sphingopyxis macrogoltabida, respectively.

Union of the genera Microbacterium Orla-Jensen and Aureobacterium Collins et al. in a redefined genus Microbacterium.

The 16S rRNA gene sequences of 19 strains, 11 strains representing validated Aureobacterium or Microbacterium species and eight strains of non-valid species or isolates, were determined. These sequences were aligned with the sequences of other validated Aureobacterium and Microbacterium species and related actinobacteria. A comparative sequence analysis of 43 strains revealed that the species of the genera Aureobacterium and Microbacterium form a monophyletic association in which species of both genera are intermixed. The high similarity in phylogenetic properties found in the species within both genera and the close relationship in physiological and chemotaxonomic features other than the diamino acid in the cell wall, provided strong evidence that the genera Aureobacterium and Microbacterium should be unified. An emended genus Microbacterium is proposed for the two combined genera. The following validated Aureobacterium species were combined to the genus Microbacterium: Aureobacterium arabinogalactanolyticum to Microbacterium arabinogalactanolyticum, Aureobacterium barkeri to Microbacterium barkeri, Aureobacterium esteraromaticum to Microbacterium esteraromaticum, Aureobacterium flavescens to Microbacterium flavescens, Aureobacterium keratanolyticum to Microbacterium liquefaciens, Aureobacterium luteolum to Microbacterium luteolum, Aureobacterium saperdae to Microbacterium saperdae, Aureobacterium schleiferi to Microbacterium schleiferi, Aureobacterium terrae to Microbacterium terrae, Aureobacterium terregens to Microbacterium terregens, Aureobacterium testaceum to Microbacterium testaceum, and Aureobacterium trichothecenolyticum to Microbacterium trichothecenolyticum.

Taxonomic Study of Bacteria Isolated from Plants: Proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov.

The taxonomic positions of 10 strains of 3-ketolactose-forming bacteria which were isolated from the roots of plants (Rosa sp., Psychotria nairobiensis, Ardisia crispa, Prunus persica, and apple trees) were investigated. The DNA base compositions of these strains ranged from 64.0 to 65.7 mol%, the isoprenoid quinone of each strain was ubiquinone 10, 3-hydroxy fatty acids were lacking in the cellular fatty acids of these organisms, and all of the strains contained a sphingolipid with the long-chain base dihydrosphingosin. These are characteristics of the genus Sphingomonas. On the basis of morphological, physiological, and chemotaxonomic characteristics, together with DNA-DNA hybridization and 16S ribosomal DNA sequence comparison data, we propose the following four new species of the genus Sphingomonas: Sphingomonas rosa (type strain, IFO 15208) for the strains isolated from rose plants and formerly named [Agrobacterium rhizogenes]; Sphingomonas pruni (type strain, IFO 15498) for the strains isolated from Prunus persica; and Sphingomonas asaccharolytica (type strain, IFO 15499) and Sphingomonas mali (type strain, IFO 15500) for the strains isolated from apple trees. Two strains which were isolated from Psychotria nairobiensis and formerly named [Chromobacterium lividum] were identified as Sphingomonas yanoikuyae strains.

Sphingomonas aquatilis sp. nov., Sphingomonas koreensis sp. nov. and Sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water

The taxonomic status of four strains from several mineral water sources in Taejon, Korea, was examined. The DNA base compositions of these strains ranged from 62 to 66 mol %. All of the strains contained sphingolipids and ubiquinone 10 as the main respiratory quinone. The cellular fatty acids of these strains included octadecenoic acid, hexadecanoic acid and 2-hydroxymyristic acid, without 3-hydroxy fatty acids. On the basis of morphological, physiological and chemotaxonomic characteristics, together with 16S rDNA sequence comparison and DNA-DNA reassociation data, three new species of the genus Sphingomonas are proposed for the strains isolated from natural mineral water: Sphingomonas aquatilis sp. nov. for strain JSS7T (= KCTC 2881T = KCCM 41067T), Sphingomonas koreensis sp. nov. for strains JSS26T (= KCTC 2882T = KCCM 41069T) and JSS28 (= KCTC 2883 = KCCM 41066) and Sphingomonas taejonensis sp. nov. for strain JSS54T (= KCTC 2884T = KCCM 41068T).

Leucobacter komagatae gen. nov., sp. nov., a new aerobic gram-positive, nonsporulating rod with 2,4-diaminobutyric acid in the cell wall.

A new aerobic, gram-positive, nonsporulating rod-shaped organism is described: Strain IFO 15245T (T = type strain) has the following characteristics: the menaquinone contains a side chain with 11 isoprenyl units; the guanine-plus-cytosine content of the DNA is 66.2 mol%; 2,4-diaminobutyric acid, glutamic acid, alanine, glycine, and gamma-aminobutyric acid are present in the cell wall at a molar ratio of ca. 1:1:2:1:1; and glucose and galactose are also present in the cell wall. A comparison of partial 16S rRNA sequences revealed that IFO 15245T represents a distinct line of descent within the gram-positive bacteria with high guanine-plus-cytosine contents. The taxonomic characteristics of this organism are different from those of previously described aerobic, gram-positive, nonsporulating, rod-shaped bacteria. The name Leucobacter komagatae gen. nov., sp. nov., is proposed for this organism. The type strain is strain IFO 15245.

Phylogenetic Evidence for Sphingomonas and Rhizomonas as Nonphotosynthetic Members of the Alpha-4 Subclass of the Proteobacteria

To clarify the taxonomic relationships of the genera Rhizomonas and Sphingomonas, the 16S rRNA sequence of Rhizomonas suberifaciens IFO 15211T (T = type strain) was determined. A phylogenetic analysis of aligned 16S rRNA gene sequences revealed that eight species of the genus Sphingomonas and R. suberifaciens are closely related to Erythrobacter longus and Porphyrobacter neustonensis and, therefore, belong in the alpha-4 subclass of the Proteobacteria. Within this subclass, Sphingomonas species and R. suberifaciens are phylogenetically interrelated and comprise several subgroups. Our findings show that the genus and species definitions of these organisms are in need of revision.

Proposal of six new species in the genus Aureobacterium and transfer of Flavobacterium esteraromaticum Omelianski to the genus Aureobacterium as Aureobacterium esteraromaticum comb. nov.

Twelve strains placed in the genera Flavobacterium, Pseudomonas, and Aureobacterium, including soil isolates, were characterized taxonomically. On the basis of morphological, physiological, and chemotaxonomic data, as well as DNA-DNA hybridization data, we propose that 11 of these strains should be classified in the genus Aureobacterium as new combinations or new species, as follows: Aureobacterium esteraromaticum comb. nov. (type strain, IFO 3751 [= ATCC 8091]), Aureobacterium arabinogalactanolyticum sp. nov. (type strain, IFO 14344), Aureobacterium keratanolyticum sp. nov. (type strain, IFO 13309), Aureobacterium luteolum sp. nov. (type strain, IFO 15074 [= DMS 20143]), Aureobacterium schleiferi sp. nov. (type strain, IFO 15075 [= DMS 20489]), Aureobacterium terrae sp. nov. (type strain, IFO 15300), and Aureobacterium trichothecenolyticum sp. nov. (type strain, IFO 15077 [= JCM 1358]). Whereas the peptidoglycan type of members of this genus is considered to be B2beta, the new species A. keratanolyticum was shown to have a new peptidoglycan type, murein variation B2alpha. An emended description of the genus Aureobacterium is presented.

Gordonia rhizosphera sp. nov. isolated from the mangrove rhizosphere

The taxonomic position of bacterial strain 141T, isolated from the mangrove rhizosphere, has been clarified by phenotypic, chemotaxonomic and phylogenetic studies. The strain possesses wall chemotype IV, MK-9(H2) as the predominant menaquinone, relatively long-chain mycolic acids (56-64) carbon atoms) and straight-chain saturated and monounsaturated fatty acids with a small amount of tuberculostearic acid. The G+C content of the DNA is 66.8 mol%. Similarity values for genes encoding 16S rRNA indicated that strain 141T represents a new species within the genus Gordonia for which the name Gordonia rhizosphera sp. nov. is proposed. The type strain of G. rhizosphere is 141T (IFO 16068T).

Bacillus curdlanolyticus sp. nov. and Bacillus kobensis sp. nov., which hydrolyze resistant curdlan.

Taxonomic characteristics of seven bacterial strains which were isolated from soil and hydrolyze resistant curdlan were studied. These bacteria were aerobic, spore-forming rods, contained menaquinone 7 as a major quinone, contained anteiso-C15:0 and iso-C16:0 as major cellular fatty acids, had guanine-plus-cytosine contents of 50 to 52 mol%, and could be divided into two groups on the basis of physiological and chemotaxonomic characteristics and DNA-DNA hybridization data. We propose the following two new species: Bacillus curdlanolyticus for strains YK9, YK121, YK161, YK201, and YK203, with type strain YK9 (= IFO 15724); and Bacillus kobensis for strains YK205 and YK207, with type strain YK205 (= IFO 15729).

Agromyces luteolus sp. nov., Agromyces rhizospherae sp. nov. and Agromyces bracchium sp. nov., from the mangrove rhizosphere.

The taxonomic positions of four strains isolated from the mangrove rhizosphere were studied by a polyphasic approach using phenotypic, chemotaxonomic and genetic methods. The four isolates contain 2,4-diaminobutyric acid in their peptidoglycan, and rhamnose as the major cell wall sugar. The predominant menaquinones are MK-12 and MK-11. The predominant cellular fatty acids are iso-C16:0, anteiso-C15:0 and/or anteiso-C17:0. The G+C content of the DNA ranges from 70.0 to 73.3 mol%. The four strains formed a coherent cluster with Agromyces species in a phylogenetic inference based on 16S rDNA sequences. Interestingly, the four isolates grew well in the presence of 5% NaCl. The differences in some phenotypic and chemotaxonomic characteristics, 16S rDNA sequence similarity data and DNA-DNA relatedness data indicate that the four isolates represent three new species in the genus Agromyces, for which are proposed the names Agromyces luteolus for strain 8T (IFO 16235T = VKM Ac-2085T), Agromyces bracchium for strain 65T (IFO 16238T = VKM Ac-2088T) and Agromyces rhizospherae for strains 14T (IFO 16236T = VKM Ac-2086T) and 58(5) (IFO 16237 = VKM Ac-2087).