- Volume 55, Issue 2, 2005

An aerobic, motile, Gram-positive strain, DX3-12T, was isolated from coastal sediment of the Eastern China Sea in Fujian Province, China, and was identified by means of polyphasic taxonomy. On the basis of 16S rRNA gene sequence similarity, strain DX3-12T was closely related to members of the genera Planomicrobium and Planococcus. 16S rRNA gene sequence similarities between strain DX3-12T and Planomicrobium mcmeekinii, Planomicrobium koreense, Planomicrobium okeanokoites, Planococcus psychrophilus and Planococcus alkanoclasticus were 97·8, 97·8, 97·1, 97·5 and 96·4 %, respectively. Chemotaxonomic and physiological properties of strain DX3-12T supported its affiliation to the genus Planomicrobium. Strain DX3-12T and Planomicrobium mcmeekinii exhibited common phenotypic properties such as the ability to reduce nitrate, but they could be distinguished from each other by physiological and biochemical tests, e.g. acid production from glucose, growth temperature and NaCl concentration requirements. DNA–DNA hybridization further distinguished strain DX3-12T from Planomicrobium mcmeekinii at the species level. Therefore, it is proposed that strain DX3-12T (=AS 1.3454T=JCM 12466T) represents a novel species, Planomicrobium chinense sp. nov. Based on 16S rRNA gene sequence similarities, signature nucleotides, cell morphology and physiological and biochemical properties, Planococcus psychrophilus and Planococcus alkanoclasticus have been transferred to the genus Planomicrobium as Planomicrobium psychrophilum comb. nov. (type strain DSM 14507T=MTCC 3812T) and Planomicrobium alkanoclasticum comb. nov. (type strain NCIMB 13489T=CIP 107718T), respectively.

An actinomycete, strain B60T, was isolated from a soil sample in Napier, Western Cape province of South Africa. Based on 16S rRNA gene sequence analysis and chemotaxonomy, strain B60T was identified as a member of the genus Actinomadura. Strain B60T produced an antibiotic with activity against Escherichia coli, Enterococcus faecium and Mycobacterium aurum, but not against Mycobacterium tuberculosis. Significant differences in morphological and physiological characteristics indicate that strain B60T represents a novel species of the genus Actinomadura. The name Actinomadura napierensis sp. nov. is proposed. The type strain is B60T (=DSM 44846T=NRRL B-24319T).

The taxonomic position of a rhizosphere isolate, strain 52108aT, was determined using a polyphasic approach. The strain was found to have chemical and morphological properties consistent with its assignment to the genus Kitasatospora. An almost complete 16S rRNA gene sequence determined for the strain was aligned with corresponding sequences of representatives of the genus Kitasatospora and related taxa using three tree-making algorithms. The organism formed a distinct phyletic line within the Kitasatospora clade and was most closely related to Kitasatospora arboriphila (98·9 %), Kitasatospora kifunensis (99·0 %), Kitasatospora paracochleata (98·4 %) and Kitasatospora terrestris (98·2 %), but was readily distinguished from representatives of these species using a combination of phenotypic properties. The combined genotypic and phenotypic data show that the strain should be classified in the genus Kitasatospora as a novel species. The name proposed is Kitasatospora viridis sp. nov., with the type strain 52108aT (=AS 4.1878T=DSM 44826T).

Two strains of Streptosporangium were isolated from Yunnan Province, a region of China with specific geographical conditions that contribute to its great microbiological diversity. They were identified using a polyphasic approach employing phenotypic, genotypic and phylogenetic techniques, such as study of morphological and physiological properties, cell chemistry, G+C content of the genomic DNA, DNA–DNA hybridization and phylogenetic analysis. The strains belong to two novel species of Streptosporangium on the basis of 16S rRNA gene sequencing. The results of morphological, physiological and biochemical investigations and DNA–DNA hybridization indicated that the two strains are different from known members of the genus Streptosporangium. The names Streptosporangium yunnanense sp. nov. (type strain CY-11007T=CCTCC AA 97009T=CCRC 16307T=DSM 44663T) and Streptosporangium purpuratum sp. nov. (type strain CY-15110T=CCTCC AA 97010T=CCRC 16308T=DSM 44688T) are proposed. They have been deposited in CCTCC in Wuhan.

During a study of the distribution of actinomycetes in a mangrove zone, a strain forming spore chains borne on the tip of short sporophores arising directly from the agar surface was isolated from soil. The isolate contained glutamic acid, glycine, alanine and meso-diaminopimelic acid as cell-wall amino acids, menaquinone MK-10(H6, H8), fatty acid type 2d and xylose in the whole-cell hydrolysate. The 16S rRNA gene sequence of the isolate formed a monophyletic cluster with the members of the genus Asanoa in the family Micromonosporaceae. On the basis of morphological and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA hybridization, a novel species of the genus Asanoa is proposed for strain TT 97-02T (=NBRC 100142T=DSM 44745T), Asanoa iriomotensis sp. nov.

A DNA–DNA hybridization survey was performed on 13 Streptomyces species and two subspecies, dispersed over five genotypically defined clusters as delineated by Lanoot et al. [Syst Appl Microbiol 27 (2004), 84–92] . Within each of the latter clusters, strains shared DNA–DNA relatedness values above 70 %. On the basis of published recommendations, the following eight Streptomyces species with validly published names are considered as later synonyms: Streptomyces nigrifaciens as a synonym of Streptomyces flavovirens; Streptomyces citreofluorescens, Streptomyces chrysomallus subsp. chrysomallus and Streptomyces fluorescens as synonyms of Streptomyces anulatus; Streptomyces chibaensis as a synonym of Streptomyces corchorusii; Streptomyces flaviscleroticus as a synonym of Streptomyces minutiscleroticus; and Streptomyces lipmanii, Streptomyces griseus subsp. alpha, Streptomyces griseus subsp. cretosus and Streptomyces willmorei as synonyms of Streptomyces microflavus. Emended descriptions are proposed.

A Gram-variable, motile, endospore-forming, halotolerant bacillus, strain JG-30T, was isolated from the traditional Korean fermented seafood jeotgal, and was subjected to a polyphasic taxonomic study. This organism grew optimally at 37 °C and in the presence of 0–1 % (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain JG-30T forms a distinct phylogenetic lineage within the evolutionary radiation encompassed by the genus Bacillus. Strain JG-30T was characterized chemotaxonomically as having cell-wall peptidoglycan based on meso-diaminopimelic acid, MK-7 as the predominant menaquinone and iso-C15 : 0 and iso-C14 : 0 as the major fatty acids. The DNA G+C content was 45 mol%. Strain JG-30T exhibited levels of 16S rRNA gene sequence similarity of less than 95·7 % to Bacillus species with validly published names. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain JG-30T (=KCTC 3880T=DSM 16189T) was classified within the genus Bacillus as a novel species, for which the name Bacillus cibi sp. nov. is proposed.

Sphaerotilus natans is a sheathed bacterium often found in activated sludge that has a bulking problem. A bacterial strain that is able to degrade the extracellular polysaccharide produced by S. natans was isolated. The isolate was a spore-forming, aerobic, rod-shaped bacterium. The Gram reaction was variable or negative. The optimum growth temperature was 30 °C and the optimum pH was 8. The G+C content of the DNA was 55 mol%. The major cellular fatty acid and respiratory quinone were anteiso-C15 : 0 and MK-7, respectively. Phylogenetic analysis based on the 16S rRNA gene indicated that the isolate was a member of the genus Paenibacillus. The nearest relative, with a similarity of 94·2 %, was Paenibacillus koleovorans, a bacterium capable of degrading the sheath of S. natans. The phenotypic characteristics of the isolate were apparently different from those of related species in the genus Paenibacillus. It is proposed that the isolate be designated Paenibacillus hodogayensis sp. nov. The type strain is SGT (=JCM 12520T=KCTC 3919T).

A bacterial strain, designated PALXIL04T, was isolated from the phyllosphere of Phoenix dactylifera. Phylogenetic analysis placed the isolate within the genus Paenibacillus with the closest relatives being Paenibacillus curdlanolyticus and Paenibacillus kobensis. DNA–DNA hybridization measurements showed low DNA relatedness (15–20 %) between the isolate and its closest relatives. Cells were Gram-variable, facultatively anaerobic, motile, sporulating rods. Catalase and oxidase were produced by the organism. Cellulose, starch, aesculin and xylan were hydrolysed. Growth was supported by many carbohydrates as the carbon source. MK-7 was the predominant menaquinone and anteiso-C15 : 0 the major fatty acid. The G+C content of the DNA was 50·7 mol%. Phylogenetic, DNA–DNA relatedness and phenotypic analyses indicated that strain PALXIL04T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus phyllosphaerae sp. nov. is proposed. The type strain is PALXIL04T (=LMG 22192T=CECT 5862T).

Twenty morphologically different strains were chosen from French wheat sourdough isolates. Cells were Gram-positive, non-spore-forming, non-motile rods. The isolates were identified using amplified-fragment length polymorphism, randomly amplified polymorphic DNA and 16S rRNA gene sequence analysis. All isolates were members of the genus Lactobacillus. They were identified as representing Lactobacillus plantarum, Lactobacillus paralimentarius, Lactobacillus sanfranciscensis, Lactobacillus spicheri and Lactobacillus sakei. However, two isolates (LP38T and LP39) could be clearly discriminated from recognized Lactobacillus species on the basis of genotyping methods. 16S rRNA gene sequence similarity and DNA–DNA relatedness data indicate that the two strains belong to a novel Lactobacillus species, for which the name Lactobacillus hammesii is proposed. The type strain is LP38T (=DSM 16381T=CIP 108387T=TMW 1.1236T).

Two novel anaerobes, strains GB4-38T and SB9-1, were isolated from an upflow anaerobic sludge blanket reactor for treating bean-curd farm wastewater and lotus field mud, respectively. The strains degraded straight-chain fatty acids with 4–8 carbon atoms in syntrophic association with methanogens and converted 1 mol butyrate into about 2 mol acetate and presumably 2 mol H2. None of the branched-chain fatty acids tested could be degraded. Benzoate was not degraded. Fumarate, sulfate, thiosulfate, sulfur and nitrate did not serve as electron acceptors for butyrate degradation. In the absence of a methanogen partner, strain GB4-38T grew on crotonate in pure culture; the generation time was about 5 h at 37 °C. However, strain SB9-1 grew on butyrate plus pentenoate, but not crotonate, in pure culture and the generation time was 18 h at 37 °C. Cells of GB4-38T and SB9-1 were straight rods and stained Gram-negative. The major cellular fatty acids of GB4-38T were C14 : 0 (29·74 %), C16 : 0 (17·00 %), C16 : 1 ω5c (16·63 %) and isoC17 : 1 I (15·34 %). ll-Diaminopimelic acid existed in the cellular peptidoglycan. The genomic DNA G+C content of strain GB4-38T was 43·2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences supported clustering of the two strains with syntrophic bacterial species of the genus Syntrophomonas (89·6–92·4 % sequence similarity), but phenotypic, chemotaxonomic and genetic characters differentiated the two strains from members of this genus. Therefore, it is proposed that the two strains are representatives of a novel species, Syntrophomonas erecta sp. nov. The type strain is GB4-38T (=CGMCC 1.5013T=DSM 16215T).

Strain CCM 2783, previously classified as representing Arthrobacter aurescens, was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence analysis and chemotaxonomic characteristics such as peptidoglycan type A3α Lys–Ala2, major menaquinone MK-9(H2) and fatty acid composition confirmed assignment of the strain to the genus Arthrobacter. The results of phylogenetic analysis, DNA–DNA relatedness experiments and physiological and chemotaxonomic characteristics indicate that CCM 2783 differs from its nearest phylogenetic relative Arthrobacter psychrolactophilus and from other recognized Arthrobacter species. Therefore, a novel species, Arthrobacter stackebrandtii sp. nov., is proposed with the type strain CCM 2783T (=DSM 16005T).

Four Gram-positive, rod- or coccus-shaped bacterial strains, KSL-1T, KSL-9, KSL-10 and KSL-12, were isolated from an alkaline serpentinite soil in Korea, and their taxonomic positions were investigated in a polyphasic study. The four strains exhibited no difference in their 16S rRNA gene sequences. Phylogenetic analyses based on 16S rRNA gene sequences showed that the four strains were phylogenetically affiliated to the genus Nocardioides. The four strains had cell-wall peptidoglycan based on ll-diaminopimelic acid as the diamino acid, indicating wall chemotype I. The predominant menaquinone detected in the four strains was MK-8(H4). The major fatty acid components were iso-C16 : 0, 10-methyl-C18 : 0, C18 : 1 ω9c and C17 : 1 ω6c. The DNA G+C contents were 72·4–73·6 mol%. The four strains exhibited 16S rRNA gene sequence similarity levels of 94·0–96·3 % to the type strains of Nocardioides species with validly published names. DNA–DNA relatedness levels between the four strains were 85–91 %. On the basis of phenotypic properties, phylogenetic distinctiveness and genotypic relatedness, strains KSL-1T, KSL-9, KSL-10 and KSL-12 were classified in the genus Nocardioides as members of a novel species, Nocardioides alkalitolerans sp. nov. The type strain is strain KSL-1T (=KCTC 19037T=DSM 16699T).

A previously undescribed, Gram-positive, catalase-negative, Streptococcus-like organism originating from a European beaver (Castor fiber) was subjected to a taxonomic study. The organism displayed β-haemolytic activity and gave a positive reaction with Lancefield group A antisera. Based on the results of biochemical testing, the organism was tentatively identified as a member of the genus Streptococcus, but it did not correspond phenotypically to any recognized species of this genus. Comparative 16S rRNA gene sequencing studies confirmed this assignment, with the bacterium forming a hitherto unknown subline within the genus. Sequence divergence values of greater than 3 % from other reference streptococcal species, however, demonstrated that the unidentified coccus-shaped organism represents a hitherto unknown species. Based on phenotypic and molecular phylogenetic evidence, it is therefore proposed that the unknown organism from a beaver be classified as a novel species, Streptococcus castoreus sp. nov. The type strain is M605815/03/2T (=CCUG 48115T=CIP 108205T).

A Gram-positive, aerobic, non-motile actinomycete, strain GW 14-1925T, that formed branched substrate and aerial mycelium was studied using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity studies, strain GW 14-1925T was shown to belong to the genus Nonomuraea, being most closely related to Nonomuraea longicatena (97·9 %), Nonomuraea turkmeniaca (98·9 %), Nonomuraea helvata (98·6 %), Nonomuraea polychroma (98·5 %), Nonomuraea salmonaea (98·3 %), Nonomuraea roseoviolacea subsp. roseoviolacea (98·1 %) and Nonomuraea roseoviolacea subsp. carminata (97·7 %). The 16S rRNA gene sequence similarity to other Nonomuraea species was <97·5 %. Chemotaxonomic data [major menaquinones of the MK-9 series with minor amounts of MK-8(H4); major polar lipids of phospholipid type IV; fatty acids with major amounts of iso- and anteiso- and 10-methyl-branched fatty acids in combination with iso-branched 2-hydroxy fatty acids] supported allocation of the strain to the genus Nonomuraea. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW 14-1925T from closely related species; thus, GW 14-1925T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea kuesteri sp. nov. is proposed, with GW 14-1925T (=DSM 44753T=NRRL B-24325T) as the type strain.

Phenotypic and phylogenetic studies were performed on two strains of an unidentified Gram-positive, fastidious, non-spore-forming, coccus-shaped bacterium recovered from human blood. The organism was catalase-negative and grew under strictly anaerobic conditions and in the presence of 2 and 6 % O2. Comparative 16S rRNA gene sequencing demonstrated that the unidentified bacterium was, phylogenetically, far removed from peptostreptococci and related Gram-positive coccus-shaped organisms, but exhibited a phylogenetic association with Clostridium rRNA cluster III [as defined by Collins et al., Int J Syst Bacteriol 44 (1994), 812–826 ]. Sequence divergence values of 15 % or more were observed between the unidentified bacterium and all other recognized species within this and related rRNA clostridial clusters. Treeing analysis showed that the unknown bacterium formed a deep line branching at the periphery of rRNA cluster III and represents a hitherto unknown genus within this supra-generic grouping. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium from blood be classified in a new genus, Fastidiosipila gen. nov., as Fastidiosipila sanguinis sp. nov. The type strain of Fastidiosipila sanguinis is CCUG 47711T (=CIP 108292T).

A polyphasic study was carried out to clarify the taxonomic positions of three Gram-positive isolates from the Catacombs of Domitilla, Rome (Italy). 16S rRNA gene sequence comparisons placed these strains within the genus Agromyces. The morphological and chemotaxonomic characteristics of these isolates were consistent with the description of the genus Agromyces. The three isolates could be readily distinguished from one another and from representatives of all Agromyces species with validly published names by a broad range of phenotypic characteristics and DNA–DNA relatedness studies. Therefore, these isolates are proposed to represent three novel species of the genus Agromyces, Agromyces italicus sp. nov. (type strain CD1T=HKI 0325T=DSM 16388T=NCIMB 14011T), Agromyces humatus sp. nov. (type strain CD5T=HKI 0327T=DSM 16389T=NCIMB 14012T) and Agromyces lapidis sp. nov. (type strain CD55T=HKI 0324T=DSM 16390T=NCIMB 14013T).

An actinomycete strain was recovered from a pond where radon is known to be dissolved. A polyphasic study was undertaken to identify the new isolate. The 16S rRNA gene sequence of strain WA201T showed closest similarity to the type strains of Micromonospora carbonacea (98·5 %) and Micromonospora matsumotoense (98·1 %). The chemotaxonomic results confirmed the taxonomic position of the isolate in the genus Micromonospora. DNA–DNA relatedness values supported the classification of this isolate as a novel species. A number of physiological and biochemical tests were able to distinguish strain WA201T from its closest phylogenetic neighbours. Therefore, it is proposed that isolate WA201T (=DSM 44830T=LMG 22229T) be considered the type strain representing a novel species, Micromonospora mirobrigensis sp. nov.

A novel actinomycete strain, designated YIM 002T, was isolated from a desert soil sample in Gansu Province, north-west China. This actinomycete isolate formed well-differentiated aerial and substrate mycelia. In the early stages of growth, the substrate mycelia fragmented into short or elongated rods. Chemotaxonomically, it contained ll-2,6-diaminopimelic acid in the cell wall. The cell-wall sugars contained ribose and glucose. Phospholipids present were phosphatidylinositol mannosides, phosphatidylinositol and diphosphatidylglycerol. MK-9(H4) was the predominant menaquinone. The major fatty acids were anteiso C15 : 0 (35·92 %), anteiso C17 : 0 (15·84 %), iso C15 : 0 (10·40 %), iso C16 : 0 (7·07 %) and C17 : 1 ω8c (9·37 %). The G+C content of the DNA was 70 mol%. Phylogenetic analysis and signature nucleotide data based on 16S rRNA gene sequences showed that strain YIM 002T is distinct from all recognized genera of the family Nocardioidaceae in the suborder Propionibacterineae. On the basis of the phenotypic and genotypic characteristics, it is proposed that isolate YIM 002T be classified as a novel species in a new genus, Jiangella gansuensis gen. nov., sp. nov. The type strain is YIM 002T (=DSM 44835T=CCTCC AA 204001T=KCTC 19044T).