- Volume 54, Issue 6, 2004

Obligately thermophilic, aerobic, proteolytic, endospore-forming strain N-3T was isolated from a high-temperature oilfield in Lithuania. 16S rRNA gene sequence analysis placed this strain in genetic group 5 of the endospore formers. Geobacillus thermoleovorans appeared to be the closest phylogenetic neighbour (99·4 % sequence similarity). The G+C content of strain N-3T was 52·5 mol% and matched the range established for the genus Geobacillus. Studies of DNA–DNA relatedness and morphological and physiological analyses enabled strain N-3T to be described as a member of the genus Geobacillus, but could not assign this strain to any other known species of this genus. Results of this polyphasic study allowed characterization of strain N-3T as a novel species in the genus Geobacillus – Geobacillus lituanicus sp. nov. This species can be distinguished from G. thermoleovorans and Geobacillus stearothermophilus on the basis of 16S rRNA gene PCR-RFLP assays with the restriction endonucleases AluI, HaeIII and TaqI. The type strain of the novel species is N-3T (=DSM 15325T=VKM B-2294T).

In a screening campaign to isolate strains with the ability to remove the bad smell associated with animal faeces, strain MA001T was isolated from a soil sample obtained from Shizuoka prefecture, Japan. The isolate grew at pH 6–9 but not at pH 10. Cells were Gram-positive, straight rods with peritrichous flagella and produced ellipsoidal spores. The isolate was positive for catalase and oxidase tests but negative for indole production, deamination of phenylalanine and H2S production. The isolate did not produce acid from any carbohydrates tested and could not grow in more than 2 % NaCl. The DNA G+C content was 39·4 mol%. The cellular fatty acids profile consisted of significant amount of C15 branched-chain fatty acids, iso-C15 : 0 and anteiso-C15 : 0. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain MA001T was closely related to Bacillus simplex and Bacillus psychrosaccharolyticus. DNA–DNA hybridization revealed a low relatedness of the isolate to several phylogenetically close neighbours (less than 9 %). On the basis of the phenotypic characteristics observed, phylogenetic data based on 16S rRNA gene sequencing and DNA–DNA relatedness data, it is concluded that the isolate should be classified as representing a novel species, for which the name Bacillus asahii is proposed. The type strain is MA001T (=JCM 12112T=NCIMB 13969T).

A novel alkaliphile was isolated from a drain of a fish processing plant. The isolate grew at a pH range of 7–10. Cells were Gram-positive, facultatively aerobic, motile rods with peritrichous flagella. Colonies were orange or yellow in colour. Catalase and oxidase reactions were positive. The isolate grew in 0–12 % NaCl but not above 15 % NaCl. Its cell extract exhibited 567 times higher catalase activity than an Escherichia coli cell extract. The major cellular fatty acids were iso-C13 : 0, anteiso-C13 : 0, iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, anteiso-C17 : 0 and iso-C17 : 1. Its DNA G+C content was 46·7 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing and chemotaxonomic data indicated that strain T-2-2T is a member of the genus Exiguobacterium. DNA–DNA hybridization revealed a low relatedness of the isolate to several phylogenetic neighbours (less than 25 %). On the basis of phenotypic characteristics, phylogenetic data and DNA–DNA relatedness data, the isolate merits classification as a novel species, for which the name Exiguobacterium oxidotolerans sp. nov. is proposed. The type strain is T-2-2T (=JCM 12280T=NCIMB 13980T).

A novel thermophilic spore-forming strain, GaT, was isolated from the Garga hot spring located in the northern part of the Transbaikal region (Russia). Strain GaT was found to be an aerobic, Gram-positive, rod-shaped, thermophilic (optimum growth temperature is 60–65 °C), chemo-organotrophic bacterium that grows on various sugars, carboxylic acids and hydrocarbons. The G+C content of its DNA is 52·9 mol%. The 16S rRNA gene sequence similarity data show that strain GaT is closely related to members of the genus Geobacillus. Relevant chemotaxonomic data (in particular, the major fatty acid profile of strain GaT, which includes iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0 acids) support the assignment of this strain to the genus Geobacillus. The physiological, biochemical and DNA–DNA hybridization studies of strain GaT showed that it differs both genotypically and phenotypically from the recognized Geobacillus species. Based on these data, strain GaT belongs to a novel species, Geobacillus gargensis sp. nov. (type strain, GaT=VKM B-2300T=DSM 15378T). The analysis of the phenotypic characteristics (additional to those given in the original description) of the type strain of Bacillus vulcani (DSM 13174T) showed that they are very similar to the major phenotypic characteristics of the genus Geobacillus. The low DNA–DNA reassociation values of strain DSM 13174T with various species of this genus (from 38 to 54 %) clearly demonstrate a sufficient genomic distinction of this strain and its taxonomic status as a species. The physiological characteristics, phylogenetic position and DNA–DNA reassociation values of B. vulcani allow this species to be reclassified as Geobacillus vulcani comb. nov. The main properties that differentiate G. vulcani from the other species of the genus are its ability to produce acids from glycerol, lactose and ribose.

Two actinomycete strains isolated from two patients with lung nocardiosis between 1995 and 1997 in Japan were assigned to novel species of the genus Nocardia based on morphological and chemical criteria. Comparative 16S rRNA gene sequence analysis of the two strains revealed that they belong to the genus Nocardia and are most closely related to the species Nocardia beijingensis. Determination of DNA–DNA relatedness indicated that these strains could be assigned to two novel species. Based on their phenotypic and phylogenetic characters, two novel species of the genus Nocardia are proposed: Nocardia araoensis sp. nov. for IFM 0575T (=NBRC 100135T=JCM 12118T=DSM 44729T) and Nocardia pneumoniae sp. nov. for IFM 0784T (=NBRC 100136T=JCM 12119T=DSM 44730T).

Two novel spore-forming bacteria with broad antimicrobial activity were isolated from roots of Perilla frutescens. The isolates, SD17T and SD18, were facultatively anaerobic and showed variable Gram reaction. Growth was observed between 20 and 45 °C. DNA G+C content of SD17T was 51·7 mol%, and the major fatty acid was anteiso-C15 : 0 (54·1 %). 16S rRNA gene sequence similarity of SD17T ranged from 98·6 to 91·3 % with other Paenibacillus species. The phylogenetic tree showed that isolate SD17T formed a significant monophyletic clade with Paenibacillus koreensis KCTC 2393T and Paenibacillus ehimensis IFO 15659T. DNA–DNA relatedness values for strain SD17T with Paenibacillus koreensis KCTC 2393T and Paenibacillus ehimensis IFO 15659T were 17·4 and 19·8 %, respectively. These isolates thus merit species status within Paenibacillus, for which the name Paenibacillus elgii sp. nov. is proposed. The type strain is SD17T (=KCTC 10016BPT=NBRC 100335T).

A novel anaerobic, thermophilic and cellulolytic bacterium (strain CSK1T) was isolated from a cellulose-degrading bacterial community. On the basis of 16S rRNA gene sequence similarity, strain CSK1T was mapped to cluster III of the genus Clostridium. Strain CSK1T is closely related to Clostridium thermocellum (96·2 %) and Clostridium aldrichii (95·1 %). Strain CSK1T is a non-motile, spore-forming, straight or slightly curved rod. The optimum temperature and initial pH for its growth and cellulose degradation are 50–55 °C and pH 7·5. Strain CSK1T grew under a gas phase containing up to 4 % O2. Phylogenetic and phenotypic analyses support the differentiation of strain CSK1T from its closest relatives. Strain CSK1T therefore represents a novel species, for which the name Clostridium straminisolvens sp. nov. is proposed, with CSK1T (=DSM 16021T=IAM 15070T) as the type strain.

Sphaerobacter thermophilus was originally classified as the deepest branching member of the phylum Actinobacteria (high-G+C, Gram-positive bacteria) based on 16S rRNA gene comparative analysis. However, the analysis lacked suitable outgroups, and additional 16S rRNA gene sequences indicate that it is most closely related to Thermomicrobium roseum, which it also resembles phenotypically. Furthermore, both species are reproducibly affiliated with the phylum Chloroflexi (green non-sulfur bacteria), despite T. roseum currently being classified in its own phylum, the Thermomicrobia. Transfer of Sphaerobacter to the class Thermomicrobia, and transfer of the class Thermomicrobia to the phylum Chloroflexi, are proposed. Descriptions for the phylum Chloroflexi and the class Thermomicrobia are emended to reflect the proposed changes in classification.

An actinomycete that developed sporangia containing four spores in a single row at the ends of short sporangiophores on branched aerial hyphae was isolated from subtropical forest soil. The isolate contained menaquinone MK-9(H4), glutamic acid, alanine and meso-diaminopimelic acid as cell-wall amino acids and madurose in the whole-cell hydrolysate. The 16S rRNA gene sequence indicated that the isolate formed a monophyletic cluster with Planotetraspora mira. On the basis of morphological and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, a novel species of the genus Planotetraspora is proposed, Planotetraspora silvatica sp. nov. (type strain, TT 00-51T=NBRC 100141T=DSM 44746T).

The characterization of a novel slowly growing, scotochromogenic Mycobacterium species is reported. This previously undescribed mycobacterial species was isolated from five different patients with symptomatic pulmonary infections. All isolates were acid-fast-positive and the mycolic acid profiles were unique and supported placement into the genus Mycobacterium. Phenotypic characteristics of each strain included optimal growth after 3 weeks at a temperature range of 30–35 °C, yellow pigmentation after incubation in the dark and production of a heat-stable catalase. The 16S rRNA gene and internal transcribed spacer 1 sequences were identical for all five strains, but distinct from all known mycobacterial species. Phylogenetic analysis based on the 16S rRNA gene sequence placed the novel species within the slowly growing mycobacteria group in close proximity to Mycobacterium malmoense, Mycobacterium avium, Mycobacterium kansasii and Mycobacterium scrofulaceum. These data support the conclusion that the related five described organisms represent a novel Mycobacterium species, for which the name Mycobacterium nebraskense sp. nov. is proposed, with the type strain UNMC-MY1349T (=ATCC BAA-837T=DSM 44803T).

The taxonomic position of an actinomycete isolated from an ultramafic soil in New Caledonia was determined using a polyphasic approach. The isolate, which was designated SFOp68T, was shown to have chemical and morphological properties typical of streptomycetes. An almost complete 16S rRNA gene sequence of the isolate was generated and compared with sequences of representative streptomycetes. The 16S rRNA data not only supported the classification of the strain in the genus Streptomyces, but also showed that it formed a distinct phyletic line that was most closely related to one composed of the type strain of Streptomyces rimosus. The two organisms can be readily separated using a diverse range of phenotypic properties. It is proposed that strain SFOp68T (=DSM 41836T=NCIMB 13954T) be classified in the genus Streptomyces as Streptomyces ferralitis sp. nov.

On the basis of phenotypic, genotypic and chemotaxonomic characteristics, a novel species belonging to the genus Arthrobacter is described. A facultatively psychrophilic bacterium, strain AG31T, was isolated from an alpine ice cave. The aerobic, Gram-positive, non-spore-forming, non-motile strain exhibited a rod–coccus growth cycle and produced a yellow pigment. Good growth and phenol biodegradation occurred at a temperature range of 1–25 °C. Up to 10 mM phenol was utilized as a sole carbon source. Glucose was not assimilated. Analysis of the 16S rRNA gene revealed that strain AG31T represents a distinct lineage within the genus Arthrobacter, being most closely related to Arthrobacter sulfureus. The level of DNA–DNA relatedness to the type strain of A. sulfureus was 29·9 %. Anteiso-C15 : 0 was the predominant fatty acid (72 %). Strain AG31T exhibited A4α l-lys–l-Glu-type peptidoglycan and contained glucose as the only cell-wall sugar. MK-10 was the predominant menaquinone, and the polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. Strain AG31T (=DSM 15454T=LMG 21914T) is assigned as the type strain of a novel Arthrobacter species, Arthrobacter psychrophenolicus sp. nov.

A polyphasic study was undertaken to establish the taxonomic status of a soil isolate. The organism, strain FXJ14T, was found to have chemical and morphological properties characteristic of streptomycetes. Phylogenetic analyses based on an almost complete 16S rRNA gene sequence of the strain and on the 120 nt variable γ-region of the 16S rRNA molecule showed that it formed a distinct phyletic line within the range of variation encompassed by the genus Streptomyces. The sharp separation of the organism from representatives of the genus Streptomyces was strengthened by the fact that its BOX-PCR and RFLP of 16S rDNA-ITS fingerprints differed from those of over 450 recognized Streptomyces species. The isolate also had a profile of phenotypic properties that readily distinguished it from the genotypically close type strains. It is evident from the combination of genotypic and phenotypic data that strain FXJ14T (=AS 4.1858T=JCM 12278T=LMG 22082T) should be classified as the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces glauciniger sp. nov. is proposed.

A pyrene-degrading isolate, strain PYX-6T, was obtained from Tianchi Lake, Xinjiang Uygur Autonomous Region, China, and was identified by means of polyphasic taxonomy. On the basis of 16S rRNA gene sequence similarity, strain PYX-6T was closely related to members of the genus Saccharothrix. Its 16S rRNA gene sequence similarity to each of Saccharothrix syringae, Saccharothrix australiensis, Saccharothrix algeriensis and Saccharothrix coeruleofusca was 98 %. Chemotaxonomic and physiological properties of strain PYX-6T further supported its affiliation to the genus Saccharothrix. DNA–DNA hybridization results and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain PYX-6T from recognized Saccharothrix species. Therefore, strain PYX-6T represents a novel species, for which the name Saccharothrix xinjiangensis sp. nov. is proposed, with type strain PYX-6T (=AS 4.1731T=JCM 12329T).

Two whitish yellow, Gram-positive, non-motile, aerobic bacteria were isolated from enrichment culture during degradation of the thallus of the brown alga Fucus evanescens. The bacteria studied were chemo-organotrophic, mesophilic and grew well on nutrient media containing up to 15 % (w/v) NaCl. The DNA G+C content was 61 mol%. The two isolates exhibited a conspecific DNA–DNA relatedness value of 98 %, indicating that they belong to the same species. A comparative analysis of 16S rRNA gene sequences revealed that strain KMM 3637T formed a distinct phyletic lineage in the genus Brevibacterium (family Brevibacteriaceae, class Actinobacteria) and showed the highest sequence similarity (about 97 %) to Brevibacterium casei. DNA–DNA hybridization experiments demonstrated 45 % binding with the DNA of B. casei DSM 20657T. Physiological and chemotaxonomic characteristics (meso-diaminopimelic acid in the peptidoglycan, major cellular fatty acids 15 : 0ai and 17 : 0ai) of the bacteria studied were consistent with the genomic and phylogenetic data. On the basis of the results of this study, a novel species, Brevibacterium celere sp. nov., is proposed. The type strain is KMM 3637T (=DSM 15453T=ATCC BAA-809T).

Five strains of Gram-positive, endospore-forming, moderately halotolerant bacteria were studied taxonomically. Four were isolated from Vietnamese fish sauce and one from the Gulf of Mexico. Phylogenetic analysis based on 16S rRNA gene sequences showed that these strains clustered within the radiation of the genus Bacillus but separately from recognized Bacillus species. DNA G+C composition of the isolates ranged from 43 to 44 mol%. Strains 15-1T and NRRL B-14850 showed high levels of DNA–DNA relatedness (82–100 %) to each other and to the other strains isolated here; they displayed low levels of DNA–DNA relatedness (<29 %) to the type strains of selected recognized Bacillus species. They grew in 15 % NaCl and optimally in 1 % NaCl, which is characteristic of moderately halotolerant bacteria. The isolates grew at pH 6·5 to 10·0 but not at pH 6·0. Their cell walls contained meso-diaminopimelic acid. The major isoprenoid quinone was MK-7 and the principal cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. Based on these results, the strains tested were regarded as members of a novel Bacillus species for which the name Bacillus vietnamensis sp. nov. is proposed. The type strain is 15-1T (=JCM 11124T=NRIC 0531T=NRRL 23890T).

A polyphasic study was carried out to establish the taxonomic positions of six strains isolated from diverse soil samples and provisionally assigned to the genus Kitasatospora. The isolates were found to have chemical and morphological properties consistent with their classification as Kitasatospora strains. Direct 16S rRNA gene sequence data confirmed the taxonomic position of the strains following the generation of phylogenetic trees by using three tree-making algorithms. Five of the isolates were considered to merit species status using complementary genotypic and phenotypic data. These organisms were designated Kitasatospora arboriphila sp. nov. (HKI 0189T=2291-120T=DSM 44785T=NCIMB 13973T), Kitasatospora gansuensis sp. nov. (HKI 0314T=2050-015T=DSM 44786T=NCIMB 13974T), Kitasatospora nipponensis sp. nov. (HKI 0315T=2148-013T=DSM 44787T=NCIMB 13975T), Kitasatospora paranensis sp. nov. (HKI 0190T=2292-041T=DSM 44788T=NCIMB 13976T) and Kitasatospora terrestris sp. nov. (HKI 0186T=2293-012T=DSM 44789T=NCIMB 13977T). The remaining organism, isolate HKI 0316 (=2122-022=DSM 44790=NCIMB 13978), was considered to be a strain of Kitasatospora kifunensis on the basis of 16S rRNA gene sequence, DNA–DNA relatedness and phenotypic data.

A strictly aerobic, non-motile, rod-shaped actinomycete, designated strain JC2056T, was isolated from a sediment sample of getbol, the tidal flat of Korea. Results of 16S rRNA gene sequence analysis indicated that the isolate belonged to the genus Nocardioides, with the highest similarity being to Nocardioides luteus KCTC 9575T (95·7 %). The major menaquinone was MK-8(H4), and predominant cellular fatty acids were iso-16 : 0 and iso-16 : 1 H. The DNA G+C content was 70 mol%. Based on the morphological, physiological, biochemical and chemotaxonomical data presented in this study, strain JC2056T should be classified as a novel species, for which the name Nocardioides aestuarii sp. nov. is proposed; the type strain is JC2056T (=IMSNU 14029T=KCTC 9921T=JCM 12125T).

A Gram-variable, endospore-forming moderately halophilic rod, strain SF-121, was isolated from a marine solar saltern of the Yellow Sea in Korea. The result of 16S rRNA gene sequence analysis showed that strain SF-121 has highest sequence similarity (99·7 %) with the type strain of Bacillus halodenitrificans. Phylogenetic analyses based on 16S rRNA gene sequences revealed that B. halodenitrificans DSM 10037T and strain SF-121 are more closely related to the genus Virgibacillus than to the genus Bacillus. Strain SF-121 and B. halodenitrificans DSM 10037T exhibited 16S rRNA gene similarity levels of 95·3–97·5 % with the type strains of Virgibacillus species and 94·0 % with the type strain of Bacillus subtilis. DNA–DNA relatedness and phenotypic data indicated that B. halodenitrificans DSM 10037T and strain SF-121 are members of the same species. B. halodenitrificans DSM 10037T and strain SF-121 exhibited DNA–DNA relatedness values of 9–11 % with the type strains of Virgibacillus carmonensis and Virgibacillus marismortui. On the basis of the phenotypic, chemotaxonomic, phylogenetic and genetic data, B. halodenitrificans should be reclassified in the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov.