- Volume 60, Issue 10, 2010

Four nocardioform bacterial strains isolated from clinical respiratory sources were characterized using a polyphasic taxonomic approach. On the basis of 16S rRNA gene sequence analyses, these strains were found to be 100 % similar to each other and were shown to belong to the genus Nocardia. Chemotaxonomic data [major menaquinone: ω-cyclic isoprene side chain MK-8(H4cycl ); major polar lipids: diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides; major fatty acids: monounsaturated fatty acids with a considerable amount of tuberculostearic acid; and mycolic acids (52–62 carbon atoms)] were consistent with the assignment of the novel strains to the genus Nocardia. Comparative phylogenetic analysis of the 16S rRNA gene sequences showed that the novel strains were related to Nocardia cerradoensis DSM 44546T (99.8 %) and Nocardia aobensis JCM 12352T (99.6 %). Analysis of gyrB gene sequences showed these strains were related to N. aobensis (96.6 %) and to N. cerradoensis (96.3 %). The results suggest that gyrB gene sequencing is a more powerful tool than 16S rRNA gene sequencing for taxonomic identification within the genus Nocardia. DNA–DNA hybridization and physiological and biochemical tests supported the genotypic and phenotypic differentiation of the novel strains from related species. These data indicated that the new strains represent a novel species within the genus Nocardia, for which the name Nocardia mikamii sp. nov. is proposed, with strain W8061T (=DSM 45174T=JCM 15508T) as the type strain.

A short coccoid- to rod-shaped, motile, mesophilic actinobacterium, strain MSL-22T, was isolated from soil on Bigeum Island, Korea. A polyphasic study was undertaken to establish the taxonomic position of this strain. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MSL-22T formed an evolutionary lineage within the radiation of the genus Nocardioides. In particular, it formed a monophyletic lineage with Nocardioides jensenii KCTC 9134T with which it shared the highest sequence similarity of about 97.3%. However, DNA–DNA relatedness demonstrated that strain MSL-22T was distinct from its closest phylogenetic neighbours. The cell-wall peptidoglycan of strain MSL-22T contained ll-diaminopimelic acid. The predominant menaquinone was MK-8(H4). Strain MSL-22T had a cellular fatty acid profile containing straight-chain, branched, unsaturated and 10-methyl fatty acids, with iso-C16 : 0 as the major fatty acid. The DNA G+C content of the strain was 68.7 mol%. On the basis of phenotypic and phylogenetic evidence, the strain is separate from previously described members of the genus Nocardioides and represents a novel species in this genus, for which the name Nocardioides mesophilus sp. nov. is proposed. The type strain is MSL-22T (=DSM 19432T=KCTC 19310T).

The omission of the name ‘Mycobacterium paraffinicum’ from the Approved Lists of Bacterial Names was due to phenotypic confusion surrounding a close relationship with Mycobacterium scrofulaceum. Correspondingly, ‘M. paraffinicum’ strains grew slowly in >7 days, stained acid–alcohol-fast and produced yellow-pigmented, smooth, waxy colonies in the dark at an optimal temperature of 35 °C. However, ‘M. paraffinicum’ strains demonstrated no activity for urease, nicotinamidase or pyrazinamidase and lacked growth at 42 °C, unlike M. scrofulaceum. The mycolic acid pattern, as determined by HPLC, clustered ‘M. paraffinicum’ with M. scrofulaceum, Mycobacterium avium and Mycobacterium parascrofulaceum. Strains were fully susceptible to linezolid, rifabutin, clarithromycin and amikacin. Examination of the historical reference strain of ‘M. paraffinicum’, ATCC 12670, and five additional isolates using comparative studies with 16S rRNA, hsp65 and rpoB gene and concatenated sequences showed that they formed a tight taxonomic group that was distinct from similar non-tuberculous mycobacteria. Multilocus enzyme electrophoresis (MEE) analysis confirmed a close association of the five additional isolates with the reference strain of ‘M. paraffinicum’ with a genetic distance of 0.12 and showed that all six strains were distinct from other closely related species. These genetic results provided unambiguous evidence of the uniqueness of this slowly growing, scotochromogenic species and supported the revival of the name as Mycobacterium paraffinicum (ex Davis, Chase and Raymond 1956) sp. nov., nom. rev. We propose the previously deposited reference strain ATCC 12670T =DSM 44181T =NCIMB 10420T, located in collections worldwide, as the type strain.

A tangerine-coloured, Gram-positive actinobacterial strain, designated F10T, was isolated from the abdominal epidermis of a sea cucumber, Holothuria edulis, collected in seawater off the coast of Japan. A 16S rRNA gene sequence analysis indicated that strain F10T was a member of the class Actinobacteria and was most closely related to Nitriliruptor alkaliphilus ANL-iso2T (87.4 % sequence similarity). Phylogenetic analyses showed that strain F10T represented a novel, deep-rooted, and distinct phylogenetic lineage within the class Actinobacteria and clustered with N. alkaliphilus and uncultured bacteria. The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and rhamnose and galactose as the diagnostic cell-wall sugars. Strain F10T contained C16 : 1 ω7c, C16 : 0 and C17 : 1 ω8c as the major cellular fatty acids. The predominant isoprenoid quinone was MK-9 (H4). The G+C content of the DNA was 68.3 mol%. Based on data from the current polyphasic study, it is proposed that the new marine isolate be placed in a novel genus and be considered a novel species designated Euzebya tangerina gen. nov., sp. nov. within the new family, order and subclass Euzebyaceae fam. nov., Euzebyales ord. nov. and Nitriliruptoridae subclassis nov. in the class Actinobacteria. The type strain of Euzebya tangerina is F10T (=NBRC 105439T =KCTC 19736T).

Six actinomycete strains isolated from soil and plant-litter samples in Indonesia were studied for their taxonomic position by using a polyphasic approach. Phylogenetically, all the strains were located in the broad cluster of the genus Actinokineospora. Chemotaxonomic data [cell-wall diamino acid, meso-diaminopimelic acid; cell-wall peptidoglycan, type III (A1γ); major sugars, galactose and arabinose; major menaquinone, MK-9(H4); major fatty acid, iso-C16 : 0; major phospholipid, phosphatidylethanolamine] supported the affiliation of all six strains to the genus Actinokineospora. The results of DNA–DNA hybridization with DNA from type strains of Actinokineospora species with validly published names revealed three DNA–DNA relatedness groups. Group I (ID03-0561T) showed low relatedness to the other strains studied. The three strains in group II (ID03-0784T, ID03-0808 and ID03-0809) formed a group with high relatedness (98–100 %) and showed low relatedness to the other strains studied. The two strains in group III (ID03-0810T and ID03-0813) showed 58–68 % relatedness to Actinokineospora terrae NBRC 15668T and showed low relatedness (2–24 %) to the other strains studied. The description of three novel species is proposed: Actinokineospora baliensis sp. nov., for the single strain in group I (type strain ID03-0561T =BTCC B-554T =NBRC 104211T), Actinokineospora cibodasensis sp. nov., for the strains in group II (type strain ID03-0784T =BTCC B-555T =NBRC 104212T), and Actinokineospora cianjurensis sp. nov., for the strains in group III (type strain ID03-0810T =BTCC B-558T =NBRC 105526T).

A novel actinomycete, designated strain VN05A0561T, was isolated from plant litter collected at Ba Be National Park, Vietnam. The substrate mycelia and spore chains fragmented in a manner similar to nocardioform actinomycetes; the spores had smooth surfaces and were rod-shaped. Strain VN05A0561T had the following chemotaxonomic characteristics: meso-diaminopimelic acid in the cell-wall peptidoglycan, arabinose and galactose as characteristic sugars, MK-8(H4) as the major isoprenoid quinone, phosphatidylcholine as the diagnostic phospholipid and iso-C16 : 0 as the major cellular fatty acid. Strain VN05A0561T shared low levels of 16S rRNA gene sequence similarity (<97 %) with the type strains of recognized species of the genus Pseudonocardia and could be differentiated from its closest phylogenetic relatives based on phenotypic characteristics. These results suggested that strain VN05A0561T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia babensis sp. nov. is proposed. The type strain is VN05A0561T (=VTCC-A-1757T=NBRC 105793T).

A Gram-stain-positive, aerobic bacterium, designated strain BZ41T, was isolated from hydrocarbon-contaminated soil. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ41T was related to members of the genus Agromyces and showed highest similarity with the type strain of Agromyces ramosus (96.8 %). The morphological, biochemical and chemotaxonomic characteristics of the new isolate were consistent with the description of the genus Agromyces. The cell-wall peptidoglycan of strain BZ41T was of type B2γ and contained the amino acids 2,4-diaminobutyric acid, alanine, glycine and glutamic acid in an approximate molar ratio of 1.8 : 0.7 : 1.1 : 1.0. The predominant cell-wall sugars were galactose, glucose, mannose and rhamnose. Strain BZ41T had MK-12 and MK-11 as major menaquinones and contained anteiso-C15 : 0 and anteiso-C17 : 0 as major fatty acids. The genomic DNA G+C content of strain BZ41T was 69.7 mol%. On the basis of phenotypic characteristics and genotypic analysis, strain BZ41T is considered to represent a novel species of the genus Agromyces, for which the name Agromyces bauzanensis sp. nov. is proposed. The type strain is BZ41T (=DSM 22275T =CGMCC 1.8984T).

A polyphasic taxonomic study of a halotolerant bacterium, isolated from sandy rhizospheric soil in Sarbandar, Persian Gulf, Iran, revealed that strain HM6T represents a novel species within the genus Nocardiopsis. Results of the 16S rRNA gene sequence comparison revealed that strain HM6T clustered with strains of the genus Nocardiopsis, showing the highest degree of 16S rRNA gene sequence similarity to Nocardiopsis quinghaiensis (99.2 %), Nocardiopsis aegyptia (98.5 %) and Nocardiopsis halotolerans (98.3 %). However, DNA–DNA hybridization studies with these type strains revealed less than 39.6 % similarity. Rather than genotypic differences, there are some phenotypic discrepancies between strain HM6T and closely related species of the genus Nocardiopsis. Main morphological and chemotaxonomical features of strain HM6T include: (i) growth characteristics, i.e. the formation of a scant light-yellow to white aerial mycelium and the typical zig-zag form of the hyphae, which fragment during ageing into smooth rod-shaped spores; (ii) the presence of meso-diaminopimelic acid and glucose plus ribose in whole-cell hydrolysates; (iii) the presence of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylinositol, together with three unknown Nocardiopsis-specific phospholipids (close to diphosphatidylglycerol in position) in polar lipid extracts; (iv) the presence of the major menaquinones MK-10(H0), MK-10(H2) and MK-9(H0) in the non-polar fraction; (v) the presence of iso/anteiso-branched plus 10-methyl-branched fatty acids, showing the diagnostic combination for species of the genus Nocardiopsis of iso-16 : 0 (31.1 %), anteiso-17 : 0 (19.2 %), 10-methyl-17 : 0 (5.8 %) and tuberculostearic acid (8.8 %); and (vi) the absence of mycolic acids. Analysis of the 16S rRNA gene sequence revealed that strain HM6T represents a distinct taxon within the genus Nocardiopsis. Based upon genotypic and phenotypic differences from other members of the genus, a novel species, Nocardiopsis sinuspersici sp. nov., is proposed. The type strain is HM6T (=UTMC 00102T =DSM 45277T =CCUG 57624T).

A Gram-positive, coccoid, non-endospore-forming actinobacterium (strain 12-Be-011T) was isolated from indoor wall material. Based on 16S rRNA gene sequence comparisons, strain 12-Be-011T was clearly shown to belong to the genus Microlunatus and was most closely related to Microlunatus panaciterrae Gsoil 954T (95.7 %), Microlunatus soli CC-12602T (94.9 %), Microlunatus ginsengisoli Gsoil 633T (94.8 %), Microlunatus aurantiacus YIM 45721T (95.5 %) and Microlunatus phosphovorus DSM 10555T (94.7 %). The cell-wall peptidoglycan contained ll-diaminopimelic acid as the diagnostic diamino acid. Mycolic acids were absent. The major menaquinone was MK-9(H4). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unknown phospholipids and one unknown glycolipid. The major fatty acids of iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0 supported the affiliation of strain 12-Be-011T to the genus Microlunatus. Physiological and biochemical test results allowed a clear phenotypic differentiation of strain 12-Be-011T from all other species of the genus Microlunatus. Hence, strain 12-Be-011T can be regarded as a representative of a novel species, for which the name Microlunatus parietis sp. nov. is proposed, with the type strain 12-Be-011T (=DSM 22083T=CCM 7636T).

An actinobacterial strain was isolated from subarctic forest soil, and subjected to polyphasic taxonomic characterization. The cell-wall peptidoglycan comprised meso-diaminopimelic acid, alanine and glutamic acid. MK-9(H4) was the predominant isoprenoid quinone, and iso-C17 : 0, iso-C15 : 0 and C16 : 0 were detected as the major cellular fatty acids. Phylogenetic analyses based on 16S rRNA gene sequences showed that this organism was related to members of the suborders Kineosporiineae and Micrococcineae. The phenotypic properties readily differentiated this organism from the phylogenetic neighbours. Based on the phenotypic and genotypic evidence, the strain is assigned to a novel species of a novel genus: Angustibacter luteus gen. nov., sp. nov. with type strain TT07R-79T (=NBRC 105387T =KACC 14249T).

A haloalkaliphilic archaeon, strain JX313T, was isolated from a saline–alkaline soil from Daqing, Heilongjiang Province, China. Its morphological, physiological and biochemical features and 16S rRNA gene sequence were determined. Colonies of the strain were orange–red and cells were non-motile cocci and Gram-stain-variable. The strain required at least 1.7 M NaCl for growth, with optimal growth occurring in 2.0–2.5 M NaCl. Growth was observed at 20–50 °C and pH 8.0–10.5, with optimal growth at 35 °C and pH 10.0. The G+C content of its genomic DNA was 59.3 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed that strain JX313T is associated with the genera Haloterrigena and Natrinema and is most closely related to Haloterrigena salina XH-65T (96.2 % sequence similarity) and Haloterrigena hispanica FP1T (96.2 %). DNA–DNA hybridization experiments revealed that the relatedness of strain JX313T to type strains of related species of the genus Haloterrigena or Natrinema was less than 50 %. Furthermore, the cellular polar lipids of strain JX313T, identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and mannose-2,6-disulfate (1→2)-glucose glycerol diether (S2-DGD), were consistent with the polar lipid characteristics of the genus Haloterrigena. Therefore, phylogenetic analysis, phenotypic assessment and chemotaxonomic data showed that JX313T represents a novel species within the genus Haloterrigena, for which the name Haloterrigena daqingensis sp. nov. is proposed. The type strain is JX313T (=CGMCC 1.8909T =NBRC 105739T).

A halophilic archaeon, strain RO1-6T, was isolated from a marine solar saltern in eastern China. Cells of strain RO1-6T were pleomorphic and motile and stained Gram-negative. Strain RO1-6T grew well on complex medium and colonies were red-pigmented. It was able to grow at 20–50 °C (optimum 37 °C), in 2.1–5.1 M NaCl (optimum 3.9 M NaCl), in 0.05–0.70 M MgCl2 (optimum 0.30 M MgCl2) and at pH 6.5–8.0 (optimum pH 7.0). Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 12 % (w/v). The major polar lipids of strain RO1-6T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and two glycolipids that were chromatographically identical to S-DGD-1 and S2-DGD. The 16S rRNA gene sequence of strain RO1-6T showed similarities of 96.9 and 96.4 % to those of the type strains of Halosarcina pallida and Halogeometricum borinquense, respectively, members of the most closely related recognized genera within the family Halobacteriaceae. The DNA G+C content of strain RO1-6T was 61.2 mol%. Phenotypic characterization and phylogenetic analysis revealed that strain RO1-6T is related to Halosarcina pallida and represents a novel species of the genus Halosarcina, for which the name Halosarcina limi sp. nov. is proposed; the type strain is RO1-6T (=CGMCC 1.8711T =JCM 16054T).

A Gram-negative, rod-shaped, non-spore-forming, strictly aerobic strain with gliding motility, designated JAMB N27T, was isolated from sediment adjacent to sperm whale carcasses off Kagoshima, Japan, at a depth of 219 m. Strain JAMB N27T contained MK-6 as the major isoprenoid quinone and iso-C15 : 0, iso-C15 : 1, C16 : 1 and iso-C17 : 1 as the predominant fatty acids. Casein, chitin, gelatin and starch were degraded. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JAMB N27T represented a separate lineage within the genus Aquimarina. The DNA G+C content of strain JAMB N27T was 33.1 mol%. DNA–DNA relatedness values between strain JAMB N27T and type strains of species of the genus Aquimarina were significantly lower than the cut-off value accepted for the definition of a novel species. Therefore, strain JAMB N27T represents a novel species, for which the name Aquimarina macrocephali sp. nov. is proposed. The type strain is JAMB N27T (=JCM 15542T=NCIMB 14508T).

Two novel heterotrophic, facultatively anaerobic, gliding and yellow-pigmented bacteria, designated strains KMM 6270T and KMM 6320, were isolated from different marine environments and studied using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis placed the strains within the family Flavobacteriaceae. Strains KMM 6270T and KMM 6320 were most closely related to the type strains of recognized species of the genus Salinimicrobium (95.0–96.6 % 16S rRNA gene sequence similarity). The G+C content of the genomic DNA was 40–41 mol%. The strains grew with 0.5–15 % (w/v) NaCl (optimum 4 % NaCl) and at 4–41 °C (optimum 28–32 °C). Aesculin and gelatin were hydrolysed, but agar, casein, DNA and chitin were not. The phylogenetic data taken together with the results of the genotypic and phenotypic studies permit the classification of strains KMM 6270T and KMM 6320 as members of a novel species of the genus Salinimicrobium, for which the name Salinimicrobium marinum sp. nov. is proposed. The type strain is KMM 6270T (=KCTC 12719T=LMG 25395T).

A novel Gram-negative, rod-shaped, non-motile bacterium, designated strain LW7T, was isolated from a water sample collected at a depth of 4.5 m from Lonar Lake in Buldhana district, Maharastra, India. The cell suspension was dark-reddish orange due to the presence of carotenoids. The fatty acids were dominated by large amounts of iso-C15 : 0 (59.6 %) and iso-C17 : 0 3-OH (8.9 %). Strain LW7T contained MK-4 and MK-5 as the major respiratory quinones and phosphatidylglycerol and phosphatidylethanolamine as the major phospholipids. 16S rRNA gene sequence analysis indicated that Belliella baltica, a member of family ‘Cyclobacteriaceae’ (phylum Bacteroidetes), is the closest related species, with a sequence similarity of 94.0 % to the type strain. Other members of the family ‘Cyclobacteriaceae’ had sequence similarities of <93.3 %. Based on the above-mentioned phenotypic and phylogenetic characteristics, strain LW7T is proposed as a representative of a new genus and species, Nitritalea halalkaliphila gen. nov., sp. nov. The type strain of Nitritalea halalkaliphila is LW7T (=CCUG 57665T =JCM 15946T =NCCB 100279T). The genomic DNA G+C of strain LW7T is 49 mol%.

A Gram-staining-negative, yellow-coloured, strictly aerobic, non-spore-forming, rod-shaped bacterium, designated HS39T, isolated from a soil sample collected from a natural Populus euphratica forest in Xinjiang, China, was characterized using a polyphasic approach. The isolate grew optimally at 30–37 °C, at pH 6.5–8.0 and with 0–3 % NaCl. Analysis of the 16S rRNA gene sequence of strain HS39T revealed that it is a member of the genus Sphingobacterium. Sphingobacterium mizutaii ATCC 33299T was the nearest relative (94.0 % 16S rRNA gene sequence similarity). The G+C content of the genomic DNA was 40.2 mol%. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c). The predominant isoprenoid quinone was MK-7. On the basis of phenotypic properties and phylogenetic inference, strain HS39T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium shayense sp. nov. is proposed. The type strain is HS39T (=CCTCC AB 209006T =NRRL B-59203T).

A yellow-pigmented bacterial strain, R4-1AT, isolated from the midgut of the mosquito Culex quinquefasciatus (a vector of lymphatic filariasis), was studied using a polyphasic approach. Cells of the isolate were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequence of this organism with sequences of type strains of the most closely related species clearly showed an allocation to the genus Chryseobacterium, with the highest sequence similarities (all 97.9 %) to Chryseobacterium jejuense JS17-8T, C. indologenes ATCC 29897T, C. arthrosphaerae CC-VM-7T and C. aquifrigidense CW9T. 16S rRNA gene sequence similarities to type strains of other Chryseobacterium species were below 97.5 %. The fatty acid profile of strain R4-1AT included the major fatty acids iso-15 : 0, summed feature 4 (comprising iso-15 : 0 2-OH and/or 16 : 1ω7c), iso-17 : 1ω9c and iso-17 : 0 3-OH. DNA–DNA hybridizations with C. jejuense KACC 12501T, C. indologenes CCUG 14556T, C. arthrosphaerae CC-VM-7T and C. aquifrigidense KCTC 12894T resulted in relatedness values of 38.3 % (reciprocal 30.5 %), 29.4 % (32.1 %), 23.2 % (37.2 %) and 29.5 % (47.1 %), respectively. These results and the differentiating biochemical and chemotaxonomic properties show that strain R4-1AT represents a novel species, for which the name Chryseobacterium culicis sp. nov. is proposed. The type strain is R4-1AT (=LMG 25442T =CCM 7716T).

Three bacterial isolates from air samples in Korea, designated strains 6424S-25T, 6515J-31T and 6424S-61T, were characterized using a polyphasic approach. The cells were strictly aerobic, Gram-stain-negative, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis of their 16S rRNA gene sequences revealed a clear affiliation with the phylum Bacteroidetes. Strains 6424S-25T and 6515J-31T showed 16S rRNA gene sequence similarities of 92.7–94.8 % to type strains of recognized species of the genus Adhaeribacter and strain 6424S-61T was closely related to Segetibacter koreensis Gsoil 664T (93.9 % similarity). The G+C contents of the DNA of strains 6424S-25T, 6515J-31T and 6424S-61T were 44.5, 43.9 and 38.4 mol%, respectively. Major fatty acids of strains 6424S-25T and 6515J-31T were summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), iso-C15 : 0 and C16 : 1 ω5c. The fatty acid content of strain 6424S-61T mainly comprised iso-C15 : 1 G and iso-C15 : 0. Comparative analysis of phenotypic and phylogenetic traits indicated that strains 6424S-25T and 6515J-31T represented two novel species of the genus Adhaeribacter and that strain 6424S-61T should be considered as a novel species of the genus Segetibacter. The names Adhaeribacter aerophilus sp. nov. (type strain 6424S-25T =KACC 14118T =NBRC 106134T), Adhaeribacter aerolatus sp. nov. (type strain 6515J-31T =KACC 14117T =NBRC 106133T) and Segetibacter aerophilus sp. nov. (type strain 6424S-61T =KACC 14119T =NBRC 106135T) are proposed for these organisms.