- Volume 61, Issue 4, 2011
Volume 61, Issue 4, 2011
- Notification List
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Notification that new names and new combinations have appeared in volume 61, part 1, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- New Taxa
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- Actinobacteria
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Actinoallomurus oryzae sp. nov., an endophytic actinomycete isolated from roots of a Thai jasmine rice plant
The novel strain GMKU 370T was isolated from roots of a Thai jasmine rice plant (Oryza sativa L. ‘KDML 105’) collected from Pathum Thani Rice Research Center, Pathum Thani province, Thailand. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GMKU 370T formed a distinct clade within the genus Actinoallomurus. Strain GMKU 370T contained meso-diaminopimelic acid and lysine in the cell-wall peptidoglycan and galactose and madurose as whole-cell sugars. No mycolic acids were detected. The predominant menaquinones were MK-9(H6) and MK-9(H8). The polar phospholipids consisted of phosphatidylglycerol and phosphatidylinositol. These chemical properties reveal that strain GMKU 370T belongs to the genus Actinoallomurus. Strain GMKU 370T is distinct from the phylogenetically closely related type strains Actinoallomurus iriomotensis NBRC 103685T and Actinoallomurus coprocola NBRC 103688T (99.20 % 16S rRNA gene sequence similarity to both) in terms of differences in phenotypic characteristics and DNA–DNA relatedness (51 and 17 %, respectively). It is proposed that strain GMKU 370T represents a novel species of the genus Actinoallomurus, for which the name Actinoallomurus oryzae sp. nov. is proposed. The type strain is GMKU 370T ( = BCC 31373T = NBRC 105246T).
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Pseudonocardia eucalypti sp. nov., an endophytic actinobacterium with a unique knobby spore surface, isolated from roots of a native Australian eucalyptus tree
More LessA novel strain, designated EUM 374T, was isolated from the root of a native Australian eucalyptus tree, Eucalyptus microcarpa, and subjected to a range of morphological, phylogenetic and chemotaxonomic analyses. The strain was Gram-reaction-positive with well-developed aerial mycelia, which fragmented into rod-shaped spores that had unique knobby protrusions on the spore surface. Substrate mycelia were not present in the media used. Strain EUM 374T grew as a film on the surface of static liquid culture medium but did not grow under shaking conditions. Phylogenetic evaluation based on 16S rRNA gene sequences identified the new isolate as belonging to the family Pseudonocardiaceae with sequence similarities of 96.1 and 96.3 % to Pseudonocardia acaciae GMKU095T and Pseudonocardia spinosispora LM 141T, respectively, and 93–96 % sequence similarity to other members of the genus Pseudonocardia. The results of comprehensive phylogenetic analyses, including physiological and biochemical tests, differentiated strain EUM 374T from related members of the genus Pseudonocardia. Based on the phenotypic, phylogenetic and chemotaxonomic evidence, strain EUM 374T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia eucalypti sp. nov. is proposed. The type strain is EUM 374T ( = DSM 45351T = ACM 5285T).
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Pseudonocardia mongoliensis sp. nov. and Pseudonocardia khuvsgulensis sp. nov., isolated from soil
More LessTwo actinomycetes, designated MN08-A0270T and MN08-A0297T, were isolated from soil from the area around Khuvsgul Lake, Khuvsgul province, Mongolia, and subjected to phenotypic and genotypic characterization. They produced well-developed, branched substrate hyphae and, similar to closely related species of the genus Pseudonocardia, produced zigzag-shaped aerial hyphae by acropetal budding and blastospores. A comparative analysis of 16S rRNA gene sequences indicated that strains MN08-A0270T and MN08-A0297T formed two distinct clades within the genus Pseudonocardia and were respectively most closely related to Pseudonocardia yunnanensis NBRC 15681T (97.3 % similarity) and Pseudonocardia thermophila IMSNU 20112T (97.1 %). Chemotaxonomic characteristics, including cell-wall diaminopimelic acid, whole-cell sugars, fatty acid components and major menaquinones, suggested that the two organisms belonged to the genus Pseudonocardia. Strains MN08-A0270T and MN08-A0297T could be differentiated from each other and from closely related species of the genus Pseudonocardia by physiological and biochemical characteristics, predominant fatty acids, menaquinones and whole-cell sugar components. Combined with the results of a broad range of phenotypic tests and DNA–DNA hybridization data and phylogenetic analysis, these results support the conclusion that these strains represent two novel species of the genus Pseudonocardia, for which we propose the names Pseudonocardia mongoliensis sp. nov. (type strain MN08-A0270T = NBRC 105885T = VTCC D9-25T) and Pseudonocardia khuvsgulensis sp. nov. (type strain MN08-A0297T = NBRC 105886T = VTCC D9-26T).
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Nonomuraea endophytica sp. nov., an endophytic actinomycete isolated from Artemisia annua L.
A Gram-stain-positive, aerobic, non-motile actinomycete strain, designated YIM 65601T, was studied by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain YIM 65601T should be assigned to the genus Nonomuraea, with highest 16S rRNA gene sequence similarities to Nonomuraea candida HMC10T (98.8 %), N. salmonea DSM 43678T (98.7 %), N. turkmeniaca DSM 43926T (98.5 %), N. roseola DSM 43767T (98.4 %), N. dietziae IFO 14309T (98.2 %) and N. kuesteri GW 14-1925T (98.1 %). 16S rRNA gene sequence similarities to strains of other Nonomuraea species were below 98.0 %. Morphological and chemotaxonomic properties of the isolate were consistent with those of members of the genus Nonomuraea. The results of DNA–DNA hybridization and physiological and biochemical tests and fatty acid profiles allowed genotypic and phenotypic differentiation of strain YIM 65601T from closely related species. Thus, YIM 65601T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea endophytica sp. nov. is proposed, with YIM 65601T ( = CCTCC AA 209037T = DSM 45385T) as the type strain.
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Herbidospora sakaeratensis sp. nov., isolated from soil, and reclassification of Streptosporangium claviforme as a later synonym of Herbidospora cretacea
An actinomycete strain, DMKUA 205T, was isolated from a soil sample collected from the Sakaerat Biosphere Reserve in Nakhonratchasima Province, Thailand. The novel strain produced short chains of non-motile spores on the tips of long sporophores branching from the vegetative hyphae. The morphological and chemotaxonomic properties of this new isolate corresponded to those of members of the genus Herbidospora. Furthermore, 16S rRNA gene sequence analysis showed that the strain was closely related to members of the genus Herbidospora. Phenotypic properties and DNA–DNA relatedness values differentiated the new strain from its closest phylogenetic relatives Herbidospora yilanensis 0351M-12T (35–54 % DNA–DNA relatedness) and Herbidospora daliensis 0385M-1T (58–65 % relatedness). On the basis of phenotypic, genotypic and phylogenetic data, strain DMKUA 205T could be clearly distinguished from the type strains of H. yilanensis and H. daliensis. Therefore, strain DMKUA 205T represents a novel species, for which the name Herbidospora sakaeratensis sp. nov. is proposed. The type strain is strain DMKUA 205T ( = BCC 11662T = NBRC 102641T). In addition, the DNA–DNA hybridization results from this study revealed that Streptosporangium claviforme is a later synonym of Herbidospora cretacea.
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Olsenella umbonata sp. nov., a microaerotolerant anaerobic lactic acid bacterium from the sheep rumen and pig jejunum, and emended descriptions of Olsenella, Olsenella uli and Olsenella profusa
More LessStrain A2 is an anaerobic, variably Gram-stain-positive, non-spore-forming, small and irregularly rod-shaped bacterium from the ruminal fluid of a sheep that has been described informally as a representative of ‘Olsenella (basonym Atopobium) oviles’. Three phenotypically similar bacterial strains (lac15, lac16 and lac31T) were isolated in concert with Veillonella magna lac18T from the mucosal jejunum of a pig. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strains A2, lac15, lac16 and lac31T formed a genetically coherent group (100 % interstrain sequence similarity) within the bigeneric Olsenella–Atopobium branch of the family Coriobacteriaceae, class Actinobacteria. This group was most closely related to the type strains of the two recognized Olsenella species, namely Olsenella uli (sequence similarity of 96.85 %) and Olsenella profusa (sequence similarity of 97.20 %). The sequence similarity to the type strain of Atopobium minutum, the type species of the genus Atopobium, was 92.33 %. Unlike those of O. uli and O. profusa, outgrown colonies of strains A2, lac15, lac16 and lac31T were opaque and greyish-white with an umbonate elevation on solid culture media. The four novel strains were characterized as being well-adapted and presumably indigenous to the gastrointestinal tract of homoeothermic vertebrates: they were mesophilic, microaerotolerant, neutrophilic and acidotolerant, bile-resistant, mucin-utilizing and markedly peptidolytic lactic acid bacteria. The results of DNA–DNA hybridizations, cellular fatty acid analysis and other differential phenotypic (physiological and biochemical) tests confirmed that strains A2, lac15, lac16 and lac31T represent a novel species of the genus Olsenella. On the basis of the genotypic and phenotypic results, we therefore describe Olsenella umbonata sp. nov., with lac31T ( = CCUG 58604T = DSM 22620T = JCM 16156T) as the type strain and A2 ( = CCUG 58212 = DSM 22619 = JCM 16157) as an additionally available reference strain. Also, based on our data, we propose emended descriptions of the genus Olsenella and the species Olsenella uli and Olsenella profusa.
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Longispora fulva sp. nov., isolated from a forest soil, and emended description of the genus Longispora
More LessA novel actinomycete, strain KZ0017T, was isolated from a forest soil collected in Ohnuma, Fukushima, Japan. Strain KZ0017T formed spore chains borne on top of short sporophores arising from vegetative hyphae. Spores were non-motile and cylindrical with smooth surfaces. Strain KZ0017T contained meso-diaminopimelic (A2pm) acid, 3-OH A2pm, d-glutamic acid, glycine and l-alanine in the cell-wall peptidoglycan, and xylose, mannose, galactose, rhamnose and ribose in cell-wall hydrolysates. The acyl type of the cell-wall polysaccharides was glycolyl. The predominant menaquinones were MK-10(H4) and MK-10(H6); MK-10(H8) was a minor component. The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol and several unknown lipids and glycolipids. The major fatty acids were iso-C16 : 0, 10-methyl-C17 : 0 and iso-C17 : 1ω9c. The DNA G+C content was 70.7 mol%. The 16S rRNA gene sequence of the isolate formed a monophyletic cluster with the single member of the genus Longispora in the family Micromonosporaceae. On the basis of morphological, chemotaxonomic and phylogenetic properties, strain KZ0017T represents a novel species of the genus Longispora, for which the name Longispora fulva sp. nov. is proposed; the type strain is KZ0017T ( = NBRC 105670T = DSM 45356T).
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Actinophytocola timorensis sp. nov. and Actinophytocola corallina sp. nov., isolated from soil
Two actinomycete strains, ID05-A0653T and ID06-A0464T, were isolated from soils of West Timor and Lombok island, respectively, in Indonesia. 16S rRNA gene sequence analysis clearly demonstrated that the isolates belonged to the family Pseudonocardiaceae and were closely related to the genus Actinophytocola. Strains ID05-A0653T and ID06-A0464T exhibited 98.1 and 98.2 % 16S rRNA gene sequence similarity, respectively, with Actinophytocola oryzae GMKU 367T. The isolates grew well on ISP media and produced white aerial mycelium. Short spore chains were formed directly on the substrate mycelium. The isolates contained meso-diaminopimelic acid, arabinose and galactose as cell-wall components, MK-9(H4) as the sole isoprenoid quinone, iso-C16 : 0 as the major cellular fatty acid and phosphatidylethanolamine as the diagnostic polar lipid. The DNA G+C contents of strains ID05-A0653T and ID06-A0464T were 69.7 and 71.2 mol%, respectively. On the basis of phenotypic characteristics, DNA–DNA relatedness and 16S rRNA gene sequence comparisons, strains ID05-A0653T and ID06-A0464T each represent a novel species of the genus Actinophytocola, for which the names Actinophytocola timorensis sp. nov. (type strain ID05-A0653T = BTCC B-673T = NBRC 105524T) and Actinophytocola corallina sp. nov. (type strain ID06-A0464T = BTCC B-674T = NBRC 105525T) are proposed.
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Amycolatopsis thailandensis sp. nov., a poly(l-lactic acid)-degrading actinomycete, isolated from soil
More LessA novel actinomycete that was capable of degrading poly(l-lactic acid), strain CMU-PLA07T, was isolated from soil in northern Thailand. Strain CMU-PLA07T had biochemical, chemotaxonomic, morphological and physiological properties that were consistent with its classification in the genus Amycolatopsis. 16S rRNA gene sequence analysis showed that the isolate formed a phyletic line within the genus Amycolatopsis. Strain CMU-PLA07T was most similar to Amycolatopsis coloradensis IMSNU 22096T (99.5 % 16S rRNA gene sequence similarity) and Amycolatopsis alba DSM 44262T (99.4 %). However, strain CMU-PLA07T was distinguishable from the type strains of species of the genus Amycolatopsis on the basis of DNA–DNA relatedness and phenotypic data. Therefore, strain CMU-PLA07T is considered to represent a novel species of the genus Amycolatopsis, for which the name Amycolatopsis thailandensis sp. nov. is proposed. The type strain is CMU-PLA07T ( = JCM 16380T = BCC 38279T).
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Corynebacterium humireducens sp. nov., an alkaliphilic, humic acid-reducing bacterium isolated from a microbial fuel cell
More LessA novel halotolerant, alkaliphilic, humic acid-reducing bacterium, designated MFC-5T, was isolated from a microbial fuel cell that was fed continuously with artificial wastewater (pH 10.0). Cells were Gram-positive-staining, facultatively anaerobic, non-fermentative, non-motile rods and had a G+C content of 59.0 mol%. Microbial growth was observed with <13 % (w/v) NaCl (optimum 10 %), at pH 7.0–11.0 (optimum pH 9.0) and at 25–45 °C (optimum 37 °C). Strain MFC-5T was active in the anaerobic reduction of a humic acid analogue, anthraquinone-2,6-disulphonate, with lactate, formate, acetate, ethanol or sucrose as the electron donor. The major cellular fatty acids were C18 : 1ω9c (42.68 %), C16 : 0 (33.69 %), C18 : 0 (7.56 %), C17 : 1ω8c (5.14 %) and C17 : 0 (3.39 %). Phylogenetic analysis demonstrated that strain MFC-5T displayed >3 % 16S rRNA gene sequence divergence from its closest relatives. Based on phenotypic, genetic and phylogenetic analysis, a novel species, Corynebacterium humireducens sp. nov., is proposed. The type strain is MFC-5T ( = NBRC 106098T = CGMCC 2452T = DSM 45392T).
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Streptomyces aomiensis sp. nov., isolated from a soil sample using the membrane-filter method
More LessA Gram-positive actinobacterium, designated M24DS4T, was isolated from a soil sample collected from Aomi, Tokyo, Japan, using the membrane-filter method. Strain M24DS4T exhibited low 16S rRNA gene sequence similarity (96.1 %) with Streptomyces scabrisporus NBRC 100760T. Cell hydrolysates contained the ll-isomer of diaminopimelic acid and the predominant quinones were MK-9(H8) and MK-9(H6). The genomic DNA G+C content was 75 mol%. Comparison of the characteristics of strain M24DS4T and related members of the genus Streptomyces with validly published names showed that the strain represents a novel species of the genus, for which the name Streptomyces aomiensis sp. nov. is proposed. The type strain is M24DS4T ( = NBRC 106164T = KACC 14925T).
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Amycolatopsis samaneae sp. nov., isolated from roots of Samanea saman (Jacq.) Merr.
A novel actinomycete, designated strain RM287T, was isolated from surface-sterilized roots of Samanea saman (Jacq.) Merr., collected from Bangkok, Thailand. The status of the novel strain was determined using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism formed a distinct phyletic line within the radiation of the genus Amycolatopsis. The 16S rRNA gene sequence similarity indicated that strain RM287T was most closely related to Amycolatopsis mediterranei IMSNU 20056T (97.4 %), A. rifamycinica DSM 46095T (97.2 %), A. kentuckyensis NRRL B-24129T (97.2 %), A. pretoriensis DSM 44654T (97 %) and A. australiensis DSM 44671T (97 %). The novel organism was found to have chemical properties typical of members of the genus Amycolatopsis such as meso-diaminopimelic acid as the dignostic diamino acid in the cell-wall peptidoglycan and arabinose and galactose as the diagnostic sugars. The major menaquinone was MK-9(H4). The major fatty acids were iso-C16 : 0 iso-C15 : 0, iso 2-OH-C16 : 0 and iso-C17 : 0. The DNA G+C content was 71.7 mol%. Phenotypic data clearly distinguished the novel isolate from its closest relatives. The combined genotypic and phenotypic data indicated that strain RM287T represented a novel species of the genus Amycolatopsis. The proposed name for this organism is Amycolatopsis samaneae sp. nov., with the type strain RM287T ( = TISTR 1919T = BCC 35842T = NBRC 106095T).
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Leucobacter chromiiresistens sp. nov., a chromate-resistant strain
More LessA Gram-positive, irregular rod-shaped, non-motile, yellow-pigmented bacterium, strain JG 31T, was isolated in the course of identifying chromium-resistant soil bacteria. 16S rRNA gene sequence analysis of the isolated bacterium indicated its phylogenetic position within the genus Leucobacter. Binary 16S rRNA gene sequence alignments of the isolated bacterium with the 11 species of the genus recognized at the time of writing revealed sequence similarities of more than 97 % with Leucobacter alluvii (GenBank accession no: AM072820; 99.4 %), Leucobacter iarius (AM040493; 98.2 %), Leucobacter aridicollis (AJ781047; 97.8 %), Leucobacter komagatae (AB007419; 97.4 %), Leucobacter chironomi (EU346911; 97.1 %) and Leucobacter luti (AM072819; 97.1 %). In contrast, DNA–DNA hybridization experiments showed similarity values below 28 % for DNA samples from the most closely related type strains of L. alluvii, L. aridicollis and L. iarius. Protein analysis by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and automated RiboPrinting using the restriction enzyme PvuII differentiated strain JG 31T from all type strains of the genus Leucobacter. The dominant fatty acids of the novel isolate were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, while the quinone system consisted of menaquinones MK-11, MK-10, MK-9 and MK-8. In a B-type cross-linked peptidoglycan, the cell-wall amino acids were alanine, glycine, threonine, glutamic acid and 2,4-diaminobutyric acid. Strain JG 31T was able to grow in a medium containing up to 300 mM K2CrO4 and showed cellular aggregation in response to chromate stress. From biochemical and genomic analyses, the new strain is considered to represent a novel species of the genus Leucobacter, for which the name Leucobacter chromiiresistens sp. nov. is proposed. The type strain is strain JG 31T ( = DSM 22788T = CCOS 200T).
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Myceligenerans halotolerans sp. nov., an actinomycete isolated from a salt lake, and emended description of the genus Myceligenerans
A halotolerant actinomycete strain, designated XJEEM 11063T, was isolated from a salt lake in Xinjiang province, north-western China. Strain XJEEM 11063T grew at pH 6.0–8.0 (optimal growth at pH 7.0), between 10 and 40 °C (optimal growth at 28–37 °C) and at salinities of 0–10 % (w/v) NaCl (optimal growth at 0–5 %, w/v). The peptidoglycan type was A4α, and the whole-cell hydrolysates contained glucose, mannose and arabinose. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. MK-9(H4) was the predominant menaquinone and the polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, two unknown phospholipids and three unknown glycolipids. The genomic DNA G+C content was 71.8 mol%. The chemotaxonomic properties supported the affiliation of strain XJEEM 11063T to the genus Myceligenerans. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism was most closely related to Myceligenerans xiligouense XLG9A10.2T (98.3 %) and Myceligenerans crystallogenes DSM 17134T (97.0 %). However, it had relatively low values for DNA–DNA relatedness with the above strains (56.0 % and 47.5 %, respectively). Thus, on the basis of the results from this study, a novel species, Myceligenerans halotolerans sp. nov., is proposed. The type strain is XJEEM 11063T ( = DSM 21949T = CCTCC AA 208063T).
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Arthrobacter livingstonensis sp. nov. and Arthrobacter cryotolerans sp. nov., salt-tolerant and psychrotolerant species from Antarctic soil
More LessTwo novel cold-tolerant, Gram-stain-positive, motile, facultatively anaerobic bacterial strains, LI2T and LI3T, were isolated from moss-covered soil from Livingston Island, Antarctica, near the Bulgarian station St Kliment Ohridski. A rod–coccus cycle was observed for both strains. 16S rRNA gene sequence analysis revealed an affiliation to the genus Arthrobacter, with the highest similarity to Arthrobacter stackebrandtii and Arthrobacter psychrochitiniphilus for strain LI2T (97.8 and 97.7 % similarity to the respective type strains) and to Arthrobacter kerguelensis and Arthrobacter psychrophenolicus for strain LI3T (97.4 and 97.3 % similarity to the respective type strains). The growth temperature range was −6 to 28 °C for LI2T and −6 to 24 °C for LI3T, with an optimum at 16 °C for both strains. Growth occurred at 0–10 % (w/v) NaCl, with optimum growth at 0–1 % (w/v) for LI2T and 0.5–3 % (w/v) for LI3T. The pH range for growth was pH 4–9.5 with an optimum of pH 8 for LI2T and pH 6.5 for LI3T. The predominant fatty acids were anteiso-C15 : 0, C18 : 0 and anteiso-C17 : 0 for LI2T and anteiso-C15 : 0 and C18 : 0 for LI3T. Physiological and biochemical tests clearly differentiated strain LI2T from A. stackebrandtii and A. psychrochitiniphilus and strain LI3T from A. kerguelensis and A. psychrophenolicus. Therefore, two novel species within the genus Arthrobacter are proposed: Arthrobacter livingstonensis sp. nov. (type strain LI2T = DSM 22825T = NCCB 100314T) and Arthrobacter cryotolerans sp. nov. (type strain LI3T = DSM 22826T = NCCB 100315T).
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- Archaea
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Halogranum gelatinilyticum sp. nov. and Halogranum amylolyticum sp. nov., isolated from a marine solar saltern, and emended description of the genus Halogranum
More LessTwo extremely halophilic archaeal strains, designated TNN44T and TNN58T, were isolated from Tainan marine solar saltern near Lianyungang city, Jiangsu province, China. Cells of the two strains were pleomorphic and Gram-stain-negative; colonies were red-pigmented. Strains TNN44T and TNN58T were able to grow at 20–50 °C (optimum 37 °C for both), in the presence of 1.4–5.1 M NaCl (optimum 3.4–3.9 M NaCl) and at pH 5.5–9.0 (optimum pH 6.5–7.0); neither strain required Mg2+ for growth. Cells lysed in distilled water. On the basis of 16S rRNA gene sequence analysis, strains TNN44T and TNN58T were related closely to Halogranum rubrum RO2-11T (96.2 and 97.2 % similarity, respectively). The polar lipids of the two strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate (trace), and one major glycolipid and one minor glycolipid chromatographically identical to sulfated mannosyl glucosyl diether and mannosyl glucosyl diether, respectively; other trace unidentified lipids were also detected. The DNA G+C content of strains TNN44T and TNN58T was 64.0 and 62.0 mol%, respectively. The level of DNA–DNA relatedness between strains TNN44T and TNN58T was 37.2 %, and these two strains showed a low level of DNA–DNA relatedness with Halogranum rubrum RO2-11T (40.6 and 44.4 %, respectively). Two novel species of the genus Halogranum are proposed to accommodate these two strains, Halogranum gelatinilyticum sp. nov. (type strain TNN44T = CGMCC 1.10119T = JCM 16426T) and Halogranum amylolyticum sp. nov. (type strain TNN58T = CGMCC 1.10121T = JCM 16428T).
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Halomarina oriensis gen. nov., sp. nov., a halophilic archaeon isolated from a seawater aquarium
More LessA novel halophilic archaeon, strain KeC-11T, was isolated from a seawater aquarium at the Ocean Research Institute, University of Tokyo, Japan. The strain was aerobic, Gram-negative and chemo-organotrophic, growing optimally at 37 °C, at pH 7.0–8.0 and in 2.7 M (16 %) NaCl. The strain required at least 10 mM magnesium ions for growth. Cells of strain KeC-11T were non-motile and generally irregular coccoids or discoids. The DNA G+C content of the isolate was 67.7 mol%. Phylogenetic tree reconstructions indicated that it was distantly related to the other recognized members of the family Halobacteriaceae, with the closest relative being Natronomonas pharaonis GabaraT (91 % sequence similarity). The strain contained C20C20 and C20C25 diether derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, a glycolipid chromatographically identical to the glycosyl-mannosyl-glucosyl diether (TGD-2) and at least one unidentified glycolipid. Phenotypic characterization and phylogenetic data support the placement of isolate KeC-11T in a novel species in a new genus within the family Halobacteriaceae, for which the name Halomarina oriensis gen. nov., sp. nov. is proposed; the type strain is KeC-11T ( = JCM 16495T = KCTC 4074T).
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Haloplanus aerogenes sp. nov., an extremely halophilic archaeon from a marine solar saltern
More LessHalophilic archaeal strain TBN37T was isolated from Taibei marine solar saltern near Lianyungang city of Jiangsu province, China. Cells were pleomorphic, flat and contained gas vesicles. Cells of strain TBN37T stained Gram-negative and the colonies were pink-pigmented. The strain was able to grow at 25–50 °C (optimum, 37–40 °C), with 1.4–5.1 M NaCl (optimum, 2.1 M NaCl), with 0–1.0 M MgCl2 (optimum, 0.01 M MgCl2) and at pH 6.0–9.0 (optimum, pH 7.5). Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8 % (w/v). The major polar lipids of strain TBN37T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and one major glycolipid chromatographically identical to sulfated mannosyl glucosyl diether (S-DGD-1). On the basis of 16S rRNA gene sequence analysis, strain TBN37T was closely related to Haloplanus natans and Haloplanus vescus, with the same similarity of 97.4 %. The DNA G+C content of strain TBN37T is 64.1 mol%. DNA–DNA hybridization values between strain TBN37T and Haloplanus natans JCM 14081T and between strain TBN37T and Haloplanus vescus RO5-8T were 37.6 % and 42.1 %, respectively. It was concluded that strain TBN37T represents a novel species of the genus Haloplanus, for which the name Haloplanus aerogenes sp. nov. is proposed. The type strain is TBN37T ( = CGMCC 1.10124T = JCM 16430T).
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- Bacteroidetes
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Prevotella fusca sp. nov. and Prevotella scopos sp. nov., isolated from the human oral cavity
More LessTwo strains of anaerobic, Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to belong to two separate taxa. Phylogenetic analysis of full-length 16S rRNA gene sequences showed that the strains were both related to, but distinct from, the type strain of Prevotella melaninogenica. Two novel species, Prevotella fusca sp. nov. and Prevotella scopos sp. nov., are proposed to accommodate these strains. Both strains were saccharolytic and produced acetic and succinic acids, with lesser amounts of lactic and isovaleric acids, as end products of fermentation, and both were sensitive to 20 % bile. The principal cellular long-chain fatty acids of both strains were ai-C15 : 0, 3-OH i-C17 : 0, 3-OH C16 : 0, i-C15 : 0 and C16 : 0. The DNA G+C contents of the type strains of Prevotella fusca (W1435T = DSM 22504T = CCUG 57946T) and Prevotella scopos (W2052T = DSM 22613T = CCUG 57945T) were 43 and 41 mol%, respectively. The two species could be differentiated by gelatin hydrolysis, cellobiose and ribose fermentation, and production of β-glucosidase.
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Hymenobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil
More LessA non-motile, rod-shaped, red-pigmented bacterium, designated strain BZ33rT, was isolated from soil of an industrial site. Cells stained Gram-negative and were aerobic and psychrophilic, showing good growth at 1–20 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ33rT was related to members of the genus Hymenobacter and had highest sequence similarity with Hymenobacter aerophilus DSM 13606T (97.5 %). The predominant cellular fatty acids were anteiso-C15 : 0 (20.3 %), summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH; 20.2 %), iso-C15 : 0 (20.0 %), summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B; 8.2 %) and C16 : 1ω5c (7.9 %). Strain BZ33rT had MK-7 as the major menaquinone. The polyamine pattern contained sym-homospermidine as the major compound with moderate amounts of spermidine. Phosphatidylethanolamine, three unknown aminophospholipids, two unknown aminolipids, two unknown glycolipids and five unknown polar lipids were present in the polar lipid profile. The G+C content of the DNA was 61.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain BZ33rT is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacter psychrophilus sp. nov. is proposed. The type strain is BZ33rT ( = DSM 22290T = CGMCC 1.8975T = LMG 25548T).
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Kordia periserrulae sp. nov., isolated from a marine polychaete Periserrula leucophryna,and emended description of the genus Kordia
More LessA Gram-negative, chemoheterotrophic, yellow-pigmented, non-motile, flexirubin-negative, facultatively anaerobic bacterium, designated strain IMCC1412T, was isolated from a marine polychaete Periserrula leucophryna inhabiting a tidal flat of the Yellow Sea, Korea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain IMCC1412T was most closely related to Kordia algicida, with a sequence similarity of 96.7 %, but only distantly related to other species in the family Flavobacteriaceae (<92 % similarity). The G+C content of the DNA was 37.3 mol%. The strain contained MK-6 as the major respiratory quinone and phosphatidylethanolamine, unidentified aminolipids and unidentified polar lipids as the major polar lipids. On the basis of phylogenetic distinctiveness and differential phenotypic characteristics, strain IMCC1412T ( = KACC 14311T = KCTC 22801T = NBRC 106077T) should be assigned to the genus Kordia as the type strain of a novel species, for which the name Kordia periserrulae sp. nov. is proposed. An emended description of the genus Kordia is also presented.
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Bacteroides chinchillae sp. nov. and Bacteroides rodentium sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces
Gram-negative anaerobic rods were isolated from chinchilla (Chinchilla lanigera) faeces and three strains, ST170T, ST180 and ST28T, were investigated taxonomically. On the basis of phylogenetic analyses and specific phenotypic characteristics, the three strains belonged to the genus Bacteroides. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strains ST170T and ST180 formed a single cluster and a distinct line of descent. Strain ST170T exhibited 99.7 % 16S rRNA gene sequence similarity with strain ST180 and 95.1, 94.6 and 94.4 % 16S rRNA gene sequence similarity with Bacteroides massiliensis JCM 13223T, Bacteroides dorei JCM 13471T and Bacteroides vulgatus JCM 5826T, respectively. Strain ST28T also formed a distinct line of descent and exhibited the highest 16S rRNA gene sequence similarity with Bacteroides uniformis JCM 5828T (98.1 %). Low DNA–DNA relatedness (1 %) between strain ST28T and B. uniformis JCM 5828T clearly indicated that they belonged to different species. Analysis of hsp60 sequences also supported these relationships. The DNA G+C contents of strains ST170T and ST28T were 45.2 and 41.0 mol%, respectively. On the basis of phenotypic characteristics and phylogenetic data, two novel species, Bacteroides chinchillae sp. nov. (type strain ST170T = JCM 16497T = CCUG 59335T) and Bacteroides rodentium sp. nov. (type strain ST28T = JCM 16496T = CCUG 59334T), are proposed.
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Myroides marinus sp. nov., a member of the family Flavobacteriaceae, isolated from seawater
More LessA Gram-negative, aerobic, non-motile, yellow-pigmented, rod-shaped bacterium (strain JS-08T) isolated from seawater was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence analysis indicated that strain JS-08T belongs to the genus Myroides, a member of the phylum Bacteroidetes. Its closest phylogenetic relative was Myroides odoratimimus JCM 7460T, with which it shared 97.0 % 16S RNA gene sequence similarity. Strain JS-08T contained menaquinone-6 (MK-6) as the predominant menaquinone, and the dominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and a summed feature consisting of iso-C15 : 0 2-OH and/or C16 : 1ω7c. The DNA G+C content of strain JS-08T was 34.2 mol%. Based on phenotypic, genotypic and phylogenetic evidence, it is suggested that strain JS-08T represents a novel speciesof the genus Myroides, for which the name Myroides marinus sp. nov. is proposed. The type strain is JS-08T ( = KCTC 23023T = JCM 16529T).
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- Firmicutes And Related Organisms
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Mycoplasma mucosicanis sp. nov., isolated from the mucosa of dogs
Fourteen Mycoplasma strains were isolated from the oral cavity and genital tract of asymptomatic dogs. Isolates had been preliminarily identified by conventional serological testing as Mycoplasma bovigenitalium, but in 16S–23S rRNA intergenic spacer PCR-RFLP assays the isolates exhibited an RFLP pattern distinct from M. bovigenitalium PG11T. Analysis of the 16S rRNA gene placed a representative of the isolates (strain 1642T) in the M. bovigenitalium subcluster of the Mycoplasma bovis cluster of mycoplasmas, with the highest sequence similarities to Mycoplasma californicum ST-6T (96.4 %), M. bovigenitalium PG11T (96.3 %) and Mycoplasma phocirhinis 852T (96.2 %). 16S rRNA gene sequence similarities almost equidistant from three recognized species and results obtained by sequence analysis of the 16S–23S rRNA intergenic spacer region, polar lipid profiles and serological reactions indicated that this organism represents a novel species of the genus Mycoplasma for which the name Mycoplasma mucosicanis sp. nov. is proposed, with strain 1642T ( = ATCC BAA-1895T = DSM 22457T) as the type strain.
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Paenibacillus sophorae sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sophora japonica
More LessA nitrogen-fixing bacterium, designated strain S27T, was isolated from rhizosphere soil of Sophora japonica. Phylogenetic analysis based on a fragment of the nifH gene and the full-length 16S rRNA gene sequence revealed that strain S27T is a member of the genus Paenibacillus. High levels of 16S rRNA gene sequence similarity were found between strain S27T and Paenibacillus durus DSM 1735T (97.3 %), Paenibacillus sabinae DSM 17841T (96.9 %), Paenibacillus forsythiae DSM 17842T (96.7 %) and Paenibacillus zanthoxyli DSM 18202T (96.6 %). However, DNA–DNA hybridization values between strain S27T and the four type strains were 37.64 %, 23.12 %, 25.6 % and 34.99 %, respectively. Levels of 16S rRNA gene sequence similarity between strain S27T and the type strains of other recognized members of the genus Paenibacillus were below 96.5 %. The DNA G+C content of strain S27T was 46.0 mol%. The major fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. The major isoprenoid quinone was MK-7. On the basis of its phenotypic characteristics and DNA–DNA hybridization results, strain S27T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus sophorae sp. nov. is proposed. The type strain is S27T ( = CGMCC 1.10238T = DSM 23020T).
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Lactobacillus koreensis sp. nov., isolated from the traditional Korean food kimchi
More LessA lactic acid bacterium, strain DCY50T, isolated from the traditional Korean food kimchi, was studied to determine its taxonomic position. The strain was Gram-stain-positive, catalase-negative, facultatively anaerobic, rod-shaped and motile. The genomic DNA G+C content was 49 mol% and the peptidoglycan structure was of the A4α (l–Lys–d-Asp) type. Chemotaxonomic markers of the strain were consistent with its classification in the genus Lactobacillus. Comparisons of 16S rRNA and rpoA gene sequences showed that strain DCY50T was most closely related to the type strains of Lactobacillus parabrevis (98.4 and 91.6 % similarity, respectively, for the 16S rRNA and rpoA genes), L. hammesii (98.0 and 91.2 %), L. brevis (97.6 and 93.3 %) and L. senmaizukei (97.4 and 90.5 %). DNA–DNA relatedness of strain DCY50T to these type strains was below 36 %. According to the genotypic and phenotypic data, strain DCY50T could be differentiated from all known Lactobacillus species and should be classified in a novel species, for which the name Lactobacillus koreensis sp. nov. is proposed; the type strain is DCY50T ( = KCTC 13530T = JCM 16448T).
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Bacillus nanhaiensis sp. nov., isolated from an oyster
A novel Gram-stain-positive, slightly halophilic, facultatively alkaliphilic, catalase-positive, oxidase-negative, endospore-forming, motile, rod-shaped, aerobic bacterium, designated strain JSM 082006T, was isolated from an oyster collected from Naozhou Island in the South China Sea. The isolate grew in 0–18 % (w/v) NaCl (optimum, 0.5–4.0 %), at pH 6.0–10.5 (optimum, pH 8.0) and at 15–45 °C (optimum, 30 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. Strain JSM 082006T contained MK-7 as the predominant respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genomic DNA G+C content was 40.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 082006T should be assigned to the genus Bacillus and that it was most closely related to the type strains of Bacillus barbaricus (sequence similarity 99.1 %) and Bacillus arsenicus (97.5 %), followed by those of Bacillus rigui (96.6 %) and Bacillus solisalsi (96.1 %). Phylogenetic analysis, DNA–DNA relatedness values, phenotypic characteristics and chemotaxonomic data support the view that strain JSM 082006T represents a novel species of the genus Bacillus, for which the name Bacillus nanhaiensis sp. nov. is proposed; the type strain is JSM 082006T ( = DSM 23009T = KCTC 13712T).
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Lactobacillus kimchicus sp. nov., a β-glucosidase-producing bacterium isolated from kimchi
More LessA Gram-reaction-positive, non-spore-forming, rod-shaped, non-motile, β-glucosidase-producing bacterium, designated DCY51T, was isolated from kimchi, a Korean fermented vegetable food. 16S rRNA gene sequence analysis revealed that strain DCY51T belonged to the genus Lactobacillus and exhibited highest 16S rRNA gene sequence similarity with Lactobacillus paracollinoides AB 74 (96.9 %), L. similis JCM 2765T (96.9 %), L. collinoides JCM 1123T (96.7 %) and L. hilgardii DSM 20176T (95.5 %). Subsequently, pheS sequence analysis confirmed that strain DCY51T formed a distinct lineage within the Lactobacillus plantarum group. The major polar lipid of strain DCY51T was phosphatidylethanolamine and minor amounts of phosphatidylglycerol and diphosphatidylglycerol were found. Phenotypic characteristics and DNA–DNA relatedness indicated that strain DCY51T was clearly distinguished from other type strains of species of the genus Lactobacillus. A novel species, Lactobacillus kimchicus sp. nov., is proposed, with type strain DCY51T ( = KCTC 12976T = JCM 15530T).
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Fructobacillus tropaeoli sp. nov., a fructophilic lactic acid bacterium isolated from a flower
A fructophilic lactic acid bacterium, designated strain F214-1T, was isolated from a flower of Tropaeolum majus in South Africa. Based on phylogenetic analysis of 16S rRNA gene sequences, the strain formed a subcluster with Fructobacillus ficulneus and Fructobacillus pseudoficulneus and, based on recA gene sequences, the strain formed a subcluster with F. ficulneus. DNA–DNA hybridization studies showed that strain F214-1T was phylogenetically distinct from its closest relatives. Acid was produced from the fermentation of d-glucose, d-fructose and d-mannitol only. d-Fructose was the preferred sole carbon and energy source and was fermented more rapidly than d-glucose. Growth of the strain on d-glucose under anaerobic conditions was very weak but external electron acceptors such as oxygen and pyruvate enhanced growth on d-glucose. Lactic acid and acetic acid were produced from d-glucose in equimolar amounts. Ethanol was produced at very low levels, despite the strain’s obligately heterofermentative metabolism. Based on these data, strain F214-1T represents a novel species of fructophilic bacteria in the genus Fructobacillus, for which the name Fructobacillus tropaeoli sp. nov. is proposed. The type strain is F214-1T ( = JCM 16675T = DSM 23246T).
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- Other Bacteria
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Spiroplasma eriocheiris sp. nov., associated with mortality in the Chinese mitten crab, Eriocheir sinensis
A motile bacterium, designated strain TDA-040725-5T, was isolated from the haemolymph of a Chinese mitten crab, Eriocheir sinensis, with tremor disease. Based on 16S rRNA gene sequence analysis, the strain was phylogenetically distinct from other spiroplasmas but was closely related to Spiroplasma mirum ATCC 29335T. Cells of strain TDA-040725-5T were variable in length and shape, helical and motile, as determined by phase-contrast light microscopy. Examination by electron microscopy revealed wall-less cells delimited by a single membrane. The strain grew in M1D or R-2 liquid media at 20–40 °C, with optimum growth at 30 °C. Doubling time at the optimal temperature was 24 h. The strain catabolized glucose and hydrolysed arginine but did not hydrolyse urea. The DNA G+C content was 29.7±1 mol%. The genome size was ~1.4–1.6 Mbp. Serological analysis, performed using the deformation test, did not reveal any reciprocal titres ≥320, indicating that strain TDA-040725-5T had minimal cross-reactivity to strains of recognized species of the genus Spiroplasma. Based on this evidence, strain TDA-040725-5T ( = CCTCC M 207170T = DSM 21848T) represents a novel species of the genus Spiroplasma, for which the name Spiroplasma eriocheiris sp. nov. is proposed, belonging to the novel Spiroplasma serological group XLIII.
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Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria
More LessTwo thermophilic, Gram-stain-positive, sporulating bacterial strains, which formed branched vegetative and aerial mycelia, were isolated from fallen leaves sampled from geothermal soils and designated ONI-1T and ONI-5T. Strain ONI-1T grew at 50–74 °C, with optimum growth at 60–65 °C, and strain ONI-5T grew at 45–74 °C, with optimum growth at 60–65 °C. The pH range for growth of the strains was pH 4.6–8.0, with optimum growth at pH 7.0. The DNA G+C contents of strains ONI-1T and ONI-5T were 60.2 and 58.1 mol%, respectively. The major fatty acid was iso-C17 : 0 and the major menaquinone was MK-9(H2). The cell walls of the strains contained glutamic acid, serine, glycine, histidine, alanine and ornithine. The polar lipids consisted of phosphatidylinositol, phosphatidylglycerol and a glycolipid. The cell-wall sugar was rhamnose. Detailed phylogenetic analysis based on 16S rRNA gene sequences indicated that the strains belong to the class Ktedonobacteria and that strains ONI-1T and ONI-5T are most closely related to Thermosporothrix hazakensis SK20-1T (85.3 and 84.5 % sequence similarity, respectively). 16S rRNA gene sequence similarity between the two strains was 96.6 %. Based on the phenotypic features and phylogenetic position, we propose that strains ONI-1T and ONI-5T constitute a novel genus containing two novel species, for which we propose the names Thermogemmatispora onikobensis gen. nov., sp. nov. (the type species; type strain ONI-1T = JCM 16817T = KCTC 19768T) and Thermogemmatispora foliorum sp. nov. (type strain ONI-5T = JCM 16818T = KCTC 19767T), within the new family Thermogemmatisporaceae fam. nov. and order Thermogemmatisporales ord. nov.
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- Proteobacteria
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Altererythrobacter namhicola sp. nov. and Altererythrobacter aestuarii sp. nov., isolated from seawater
Two non-motile, orange- or yellow-pigmented bacteria, designated strains KYW48T and KYW147T, were isolated from seawater collected from the South Sea, Republic of Korea. Cells of both strains were Gram-reaction-negative, aerobic and catalase- and oxidase-positive. The major fatty acids of strain KYW48T were C18 : 1ω7c (35.3 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) (22.7 %), C17 : 1ω6c (19.8 %), C14 : 0 2-OH (7.4 %) and C16 : 0 (5.9 %), and those of strain KYW147T were C18 : 1ω7c (36.0 %), summed feature 3 (18.3 %), C16 : 0 (14.7 %), 11-methyl C18 : 1ω7c (10.7 %), C16 : 0 2-OH (9.1 %) and C18 : 1ω9c (8.0 %). The predominant isoprenoid quinone of both strains was ubiquinone 10 (Q-10). The DNA G+C contents of strains KYW48T and KYW147T were 63.8 and 67.2 mol%, respectively. A phylogenetic tree based on 16S rRNA gene sequences showed that strains KYW48T and KYW147T were grouped with the members of the family Erythrobacteraceae and formed a distinct clade with the members of the genus Altererythrobacter (<95.7 % sequence similarity). On the basis of the evidence presented in this study, the novel species Altererythrobacter namhicola sp. nov. (type strain KYW48T = KCTC 22736T = JCM 16345T) and Altererythrobacter aestuarii sp. nov. (type strain KYW147T = KCTC 22735T = JCM 16339T) are proposed.
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Henriciella litoralis sp. nov., isolated from a tidal flat, transfer of Maribaculum marinum Lai et al. 2009 to the genus Henriciella as Henriciella aquimarina nom. nov. and emended description of the genus Henriciella
More LessA Gram-staining-negative, strictly aerobic bacterium, designated strain SD10T, was isolated from a tidal flat of the Yellow Sea, South Korea. Cells were non-spore-forming rods that showed catalase- and oxidase-positive reactions. Growth of strain SD10T was observed at 15–40 °C (optimum, 25–30 °C), at pH 6.0–9.0 (optimum, pH 6.5–8.5) and in the presence of 1–10 % (w/v) NaCl. Strain SD10T contained ubiquinone-10 (Q-10) as a major isoprenoid quinone and C18 : 1ω7c (39.3 %), C16 : 0 (20.2 %), C17 : 0 (8.9 %) and C17 : 1ω6c (8.1 %) as major fatty acids. The cellular polar lipids were identified as phosphatidylglycerol, monoglycosyldiglyceride, glucuronopyranosyldiglyceride and two unidentified glycolipids. The G+C content of the genomic DNA was 55.2 mol%. Based on 16S rRNA gene sequence similarities, the strain was most closely related to Henriciella marina Iso4T and Maribaculum marinum P38T, with similarities of 97.8 and 97.0 %, respectively. The DNA–DNA relatedness between strain SD10T and H. marina Iso4T was 12.0±3.2 %. A phylogenetic analysis based on 16S rRNA gene sequences showed that M. marinum P38T and H. marina Iso4T formed a monophyletic cluster and that their 16S rRNA gene sequence similarity was 98.1 %. DNA–DNA hybridization between H. marina Iso4T and M. marinum LMG 24711T was 22.9±2.7 %, indicating that the two strains belong to separate species. On the basis of chemotaxonomic data and molecular properties, we propose that strain SD10T represents a novel species of the genus Henriciella, for which the name Henriciella litoralis sp. nov. is proposed. The type strain is SD10T ( = KACC 13700T = DSM 22014T). In addition, we propose to transfer Maribaculum marinum Lai et al. 2009 to the genus Henriciella as Henriciella aquimarina nom. nov. (type strain P38T = CCTCC AB 208227T = LMG 24711T = MCCC 1A01086T), and we present an emended description of the genus Henriciella.
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Citreicella marina sp. nov., isolated from deep-sea sediment
More LessA taxonomic study was carried out on a novel strain, designated CK-I3-6T, which was isolated from deep-sea sediment of the south-west Indian Ocean Ridge. Cells were Gram-reaction-negative, oxidase- and catalase-positive, rod-shaped and non-motile. Growth was observed at 4–38 °C and in 1–12 % (w/v) NaCl. Cells were able to degrade gelatin and oxidize thiosulfate but did not reduce nitrate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CK-I3-6T belonged to the genus Citreicella with a sequence similarity of 97.3 % to Citreicella thiooxidans CHLG 1T, while similarities with other taxa were <95.7 %. DNA–DNA hybridization showed that strain CK-I3-6T and C. thiooxidans CHLG 1T showed a low DNA–DNA relatedness (48±3 %). The principal fatty acids were C16 : 0 (7.8 %), C18 : 1ω7c (66.6 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 6.3 %) and C19 : 0ω8c cyclo (10.0 %). The chromosomal DNA G+C content was 67.5 mol%. On the basis of the combined genotypic and phenotypic data, strain CK-I3-6T represents a novel species of the genus Citreicella, for which the name Citreicella marina sp. nov. is proposed. The type strain is CK-I3-6T ( = CCTCC AB 209064T = LMG 25230T = MCCC 1A03060T).
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Desulfosoma caldarium gen. nov., sp. nov., a thermophilic sulfate-reducing bacterium from a terrestrial hot spring
More LessA thermophilic, sulfate-reducing bacterium, designated strain USBA-053T, was isolated from a terrestrial hot spring located at a height of 2500 m in the Colombian Andes (5° 45′ 33.29″ N 73° 6′ 49.89″ W), Colombia. Cells of strain USBA-053T were oval- to rod-shaped, Gram-negative and motile by means of a single polar flagellum. The strain grew autotrophically with H2 as the electron donor and heterotrophically on formate, propionate, butyrate, valerate, isovalerate, lactate, pyruvate, ethanol, glycerol, serine and hexadecanoic acid in the presence of sulfate as the terminal electron acceptor. The main end products from lactate degradation, in the presence of sulfate, were acetate, CO2 and H2S. Strain USBA-053T fermented pyruvate in the absence of sulfate and grew optimally at 57 °C (growth temperature ranged from 50 °C to 62 °C) and pH 6.8 (growth pH ranged from 5.7 to 7.7). The novel strain was slightly halophilic and grew in NaCl concentrations ranging from 5 to 30 g l−1, with an optimum at 25 g l−1 NaCl. Sulfate, thiosulfate and sulfite were used as electron acceptors, but not elemental sulfur, nitrate or nitrite. The G+C content of the genomic DNA was 56±1 mol%. 16S rRNA gene sequence analysis indicated that strain USBA-053T was a member of the class Deltaproteobacteria, with Desulfacinum hydrothermale MT-96T as the closest relative (93 % gene sequence similarity). On the basis of physiological characteristics and phylogenetic analysis, it is suggested that strain USBA-053T represents a new genus and novel species for which the name Desulfosoma caldarium gen. nov., sp. nov. is proposed. The type strain of the type species is USBA-053T ( = KCTC 5670T = DSM 22027T).
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Cohaesibacter marisflavi sp. nov., isolated from sediment of a seawater pond used for sea cucumber culture, and emended description of the genus Cohaesibacter
More LessA Gram-negative, catalase-negative, oxidase-positive, rod-shaped bacterium, strain DQHS21T, was isolated from sediment of a seawater pond used for sea cucumber culture at Jimo in Qingdao province on the east coast of China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DQHS21T belonged to the genus Cohaesibacter, sharing the highest sequence similarity (96.1 %) with Cohaesibacter gelatinilyticus CL-GR15T, while the similarity to other strains was below 93.0 %. The cellular fatty acids consisted mainly of C18 : 1ω7c (60.7 %), C18 : 0 (17.8 %), C16 : 0 (8.5 %) and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH; 6.0 %), which together accounted for 93 % of the total fatty acids. Ubiquinone 10 was the major quinone. The G+C content of the chromosomal DNA of strain DQHS21T was 55.2 mol%. The combined genotypic and phenotypic data showed that strain DQHS21T represents a novel species of the genus Cohaesibacter, for which the name Cohaesibacter marisflavi sp. nov. is proposed, with the type strain DQHS21T ( = CGMCC 1.9157T = NCCB 100300T).
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Polynucleobacter rarus sp. nov., a free-living planktonic bacterium isolated from an acidic lake
More LessThe heterotrophic, aerobic, facultatively anaerobic under denitrifying conditions, catalase- and oxidase-positive, non-motile strain MT-CBb6A5T, which was isolated from an acidic lake located in Wisconsin (USA), was characterized. The strain grew on NSY medium over a temperature range of 15–30 °C and a NaCl range of 0.0–0.3 % (w/v). The predominant fatty acids were C16 : 0, C18 : 1ω7c, 11-methyl C18 : 1ω7c, feature 3 (including C16 : 1ω7c), and feature 2 (including C14 : 0 3-OH). The DNA G+C content of the strain was 40.3 mol%. Phylogenetic analysis as well as strong similarities in phenotypic and chemotaxonomic traits indicated the affiliation with the genus Polynucleobacter. 16S rRNA gene sequence similarity values with the two described species of the genus Polynucleobacter ranged from 95.6 to 96.0 %. The strain differs from the two described species of the genus Polynucleobacter in the ability to assimilate oxalic and glycolic acids, and in the presence of the fatty acids C15 : 1ω8c and C16 : 0 3-OH as well as in quantitative differences in fatty acid composition. It has to be assumed that the strain shares with other free-living bacteria of the genus Polynucleobacter a planktonic lifestyle in the water column of freshwater habitats. Based on the phylogeny revealed and the chemotaxonomic and phenotypic differences from Polynucleobacter necessarius and Polynucleobacter cosmopolitanus, we propose to establish the novel species Polynucleobacter rarus sp. nov. with the type strain MT-CBb6A5T ( = DSM 21648T = CIP 109928T).
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Polynucleobacter acidiphobus sp. nov., a representative of an abundant group of planktonic freshwater bacteria
More LessThe heterotrophic, aerobic, facultatively anaerobic, catalase- and oxidase-positive, non-motile strain MWH-PoolGreenA3T, isolated from a rock pool filled with freshwater, was characterized. The strain grew on NSY medium over a NaCl range of 0.0–0.3 % (w/v). Whole-cell fatty acids were dominated by C16 : 1ω7c (feature 3), C18 : 1ω7c and straight-chain C16 : 0; furthermore, the components C12 : 0 and C14 : 0 2-OH were present. The DNA G+C content was 48.3 mol%. Phylogenetic analysis as well as strong similarities in phenotypic and chemotaxonomic traits indicated the affiliation with the genus Polynucleobacter. 16S rRNA gene similarity values with the three described species of the genus Polynucleobacter ranged from 96.7 to 97.8 %. DNA–DNA hybridization experiments did not reveal that the strain belongs to a previously described species of the genus Polynucleobacter. The strain can be discriminated from previously established species of the genus Polynucleobacter by chemotaxonomic and phenotypic traits. The bacterium possesses a free-living lifestyle and represents a group of planktonic freshwater bacteria occurring with high cell numbers in many freshwater lakes. Based on the phylogeny revealed and the chemotaxonomic and phenotypic differences from previously described species of the genus Polynucleobacter, we propose to establish the novel species Polynucleobacter acidiphobus sp. nov. with the type strain MWH-PoolGreenA3T ( = DSM 21994T = CIP 110079T).
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Methylovulum miyakonense gen. nov., sp. nov., a type I methanotroph isolated from forest soil
More LessA novel methanotroph, designated strain HT12T, was isolated from forest soil in Japan. Cells of strain HT12T were Gram-reaction-negative, aerobic, non-motile, coccoid and formed pale-brown colonies. The strain grew only with methane and methanol as sole carbon and energy sources. Cells grew at 5–34 °C (optimum 24–32 °C). The strain possessed both particulate and soluble methane monooxygenases and assimilated formaldehyde using the ribulose monophosphate pathway. The major cellular fatty acids were C16 : 0 (46.9 %) and C14 : 0 (34.2 %), whereas unsaturated C16 fatty acids, typical of type I methanotrophs, were absent. Comparative 16S rRNA gene sequence analysis showed that the most closely related strains were Methylosoma difficile LC 2T (93.1 % sequence similarity) and Methylobacter tundripaludum SV96T (92.6 % similarity). Phylogenetic analysis based on the pmoA gene indicated that strain HT12T formed a distinct lineage within the type I methanotrophs and analysis of the deduced pmoA amino acid sequence of strain HT12T showed that it had a 7 % divergence from that of its most closely related species. The DNA G+C content was 49.3 mol%. Based on this evidence, strain HT12T represents a novel species and genus of the family Methylococcaceae, for which the name Methylovulum miyakonense gen. nov., sp. nov. is proposed. The type strain of the type species is HT12T ( = NBRC 106162T = DSM 23269T = ATCC BAA-2070T).
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Rhizobium borbori sp. nov., aniline-degrading bacteria isolated from activated sludge
Three aniline-degrading bacteria, strains DN316T, DN316-1 and DN365, were isolated from activated sludge. According to 16S rRNA gene sequence-based phylogenetic analysis, the isolates belonged to the genus Rhizobium, with Rhizobium ( = Agrobacterium) radiobacter LMG 140T as the closest relative, with 96.5 % sequence similarity. Phylogenetic analysis of the representative strain DN316T using sequences of the glnA, thrC and recA genes and the 16S–23S intergenic spacer region confirmed the phylogenetic arrangement obtained from analysis of the 16S rRNA gene. DNA–DNA relatedness between DN316T and R. radiobacter LMG 140T was 43.7 %, clearly indicating that the representative strain DN316T represents a novel species. Phenotypic and biochemical characterization of the isolates and insertion sequence-PCR fingerprinting patterns showed several distinctive features that differentiated them from closely related species. The major components of the cellular fatty acids were C18 : 1ω7c (57.10 %), C16 : 0 (11.31 %) and C19 : 0 cyclo ω8c (10.13 %). Based on our taxonomic analysis, the three isolates from activated sludge represent a novel species of the genus Rhizobium, for which the name Rhizobium borbori sp. nov. is proposed. The type strain is DN316T ( = CICC 10378T = LMG 23925T).
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Shimia isoporae sp. nov., isolated from the reef-building coral Isopora palifera
More LessA bacterial strain, designated SW6T, was isolated from the reef-building coral Isopora palifera, collected from seawater off the coast of southern Taiwan, and characterized using a polyphasic taxonomic approach. Strain SW6T was Gram-negative, aerobic, beige coloured, rod-shaped and motile by monopolar flagella. 16S rRNA gene sequence studies showed that the strain clustered closely with Shimia marina JCM 13038T (97.9 % 16S rRNA gene sequence similarity). Strain SW6T required NaCl for growth and exhibited optimal growth at 25–30 °C and 3–4 % NaCl. The predominant cellular fatty acid was summed feature 8 (C18 : 1ω7c/C18 : 1ω6c; 64.1 %). The major respiratory quinone was ubiquinone Q-10 and the DNA G+C content was 54.9 mol%. The results of physiological and biochemical tests allowed clear phenotypic differentiation of this isolate from previously described species of the genus Shimia. It is evident from the genotypic, phenotypic and chemotaxonomic data that the new strain should be classified as a representative of a novel species in the genus Shimia. The name proposed for this taxon is Shimia isoporae sp. nov.; the type strain is SW6T ( = LMG 25377T = BCRC 80085T).
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Phaeovibrio sulfidiphilus gen. nov., sp. nov., phototrophic alphaproteobacteria isolated from brackish water
More LessTwo strains (JA480T and JA481) of phototrophic alphaproteobacteria were isolated from sediment samples collected from brackish water near Nagapattinam, India. They were Gram-negative, vibrioid cells containing bacteriochlorophyll a and rhodopin as major photosynthetic pigments. Most cells of both strains were non-flagellated; 1 % of cells showed two monopolar flagella. Cells showed positive phototaxis. Both strains showed chimeric intracellular photosynthetic membranes, where both lamellar stacks and vesicles were present together in a single cell. The major fatty acids were C18 : 1ω7c and C16 : 0 in both strains. The genomic G+C content was 67.2–68.8 mol% and the two strains were closely related (mean DNA–DNA hybridization >85 %). 16S rRNA gene sequence comparisons indicated that the isolates represent members of the Rhodospirillaceae within the class Alphaproteobacteria. According to the sequence comparison data, strain JA480T is positioned distinctly outside the group formed by the phototrophic genera Rhodospirillum, Rhodocista, Phaeospirillum, Rhodovibrio, Rhodospira and Roseospira, with only 80–92 % 16S rRNA gene sequence similarity. Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of this isolate as a representative of a novel species in a new genus, for which the name Phaeovibrio sulfidiphilus gen. nov., sp. nov. is proposed. The type strain of Phaeovibrio sulfidiphilus is JA480T ( = KCTC 5825T = NBRC 106163T = DSM 23193T).
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Yersinia entomophaga sp. nov., isolated from the New Zealand grass grub Costelytra zealandica
More LessA Gram-negative, rod-shaped, non-spore-forming bacterium (MH96T) was isolated from diseased larvae of the New Zealand grass grub, Costelytra zealandica (Coleoptera: Scarabaeidae). On the basis of 16S rRNA gene sequence similarity, strain MH96T is a member of the genus Yersinia, which is a member of the class Gammaproteobacteria. The most similar 16S rRNA gene sequence to that of MH96T is that of the type strain of Yersinia mollaretii (98.5 % similarity) followed by those of the type strains of Yersinia aldovae, Y. frederiksenii and Y. rohdei (all 98.4 % similarity). Multilocus sequence typing of five housekeeping genes (dnaJ, glnA, gyrB, groEL and recA) identified Yersinia ruckeri (81–92 % similarity) as the closest relative. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain MH96T from the four most closely related Yersinia species with validly published names, including a Y. ruckeri isolate. Strain MH96T therefore represents a novel species, for which the name Yersinia entomophaga sp. nov. is proposed, with the type strain MH96T ( = DSM 22339T = ATCC BAA-1678T).
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Colwellia chukchiensis sp. nov., a psychrotolerant bacterium isolated from the Arctic Ocean
More LessA novel psychrotolerant bacterial strain, BCw111T, was isolated from seawater samples from the Chukchi Sea in the Arctic Ocean. Cells of strain BCw111T were Gram-negative, motile, facultatively anaerobic, curved rods and were able to grow at 0–30 °C (optimum 23–25 °C). Strain BCw111T had Q-8 as the major respiratory quinone and contained iso-C15 : 0 2-OH and/or C16 : 1ω7c (28.13 %), C16 : 0 (13.28 %) and C17 : 1 (12.90 %) as the major cellular fatty acids. The genomic DNA G+C content was 41.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BCw11T formed a distinct lineage within the genus Colwellia and exhibited the highest 16S rRNA gene sequence similarity with Colwellia polaris 537T (97.8 %) and Colwellia aestuarii SMK-10T (97.1 %). Based on phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, a novel species, Colwellia chukchiensis sp. nov., is proposed. The type strain is BCw111T ( = CGMCC 1.9127T = LMG 25329T = DSM 22576T).
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Methylobacterium marchantiae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the thallus of a liverwort
More LessA pink-pigmented, facultatively methylotrophic bacterium, designated strain JT1T, was isolated from a thallus of the liverwort Marchantia polymorpha L. and was analysed by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis placed the strain in a clade with Methylobacterium adhaesivum AR27T, Methylobacterium fujisawaense DSM 5686T, Methylobacterium radiotolerans JCM 2831T and Methylobacterium jeotgali S2R03-9T, with which it showed sequence similarities of 97.8, 97.7, 97.2 and 97.4 %, respectively. However, levels of DNA–DNA relatedness between strain JT1T and these and the type strains of other closely related species were lower than 70 %. Cells of JT1T stained Gram-negative and were motile, rod-shaped and characterized by numerous fimbriae-like appendages on the outer surface of their wall (density up to 200 µm−2). Major fatty acids were C18 : 1ω7c and C16 : 0. Based on the morphological, physiological and biochemical data presented, strain JT1T is considered to represent a novel species of the genus Methylobacterium, for which the name Methylobacterium marchantiae sp. nov. is proposed. The type strain is JT1T ( = DSM 21328T = CCUG 56108T).
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Taxonomic investigation of representatives of the genus Sphaerotilus: descriptions of Sphaerotilus montanus sp. nov., Sphaerotilus hippei sp. nov., Sphaerotilus natans subsp. natans subsp. nov. and Sphaerotilus natans subsp. sulfidivorans subsp. nov., and an emended description of the genus Sphaerotilus
Seven strains of the genus Sphaerotilus were obtained from natural thermal sulfide (strains D-501T, D-502, D-504, D-505 and D-507) and low-temperature ferrous (strain HST) springs and from an activated sludge system (strain D-380). These Sphaerotilus isolates and strainsof Sphaerotilus natans obtained from the DSMZ (S. natans DSM 6575T, DSM 565 and DSM 566) were studied using a polyphasic taxonomic approach. All strains had Q-8 as the major quinone and C16 : 1ω7, C16 : 0 and C18 : 1ω7 as the major fatty acids. The DNA–DNA hybridization results and 16S rRNA, hsp60 and gyrB gene sequencing experiments showed that isolates D-501T, D-502, D-504, D-505, D-507 and D-380 were closely related to the type strain of S. natans DSM 6575T. However, strains D-501T, D-502, D-504, D-505 and D-507 significantly differed from the heterotrophic strain S. natans DSM 6575T by their capability for lithotrophic growth with reduced sulfur compounds as an electron donor for energy conservation and some other phenotypic features. For this reason, strains D-501T, D-502, D-504, D-505 and D-507 merit a separate taxonomic classification at the subspecies level. The name Sphaerotilus natans subsp. sulfidivorans subsp. nov. (type strain D-501T = DSM 22545T = VKM B-2573T) is proposed. The subspecies Sphaerotilus natans subsp. natans subsp. nov. is automatically created as a result of this proposal. Strain D-380 was phenotypically closely related to S. natans DSM 6575T. Strains D-380 and S. natans DSM 6575T were assigned to the subspecies Sphaerotilus natans subsp. natans subsp. nov. (type strain DSM 6575T = ATCC 13338T). The 16S rRNA, hsp60 and gyrB gene sequences obtained for strains HST and DSM 565 showed very low sequence similarity values of 97.3 %, 89.7 % and 88.4 %, respectively, with S. natans DSM 6575T. Strain HST shared 99 % DNA–DNA relatedness with strain
DSM 565 and 48 % with S. natans DSM 6575T. The 16S rRNA, hsp60 and gyrB gene sequence similarities between strain DSM 566T and S. natans DSM 6575T were 97.5 %, 91.5 % and 87.0 %, respectively. Strain DSM 566T had 52 % DNA–DNA relatedness to S. natans DSM 6575T and shared 44 % DNA–DNA similarity with strain HST. The creation of two novel species is proposed, Sphaerotilus montanus sp. nov. for strains HST and DSM 565 (type strain HST = DSM 21226T = VKM B-2519T) and Sphaerotilus hippei sp. nov. for strain DSM 566T (type strain DSM 566T = ATCC 29330T). Emended descriptions of the genus Sphaerotilus and of Sphaerotilus natans are presented.
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Screening for endophytic nitrogen-fixing bacteria in Brazilian sugar cane varieties used in organic farming and description of Stenotrophomonas pavanii sp. nov.
A Gram-negative, rod-shaped, non-spore-forming and nitrogen-fixing bacterium, designated ICB 89T, was isolated from stems of a Brazilian sugar cane variety widely used in organic farming. 16S rRNA gene sequence analysis revealed that strain ICB 89T belonged to the genus Stenotrophomonas and was most closely related to Stenotrophomonas maltophilia LMG 958T, Stenotrophomonas rhizophila LMG 22075T, Stenotrophomonas nitritireducens L2T, [Pseudomonas] geniculata ATCC 19374T, [Pseudomonas] hibiscicola ATCC 19867T and [Pseudomonas] beteli ATCC 19861T. DNA–DNA hybridization together with chemotaxonomic data and biochemical characteristics allowed the differentiation of strain ICB 89T from its nearest phylogenetic neighbours. Therefore, strain ICB 89T represents a novel species, for which the name Stenotrophomonas pavanii sp. nov. is proposed. The type strain is ICB 89T ( = CBMAI 564T = LMG 25348T).
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Pantoea allii sp. nov., isolated from onion plants and seed
Eight yellow-pigmented, Gram-negative, rod-shaped, oxidase-negative, motile, facultatively anaerobic bacteria were isolated from onion seed in South Africa and from an onion plant exhibiting centre rot symptoms in the USA. The isolates were assigned to the genus Pantoea on the basis of phenotypic and biochemical tests. 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA), based on gyrB, rpoB, infB and atpD sequences, confirmed the allocation of the isolates to the genus Pantoea. MLSA further indicated that the isolates represented a novel species, which was phylogenetically most closely related to Pantoea ananatis and Pantoea stewartii. Amplified fragment length polymorphism analysis also placed the isolates into a cluster separate from P. ananatis and P. stewartii. Compared with type strains of species of the genus Pantoea that showed >97 % 16S rRNA gene sequence similarity with strain BD 390T, the isolates exhibited 11–55 % whole-genome DNA–DNA relatedness, which confirmed the classification of the isolates in a novel species. The most useful phenotypic characteristics for the differentiation of the isolates from their closest phylogenetic neighbours are production of acid from amygdalin and utilization of adonitol and sorbitol. A novel species, Pantoea allii sp. nov., is proposed, with type strain BD 390T ( = LMG 24248T).
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Kangiella spongicola sp. nov., a halophilic marine bacterium isolated from the sponge Chondrilla nucula
More LessA novel halophilic bacterium of the genus Kangiella was isolated from a marine sponge collected from the Florida Keys, USA. Strain A79T, an aerobic, Gram-negative, non-motile, rod-shaped bacterium, grew in 2–15 % (w/v) NaCl, at a temperature of 10–49 °C and at pH 4.5–10. Phylogenetic analysis placed strain A79T in the family Alcanivoraceae in the class Gammaproteobacteria. Strain A79T showed 98.5 % 16S rRNA gene sequence similarity to Kangiella japonica KMM 3899T, 96.6 % similarity to Kangiella koreensis DSM 16069T and 95.6 % similarity to Kangiella aquimarina DSM 16071T. The major cellular fatty acids were iso-C11 : 0, iso-C11 : 0 3-OH, iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c and the G+C content of the genomic DNA was 44.9 mol%. On the basis of physiological, chemotaxonomic and phylogenetic comparisons, strain A79T represents a novel species in the genus Kangiella, for which the name Kangiella spongicola sp. nov. is proposed. The type strain is A79T ( = ATCC BAA-2076T = DSM 23219T).
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Idiomarina xiamenensis sp. nov., isolated from surface seawater, and proposal to transfer Pseudidiomarina aestuarii to the genus Idiomarina as Idiomarina aestuarii comb. nov.
A taxonomic study was carried out on strain 10-D-4T, which was isolated from a crude oil-degrading consortium enriched from surface seawater collected around Xiamen Island, PR China. Strain 10-D-4T grew optimally at pH 7.0–8.0 and at 25 °C. The 16S rRNA gene sequence of strain 10-D-4T showed the highest similarity to those of Idiomarina salinarum ISL-52T (94.6 %), Idiomarina tainanensis PIN1T (94.2 %) and Idiomarina seosinensis CL-SP19T (94.1 %), and showed lower similarity (92.3–94.0 %) to other members of the genus Idiomarina. The major isoprenoid quinone was ubiquinone 8 (Q-8). The major fatty acids were iso-C13 : 0 (5.2 %), iso-C15 : 0 (15.3 %), C16 : 0 (14.3 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) (6.6 %), iso-C17 : 0 (15.4 %) and C18 : 1ω7c (13.5 %). The G+C content of the chromosomal DNA was 50.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences, together with data from phenotypic and chemotaxonomic characterization, revealed that strain 10-D-4T represents a novel species of the genus Idiomarina, for which the name Idiomarina xiamenensis sp. nov. is proposed. The type strain is 10-D-4T ( = CCTCC AB 209061T = LMG 25227T = MCCC 1A01370T). We also propose the transfer of Pseudidiomarina aestuarii, described recently, to the genus Idiomarina as Idiomarina aestuarii comb. nov. (type strain KYW314T = KCTC 22740T = JCM 16344T).
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- Eukaryotic Micro-Organisms
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Lindnera rhizosphaerae sp. nov., a yeast species isolated from rhizospheric soil
More LessTwo strains of a novel yeast species were isolated from ectomycorrhizal Nothofagus pumilio rhizospheric soil in a native forest of Patagonia, Argentina. Analysis of the D1/D2 large-subunit rRNA gene sequences indicated that the novel species belongs to the recently described genus Lindnera. The name Lindnera rhizosphaerae sp. nov. is proposed to accommodate these isolates, and the type strain is CRUB 1796T ( = CBS 11400T = JCM 16499T).
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Lachancea mirantina sp. nov., an ascomycetous yeast isolated from the cachaça fermentation process
In the present work, a novel ascomycete species, Lachancea mirantina sp. nov., isolated from the fermentation process that produces cachaça, a Brazilian spirit, is proposed. Nucleotide sequence analysis of the 26S D1/D2 rDNA locus showed that L. mirantina sp. nov. was genetically related to Lachancea cidri and Lachancea fermentati, although some physiological traits showed remarkable differences. Analysis of the D1/D2 large-subunit rDNA molecular marker showed a clear distinction among all three species, confirming that L. mirantina sp. nov. belongs to a separate taxonomic species in the Lachancea clade. The type strain of Lachancea mirantina sp. nov. is URM 5925T ( = CLIB 1160T = CBS 11717T).
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Spencermartinsiella europaea gen. nov., sp. nov., a new member of the family Trichomonascaceae
More LessTen strains of a novel heterothallic yeast species were isolated from rotten wood collected at different locations in Hungary. Analysis of gene sequences for the D1/D2 domain of the large subunit rRNA, as well as analysis of concatenated gene sequences for the nearly complete nuclear large subunit rRNA, nuclear small subunit rRNA and translation elongation factor 1-α, placed the novel species in the family Trichomonascaceae, but showed that it was distinct from all currently recognized genera. The name Spencermartinsiella europaea gen. nov., sp. nov. is proposed to accommodate the new genus and novel species. The novel species could be distinguished from recognized species of neighbouring genera on the basis of standard phenotypic characteristics. The type and isotype strains of Spencermartinsiella europaea are NCAIM Y.01817T ( = NRRL Y-48265T = CBS 11730T) and NCAIM Y.01819I ( = NRRL Y-48266I = CBS 11731I), respectively.
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- Evolution, Phylogeny And Biodiversity
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Molecular phylogeny of the family Vorticellidae (Ciliophora, Peritrichia) using combined datasets with a special emphasis on the three morphologically similar genera Carchesium, Epicarchesium and Apocarchesium
More LessLittle is known about the phylogeny of the family Vorticellidae at the generic level because few comprehensive analyses of molecular phylogenetic relationships between members of this group have, so far, been done. As a result, the phylogenetic positions of some genera that were based originally on morphological analyses remain controversial. In the present study, we performed phylogenetic analyses of vorticellids based on the sequence of the small-subunit (SSU) rRNA gene, including one species of the genus Apocarchesium, for which no sequence has previously been reported. Phylogenetic trees were reconstructed with SSU rRNA gene sequences by using four different methods (Bayesian analysis, maximum-likelihood, neighbour-joining and maximum-parsimony) and had a consistent branching pattern. Members of the genera Vorticella (except V. microstoma) and Carchesium formed a clearly defined, well supported clade that was divergent from the clade comprising members of the genera Pseudovorticella and Epicarchesium, suggesting that the differences in the silverline system (transverse vs reticulate) among vorticellids may be the result of genuine evolutionary divergence. Members of the newly established genus Apocarchesium clustered within the family Vorticellidae basal to the clade containing members of the genera Pseudovorticella and Epicarchesium and were distinct from members of the genus Carchesium, supporting the validity of Apocarchesium as a novel genus. Additional phylogenetic analyses of 21 strains representing seven genera from the families Vorticellidae and Zoothamniidae were performed with single datasets (ITS1–5.8S–ITS2, ITS2 alone) and combined datasets (SSU rRNA+ITS1–5.8S–ITS2, SSU rRNA+ITS2) to explore further the phylogenetic relationship between the three morphologically similar genera Carchesium, Epicarchesium and Apocarchesium, using characteristics not included in previous analyses. The phylogenetic trees reconstructed with combined datasets were more robust and therefore more reliable than those based on single datasets and supported the results of trees based on SSU rRNA sequences.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 66 (2016)
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Volume 31 (1981)
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Volume 26 (1976)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)