- Volume 62, Issue Pt_11, 2012
Volume 62, Issue Pt_11, 2012
- Validation List
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List of new names and new combinations previously effectively, but not validly, published
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors’ names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names and new combinations have appeared in volume 62, part 8, 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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- Editorial
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- New Taxa
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- Actinobacteria
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Catenulispora graminis sp. nov., a rhizobacterium from bamboo (Phyllostachys nigro var. henonis) rhizosphere soil
More LessA novel actinobacterium, designated strain BR-34T, was isolated from rhizosphere soil of bamboo (Phyllostachys nigro var. henonis) sampled in Damyang, Korea. The strain was found to have morphological and chemotaxonomic characteristics typical of the genus Catenulispora . The strain contained iso-C16 : 0 as the major fatty acid and MK-9(H4), MK-9(H6) and MK-9(H8) as major isoprenoid quinones. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BR-34T formed a cluster separate from members of the genus Catenulispora and was related most closely to Catenulispora acidiphila ID139908T (97.4 % similarity), Catenulispora rubra Aac-30T (97.3 %), Catenulispora yoronensis TT N02-20T (97.3 %) and Catenulispora subtropica TT 99-48T (97 %). However, the level of DNA–DNA relatedness between strain BR-34T and C. acidiphila ID139908T was only 45.32 %. Based on DNA–DNA relatedness, morphological and phenotypic data, strain BR-34T could be distinguished from the type strains of phylogenetically related species. It is therefore considered to represent a novel species of the genus Catenulispora , for which the name Catenulispora graminis sp. nov. is proposed. The type strain is BR-34T ( = KACC 15070T = NBRC 107755T).
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Amycolatopsis dongchuanensis sp. nov., an actinobacterium isolated from soil
A novel actinomycete strain, designated YIM 75904T, was isolated from a soil sample that had been collected from a dry and hot river valley in Dongchuan county, Yunnan province, south-western China. The taxonomic position of the novel strain was investigated by a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strain YIM 75904T formed a distinct clade within the genus Amycolatopsis and appeared to be closely related to Amycolatopsis sacchari K24T (99.3 % sequence similarity). Strain YIM 75904T had a type-IV cell wall, with no detectable mycolic acids, and had MK-9(H4) as its predominant menaquonine. Its cell wall contained meso-diaminopimelic acid, galactose, glucose and arabinose, and its major cellular fatty acids were iso-C16 : 0, iso-C15 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. The genomic DNA G+C content of the novel strain was 68.5 mol%. Based on the results of physiological and biochemical tests and DNA–DNA hybridizations, strain YIM 75904T represents a novel species of the genus Amycolatopsis for which the name Amycolatopsis dongchuanensis sp. nov. is proposed. The type strain is YIM 75904T ( = CCTCC AA 2011016T = JCM 18054T).
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Microbacterium murale sp. nov., isolated from an indoor wall
More LessA Gram-positive rod, designated 01-Gi-001T, was isolated from a wall colonized with moulds. The 16S rRNA gene sequence analysis clearly showed that the isolate belonged to the genus Microbacterium . On the basis of pairwise comparisons of 16S rRNA gene sequences, strain 01-Gi-001T was most closely related to Microbacterium hydrocarbonoxydans DSM 16089T (98.9 % sequence similarity), Microbacterium profundi Shh49T (98.7 %), Microbacterium phyllosphaerae DSM 13468T (98.3 %) and Microbacterium foliorum DSM 12966T (98.1 %). The diagnostic diamino acid of the peptidoglycan was ornithine. The major menaquinones detected were MK-13 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unknown phospholipid and one unknown glycolipid. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, which were in agreement with those reported for other members of the genus Microbacterium . Physiological and biochemical characteristics and DNA–DNA relatedness between strain 01-Gi-001T and the type strains of its closest phylogenetic neighbours showed clear differences. For this reason, strain 01-Gi-001T ( = DSM 22178T = CCM 7640T) is proposed as the type strain of a novel species, Microbacterium murale sp. nov.
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Streptomyces atacamensis sp. nov., isolated from an extreme hyper-arid soil of the Atacama Desert, Chile
The taxonomic position of a Streptomyces strain isolated from an extreme hyper-arid soil sample collected from the Atacama Desert was determined using a polyphasic approach. The strain, isolate C60T, had chemical and morphological features typical of members of the genus Streptomyces and formed a distinct phyletic line in the Streptomyces 16S rRNA gene tree, together with the type strain of Streptomyces radiopugnans . The two strains were distinguished readily using a combination of phenotypic properties and by a DNA–DNA relatedness value of 23.17 (±0.95) %. On the basis of these genotypic and phenotypic data, it is proposed that isolate C60T ( = CGMCC 4.7018T = KACC 15492T) be classified in the genus Streptomyces as Streptomyces atacamensis sp. nov.
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Nocardioides lianchengensis sp. nov., an actinomycete isolated from soil
Jian Zhang, Yuchao Ma and Huimin YuA novel Gram-stain-positive, aerobic, rod-shaped bacterium, designated strain D94-1T, was isolated from soil collected in Liancheng county, Fujian province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain D94-1T was a member of the genus Nocardioides and was most closely related to Nocardioides salarius DSM 18239T (98.54 % 16S rRNA gene sequence similarity), Nocardioides marinisabuli DSM 18965T (98.30 %), Nocardioides basaltis KCTC 19365T (98.10 %) and Nocardioides dokdonensis KCTC 19309T (97.76 %). Phenotypic characteristics and DNA–DNA relatedness data served to distinguish strain D94-1T from N. salarius , N. marinisabuli , N. basaltis and N. dokdonensis . The chemotaxonomic properties of strain D94-1T were consistent with those of the genus Nocardioides : the cell-wall peptidoglycan type was based on ll-diaminopimelic acid, the predominant menaquinone was MK-8(H4) and the major fatty acids were iso-C16 : 0 (29.15 %) and anteiso-C17 : 0 (21.0 %). The DNA G+C content was 71.8 mol%. On the basis of the evidence presented in this study, strain D94-1T represents a novel species of the genus Nocardioides , for which the name Nocardioides lianchengensis sp. nov. is proposed. The type strain is D94-1T ( = DSM 24663T = CGMCC 4.6858T).
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Gordonia caeni sp. nov., isolated from sludge of a sewage disposal plant
A Gram-stain-positive, strictly aerobic, short-rod-shaped, non-motile strain (designated MJ32T) was isolated from a sludge sample of the Daejeon sewage disposal plant in South Korea. A polyphasic approach was applied to study the taxonomic position of strain MJ32T. Strain MJ32T showed highest 16S rRNA gene sequence similarity to Gordonia hirsuta DSM 44140T (98.1 %) and Gordonia hydrophobica DSM 44015T (97.0 %); levels of sequence similarity to the type strains of other recognized Gordonia species were less than 97.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ32T belonged to the clade formed by members of the genus Gordonia in the family Gordoniaceae . The G+C content of the genomic DNA of strain MJ32T was 69.2 mol%. Chemotaxonomically, strain MJ32T showed features typical of the genus Gordonia . The predominant respiratory quinone was MK-9(H2), the mycolic acids present had C56–C60 carbon atoms, and the major fatty acids were C16 : 0 (34.6 %), tuberculostearic acid (21.8 %), C16 : 1ω7c (19.5 %) and C18 : 1ω9c (12.7 %). The peptidoglycan type was based on meso-2,6-diaminopimelic acid as the diagnostic diamino acid with glycolated sugars. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, strain MJ32T is considered to represent a novel species of the genus Gordonia , for which the name Gordonia caeni sp. nov. is proposed. The type strain is MJ32T ( = KCTC 19771T = JCM 16923T).
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Enteractinococcus coprophilus gen. nov., sp. nov., of the family Micrococcaceae , isolated from Panthera tigris amoyensis faeces, and transfer of Yaniella fodinae Dhanjal et al. 2011 to the genus Enteractinococcus as Enteractinococcus fodinae comb. nov.
A novel actinobacterium, designated strain YIM 100590T, was isolated from Panthera tigris amoyensis faeces collected from Yunnan Wild Animal Park in Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain YIM 100590T is a member of the family Micrococcaceae . Cells were coccoid to oval (0.7–1.5 µm in diameter) occurring singly or in clusters. Growth was observed at 10–37 °C (optimum 28 °C) and at pH 7.0–11.0 (optimum pH 8.0). The major fatty acids were iso-C15 : 0 (32.22 %), anteiso-C15 : 0 (31.64 %) and iso-C16 : 0 (17.38 %). The peptidoglycan was of A4α type (l-Lys–Gly–l-Glu). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, dimannosyl diacylglycerol, an unknown glycolipid and two unknown phospholipids. The quinone system comprised menaquinones MK-7 (91.9 %) and MK-8 (8.3 %). The DNA G+C content of strain YIM 100590T was 56.2 mol%. Chemotaxonomic data indicated that the strain belongs to the family Micrococcaceae . On the basis of morphological and chemotaxonomic data and phylogenetic analysis, strain YIM 100590T is considered to represent a novel species of a new genus within the family Micrococcaceae , for which the name Enteractinococcus coprophilus gen. nov., sp. nov. is proposed. The type strain of Enteractinococcus coprophilus is YIM 100590T ( = DSM 24083T = JCM 17352T). Yaniella fodinae DSM 22966T was transferred to the new genus as Enteractinococcus fodinae comb. nov. (type strain G5T = DSM 22966T = JCM 17931T = MTCC 9846T).
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Phytohabitans flavus sp. nov., Phytohabitans rumicis sp. nov. and Phytohabitans houttuyneae sp. nov., isolated from plant roots, and emended description of the genus Phytohabitans
More LessAn actinomycete strain, designated K09-0627T, was isolated from the roots of an orchid collected in Okinawa Prefecture, Japan. Two actinomycete strains K11-0047T and K11-0057T were isolated from the roots of Rumex acetosa and Houttuynia cordata collected in Kanagawa Prefecture, Japan. 16S rRNA gene sequence analyses indicated that the isolates belonged to the genus Phytohabitans, and that they were closely related to each other and to Phytohabitans suffuscus K07-0523T. The DNA–DNA relatedness values between the three isolates and Phytohabitans suffuscus were below 70 %. On the basis of phylogenetic analysis, DNA–DNA relatedness values and phenotypic characteristics, the strains should be classified as novel species in the genus Phytohabitans , for which the names Phytohabitans flavus sp. nov. (type strain, K09-0627T = JCM 17387T = NBRC 107702T = DSM 45551T), Phytohabitans rumicis sp. nov. (type strain, K11-0047T = JCM 17829T = NBRC 108638T = BCC 48146T) and Phytohabitans houttuyneae sp. nov. (type strain, K11-0057T = JCM 17830T = NBRC 108639T = BCC 48147T) are proposed.
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Alpinimonas psychrophila gen. nov., sp. nov., an actinobacterium of the family Microbacteriaceae isolated from alpine glacier cryoconite
More LessA Gram-type positive, Gram-reaction variable, non-motile, psychrophilic actinobacterium, designated Cr8-25T, was isolated from alpine glacier cryoconite and was able to grow well over a temperature range of 1–15 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Cr8-25T belonged to the family Microbacteriaceae and showed highest 16S rRNA gene sequence similarity with Klugiella xanthotipulae 44C3T (97.0 %). However, strain Cr8-25T could be differentiated from the type strain of K. xanthotipulae on the level of genomospecies by a DNA–DNA relatedness value of only 37.2 %. Strain Cr8-25T contained a cell-wall peptidoglycan that was cross-linked according to the B-type, which is based on 2,4-diaminobutyric acid. The cell wall contained the sugars galactose, fucose and rhamnose. The predominant cellular fatty acids of strain Cr8-25T were C15 : 0 anteiso (64.6 %) and iso-C16 : 0 (22.5 %) and the major menaquinones were MK-11 and MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and unknown glycolipids. The G+C content of the genomic DNA was 58.8 mol%. On the basis of the phenotypic characteristics, phylogenetic and chemotaxonomic analyses and DNA–DNA relatedness data, strain Cr8-25T represents a novel species of a new genus in the family Microbacteriaceae , for which the name Alpinimonas psychrophila gen. nov., sp. nov. is proposed. The type strain is Cr8-25T ( = DSM 23737T = LMG 26215T).
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Arthrobacter cupressi sp. nov., an actinomycete isolated from the rhizosphere soil of Cupressus sempervirens
Jian Zhang, Yuchao Ma and Huimin YuAn actinobacterial strain, designated D48T, was isolated from the rhizosphere soil of a cypress tree collected from Mianyang in Sichuan province, China. The strain was Gram-stain-positive, catalase-positive, oxidase-negative and non-motile, with lysine as the peptidoglycan diagnostic diamino acid and acetyl as the peptidoglycan acyl type. The predominant menaquinone was MK-9(H2); small amounts of MK-7(H2), MK-10(H2) and MK-6 were also present. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The isolate underwent a rod–coccus morphological cycle, had a high DNA G+C content, was aerobic and grew between 12 and 37 °C (optimum, 28 °C). On the basis of the phenotypic and chemotaxonomic analyses, 16S rRNA gene sequence comparisons and DNA–DNA hybridization data, the isolate represents a novel species of the genus Arthrobacter , for which the name Arthrobacter cupressi sp. nov. is proposed. The type strain is D48T ( = DSM 24664T = CGMCC 1.10783T).
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- Firmicutes and Related Organisms
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Lactobacillus delbrueckii subsp. sunkii subsp. nov., isolated from sunki, a traditional Japanese pickle
More LessAlthough four strains of bacteria isolated from sunki, a traditional Japanese, non-salted pickle, were initially identified as Lactobacillus delbrueckii , the molecular and phenotypic characteristics of the strains did not match those of any of the four recognized subspecies of L. delbrueckii . Together, the results of phenotypic characterization, DNA–DNA hybridizations (in which the relatedness values between the novel strains and type strains of the recognized subspecies of L. delbrueckii were all >88.7 %) and 16S rRNA gene sequence, amplified fragment length polymorphism (AFLP) and whole-cell MALDI-TOF/MS spectral pattern analyses indicated that the four novel strains represented a single, novel subspecies, for which the name Lactobacillus delbrueckii subsp. sunkii subsp. nov. is proposed. The type strain is YIT 11221T ( = JCM 17838T = DSM 24966T).
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Lachnoanaerobaculum gen. nov., a new genus in the Lachnospiraceae : characterization of Lachnoanaerobaculum umeaense gen. nov., sp. nov., isolated from the human small intestine, and Lachnoanaerobaculum orale sp. nov., isolated from saliva, and reclassification of Eubacterium saburreum (Prévot 1966) Holdeman and Moore 1970 as Lachnoanaerobaculum saburreum comb. nov.
Two novel obligately anaerobic, Gram-stain-positive, saccharolytic and non-proteolytic spore-forming bacilli (strains CD3 : 22T and N1T) are described. Strain CD3 : 22T was isolated from a biopsy of the small intestine of a child with coeliac disease, and strain N1T from the saliva of a healthy young man. The cells of both strains were observed to be filamentous, approximately 5 to >20 µm long, some of them curving and with swellings. The novel organisms produced H2S, NH3, butyric acid and acetic acid as major metabolic end products. Phylogenetic analyses, based on comparative 16S rRNA gene sequencing, revealed close relationships (98 % sequence similarity) between the two isolates, as well as the type strain of Eubacterium saburreum and four other Lachnospiraceae bacterium-/ E. saburreum -like organisms. This group of bacteria were clearly different from any of the 19 known genera in the family Lachnospiraceae . While Eubacterium species are reported to be non-spore-forming, reanalysis of E. saburreum CCUG 28089T confirmed that the bacterium is indeed able to form spores. Based on 16S rRNA gene sequencing, phenotypic and biochemical properties, strains CD3 : 22T and N1T represent novel species of a new and distinct genus, named Lachnoanaerobaculum gen. nov., in the family Lachnospiraceae [within the order Clostridiales , class Clostridia , phylum Firmicutes ]. Strain CD3 : 22T ( = CCUG 58757T = DSM 23576T) is the type strain of the type species, Lachnoanaerobaculum umeaense gen. nov., sp. nov., of the proposed new genus. Strain N1T ( = CCUG 60305T = DSM 24553T) is the type strain of Lachnoanaerobaculum orale sp. nov. Moreover, Eubacterium saburreum is reclassified as Lachnoanaerobaculum saburreum comb. nov. (type strain CCUG 28089T = ATCC 33271T = CIP 105341T = DSM 3986T = JCM 11021T = VPI 11763T).
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Alteribacillus bidgolensis gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Bacillus persepolensis as Alteribacillus persepolensis comb. nov.
A novel Gram-stain-positive, moderately halophilic bacterium, designated strain P4BT, was isolated from water of the hypersaline Aran-Bidgol lake in Iran and characterized taxonomically by using a polyphasic approach. Cells of strain P4BT were non-motile rods producing ellipsoidal endospores at a central position in non-swollen sporangia. Strain P4BT was strictly aerobic and catalase- and oxidase-positive. It was able to grow at NaCl concentrations of 0.5–12.5 % (w/v), with optimum growth occurring at 5–7.5 % (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain P4BT was shown to belong to the phylum Firmicutes and shared highest similarity with Bacillus persepolensis HS136T (97.1 %) and Bacillus salarius BH169T (95.1 %). However, it shared only 91.3 % 16S rRNA gene sequence similarity with Bacillus subtilis subsp. subtilis DSM 10T, indicating that strain P4BT might not be a member of the genus Bacillus . The DNA G+C content of this new isolate was 38.9 mol%. DNA–DNA hybridization experiments revealed a low level of relatedness between strain P4BT and B. persepolensis HS136T (6 %). The major cellular fatty acids of strain P4BT were iso-C15 : 0 and anteiso-C15 : 0, as for B. persepolensis HS136T but in contrast to B. salarius DSM 16461T and B. subtilis subsp. subtilis DSM 10T. Its polar lipid pattern consisted of phosphatidylglycerol, an aminoglycolipid and an unknown phospholipid. This polar lipid profile was similar to that obtained for B. persepolensis DSM 21632T but different from those of B. salarius DSM 16461T and B. subtilis subsp. subtilis DSM 10T. The isoprenoid quinones were MK-7 (88 %) and MK-8 (2 %). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All these features indicate placement of strain P4BT within the Firmicutes , closely related to B. persepolensis but with features clearly distinct from those of the genus Bacillus and other related genera. On the basis of these data, strain P4BT is considered to represent a novel species of a new genus, for which the name Alteribacillus bidgolensis gen. nov., sp. nov. is proposed. The type strain of Alteribacillus bidgolensis is P4BT ( = CCM 7963T = CECT 7998T = DSM 25260T = IBRC-M 10614T = KCTC 13821T). It is also suggested to transfer B. persepolensis to this new genus, as Alteribacillus persepolensis comb. nov. The type strain of Alteribacillus persepolensis is HS136T ( = CCM 7595T = DSM 21632T = JCM 15720T = LMG 25222T).
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- Proteobacteria
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Otariodibacter oris gen. nov., sp. nov., a member of the family Pasteurellaceae isolated from the oral cavity of pinnipeds
A total of 27 bacterial isolates from California sea lions and a walrus tentatively classified within the family Pasteurellaceae was further characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the isolates investigated formed a monophyletic group, tentatively designated Bisgaard taxon 57. According to 16S rRNA gene sequences, the most closely related species with a validly published name was Bisgaardia hudsonensis and the most closely related species based on rpoB sequence comparison was Pasteurella multocida subsp. multocida; highest similarities between the isolates and the type strains of B. hudsonensis and P. multocida subsp. multocida were 95.0 and 88.2%. respectively. All isolates of Bisgaard taxon 57 exhibit the phenotypic characters of the family Pasteurellaceae . Members of Bisgaard taxon 57 can be separated from existing genera of the Pasteurellaceae by the following tests: positive reactions for catalase, oxidase, Voges–Proskauer and indole; no X- or V-factor dependency; and acid production from l-arabinose (slow), l-fucose, maltose and trehalose, but not from dulcitol, d-mannitol, d-mannose or sucrose. The main fatty acids of Bisgaard taxon 57 (CCUG 59994T) are C14 : 0, C16 : 0, C16 : 1ω7c and the summed feature C14 : 0 3-OH/iso-C16 : 1 I. This fatty acid profile is characteristic of members of the Pasteurellaceae . The quinone profile of Bisgaard taxon 57 (DSM 23800T) was similar to that of other genera in the Pasteurellaceae . The DNA G+C content of strain Baika1T is 36.2 mol%, which is at the lower end of the range for members of the family Pasteurellaceae . On the basis of both phylogenetic and phenotypic evidence, it is proposed that members of Bisgaard taxon 57 should be classified as representatives of a novel species in a new genus, Otariodibacter oris gen. nov., sp. nov. The type strain of Otariodibacter oris is Baika1T ( = CCUG 59994T = DSM 23800T), which was isolated from the oral cavity of a healthy California sea lion in Copenhagen Zoo, Denmark, in 2007.
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Microvirga lupini sp. nov., Microvirga lotononidis sp. nov. and Microvirga zambiensis sp. nov. are alphaproteobacterial root-nodule bacteria that specifically nodulate and fix nitrogen with geographically and taxonomically separate legume hosts
Strains of Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from nitrogen-fixing nodules of the native legumes Listia angolensis (from Zambia) and Lupinus texensis (from Texas, USA). Phylogenetic analysis of the 16S rRNA gene showed that the novel strains belong to the genus Microvirga , with ≥96.1 % sequence similarity with type strains of this genus. The closest relative of the representative strains Lut6T and WSM3557T was Microvirga flocculans TFBT, with 97.6–98.0 % similarity, while WSM3693T was most closely related to Microvirga aerilata 5420S-16T, with 98.8 % similarity. Analysis of the concatenated sequences of four housekeeping gene loci (dnaK, gyrB, recA and rpoB) and cellular fatty acid profiles confirmed the placement of Lut6T, WSM3557T and WSM3693T within the genus Microvirga . DNA–DNA relatedness values, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of Lut6T, WSM3557T and WSM3693T from each other and from other Microvirga species with validly published names. The nodA sequence of Lut6T was placed in a clade that contained strains of Rhizobium , Mesorhizobium and Sinorhizobium , while the 100 % identical nodA sequences of WSM3557T and WSM3693T clustered with Bradyrhizobium , Burkholderia and Methylobacterium strains. Concatenated sequences for nifD and nifH show that the sequences of Lut6T, WSM3557T and WSM3693T were most closely related to that of Rhizobium etli CFN42T nifDH. On the basis of genotypic, phenotypic and DNA relatedness data, three novel species of Microvirga are proposed: Microvirga lupini sp. nov. (type strain Lut6T = LMG 26460T = HAMBI 3236T), Microvirga lotononidis sp. nov. (type strain WSM3557T = LMG 26455T = HAMBI 3237T) and Microvirga zambiensis sp. nov. (type strain WSM3693T = LMG 26454T = HAMBI 3238T).
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Methylobacterium gnaphalii sp. nov., isolated from leaves of Gnaphalium spicatum
More LessA pink-pigmented, facultatively methylotrophic bacterium, strain 23eT, was isolated from the leaves of Gnaphalium spicatum (cudweed). The cells of strain 23eT were Gram-reaction negative, motile and non-spore-forming rods. On the basis of 16S rRNA gene sequence similarities, strain 23eT was related to Methylobacterium organophilum ATCC 27886T (97.1 %) and Methylobacterium marchantiae JT1T (97 %), and the phylogenetic similarities to all other Methylobacterium species with validly published names were less than 97 %. Major cellular fatty acids were C18 : 1ω7c, C16 : 00 and C18 : 0. The results of DNA–DNA hybridization, phylogenetic analyses based on 16S rRNA and cpn60 gene sequences, fatty acid profiles, whole-cell matrix-assisted laser desorption/ionization time of flight/MS analysis, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 23eT from the phylogenetically closest relatives. We propose that strain 23eT represents a novel species within the genus Methylobacterium , for which the name Methylobacterium gnaphalii sp. nov. is proposed. The type strain is 23eT ( = DSM 24027T = NBRC 107716T).
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Pseudomonas zeshuii sp. nov., isolated from herbicide-contaminated soil
More LessA Gram-stain-negative, rod-shaped, non-motile, non-spore-forming bacterium, designated strain BY-1T, was isolated from a soil sample from the city of Qiqihar in Heilongjiang Province, PR China. Strain BY-1T grew optimally at pH 7.0 and 30–35 °C in the presence of 0.5 % (w/v) NaCl. Analysis of 16S rRNA gene sequences revealed that strain BY-1T fell within the radiation of the genus Pseudomonas , and showed highest 16S rRNA gene sequence similarities to Pseudomonas luteola IAM 13000T (99.5 %) and Pseudomonas duriflava HR2T (97.3 %); the levels of sequence similarity with respect to other recognized species of the genus Pseudomonas were <96.7 %. Strain BY-1T showed low DNA–DNA relatedness values with Pseudomonas luteola IAM 13000T (29±3.1 %) and Pseudomonas duriflava HR2T (21±1.5 %). The G+C content of the genomic DNA of strain BY-1T was 55.3 mol%. The major fatty acids were C18 : 1, C16 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the major ubiquinone was Q-9. Data obtained in this study indicated that this isolate represents a novel species of the genus Pseudomonas , for which the name Pseudomonas zeshuii sp. nov. is proposed. The type strain is BY-1T ( = KACC 15471T = ACCC 05688T).
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Jannaschia aquimarina sp. nov., isolated from seawater
More LessA Gram-negative, aerobic, non-motile rod, designated GSW-M26T, was isolated from seawater from the southern coast of Korea. Strain GSW-M26T grew optimally at pH 7.0–8.0, at 30 °C and with 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GSW-M26T fell within the cluster comprising the genus Jannaschia and clustered with Jannaschia seosinensis CL-SP26T. The isolate exhibited the highest 16S rRNA gene sequence similarity (96.9 %) with J. seosinensis CL-SP26T and 93.7–95.5 % 16S rRNA gene sequence similarity with the other members of the genus Jannaschia . Strain GSW-M26T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and 11-methyl C18 : 1ω7c as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and one unidentified aminolipid. The DNA G+C content was 66.4 mol%. Phenotypic characteristics demonstrated that strain GSW-M26T could be differentiated from recognized members of the genus Jannaschia . On the basis of the data presented, strain GSW-M26T is considered to represent a novel species of the genus Jannaschia , for which the name Jannaschia aquimarina sp. nov. is proposed. The type strain is GSW-M26T ( = KCTC 23555T = CCUG 60899T).
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Neptunomonas concharum sp. nov., isolated from a dead ark clam, and emended description of the genus Neptunomonas
More LessA novel Gram-staining-negative, facultatively anaerobic, motile and rod-shaped bacterium, designated strain LHW37T, was isolated from a dead ark clam collected on the south coast of Korea. The novel strain grew optimally at 37 °C, at pH 7.0–8.0 and with 2 % (w/v) NaCl. The predominant cellular fatty acids were C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major isoprenoid quinone was ubiquinone-8 (Q-8) and the predominant polar lipids were phosphatidylethanolamine and phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel strain was most closely related to Neptunomonas japonica JAMM 0745T (97.1 % sequence similarity). The genomic DNA G+C content of strain LHW37T was 48.2 mol%. The DNA–DNA relatedness values recorded in hybridization experiments between the novel strain and its closest known relative were ≤18 %. Based on the phenotypic, genotypic and phylogenetic data, strain LHW37T represents a novel species belonging to the genus Neptunomonas for which the name Neptunomonas concharum sp. nov. is proposed. The type strain is LHW37T ( = KACC 15543T = JCM 17730T). An emended description of the genus Neptunomonas is also provided.
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Polaromonas glacialis sp. nov. and Polaromonas cryoconiti sp. nov., isolated from alpine glacier cryoconite
More LessThe taxonomic positions of two Gram-staining-negative, psychrophilic bacteria, which were isolated from alpine glacier cryoconite and designated strains Cr4-12T and Cr4-35T, were investigated using a polyphasic approach. Both novel strains contained ubiquinone Q-8 as the sole quinone, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the dominant cellular fatty acids, putrescine and 2-hydroxyputrescine as the major polyamines, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. The genomic DNA G+C contents of strains Cr4-12T and Cr4-35T were 61.3 mol% and 60.7 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains belonged to the genus Polaromonas . Although the 16S rRNA gene sequences of strains Cr4-12T and Cr4-35T were very similar (98.7 % sequence similarity), hybridizations indicated a DNA–DNA relatedness value of only 26.9 % between the two novel strains. In pairwise comparisons with the type strains of recognized Polaromonas species, strains Cr4-12T and Cr4-35T showed 16S rRNA gene sequence similarities of 96.4–98.5 % and 96.5–98.4 %, respectively. Based on the phenotypic and phylogenetic evidence and DNA–DNA relatedness data, strains Cr4-12T and Cr4-35T represent two novel species within the genus Polaromonas , for which the names Polaromonas glacialis sp. nov. and Polaromonas cryoconiti sp. nov., respectively, are proposed. The type strain of Polaromonas glacialis sp. nov. is Cr4-12T ( = DSM 24062T = LMG 26049T = KACC 15089T) and that of Polaromonas cryoconiti sp. nov. is Cr4-35T ( = DSM 24248T = LMG 26050T = KACC 15090T).
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Mesorhizobium muleiense sp. nov., nodulating with Cicer arietinum L.
Three chickpea rhizobial strains (CCBAU 83963T, CCBAU 83939 and CCBAU 83908), which were identified previously as representing a distinctive genospecies, were further studied here and compared taxonomically with related species in the genus Mesorhizobium . Results from SDS-PAGE of whole-cell soluble proteins revealed differences from closely related recognized species of the genus Mesorhizobium . Levels of DNA–DNA relatedness were 15.28–50.97 % between strain CCBAU 83963T and the type strains of recognized Mesorhizobium species (except for Mesorhizobium thiogangeticum ). Strain CCBAU 83963T contained fatty acids characteristic of members of the genus Mesorhizobium , but it possessed high concentrations of C19 : 0 cyclo ω8c and iso-C17 : 0. Strain CCBAU 83963T had phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol as major polar lipids, and an ornithine-containing lipid, phosphatidyl-N-dimethylethanolamine and cardiolipin as minor components. Nodulation tests demonstrated the distinct symbiotic character of strain CCBAU 83963T; only Cicer arietinum, its host plant, could be invaded to form effective nitrogen-fixing nodules. The narrow spectrum of utilization of sole carbon sources, lower resistance to antibiotics, and NaCl, pH and temperature growth ranges differentiated these novel rhizobia from recognized species of the genus Mesorhizobium . Based on the data presented, the three novel rhizobial strains are considered to represent a novel species of the genus Mesorhizobium , for which the name Mesorhizobium muleiense sp. nov. is proposed. The type strain is CCBAU 83963T ( = HAMBI 3264T = CGMCC 1.11022T).
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Algiphilus aromaticivorans gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from a culture of the marine dinoflagellate Lingulodinium polyedrum, and proposal of Algiphilaceae fam. nov.
A strictly aerobic, halotolerant, Gram-stain-negative, rod-shaped bacterium, designated strain DG1253T, was isolated from a laboratory culture of the marine dinoflagellate Lingulodinium polyedrum (CCAP 1121/2). The strain was able to degrade two- and three-ring polycyclic aromatic hydrocarbons. It exhibited a narrow nutritional spectrum, preferring to utilize aliphatic and aromatic hydrocarbon compounds and small organic acids. Cells produced surface blebs and contained a single polar flagellum. The predominant isoprenoid quinone of strain DG1253T was Q-8. The fatty acid profile was dominated by C18 : 1ω7c. The mean DNA G+C content of strain DG1253T was 63.6±0.25 mol%. 16S rRNA gene sequence analysis placed this organism within the order Xanthomonadales of the class Gammaproteobacteria . Its closest relatives included representatives of the Hydrocarboniphaga – Nevskia – Sinobacter clade (≤89.9 % 16S rRNA gene sequence similarity) in the family Sinobacteraceae . On the basis of distinct phenotypic and genotypic characteristics, strain DG1253T is considered to represent a novel species of a new genus in the class Gammaproteobacteria , for which the name Algiphilus aromaticivorans gen. nov., sp. nov. is proposed. The type strain of the type species, Algiphilus aromaticivorans, is DG1253T ( = ATCC BAA-2243T = DSM 24793T). In addition, a new family, Algiphilaceae fam. nov., is proposed to accommodate the genus Algiphilus.
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Paracoccus rhizosphaerae sp. nov., isolated from the rhizosphere of the plant Crossostephium chinense (L.) Makino (Seremban)
A Gram-negative, coccoid-shaped bacterium, strain CC-CCM15-8T, was isolated from a rhizosphere soil sample of the plant Crossostephium chinense (L.) Makino (Seremban) from Budai Township, Chiayi County, Taiwan. 16S rRNA gene sequence analysis clearly allocated strain CC-CCM15-8T to the Paracoccus cluster, showing highest similarities to the type strains of ‘Paracoccus beibuensis’ (98.8 %), Paracoccus homiensis (97.6 %), Paracoccus aestuarii (97.7 %) and Paracoccus zeaxanthinifaciens (97.7 %). The fatty acid profile, comprising C18 : 1ω7c as the major component and C10 : 0 3-OH as the characteristic hydroxylated fatty acid, supported the placement of strain CC-CCM15-8T within the genus Paracoccus . The polyamine pattern consisted of putrescine and spermidine as major components. Ubiqinone Q-10 was the major quinone type (95 %); ubiquinone Q-9 was also detected (5 %). The complex polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, and unidentified phospholipids, lipids and glycolipids. Levels of DNA–DNA relatedness between strain CC-CCM15-8T and ‘P. beibuensis’ LMG 25871T, P. aestuarii DSM 19484T, P. zeaxanthinifaciens LMG 21993T and P. homiensis KACC 11518T were 24.9 % (34.8 %, reciprocal analysis), 15.7 % (17.5 %), 17.7 % (23.4 %) and 16.0 % (25.4 %), respectively. Physiological and biochemical test results allowed the phenotypic differentiation of strain CC-CCM15-8T from its closest relatives in the genus Paracoccus . Based on the data presented, it is concluded that strain CC-CCM15-8T represents a novel species of the genus Paracoccus , for which the name Paracoccus rhizosphaerae sp. nov. is proposed. The type strain is CC-CCM15-8T ( = LMG 26205T = CCM 7904T).
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- Bacteroidetes
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Sphingobacterium kyonggiense sp. nov., isolated from chloroethene-contaminated soil, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium mizutaii
More LessA Gram-reaction-negative, strictly aerobic, rod-shaped, non-motile strain, designated 2-1-2T, was isolated from perchloroethylene/trichloroethene-contaminated soil in Suwon, South Korea. A polyphasic approach was used to study the taxonomic position of strain 2-1-2T. Strain 2-1-2T showed highest 16S rRNA gene sequence similarities to Sphingobacterium daejeonense TR6-04T (97.9 %) and Sphingobacterium mizutaii ATCC 33299T (97.1 %); sequence similarities to other Sphingobacterium species were less than 93.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 2-1-2T belonged to the clade formed by members of the genus Sphingobacterium in the family Sphingobacteriaceae . The G+C content of the genomic DNA was 36.6 mol%. Strain 2-1-2T showed the typical chemotaxonomic features of the genus Sphingobacterium , with the presence of a ceramide phosphorylethanolamine (CerPE-2) as the major ceramide, menaquinone 7 (MK-7) as the predominant respiratory quinone and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c) as the major fatty acids. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, and DNA–DNA relatedness, strain 2-1-2T represents a novel species of the genus Sphingobacterium , for which the name Sphingobacterium kyonggiense sp. nov. is proposed; the type strain is 2-1-2T ( = KEMC 2241-005T = JCM 16704T). Emended descriptions of Sphingobacterium daejeonense and Sphingobacterium mizutaii are also proposed.
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Terrimonas rubra sp. nov., isolated from a polluted farmland soil and emended description of the genus Terrimonas
More LessA salmon-red-pigmented bacterial strain, designated M-8T, was isolated from a polluted farmland soil sample in China and was characterized in a taxonomic study using a polyphasic approach. Strain M-8T was Gram-stain-negative, rod-shaped, non-motile and non-spore-forming. Growth occurred at 20–37 °C, at pH 5.0–10.0 and with 0–2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain M-8T belonged to the genus Terrimonas .16S rRNA gene sequence similarity values between strain M-8T and the type strains of the three recognized species of the genus Terrimonas , Terrimonas ferruginea KACC 11310T, Terrimonas aquatica LMG 24825T and Terrimonas lutea KACC 13047T, were 97.1, 96.3 and 95.3 %, respectively. The predominant respiratory quinone was menaquinone-7 (MK-7) and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content of strain M-8T was 47.0 mol%. On the basis of genotypic and phenotypic data, strain M-8T is considered to represent a novel species of the genus Terrimonas , for which the name Terrimonas rubra sp. nov. is proposed. The type strain is M-8T ( = CCTCC AB 2010401T = KCTC 23299T). An emended description of the genus Terrimonas is also presented.
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Isolates belonging to CDC group II-i belong predominantly to Sphingobacterium mizutaii Yabuuchi et al. 1983: emended descriptions of S. mizutaii and of the genus Sphingobacterium
More LessTwo clinical strains, NF 296 and NF 931, present in our collection, were identified biochemically as members of CDC group II-i. Determination of the 16S rRNA gene sequence revealed highest similarity with strains of Sphingobacterium mizutaii . Because these strains produced indole, whereas S. mizutaii has been described as indole-negative, we also investigated the type strain and a reference strain of S. mizutaii , LMG 8340T ( = CCUG 15907T) and LMG 8341 ( = CCUG 15908), and found both strains also to be positive for indole production. These data warrant inclusion of some of the CDC group II-i strains into S. mizutaii and emended descriptions of Sphingobacterium mizutaii as indole-production-positive and of the genus Sphingobacterium as variable for indole production.
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Parabacteroides chartae sp. nov., an obligately anaerobic species from wastewater of a paper mill
More LessA bacterial strain, designated NS31-3T, was isolated from the wastewater of a paper mill. Cells of the isolate were obligately anaerobic, non-pigmented, non-motile, Gram-negative, short rods (0.7–1.0×1.4–2.5 µm). The isolate was able to grow on media containing 20 % bile salts. API 20A tests showed that acid was produced from glucose, lactose, sucrose, maltose, d-xylose, l-arabinose, cellobiose, d-mannose, d-melezitose, d-raffinose, d-trehalose, d-mannitol, salicin and d-sorbitol. The main fermentation products from PYG broth were lactic acid, propionic acid, formic acid and acetic acid. Chemotaxonomic analysis showed that the major fatty acids were anteiso-C15 : 0, C15 : 0 and iso-C17 : 0 3-OH and the predominant respiratory quinones were MK-9 and MK-10. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NS31-3T was related to members of genus Parabacteroides (91.2–93.2 % sequence similarity); the isolate had the closest affinity with Parabacteroides merdae JCM 9497T. The G+C content of the genomic DNA was 37.2 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analysis, strain NS31-3T represents a novel species of the genus Parabacteroides , for which the name Parabacteroides chartae sp. nov. is proposed. The type strain is NS31-3T ( = JCM 17797T = DSM 24967T).
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Alkalitalea saponilacus gen. nov., sp. nov., an obligately anaerobic, alkaliphilic, xylanolytic bacterium from a meromictic soda lake
More LessA Gram-positive, obligately anaerobic, motile, slender, flexible rod, designated SC/BZ-SP2T, was isolated from mixed alkaline water and sediment of Soap Lake, Washington State, USA. Strain SC/BZ-SP2T formed salmon to pink colonies and was alkaliphilic. The isolate grew at pH35 °C 7.5–10.5 (optimum pH35 °C 9.7), at 8–40 °C (optimum 35–37 °C) and with 0.35–1.38 M Na+ (optimum 0.44–0.69 M Na+). The isolate utilized l-arabinose, d-ribose, d-xylose, d-fructose, d-mannose, d-galactose, cellobiose, maltose, sucrose, trehalose, sorbitol, xylan, malate and yeast extract as carbon and energy sources; best growth was observed with l-arabinose, cellobiose, maltose and trehalose. The major fermentation products from beechwood xylan were propionate and acetate. The dominant fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH, C17 : 0 3-OH and C15 : 0 3-OH. The cell-wall sugars were ribose, xylose, galactose and glucose. Thiosulfate and sulfite could be reduced to sulfide. The genomic DNA G+C content was 39.5±0.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SC/BZ-SP2T belonged to the family Marinilabiliaceae of the order Bacteroidales , class Bacteroidia . The most closely related strains were Alkaliflexus imshenetskii Z-7010T (91.8 % 16S rRNA gene sequence similarity), Marinilabilia salmonicolor Cy s1T (91.0 %) and Anaerophaga thermohalophila Fru22T (90.4 %). On the basis of phenotypic, chemotaxonomic and phylogenetic features, strain SC/BZ-SP2T represents a novel species in a new genus of the family Marinilabiliaceae , for which the name Alkalitalea saponilacus gen. nov., sp. nov. is proposed. The type strain of Alkalitalea saponilacus is SC/BZ-SP2T ( = ATCC BAA-2172T = DSM 24412T).
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Imtechella halotolerans gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from estuarine water
More LessA novel Gram-negative, rod-shaped, non-motile, non-sporulating bacterium, designated strain K1T, was isolated from an estuarine water sample collected from Kochi, Kerala, India. Colonies on marine agar were circular, 2.0–2.5 mm in diameter, shiny, yellow, translucent and convex with entire margins. Strain K1T was negative for ornithine decarboxylase, lysine decarboxylase, nitrate reduction and H2S production. The fatty acids were dominated by iso-branched components with a high abundance of iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH; MK-6 (64 %) and MK-7 (34 %) were found as major respiratory quinones; and phosphatidylethanolamine, two unidentified aminolipids, four unidentified phospholipids and two unidentified lipids were major polar lipids. The DNA G+C content of strain K1T was 46.1 mol%. 16S rRNA gene sequence analysis indicated that strain K1T was related most closely to the type strain of Zhouia amylolytica (pairwise sequence similarity of 93.0 %). Phylogenetic analysis showed that strain K1T formed a distinct branch within the family Flavobacteriaceae and clustered with the clade comprising species of the genera Zhouia , Coenonia and Capnocytophaga , being phylogenetically most closely related to the type strain of Zhouia amylolytica at a distance of 9.2 % (90.8 % similarity). Other species of the genera within the same clade were related to strain K1T at distances of 15.0–23.1 %. Based on phenotypic and chemotaxonomic characteristics and on phylogenetic inference, strain K1T is considered to represent a novel species of a new genus in the family Flavobacteriaceae , for which the name Imtechella halotolerans gen. nov., sp. nov. is proposed. The type strain of Imtechella halotolerans is K1T ( = MTCC 11055T = JCM 17677T).
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Reclassification of Xylanibacter oryzae Ueki et al. 2006 as Prevotella oryzae comb. nov., with an emended description of the genus Prevotella
More Less16S rRNA gene sequence information has indicated that Xylanibacter oryzae has a close relationship with the genus Prevotella . To clarify the taxonomic position of X. oryzae , we determined the sequence of hsp60 as it represents an alternative phylogenetic marker for identification and classification of Gram-negative anaerobic rods. On the basis of hsp60 sequences, X. oryzae was located within the genus Prevotella , indicating that the species does not represent a distinct taxon at the genus level. Statistical tests (the Shimodaira–Hasegawa test and the approximately unbiased test) supported the finding that X. oryzae is monophyletic with members of the genus Prevotella and thus belongs to the genus. On the basis of the phylogenetic findings, we propose that X. oryzae should be reclassified as Prevotella oryzae comb. nov.; the type strain is KB3T ( = JCM 13648T = DSM 17970T). An emended description of the genus Prevotella is also provided.
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Flavobacterium ummariense sp. nov., isolated from hexachlorocyclohexane-contaminated soil, and emended description of Flavobacterium ceti Vela et al. 2007
Pushp Lata, Devi Lal and Rup LalA Gram-negative, strictly aerobic, yellow bacterial strain, designated DS-12T, was isolated from hexachlorocyclohexane-contaminated soil in Lucknow, Uttar Pradesh, India. Strain DS-12T showed the highest 16S rRNA gene sequence similarity with Flavobacterium ceti 454-2T (94.2 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-12T belonged to the genus Flavobacterium . Strain DS-12T produced flexirubin-type pigments. Gliding motility was not observed. The major fatty acids of strain DS-12T were iso-C15 : 0 (48.0 %), summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl; 19.3 %), iso-C17 : 0 3-OH (8.5 %) and summed feature 3 (comprising one or more of C16 : 1ω7c, C16 : 1ω6c and iso-C15 : 0 2-OH; 7.2 %). The only respiratory quinone was menaquinone-6 and the major polyamine was homospermidine. Strain DS-12T contained phosphatidyldimethylethanolamine, phosphatidylserine, phosphatidylethanolamine, one unknown phospholipid and one unknown aminolipid. The DNA G+C content was 37.4 mol%. Phylogenetic inference and phenotypic properties indicated that strain DS-12T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium ummariense sp. nov. is proposed. The type strain is DS-12T ( = CCM 7847T = MTCC 10766T). An emended description of Flavobacterium ceti is also given.
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- Other Bacteria
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Thermosulfurimonas dismutans gen. nov., sp. nov., an extremely thermophilic sulfur-disproportionating bacterium from a deep-sea hydrothermal vent
An extremely thermophilic, anaerobic, chemolithoautotrophic bacterium (strain S95T) was isolated from a deep-sea hydrothermal vent chimney located on the Eastern Lau Spreading Center, Pacific Ocean, at a depth of 1910 m. Cells of strain S95T were oval to short Gram-negative rods, 0.5–0.6 µm in diameter and 1.0–1.5 µm in length, growing singly or in pairs. Cells were motile with a single polar flagellum. The temperature range for growth was 50–92 °C, with an optimum at 74 °C. The pH range for growth was 5.5–8.0, with an optimum at pH 7.0. Growth of strain S95T was observed at NaCl concentrations ranging from 1.5 to 3.5 % (w/v). Strain S95T grew anaerobically with elemental sulfur as an energy source and bicarbonate/CO2 as a carbon source. Elemental sulfur was disproportionated to sulfide and sulfate. Growth was enhanced in the presence of poorly crystalline iron(III) oxide (ferrihydrite) as a sulfide-scavenging agent. Strain S95T was also able to grow by disproportionation of thiosulfate and sulfite. Sulfate was not used as an electron acceptor. Analysis of the 16S rRNA gene sequence revealed that the isolate belongs to the phylum Thermodesulfobacteria . On the basis of its physiological properties and results of phylogenetic analyses, it is proposed that the isolate represents the sole species of a new genus, Thermosulfurimonas dismutans gen. nov., sp. nov.; S95T ( = DSM 24515T = VKM B-2683T) is the type strain of the type species. This is the first description of a thermophilic micro-organism that disproportionates elemental sulfur.
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- Eukaryotic Micro-organisms
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The morphology and phylogeny of two euplotid ciliates, Diophrys blakeneyensis spec. nov. and Diophrys oligothrix Borror, 1965 (Protozoa, Ciliophora, Euplotida)
More LessThe morphology, infraciliature and molecular phylogeny of two marine ciliated protozoans, Diophrys blakeneyensis spec. nov. and Diophrys oligothrix Borror, 1965, isolated from British salt marshes, were investigated using microscopic observations of live and protargol-impregnated specimens, and by small subunit (SSU) rRNA gene sequence analysis. Diophrys blakeneyensis spec. nov. is characterized as follows: cell oval to rectangular in outline; size variable, approximately 60–180 × 30–80 µm in vivo; adoral zone comprising about 45 membranelles; usually five frontal, two ventral, five transverse, two left marginal and three caudal cirri; five dorsal kineties with more than 10 dikinetids each; 7–23 spherical to ellipsoid macronuclear nodules in a ring-like pattern; marine biotope. The population of Diophrys oligothrix described here corresponds well with previous populations in terms of its general morphology and ciliary pattern, in particular the continuous ciliary rows on the dorsal side with loosely arranged cilia. The main differences between the present and previously reported populations are the broader buccal field and greater number of dorsal kineties in the present population, both of which are regarded as population-dependent features. Phylogenetic analyses based on SSU rRNA gene sequence data demonstrate that Diophrys blakeneyensis is most closely related to Diophrys oligothrix, and both organisms cluster with two congeners with high bootstrap support within a larger group that contain the core species of the Diophrys-complex. Cladistic analysis based on morphological and morphogenetic data broadly agree with the SSU rRNA gene sequence phylogeny. Both analyses suggest that the genus Diophrys may be polyphyletic.
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Kwoniella shandongensis sp. nov., a basidiomycetous yeast isolated from soil and bark from an apple orchard
More LessFour basidiomycetous yeast strains (Y13-1T, Y2-1, Y6-3 and Y8-2) were isolated from soil and bark collected from an apple orchard in Tai’an, Shandong province, PR China. Phylogenetic analysis based on 26S rRNA gene D1/D2 domains and ITS regions revealed that these novel strains were located in the Kwoniella clade in the class Tremellomycetes and were closely related to Cryptococcus cuniculi and Kwoniella heveanensis, but were clearly distinct from these species. Therefore, it is proposed that the new strains represent a novel species, Kwoniella shandongensis sp. nov., with the type strain Y13-1T( = CGMCC 2.04458T = CBS 12478T). The MycoBank number for the novel species is MB 564868.
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Aspergillus baeticus sp. nov. and Aspergillus thesauricus sp. nov., two species in section Usti from Spanish caves
More LessTwo novel species of Aspergillus that are clearly distinct from all known species in section Usti were revealed during a study of microfungal communities in Spanish caves. The novel species identified in this study and additional species of Aspergillus section Usti are associated with places and substrates related to human activities in caves. Novel species are described using data from four loci (ITS, benA, caM and rpb2), morphology and basic chemical and physiological analyses. Members of the species Aspergillus thesauricus sp. nov. were isolated from various substrates, including decaying organic matter, cave air and cave sediment of the Cueva del Tesoro Cave (the Treasure cave); the species is represented by twelve isolates and is most closely related to the recently described Aspergillus germanicus. Members of the species Aspergillus baeticus sp. nov. were isolated from cave sediment in the Gruta de las Maravillas Cave (the Grotto of the Marvels); the species is represented by two isolates. An additional isolate was found in the Cueva del Tesoro Cave and in the Demänovská Peace Cave (Slovakia), suggesting a potentially wide distribution of this micro-organism. The species is related to Aspergillus ustus and Aspergillus pseudoustus. Both species were unable to grow at 37 °C, and a weakly positive, light greenish yellow Ehrlich reaction was observed in A. thesauricus. Unique morphological features alone are sufficient to distinguish both species from related taxa.
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Wickerhamomyces xylosica sp. nov. and Candida phayaonensis sp. nov., two xylose-assimilating yeast species from soil
Two strains (NT29T and NT31T) of xylose-assimilating yeasts were obtained from soils collected in northern Thailand. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, and sequence analysis of the D1/D2 domain of the large subunit rRNA gene and the internal transcribed spacer region, the two strains were found to represent two novel ascomycete yeast species. Strain NT29T was assigned to the genus Candida belonging to the Pichia clade as a representative of Candida phayaonensis sp. nov.; the type strain is NT29T ( = BCC 47634T = NBRC 108868T = CBS 12319T). Strain NT31T represented a novel Wickerhamomyces species, which was named Wickerhamomyces xylosica sp. nov.; the type strain is NT31T ( = BCC 47635T = NBRC 108869T = CBS 12320T).
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Saccharomycopsis fodiens sp. nov., a rare predacious yeast from three distant localities
Three strains representing a novel yeast species were recovered as part of independent collections from flower-associated nitidulid beetles in Australia, Costa Rica and the Galapagos Islands, Ecuador. Analysis of the D1/D2 domains of the large subunit rRNA gene indicated that the species belongs to the genus Saccharomycopsis, although the formation of ascospores was not observed. The yeast is capable of necrotrophic parasitism by means of infection pegs when mixed with other yeasts or filamentous fungi. Of particular interest is the fact that despite the large distances separating the isolation sites of the three strains, other strains of the species have not been recovered in other samples of flower-associated nitidulids even though these habitats have been sampled extensively. It is suggested that the dispersal of the yeast may be linked to human historical factors. The name Saccharomycopsis fodiens sp. nov. is proposed for the yeast. The type strain is UWOPS 95-697.4T ( = CBS 8332T = NRRL Y-48786T).
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Spencermartinsiella ligniputridi sp. nov., a yeast species isolated from rotten wood
More LessFour strains of a novel heterothallic yeast species were isolated from rotten wood samples collected at different locations in Hungary. Analysis of sequences of the D1/D2 domain of the large subunit rRNA gene placed the novel species in the genus Spencermartinsiella. The novel species can be distinguished from Spencermartinsiella europaea, the single species of the genus, and from Candida cellulosicola, the only recognized anamorphic species of the Spencermartinsiella clade, on the basis of standard phenotypic characteristics. The relatedness among the four strains of the novel species and two closely related strains representing undescribed yeast species is discussed. The name Spencermartinsiella ligniputridi sp. nov. is proposed to accommodate the four novel strains. The type and isotype strains of Spencermartinsiella ligniputridi sp. nov. are NCAIM Y.01992T ( = CBS 12585T = NRRL Y-48818T) and NCAIM Y.01936I ( = CBS 12586I = NRRL Y-48819I), respectively. Two additional strains are NCAIM Y.01991 and NCAIM Y.01993.
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Candida ficus sp. nov., a novel yeast species from the gut of Apriona germari larvae
More LessA novel yeast species is described based on three strains from the gut of wood-boring larvae collected in a tree trunk of Ficus carica cultivated in parks near Nanyang, central China. Phylogenetic analysis based on sequences of the D1/D2 domains of the large subunit rRNA gene showed that these strains occurred in a separate clade that was genetically distinct from all known ascomycetous yeasts. In terms of pairwise sequence divergence, the novel strains differed by 15.3 % divergence from the type strain of Pichia terricola, and by 15.8 % divergence from the type strains of Pichia exigua and Candida rugopelliculosa in the D1/D2 domains. All three are ascomycetous yeasts in the Pichia clade. Unlike P. terricola, P. exigua and C. rugopelliculosa, the novel isolates did not ferment glucose. The name Candida ficus sp. nov. is proposed to accommodate these highly divergent organisms, with STN-8T ( = CICC 1980T = CBS 12638T) as the type strain.
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