- Volume 60, Issue 3, 2010
Volume 60, Issue 3, 2010
- Editorial
- 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 59, part 12, 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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Microbacterium soli sp. nov., an α-glucosidase-producing bacterium isolated from soil of a ginseng field
Five Gram-type-positive, aerobic, rod-shaped, non-motile strains of Microbacterium (DCY 17T, Ms1, Ms2, Ms3 and Ms4) were isolated from soil from a ginseng field in Daejeon, South Korea. On the basis of 16S rRNA gene sequence similarity, these strains were shown to be related to Microbacterium esteraromaticum DSM 8609T (96.1 %), M. xylanilyticum DSM 16914T (96.0 %), M. aquimaris JS54-2T (95.6 %), M. insulae DS-66T (95.5 %), M. ketosireducens IFO 14548T (95.5 %) and M. arabinogalactanolyticum DSM 8611T (95.4 %). Chemotaxonomic data revealed that the type strain, DCY 17T, possesses menaquinones MK-12, MK-11 and MK-13 and the predominant fatty acids C15 : 0 anteiso (32.5 %), C15 : 0 iso (27.5 %), C16 : 0 iso (17.0 %), C17 : 0 anteiso (13.2 %), C17 : 0 iso (6.1 %) and C14 : 0 iso (2.1 %). The DNA G+C content of strain DCY 17T is 70.2 mol% and those of strains Ms1 to Ms4 are in the range 68.9–73.5 mol%. The physiological and biochemical tests suggested that these strains represent a novel species. Based on these data, DCY 17T (=KCTC 19237T =LMG 24010T) is classified as the type strain of a novel Microbacterium species, for which the name Microbacterium soli sp. nov. is proposed.
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Citricoccus zhacaiensis sp. nov., isolated from a bioreactor for saline wastewater treatment
More LessA Gram-positive, neutrophilic, non-motile and non-spore-forming actinobacterium, strain FS24T, was isolated from a bioreactor treating salt-containing wastewater. This isolate grew in the presence of 0–15 % (w/v) NaCl and at 10-37 °C. The optimum NaCl concentration for growth of FS24T was 5 % (w/v) at 37 °C or 1 % (w/v) at 25 °C. Chemotaxonomic analysis revealed MK-9(H2) as the predominant menaquinone and the major cellular polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, four unknown glycolipids, two unknown phospholipids and an unknown lipid. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The genomic DNA G+C content was 66.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FS24T clustered with members of the genus Citricoccus, exhibiting high sequence similarity to the 16S rRNA gene sequences of the type strains of Citricoccus alkalitolerans (98.9 %) and Citricoccus muralis (98.8 %), respectively. The DNA–DNA relatedness values of strain FS24T to C. alkalitolerans DSM 15665T and C. muralis DSM 14442T were 54 and 39 %, respectively. On the basis of phenotypic and genotypic data, strain FS24T represents a novel species of the genus Citricoccus, for which the name Citricoccus zhacaiensis sp. nov. is proposed. The type strain is FS24T (=CGMCC 1.7064T =JCM 15136T).
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Promicromonospora umidemergens sp. nov., isolated from moisture from indoor wall material
More LessA Gram-positive, yellow-pigmented, branched-hyphae-forming micro-organism, strain 09-Be-007T, was isolated from the wall of an indoor environment. Based on 16S rRNA gene sequence similarity studies, strain 09-Be-007T belonged to the genus Promicromonospora. The novel isolate showed sequence similarities of 98.8 % to Promicromonospora aerolata V54AT, 98.9 % to Promicromonospora vindobonensis V45T, 98.1 % to Promicromonospora sukumoe DSM 44121T, 98.2 % to Promicromonospora kroppenstedtii RS16T, 96.7 % to Promicromonospora flava CC 0387T and 97.8 % to Promicromonospora citrea DSM 43110T, the type strain of the type species of this genus. Cell wall sugars of strain 09-Be-007T were galactose, rhamnose and glucose. The diagnostic diamino acid of the cell-wall peptidoglycan was lysine. The major menaquinones detected were MK-9(H4) and MK-9(H6). Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. Major fatty acids were iso-C15 : 0 and anteiso-C15 : 0; moderate amounts of anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 1 were also found. All these data supported the affiliation of strain 09-Be-007T to the genus Promicromonospora. DNA–DNA hybridization values and physiological and biochemical data enabled strain 09-Be-007T to be differentiated genotypically and phenotypically from the six recognized species of the genus Promicromonospora. For these reasons, strain 09-Be-007T represents a novel species, for which the name Promicromonospora umidemergens sp. nov. is proposed, with 09-Be-007T (=DSM 22081T=CCM 7634T) as the type strain.
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Actinoallomurus acaciae sp. nov., an endophytic actinomycete isolated from Acacia auriculiformis A. Cunn. ex Benth.
A novel endophytic actinomycete, strain GMKU 931T, was isolated from the root of a wattle tree, Acacia auriculiformis A. Cunn. ex Benth., collected at Kasetsart University, Bangkok, Thailand. Strain GMKU 931T produced short spiral chains of smooth-surfaced spores on the aerial mycelium. Lysine and meso-diaminopimelic acid were present in the cell-wall peptidoglycan. Whole-cell hydrolysates contained galactose, madurose and mannose. The predominant menaquinones were MK-9(H6) and MK-9(H8). The major fatty acids were iso-C16 : 0 and iso-C16 : 1. The major phospholipids were phosphatidylinositol and phosphatidylglycerol. A phylogenetic analysis based on 16S rRNA gene sequences suggested that strain GMKU 931T forms a distinct phyletic line within the recently proposed genus Actinoallomurus. The significant differences in phenotypic and genotypic data indicate that strain GMKU 931T represents a novel species of the genus Actinoallomurus, for which the name Actinoallomurus acaciae sp. nov. is proposed. The type strain is GMKU 931T (=BCC 28622T =NBRC 104354T =NRRL B-24610T).
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Luteipulveratus mongoliensis gen. nov., sp. nov., an actinobacterial taxon in the family Dermacoccaceae
More LessA novel actinobacterial strain, MN07-A0370T, was isolated from Mongolian soil and its taxonomic status was determined using a polyphasic approach. Comparative 16S rRNA gene sequence studies revealed that strain MN07-A0370T represented a novel lineage within the actinobacteria. Strain MN07-A0370T formed a distinct clade in the family Dermacoccaceae and was most closely related to the members of the genera Dermacoccus (16S rRNA gene sequence similarity, 96.2 %–96.4 %), Demetria (94.1 %) and Kytococcus (93.7 %). The cell-wall peptidoglycan of the novel strain contained l-lysine, alanine, aspartic acid, glutamic acid and serine and represented peptidoglycan type A4α. The menaquinones were MK-8(H4) and MK-8(H6). The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol and the whole-cell sugars were galactose, mannose, rhamnose, ribose and glucose. Mycolic acids were absent. The fatty acid profile was characterized by the presence of large amounts of saturated iso- and anteiso-branched-chain fatty acids as well as smaller amounts of saturated straight-chain and unsaturated acids. The major fatty acids were iso-C16 : 0, anteiso-C17 : 0, iso-C16 : 1 H, C17 : 1 ω9c and C17 : 0 10-methyl. The G+C content of the DNA was 68.2 mol%. On the basis of chemotaxonomic, physiological and biochemical differences from other genera of the family Dermacoccaceae, strain MN07-A0370T should be classified as representing a novel species in a new genus, for which we propose the name Luteipulveratus mongoliensis gen. nov., sp. nov. The type strain is MN07-A0370T (=NBRC 105296T=VTCC D9-09T).
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Amycolicicoccus subflavus gen. nov., sp. nov., an actinomycete isolated from a saline soil contaminated by crude oil
Two novel actinomycetes, designated DQS3-9A1T and DQS3-9A2, were isolated from a saline soil contaminated with crude oil in the Shengli Oilfield in China. On the basis of 16S rRNA gene sequence analysis, the two strains were most closely related to Mycobacterium species (92.7–94.9 % similarities), and formed a distinct lineage in the suborder Corynebacterineae. In addition, the major sugars in the cell wall, arabinose and galactose, supported the affiliation of strain DQS3-9A1T with members of the family Mycobacteriaceae. However, strain DQS3-9A1T did not contain mycolic acids and MK-8 (85.5 %) was the major menaquinone for both isolates. The major cellular fatty acids for strain DQS3-9A1T were C16 : 0 (20.5 %), 10-methyl C17 : 0 (19.3 %), 10-methyl C18 : 0 (16.1 %), summed feature 3 (11.4 %), C15 : 0 (11.3 %), C17 : 0 (5.0 %) and C17 : 1 ω8c (5.0 %). The polar lipids of strain DQS3-9A1T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and an unknown glucosamine-containing phospholipid. These chemotaxonomic data indicated that strain DQS3-9A1T differs from the present members of the suborder Corynebacterineae. Therefore, the creation of Amycolicicoccus subflavus gen. nov., sp. nov. is proposed, with DQS3-9A1T (=DSM 45089T=CGMCC 4.3532T) as the type strain.
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Micromonospora marina sp. nov., isolated from sea sand
More LessTwo actinomycete strains, JSM1-1T and JSM1-3, were isolated from sea sand collected in Thailand. Their taxonomic position was determined using a polyphasic approach. The chemotaxonomic characteristics of these strains coincided with those of the genus Micromonospora, i.e. the presence of meso-diaminopimelic acid and N-glycolyl muramic acid in the peptidoglycan, whole cell sugar pattern D, phospholipids type II, and cellular fatty acid type 3b. Phylogenetic analysis of 16S rRNA gene sequences revealed a close relationship between strains JSM1-1T and JSM1-3 (99.8 %), and between JSM1-1T and Micromonospora aurantiaca JCM 10878T (99.3 %), Micromonospora chalcea JCM 3031T (99.0 %), and Micromonospora coxensis JCM 13248 T (99.0 %). However, strains JSM1-1T and JSM1-3 could be clearly distinguished from these type strains by a low DNA–DNA relatedness and by phenotypic differences. On the basis of the data presented, a new species, Micromonospora marina sp. nov., is proposed. The type strain is JSM1-1T (=JCM 12870T =PCU 269T =TISTR 1566T).
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Yimella lutea gen. nov., sp. nov., a novel actinobacterium of the family Dermacoccaceae
More LessA Gram-stain-positive, coccoid, non-motile, halotolerant actinobacterium, designated YIM 45900T, was found as a contaminant on an agar plate in the laboratory of Yunnan Institute of Microbiology, China. The peptidoglycan type was A4α with an l-Lys–l-Ser–d-Asp interpeptide bridge. The cell-wall sugars contained galactose and fucose. The predominant menaquinone was MK-8(H4). The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipids contained diphosphatidylglycerol, phosphatidylinositol, a glucosamine-containing phospholipid and an unknown phospholipid. The DNA G+C content was 65.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism falls within the radius of the suborder Micrococcineae and its closest phylogenetic neighbours are the genera of the family Dermacoccaceae. Strain YIM 45900T showed 16S rRNA gene sequences similarity values of 93.1–95.9 % with members of the genera Dermacoccus, Demetria and Kytococcus. On the basis of the phylogenetic and phenotypic characteristics of the actinobacterium, a novel genus and species, Yimella lutea gen. nov., sp. nov., are proposed. The type strain of Yimella lutea is YIM 45900T (=DSM 19828T =KCTC 19231T =CCTCC AB 207007T).
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Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA–DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species
More LessStreptomyces griseus and related species form the biggest but least well-defined clade in the whole Streptomyces 16S rRNA gene tree. Multilocus sequence analysis (MLSA) has shown promising potential for refining Streptomyces systematics. In this investigation, strains of 18 additional S. griseus clade species were analysed and data from a previous pilot study were integrated in a larger MLSA phylogeny. The results demonstrated that MLSA of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) is better than the previous six-gene scheme, as it provides equally good resolution and stability and is more cost-effective; MLSA using three or four of the genes also shows good resolution and robustness for differentiating most of the strains and is therefore of value for everyday use. MLSA is more suitable for discriminating strains that show >99 % 16S rRNA gene sequence similarity. DNA–DNA hybridization (DDH) between strains with representative MLSA distances revealed a strong correlation between the data of MLSA and DDH. The 70 % DDH value for current species definition corresponds to a five-gene MLSA distance of 0.007, which could be considered as the species cut-off for the S. griseus clade. It is concluded that the MLSA procedure can be a practical, reliable and robust alternative to DDH for the identification and classification of streptomycetes at the species and intraspecies levels. Based on the data from MLSA and DDH, as well as cultural and morphological characteristics, 18 species and three subspecies of the S. griseus clade are considered to be later heterotypic synonyms of 11 genomic species: Streptomyces griseinus and Streptomyces mediolani as synonyms of Streptomyces albovinaceus; Streptomyces praecox as a synonym of Streptomyces anulatus; Streptomyces olivoviridis as a synonym of Streptomyces atroolivaceus; Streptomyces griseobrunneus as a synonym of Streptomyces bacillaris; Streptomyces cavourensis subsp. washingtonensis as a synonym of Streptomyces cyaneofuscatus; Streptomyces acrimycini, Streptomyces baarnensis, Streptomyces caviscabies and Streptomyces flavofuscus as synonyms of Streptomyces fimicarius; Streptomyces flavogriseus as a synonym of Streptomyces flavovirens; Streptomyces erumpens, ‘Streptomyces ornatus’ and Streptomyces setonii as synonyms of Streptomyces griseus; Streptomyces graminofaciens as a synonym of Streptomyces halstedii; Streptomyces alboviridis, Streptomyces griseus subsp. alpha, Streptomyces griseus subsp. cretosus and Streptomyces luridiscabiei as synonyms of Streptomyces microflavus; and Streptomyces californicus and Streptomyces floridae as synonyms of Streptomyces puniceus.
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- Archaea
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Halopiger aswanensis sp. nov., a polymer-producing and extremely halophilic archaeon isolated from hypersaline soil
More LessStrain 56T was isolated from a hypersaline soil in Aswan (Egypt). Cells were pleomorphic rods. The organism was neutrophilic, motile and required at least 1.7 M (10 % w/v) NaCl, but not MgCl2, for growth; optimal growth occurred at ≥3.8 M (≥22.5 %) NaCl. The strain was thermotolerant with an optimum temperature for growth of 40 °C, although growth was possible up to 55 °C. The G+C content of the DNA of the novel strain was 67.1 mol%.16S rRNA gene sequence analysis revealed that strain 56T was a member of the phyletic group defined by the family Halobacteriaceae, showing the highest similarity to Halopiger xanaduensis SH-6T (99 %) and the next highest similarity of 94 % to other members of the family Halobacteriaceae. DNA–DNA hybridization revealed 27 % relatedness between strain 56T and Hpg. xanaduensis SH-6T. Polar lipid analysis revealed the presence of the bis-sulfated glycolipid S2-DGD-1 as the sole glycolipid and the absence of the glycerol diether analogue phosphatidylglycerosulfate. Both C20 . 20 and C20 . 25 core lipids were present. Strain 56T accumulated large amounts of polyhydroxybutyrate and also secreted an exopolymer. Physiological and biochemical differences suggested that Hpg. xanaduanesis and strain 56T were sufficiently different to be separated into two distinct species. It is suggested that strain 56T represents a novel species of the genus Halopiger, for which the name Halopiger aswanensis sp. nov. is proposed. The type strain is strain 56T (=DSM 13151T=JCM 11628T).
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- Bacteroidetes
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Prevotella aurantiaca sp. nov., isolated from the human oral cavity
More LessTwo anaerobic, pigmented, non-spore-forming, Gram-stain-negative, rod-shaped strains isolated from the human oral cavity, OMA31T and OMA130, were characterized by determining their phenotypic and biochemical features, cellular fatty acid profiles and phylogenetic positions based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that the new isolates belonged to a single species of the genus Prevotella. The two isolates showed 100 % 16S rRNA gene sequence similarity with each other and were most closely related to Prevotella intermedia ATCC 25611T with 96.4 % 16S rRNA gene sequence similarity; the next most closely related strains to the isolates were Prevotella pallens AHN 10371T (96.1 %) and Prevotella falsenii JCM 15124T (95.3 %). Phenotypic and biochemical characteristics of the isolates were the same as those of P. intermedia JCM 12248T, P. falsenii JCM 15124T and Prevotella nigrescens JCM 12250T. The isolates could be differentiated from P. pallens JCM 11140T by mannose fermentation and α-fucosidase activity. Conventional biochemical tests were unable to differentiate the new isolates from P. intermedia, P. falsenii and P. nigrescens. However, hsp60 gene sequence analysis suggested that strain OMA31T was not a representative of P. intermedia, P. pallens, P. falsenii or P. nigrescens. Based on these data, a novel species of the genus Prevotella, Prevotella aurantiaca sp. nov., is proposed, with OMA31T (=JCM 15754T=CCUG 57723T) as the type strain.
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Wandonia haliotis gen. nov., sp. nov., a marine bacterium of the family Cryomorphaceae, phylum Bacteroidetes
A novel, strictly aerobic, Gram-stain-negative, yellow-orange-pigmented, rod-shaped bacterium was isolated from abalone (Haliotis discus) under aquaculture in seawater off the Wando coast, Southern Korea, and subjected to a polyphasic taxonomic study. Cells of strain Haldis-1T were catalase- and oxidase-positive rods with flexirubin pigments. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Haldis-1T formed a distinct lineage within the family Cryomorphaceae and could be distinguished from the related genera Lishizhenia and Fluviicola. Strain Haldis-1T shared 16S rRNA gene sequence similarities of 92.5 and 92.4 % with Lishizhenia caseinilytica UST040201-001T and Fluviicola taffensis RW262T, respectively. The DNA G+C content was 38.1 mol% and the major respiratory quinone was MK-7. The predominant cellular fatty acids were iso-C15 : 0 (38.6 %), C15 : 0 2-OH (20.3 %) and C15 : 0 (10.7 %). Growth was observed at 25–42 °C (optimum 30–37 °C) and at pH 6.5–9.5 (optimum pH 6.5–8.0). On the basis of polyphasic analysis of phenotypic, genotypic and phylogenetic data, strain Haldis-1T represents a novel genus and species within the family Cryomorphaceae in the phylum Bacteroidetes, for which the name Wandonia haliotis gen. nov., sp. nov. is proposed. The type strain is Haldis-1T (=KCTC 22610T =NBRC 105642T).
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Niastella populi sp. nov., isolated from soil of Euphrates poplar (Populus euphratica) forest, and emended description of the genus Niastella
A novel bacterial strain, designated THYL-44T, was isolated from the soil of a Euphrates poplar (Populus euphratica) forest in Xinjiang, China. The cells were strictly aerobic, Gram-staining-negative, non-flagellated, non-motile and filamentous. Growth occurred at 17–37 °C (optimum 30 °C), at pH 5.0–8.0 (optimum pH 7.0) and with 0–1 % NaCl (w/v; optimum 0 %). Flexirubin pigments were not produced. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain THYL-44T was closely related to Niastella koreensis KACC 11465T (95.5 % sequence similarity). The major respiratory quinone was MK-7 and the predominant cellular fatty acids were iso-C15 : 0 (28.6 %), iso-C17 : 0 3-OH (23.9 %) and iso-C15 : 1 G (17.4 %). The DNA G+C content was 45.2 mol%. Therefore, the phylogenetic, physiological and chemotaxonomic data demonstrated that strain THYL-44T represents a novel species of the genus Niastella, for which the name Niastella populi sp. nov. is proposed. The type strain is THYL-44T (=CCTCC AB 208238T=KCTC 22560T). On the basis of new data, an emended description of the genus Niastella is also proposed.
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Mesonia phycicola sp. nov., isolated from seaweed, and emended description of the genus Mesonia
More LessAn aerobic, Gram-reaction-negative, non-motile, catalase- and oxidase-positive bacterium, designated strain MDSW-25T, was isolated from seaweed collected in the vicinity of Mara Island in Jeju province, Republic of Korea. Colonies were smooth, circular and convex with entire edges and yellow in colour. Growth occurred at 10–30 °C, at pH 6.1–9.1 and in the presence of 1–12 % (w/v) NaCl. The major fatty acids were iso-C15 : 0 (25.6 %) and iso-C15 : 1 G (11.3 %), and the major menaquinone was MK-6. The DNA G+C content was 30.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MDSW-25T belonged to the genus Mesonia, family Flavobacteriaceae. Sequence similarity with Mesonia mobilis and Mesonia algae was 97.5 and 95.4 %, respectively, but DNA relatedness between strain MDSW-25T and M. mobilis KCTC 12708T was only 47 %. A battery of phenotypic data, phylogenetic inference and DNA–DNA hybridization analyses supports the conclusion that strain MDSW-25T (=KCTC 22373T =DSM 21425T) represents a novel species of the genus Mesonia, for which the name Mesonia phycicola sp. nov. is proposed. On the basis of new data obtained in this study, an emended description of the genus Mesonia is also proposed.
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Lutibacter maritimus sp. nov., isolated from a tidal flat sediment
More LessA Gram-staining-negative, aerobic, non-motile, non-gliding, yellow-pigmented and rod-shaped bacterial strain, designated S7-2T, was isolated from a tidal flat sediment at Saemankum on the west coast of Korea and investigated using a polyphasic taxonomic approach. Strain S7-2T grew optimally at pH 7.0–8.0, at 25–30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain S7-2T clustered with Lutibacter litoralis CF-TF09T, a member of the family Flavobacteriaceae, with which it showed 95.8 % 16S rRNA gene sequence similarity. It contained MK-6 as the predominant menaquinone and iso-C15 : 0 and C15 : 1 ω6c as the major fatty acids. The major polar lipids of strain S7-2T and L. litoralis JCM 13034T were phosphatidylethanolamine and three unidentified lipids. The DNA G+C content was 34.6 mol%. Differential phenotypic properties and phylogenetic distinctiveness suggested that strain S7-2T represents a novel species of the genus Lutibacter, for which the name Lutibacter maritimus sp. nov. is proposed. The type strain is S7-2T (=KCTC 22635T=CCUG 57524T).
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Epilithonimonas lactis sp. nov., isolated from raw cow'smilk
More LessA Gram-staining-negative, rod-shaped, oxidase-positive, aerobic, non-motile and yellow-pigmented bacterial strain containing flexirubin type pigments, designated H1T, was isolated from raw cow'smilk in Israel.16S rRNA gene sequence analysis indicated that the isolate should be placed in the genus Epilithonimonas (family Flavobacteriaceae, phylum Bacteroidetes). The level of 16S rRNA gene sequence similarity between strain H1T and the type strain of Epilithonimonas tenax was 97.6 %. Strain H1T grew at 5–33 °C and with 0–2.0 % NaCl. The dominant cellular fatty acids of strain H1T were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c), and the DNA G+C content was 38.0 mol%. On the basis of phenotypic properties and phylogenetic distinctiveness, the milk isolate is classified as a new species in the genus Epilithonimonas, for which the name Epilithonimonas lactis sp. nov. (type strain H1T =LMG 24401T =DSM 19921T) is proposed.
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- Firmicutes And Related Organisms
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Cohnella yongneupensis sp. nov. and Cohnella ginsengisoli sp. nov., isolated from two different soils
Two aerobic, Gram-positive, rod-shaped bacterial strains, 5YN10-14T and GR21-5T, were isolated from the Yongneup wetland and ginseng soil in Korea, respectively. The two strains formed ellipsoidal or oval spores positioned centrally or paracentrally in swollen sporangia. On the basis of 16S rRNA gene sequence analysis, these strains were related to members of the genus Cohnella. 16S rRNA gene sequence similarity between strains 5YN10-14T and GR21-5T was 95.9 %. Strains 5YN10-14T and GR21-5T showed, respectively, 94.3 and 95.2 % 16S rRNA gene sequence similarity to Cohnella thermotolerans CCUG 47242T, 94.6 and 94.4 % to Cohnella hongkongensis HKU3T, 94.7 and 94.7 % to Cohnella laeviribosi RI-39T, and 95.4 and 94.8 % to Cohnella phaseoli GSPC1T. The major fatty acids of strain 5YN10-14T were anteiso-C15 : 0 (51.1 %), iso-C16 : 0 (18.5 %) and C16 : 0 (13.2 %), and the major fatty acids of strain GR21-5T were anteiso-C15 : 0 (48.9 %), iso-C16 : 0 (15.0 %) and iso-C15 : 0 (12.2 %). The two strains contained menaquinone with seven isoprene units (MK-7) as the predominant quinone, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major polar lipids; however, strain 5YN10-14T also contained lysylphosphatidylglycerol as a major polar lipid, whereas strain GR21-5T had an unknown aminophospholipid as another major polar lipid. The DNA G+C contents of strains 5YN10-14T and GR21-5T were 58.8 and 61.3 mol%, respectively. Based on the results of the phylogenetic and phenotypic data presented, it was concluded that the two strains represent two novel species of the genus Cohnella, for which the names Cohnella yongneupensis sp. nov. (type strain 5YN10-14T=KACC 11768T=DSM 18998T) and Cohnella ginsengisoli sp. nov. (type strain GR21-5T=KACC 11771T=DSM 18997T) are proposed.
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Pontibacillus litoralis sp. nov., a facultatively anaerobic bacterium isolated from a sea anemone, and emended description of the genus Pontibacillus
A facultatively anaerobic, moderately halophilic, Gram-positive, endospore-forming, motile, catalase- and oxidase-positive, rod-shaped bacterium, strain JSM 072002T, was isolated from a sea anemone (Anthopleura xanthogrammica) collected from the South China Sea. Strain JSM 072002T was able to grow with 0.5–15 % (w/v) NaCl and at pH 6.0–10.0 and 15–50 °C; optimum growth was observed with 2–5 % (w/v) NaCl and at pH 7.5 and 35 °C. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The predominant respiratory quinone was menaquinone 7 and the genomic DNA G+C content was 41.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 072002T should be assigned to the genus Pontibacillus and revealed relatively low 16S rRNA gene sequence similarities (<97 %) with the type strains of the three recognized Pontibacillus species (Pontibacillus chungwhensis BH030062T, 96.8 %; Pontibacillus marinus KCTC 3917T, 96.7 %; Pontibacillus halophilus JSM 076056T, 96.0 %). The combination of phylogenetic analysis, DNA–DNA relatedness values, phenotypic characteristics and chemotaxonomic data supports the view that strain JSM 072002T represents a novel species of the genus Pontibacillus, for which the name Pontibacillus litoralis sp. nov. is proposed. The type strain is JSM 072002T (=DSM 21186T=KCTC 13237T). An emended description of the genus Pontibacillus is also presented.
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Staphylococcus microti sp. nov., isolated from the common vole (Microtus arvalis)
Two strains of Gram-positive cocci were isolated from viscera of common voles (Microtus arvalis Pallas) with generalized Brucella microti infection in the Czech Republic. Biochemical features and phylogenetic analysis based on 16S rRNA gene sequences showed that the strains are representatives of the genus Staphylococcus and assigned Staphylococcus muscae as the nearest relative. A detailed characterization done by ribotyping, rpoB and hsp60 gene sequencing, whole-cell protein analysis and rep-PCR using the (GTG)5 primer differentiated the two strains from all described staphylococci. DNA–DNA hybridization with the type strain of S. muscae demonstrated that the two strains should be considered as members of a novel species (26.8 % reassociation). The two analysed strains were found to be coagulase-negative, novobiocin-susceptible, oxidase-negative cultures, phenotypically close to one another, but showing differences in ribotype profiles. The major fatty acids were iso-C15 : 0, iso-C17 : 0, anteiso-C15 : 0, C18 : 2 ω6,9c/anteiso-C18 : 0, C18 : 0 and C18 : 1 ω9c. MK-7 was the predominant isoprenoid quinone, with minor amounts of MK-6 and MK-8. The polar lipid profile was composed of the major lipids diphosphatidylglycerol and phosphatidylglycerol and several unknown lipids. These results proved that the two isolates represent a novel staphylococcal species. The name proposed for this novel taxon is Staphylococcus microti sp. nov.; the type strain is 4005-LJ(m)T (=CCM 4903T =CCUG 55861T =DSM 22147T).
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Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Séguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov.
More LessWe isolated several strains from various clinical samples (five samples of blood, four of intra-abdominal pus and one of infected soft tissue) that were anaerobic, motile or non-motile and Gram-positive rods. Some of the strains formed spores. Phylogenetic analysis of the 16S rRNA gene sequence showed that these organisms could be placed within clostridial cluster IV as defined by Collins et al. [(1994). Int J Syst Bacteriol 44, 812–826] and shared more than 99 % sequence similarity with Clostridium orbiscindens DSM 6740T and Eubacterium plautii DSM 4000T. Together, they formed a distinct cluster, with Bacteroides capillosus ATCC 29799T branching off from this line of descent with sequence similarities of 97.1–97.4 %. The next nearest neighbours of these organisms were Clostridium viride, Oscillibacter valericigenes, Papillibacter cinnamivorans and Sporobacter termitidis, with sequence similarities to the respective type strains of 93.1–93.4, 91.2–91.4, 89.8–90 and 88.7–89.3 %. On the basis of biochemical properties, phylogenetic position, DNA G+C content and DNA–DNA hybridization, it is proposed to unify Clostridium orbiscindens and Eubacterium plautii in a new genus as Flavonifractor plautii gen. nov., comb. nov., with the type strain Prévot S1T (=ATCC 29863T =VPI 0310T =DSM 4000T), and to reassign Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov., with the type strain CCUG 15402AT (=ATCC 29799T =VPI R2-29-1T).
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Paenibacillus aestuarii sp. nov., isolated from an estuarine wetland
More LessA novel bacterial strain designated CJ25T was isolated from the estuarine wetland of the Han river in Korea. Identification of this strain was carried out on the basis of polyphasic taxonomy. The isolate was Gram-staining-positive, rod-shaped, non-pigmented and motile. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was closely related to Paenibacillus chondroitinus DSM 5051T with 96.1 % similarity. The predominant fatty acids were anteiso-C15 : 0 (50.25 %), iso-C16 : 0 (18.54 %) and iso-C15 : 0 (10.00 %). The major isoprenoid quinone was MK-7. The G+C content of genomic DNA was 50 mol%. According to physiological data and 16S rRNA gene sequence analysis, the isolate was discriminated from related members of the genus Paenibacillus. Therefore, strain CJ25T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus aestuarii sp. nov. is proposed. The type strain is CJ25T (=KACC 13125T =JCM 15521T).
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Salinicoccus carnicancri sp. nov., a halophilic bacterium isolated from a Korean fermented seafood
More LessA novel, moderately halophilic bacterium belonging to the genus Salinicoccus was isolated from crabs preserved in soy sauce: a traditional Korean fermented seafood. Colonies of strain CrmT were ivory and the cells were non-motile, Gram-positive cocci. The organism was non-sporulating, catalase-positive and oxidase-negative. The major fatty acids of strain CrmT were iso-C15 : 0 (22.0 %), anteiso-C15 : 0 (40.6 %) and anteiso-C17 : 0 (12.1 %). The cell wall peptidoglycan contained lysine and glycine, and the major isoprenoid quinone was MK-6. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. The genomic DNA G+C content was 47.8 mol%. Strain CrmT was closely related to the type strain of Salinicoccus halodurans, with which it shared 96.9 % 16S rRNA gene sequence similarity. The DNA–DNA hybridization value between strains CrmT and S. halodurans DSM 19336T was 7.6 %. Based on phenotypic, genetic and phylogenetic data, strain CrmT should be classified as a novel species within the genus Salinicoccus, for which the name Salinicoccus carnicancri sp. nov. is proposed. The type strain is CrmT (=KCTC 13301T =JCM 15796T).
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Desulfitobacterium aromaticivorans sp. nov. and Geobacter toluenoxydans sp. nov., iron-reducing bacteria capable of anaerobic degradation of monoaromatic hydrocarbons
Dissimilatory iron reduction plays a significant role in subsurface environments. Currently, it is assumed that members of the genus Geobacter constitute the majority of the iron-reducing micro-organisms that oxidize aromatic compounds in contaminated subsurface environments. Here, we report the isolation of two phylogenetically distinct pure cultures of iron-reducing degraders of monoaromatic hydrocarbons, strain TMJ1T, which belongs to the genus Geobacter within the Deltaproteobacteria, and strain UKTLT, belonging to the genus Desulfitobacterium within the Clostridia. Both strains utilize a wide range of substrates as carbon and energy sources, including the aromatic compounds toluene, phenol and p-cresol. Additionally, strain UKTLT utilizes o-xylene and TMJ1T utilizes m-cresol. Anaerobic degradation of toluene in both strains and o-xylene in strain UKTLT is initiated by activation with fumarate addition to the methyl group. The genomic DNA G+C contents of strains TMJ1T and UKTLT are 54.4 and 47.7 mol%, respectively. Based on a detailed physiological characterization and phylogenetic analysis of the 16S rRNA genes of both strains, we propose the names Desulfitobacterium aromaticivorans sp. nov. (type strain UKTLT =DSM 19510T =JCM 15765T) and Geobacter toluenoxydans sp. nov. (type strain TMJ1T =DSM 19350T =JCM 15764T) to accommodate these strains. To the best of our knowledge, strain UKTLT is the first described spore-forming, iron-reducing bacterium that can degrade aromatic hydrocarbons.
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- Proteobacteria
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Transfer of Pantoea citrea, Pantoea punctata and Pantoea terrea to the genus Tatumella emend. as Tatumella citrea comb. nov., Tatumella punctata comb. nov. and Tatumella terrea comb. nov. and description of Tatumella morbirosei sp. nov.
Pantoea citrea, Pantoea punctata and Pantoea terrea were described for strains isolated from fruit and soil originating in Japan. These three ‘Japanese’ species have been shown to be phylogenetically distant from other species of the genus Pantoea. It has been observed previously that, using multilocus sequence analysis (MLSA), the ‘Japanese’ species consistently formed a distinct clade with an extended branch length, casting doubt on the inclusion of these species within the genus Pantoea. Furthermore, the ‘Japanese’ species are closely related to Tatumella ptyseos, strains of which originate from human clinical specimens. DNA–DNA hybridization and phenotypic tests confirmed the observed phylogenetic distance of P. citrea, P. punctata and P. terrea from the genus Pantoea and the affiliation of these species with Tatumella. In addition, strains causing pink disease of pineapple, identified previously as P. citrea, were shown to represent a separate species by using 16S rRNA gene sequence analysis, and MLSA and DNA–DNA hybridization data. The name Tatumella morbirosei sp. nov. with the type strain LMG 23360T (=BD 878T=NCPPB 4036T=CMC6T) is proposed to accommodate these strains. The new combinations Tatumella citrea (Kageyama et al. 1992) comb. nov. (type strain, SHS 2003T=ATCC 31623T=BD 875T=CCUG 30156T=CIP 105599T=DSM 13699T=JCM 8882T=LMG 22049T), Tatumella punctata (Kageyama et al. 1992) comb. nov. (type strain, SHS 2006T=ATCC 31626T=BD 876T=CCUG 30159T=CIP 105598T=DSM 13700T=JCM 8885T=LMG 22050T) and Tatumella terrea (Kageyama et al. 1992) comb. nov. (type strain, SHS 2008T=ATCC 31628T=BD 877T=CCUG 30161T=CIP 105600T=DSM 13701T=JCM 8887T=LMG 22051T) are proposed for P. citrea, P. punctata and P. terrea, respectively.
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Gallaecimonas pentaromativorans gen. nov., sp. nov., a bacterium carrying 16S rRNA gene heterogeneity and able to degrade high-molecular-mass polycyclic aromatic hydrocarbons
A Gram-negative, rod-shaped, halotolerant bacterium, designated strain CEE_131T, which degraded high-molecular-mass polycyclic aromatic hydrocarbons of four and five rings, was isolated from intertidal sediment of Corcubion Ria in Cee, A Coruña, Spain. Direct sequencing showed ambiguities and suggested heterogeneity. Cloned 16S rRNA gene sequence PCR products yielded five different sequences varying at five positions. Strain CEE_131T showed rather distant relationships to its phylogenetically closest neighbours, including the genera Rheinheimera and Serratia, exhibiting 91 % sequence similarity with Rheinheimera perlucida BA131T and Serratia proteamaculans subsp. quinovora DSM 4597T. The major fatty acids were C16 : 1 ω7c, C16 : 0 and C18 : 1 ω7c. The DNA G+C content was 41.7 mol%. On the basis of these distinct phenotypic and genotypic characteristics, strain CEE_131T is considered to represent a novel species in a new genus in the class Gammaproteobacteria, for which the name Gallaecimonas pentaromativorans gen. nov., sp. nov. is proposed. The type strain is CEE_131T (=DSM 21945T=CECT 7479T).
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Arcobacter marinus sp. nov.
More LessA slightly curved, rod-shaped marine bacterium, designated strain CL-S1T, was isolated from near Dokdo, an island in the East Sea, Korea. Cells were Gram-negative and grew well under either aerobic or microaerobic conditions. Analyses of the 16S rRNA and gyrA gene sequences of strain CL-S1T revealed an affiliation with the genus Arcobacter within the class Epsilonproteobacteria. Phylogenetic analyses based on 16S rRNA and gyrA gene sequences showed that strain CL-S1T formed a robust clade with Arcobacter halophilus LA31BT, with sequence similarities of 96.1 and 88.2 %, respectively. DNA–DNA relatedness between strain CL-S1T and A. halophilus DSM 18005T was 44 %, indicating that they represent genomically distinct species. Strain CL-S1T grew optimally at 30–37 °C, at pH 7 and in the presence of 3–5 % NaCl. The dominant cellular fatty acids were iso-C15 : 0 2-OH and/or C16 : 1 ω7c (28.4 %), C16 : 0 (26.2 %) and C18 : 1 ω7c (22.3 %). The DNA G+C content of strain CL-S1T was 28 mol%. Strain CL-S1T differed phenotypically from A. halophilus LA31BT based on its ability to grow aerobically at 10 °C and inability to grow under anaerobic conditions. Based on the data presented, strain CL-S1T is considered to represent a novel species of the genus Arcobacter, for which the name Arcobacter marinus sp. nov. is proposed. The type strain is CL-S1T (=KCCM 90072T =JCM 15502T).
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Geobacter daltonii sp. nov., an Fe(III)- and uranium(VI)-reducing bacterium isolated from a shallow subsurface exposed to mixed heavy metal and hydrocarbon contamination
An Fe(III)- and uranium(VI)-reducing bacterium, designated strain FRC-32T, was isolated from a contaminated subsurface of the USA Department of Energy Oak Ridge Field Research Center (ORFRC) in Oak Ridge, Tennessee, where the sediments are exposed to mixed waste contamination of radionuclides and hydrocarbons. Analyses of both 16S rRNA gene and the Geobacteraceae-specific citrate synthase (gltA) mRNA gene sequences retrieved from ORFRC sediments indicated that this strain was abundant and active in ORFRC subsurface sediments undergoing uranium(VI) bioremediation. The organism belonged to the subsurface clade of the genus Geobacter and shared 92–98 % 16S rRNA gene and 75–81 % rpoB gene sequence similarities with other recognized species of the genus. In comparison to its closest relative, Geobacter uraniireducens Rf4T, according to 16S rRNA gene sequence similarity, strain FRC-32T showed a DNA–DNA relatedness value of 21 %. Cells of strain FRC-32T were Gram-negative, non-spore-forming, curved rods, 1.0–1.5 μm long and 0.3–0.5 μm in diameter; the cells formed pink colonies in a semisolid cultivation medium, a characteristic feature of the genus Geobacter. The isolate was an obligate anaerobe, had temperature and pH optima for growth at 30 °C and pH 6.7–7.3, respectively, and could tolerate up to 0.7 % NaCl although growth was better in the absence of NaCl. Similar to other members of the Geobacter group, strain FRC-32T conserved energy for growth from the respiration of Fe(III)-oxyhydroxide coupled with the oxidation of acetate. Strain FRC-32T was metabolically versatile and, unlike its closest relative, G. uraniireducens, was capable of utilizing formate, butyrate and butanol as electron donors and soluble ferric iron (as ferric citrate) and elemental sulfur as electron acceptors. Growth on aromatic compounds including benzoate and toluene was predicted from preliminary genomic analyses and was confirmed through successive transfer with fumarate as the electron acceptor. Thus, based on genotypic, phylogenetic and phenotypic differences, strain FRC-32T is considered to represent a novel species of the genus Geobacter, for which the name Geobacter daltonii sp. nov. is proposed. The type strain is FRC-32T (=DSM 22248T=JCM 15807T).
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Sphingosinicella vermicomposti sp. nov., isolated from vermicompost, and emended description of the genus Sphingosinicella
More LessA Gram-stain-negative, rod-shaped bacterium, designated strain YC7378T was isolated from vermicompost (VC) collected at Masan, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain YC7378T grew optimally at 30 °C and at pH 6.5–8.5. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YC7378T belongs to the genus Sphingosinicella in the family Sphingomonadaceae. The most closely related strains are Sphingosinicella soli KSL-125T (95.7 %), Sphingosinicella xenopeptidilytica 3-2W4T (95.6 %) and Sphingosinicella microcystinivorans Y2T (95.5 %). Strain YC7378T contained ubiquinone Q-10 as the major respiratory quinone system and sym-homospermidine as the major polyamine. The major fatty acids of strain YC7378T were C18 : 1 ω7c, C16 : 1 ω7c and/or iso-C15 : 0 2-OH, C14 : 0 2-OH and C16 : 0. The major polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The total DNA G+C content was 59.4 mol%. The phenotypic, phylogenetic and chemotaxonomic data showed that strain YC7378T represents a novel species of the genus Sphingosinicella, for which the name Sphingosinicella vermicomposti sp. nov. is proposed. The type strain is YC7378T (=KCTC 22446T =DSM 21593T).
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Desulfovibrio butyratiphilus sp. nov., a Gram-negative, butyrate-oxidizing, sulfate-reducing bacterium isolated from an anaerobic municipal sewage sludge digester
More LessStrictly anaerobic, mesophilic, sulfate-reducing bacterial strains were isolated from two anaerobic municipal sewage sludge digesters. One representative strain (BSYT) was characterized phenotypically and phylogenetically. Cells were Gram-negative, motile by means of a single polar flagellum, non-spore-forming, curved rods. Cells had desulfoviridin and cytochrome type c. Catalase and oxidase activities were not detected. The optimum NaCl concentration for growth was 0.5 % (w/v). The optimum temperature was 35 °C and the optimum pH was 7.1. Strain BSYT utilized butyrate, 2-methylbutyrate, valerate, pyruvate, lactate, ethanol, 1-propanol, butanol and H2 as electron donors for sulfate reduction. This strain grew lithoautotrophically with H2/CO2 under sulfate-reducing conditions. Most organic electron donors were incompletely oxidized to mainly acetate, whereas 2-methylbutyrate and valerate were oxidized to equivalent amounts of acetate and propionate. Strain BSYT utilized thiosulfate as an electron acceptor, and grew with pyruvate in the absence of electron acceptors. The genomic DNA G+C content of strain BSYT was 63.3 mol%. Menaquinone MK-6(H2) was the major respiratory quinone. Major cellular fatty acids were C14 : 0, C16 : 0, C16 : 1 ω7 and C18 : 1 ω7. Phylogenetic analyses based on 16S rRNA and dissimilatory sulfite-reductase β-subunit gene sequences assigned strain BSYT to the genus Desulfovibrio in the family Desulfovibrionaceae within the class Deltaproteobacteria. Its closest recognized relative based on 16S rRNA gene sequences was the type strain of Desulfovibrio putealis (95.3 % similarity). On the basis of significant differences in 16S rRNA gene sequences and phenotypic characteristics, the sewage sludge strains are considered to represent a single novel species of the genus Desulfovibrio, for which the name Desulfovibrio butyratiphilus sp. nov. is proposed. The type strain is BSYT (=JCM 15519T=DSM 21556T).
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Umboniibacter marinipuniceus gen. nov., sp. nov., a marine gammaproteobacterium isolated from the mollusc Umbonium costatum from the Sea of Japan
More LessTwo bacterial strains, KMM 3891T and KMM 3892, were isolated from internal tissues of the marine mollusc Umbonium costatum collected from the Sea of Japan. The novel isolates were Gram-negative, aerobic, faint pink–reddish-pigmented, rod-shaped, non-motile, stenohaline and psychrotolerant bacteria that were unable to degrade most tested complex polysaccharides. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Fatty acid analysis revealed C17 : 1 ω6c, C17 : 0, C16 : 0 and C16 : 1 ω7c as the dominant components. The major isoprenoid quinone was Q-7. The DNA G+C content of strain KMM 3891T was 51.7 mol%. According to phylogenetic analysis of 16S rRNA gene sequences, strains KMM 3891T and KMM 3892 were positioned within the Gammaproteobacteria as a separate branch, sharing <93 % sequence similarity to their phylogenetic relatives including Saccharophagus degradans, Microbulbifer species, Endozoicomonas elysicola, Simiduia agarivorans and Teredinibacter turnerae. Based on phenotypic characterization and phylogenetic distance, the novel marine isolates KMM 3891T and KMM 3892 represent a new genus and species, for which the name Umboniibacter marinipuniceus gen. nov., sp. nov. is proposed. The type strain of Umboniibacter marinipuniceus is KMM 3891T (=NRIC 0753T =JCM 15738T).
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Jeongeupia naejangsanensis gen. nov., sp. nov., a cellulose-degrading bacterium isolated from forest soil from Naejang Mountain in Korea
More LessA Gram-stain-negative, motile, rod-shaped, cellulose-degrading bacterial strain, BIO-TAS4-2T, which belongs to the Betaproteobacteria, was isolated from forest soil from Naejang Mountain, Korea, and its taxonomic position was investigated by using a polyphasic study. Strain BIO-TAS4-2T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 0–1.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain BIO-TAS4-2T clustered with members of the genera Andreprevotia, Silvimonas and Deefgea of the family Neisseriaceae, with which it exhibited 16S rRNA gene sequence similarities of 93.5–94.2 %. Strain BIO-TAS4-2T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) and C16 : 0 as the major fatty acids. The DNA G+C content was 63.8 mol%. Strain BIO-TAS4-2T could be differentiated from members of phylogenetically related genera by differences in fatty acid composition, DNA G+C content and some phenotypic properties. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain BIO-TAS4-2T is considered to represent a novel species in a new genus, for which the name Jeongeupia naejangsanensis gen. nov., sp. nov. is proposed, with BIO-TAS4-2T (=KCTC 22633T=CCUG 57610T) as the type strain.
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Cobetia crustatorum sp. nov., a novel slightly halophilic bacterium isolated from traditional fermented seafood in Korea
More LessA slightly halophilic, Gram-stain-negative, straight-rod-shaped aerobe, strain JO1T, was isolated from jeotgal, a traditional Korean fermented seafood. Cells were observed singly or in pairs and had 2–5 peritrichous flagella. Optimal growth occurred at 25 °C, in 6.5 % (w/v) salts and at pH 5.0–6.0. Strain JO1T was oxidase-negative and catalase-positive. Cells did not reduce fumarate, nitrate or nitrite on respiration. Acid was produced from several carbohydrates and the strain utilized many sugars and amino acids as carbon and nitrogen sources. The main fatty acids were C12 : 0 3-OH, C16 : 0, C17 : 0 cyclo and summed feature 3 (C16 : 1 ω7c/iso-C15 : 0 2-OH). DNA–DNA hybridization experiments with strain JO1T and Cobetia marina DSM 4741T revealed 24 % relatedness, although high 16S rRNA gene sequence similarity (98.9 %) was observed between these strains. Based on phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolate from jeotgal should be classified as a representative of a novel species, Cobetia crustatorum sp. nov., with strain JO1T (=KCTC 22486T=JCM 15644T) as the type strain.
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Devosia yakushimensis sp. nov., isolated from root nodules of Pueraria lobata (Willd.) Ohwi
More LessA Gram-negative, strictly aerobic bacterium, comprising non-endospore-forming motile rods (1.2–2.0 μm × 0.4–0.6 μm) with polar flagellae was isolated from root nodules of the leguminous plant Pueraria lobata (Willd.) Ohwi growing on the coast of Yakushima Island, Kagoshima Prefecture, Japan. The novel strain, designated Yak96BT, grew at an optimum pH of 7.0 and an optimum temperature of 28 °C. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that the new strain was closely related to Devosia neptuniae J1T and Devosia chinhatensis IPL18T, with sequence similarities of 98.1 % and 97.8 %, respectively. However, the DNA–DNA relatedness values of strain Yak96BT with D. neptuniae LMG 21357T and D. chinhatensis CCM 7426T were 53.6 % and 34 %, respectively. The DNA G+C content of strain Yak96BT was 65.3 mol%, the predominant isoprenoid quinone was Q10 (85 %) and the polar lipids were phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids (>5 %) were 11-methyl C18 : 1 ω7c (35.0 %), C16 : 0 (22.4 %), C18 : 1 ω7c (21.8 %), C19 : 0 cyclo ω8c (6.8 %) and C18 : 0 (5.4 %). The infection/nodulation test was negative and nifH and nodD genes were not detected. Based on its chemotaxonomic and physiological characteristics, strain Yak96BT represents a novel species of the genus Devosia, for which the name Devosia yakushimensis sp. nov. is proposed. The type strain is Yak96BT (=KCTC 22147T=NBRC 103855T=LMG 24299T).
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Multilocus sequence analysis of root nodule isolates from Lotus arabicus (Senegal), Lotus creticus, Argyrolobium uniflorum and Medicago sativa (Tunisia) and description of Ensifer numidicus sp. nov. and Ensifer garamanticus sp. nov.
Nine isolates from Argyrolobium uniflorum, Lotus creticus, Medicago sativa (Tunisia) and Lotus arabicus (Senegal) were analysed by multilocus sequence analysis (MLSA) of five housekeeping genes (recA, atpD, glnA, gltA and thrC), the 16S rRNA gene and the nodulation gene nodA. Analysis of the individual and concatenated gene sequences demonstrated that the nine new strains constituted three stable, well-supported (bootstrap and gene sequence similarity values) monophyletic clusters, A, B and C, all belonging to the branch of the genus Ensifer, regardless of the phylogenetic reconstruction method used (maximum likelihood, maximum-parsimony, neighbour-joining). The three groups were further characterized by API 100 auxanographic tests, host specificity and nodA gene sequence analysis. On the basis of these data, clusters A and C are suggested as representing two novel species within the genus Ensifer, for which the names Ensifer numidicus sp. nov. (type strain ORS 1407T=LMG 24690T=CIP 109850T) and Ensifer garamanticus sp. nov. (type strain ORS 1400T=LMG 24692T=CIP 109916T) are proposed. The cluster B strains were assigned to Ensifer adhaerens genomovar A.
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Salinisphaera dokdonensis sp. nov., isolated from surface seawater
More LessA Gram-negative, strictly aerobic bacterium, designated CL-ES53T, was isolated from surface water of the East Sea in Korea. Cells of strain CL-ES53T were short rods and motile by means of monopolar flagella. Strain CL-ES53T grew with 4–21 % NaCl (optimum 10 %) and at 5–40 °C (optimum 25 °C) and pH 5.2–8.8 (optimum pH 6.3–7.2). The major isoprenoid quinone was Q-8. The major fatty acids were C18 : 1 ω7c (42.0 %), C18 : 1 ω9c (14.8 %) and C14 : 0 (9.4 %). The genomic DNA G+C content was 64.9 mol%. Analysis of the 16S rRNA gene sequence of strain CL-ES53T revealed that it was a member of the genus Salinisphaera and most closely related to Salinisphaera shabanensis E1L3A T (96.9 % sequence similarity) and Salinisphaera hydrothermalis EPR70T (93.8 %). Phylogenetic analyses based on the 16S rRNA gene sequence showed that strain CL-ES53T formed a robust cluster with S. shabanensis E1L3A T. Although the 16S rRNA gene sequence similarity between strain CL-ES53T and S. shabanensis E1L3A T was rather high (96.9 %), DNA–DNA relatedness between these strains was 12 %, suggesting that they represent genomically distinct species. Strain CL-ES53T was differentiated from S. shabanensis E1L3A T and S. hydrothermalis EPR70T on the basis of optimum temperature for growth and certain phenotypic characteristics. The phylogenetic analysis and physiological and chemotaxonomic data show that strain CL-ES53T should be classified in the genus Salinisphaera within a novel species, for which the name Salinisphaera dokdonensis sp. nov. is proposed. The type strain is CL-ES53T (=KCCM 90064T =DSM 19549T).
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- Eukaryotic Micro-Organisms
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Candida golubevii sp. nov., an asexual yeast related to Metschnikowia lunata
Two strains of a novel yeast species were isolated from insect frass and a flower in Thailand and Brazil, respectively. The strain from Thailand was isolated from insect frass collected in Than-Tong waterfall, Nong Khai Province, whereas the strain from Brazil was recovered from a flower of Ipomoea sp. collected on the banks of the Paraguai River in the state of Mato Grosso do Sul. The sequences of the D1/D2 domains of the large subunit of the rDNA of both strains were identical. This novel species belonged to the Metschnikowia clade and was related to Metschnikowia lunata. No signs of sporulation were observed for the two strains on various culture media. The novel species, Candida golubevii sp. nov., is proposed to accommodate these isolates. The type strain is BCC 8332T (=CBS 11362T=NBRC 105679T).
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Cryptococcus spencermartinsiae sp. nov., a basidiomycetous yeast isolated from glacial waters and apple fruits
Seven strains representing a novel yeast species belonging to the genus Cryptococcus were isolated from different substrates from Patagonia, Argentina, and The Netherlands. Three strains were isolated from a meltwater river draining from the Frias glacier at Mount Tronador situated in Nahuel Huapi National Park (Patagonia) and four were isolated from apple surfaces in Randwijk, The Netherlands. Analysis of the D1/D2 large-subunit rRNA gene and ITS region sequences indicated that these strains represent a single species that is distinct from other species of the Tremellales clade. The name Cryptococcus spencermartinsiae sp. nov. is proposed to accommodate these strains. The type strain is CRUB 1230T (=CBS 10760T =DBVPG 8010T).
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- Evolution, Phylogeny And Biodiversity
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Amplified fragment length polymorphism and multilocus sequence analysis-based genotypic relatedness among pathogenic variants of Xanthomonas citri pv. citri and Xanthomonas campestris pv. bilvae
Three pathogenic variants (i.e. pathotypes) have been described within Xanthomonas citri pv. citri, the causal agent of Asiatic citrus canker. Pathotype A strains naturally infect a wide range of Citrus species and members of some related genera. In contrast, pathotypes A* and Aw have narrow host ranges within the genus Citrus and have been isolated from Mexican lime (Citrus aurantifolia L.) and from Mexican lime and alemow (Citrus macrophylla L.), respectively. We used amplified fragment length polymorphism (AFLP) and multilocus sequence analysis (MLSA) based on four partial housekeeping gene sequences (atpD, dnaK, efp and gyrB) for the genotypic classification of Xanthomonas citri pv. citri and the poorly characterized citrus pathogen Xanthomonas campestris pv. bilvae. A Mantel test showed that genetic distances derived from AFLP and MLSA were highly correlated. X. campestris pv. bilvae showed a close relatedness to the type strain of X. citri, indicating that this pathovar should be reclassified as X. citri pv. bilvae. All pathotype A* and Aw strains were most closely related to X. citri pv. citri strains with a wide host range (pathotype A), confirming previous DNA–DNA hybridization data. Pathotype Aw should be considered a junior synonym of pathotype A* on the basis of pathogenicity tests, AFLP, MLSA and PCR using pathovar-specific primers. Evolutionary genome divergences computed from AFLP data suggested that pathotype A* (including Aw strains) is a group of strains that shows a wider genetic diversity than pathotype A.
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- International Committee On Systematics Of Prokaryotes
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- Minutes
- Taxonomic Note
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The reference strain Aeromonas hydrophicla CIP 57.50 should be reclassified as Aeromonas salmonicida CIP 57.50
More LessThe use of reference strains is a critical element for the quality control of different assays, from the development of molecular methods to the evaluation of antimicrobial activities. Most of the strains used in these assays are not type strains and some of them are cited erroneously because of subsequent reclassifications and descriptions of novel species. In this study, we propose that the reference strain Aeromonas hydrophila CIP 57.50 be reclassified as Aeromonas salmonicida CIP 57.50 based on phenotypic characterization and sequence analyses of the cpn60, dnaJ, gyrB and rpoD genes.
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- Errata
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