- Volume 66, Issue 3, 2016
Volume 66, Issue 3, 2016
- Validation List no. 168
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List of new names and new combinations previously effectively, but not validly, published
More LessThe 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. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. 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 of prokaryotes, new combinations and new taxonomic opinions have appeared in volume 65, part 12, of the IJSEM
More LessThis listing of names of prokaryotes 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).
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- NEW TAXA
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- Archaea
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Thermogladius calderae gen. nov., sp. nov., an anaerobic, hyperthermophilic crenarchaeote from a Kamchatka hot spring
An obligately anaerobic, hyperthermophilic, organoheterotrophic archaeon, strain 1633T, was isolated from a terrestrial hot spring of the Uzon Caldera (Kamchatka Peninsula, Russia). Cells were regular cocci, 0.5–0.9 μm in diameter, with one flagellum. The temperature range for growth was 80–95 °C, with an optimum at 84 °C. Strain 1633T grew on yeast extract, beef extract, peptone, cellulose and cellobiose. No growth was detected on other sugars or carbohydrates, organic acids, or under autotrophic conditions. The only detected growth products were CO2, acetate, and H2. The growth rate was stimulated by elemental sulfur, which was reduced to hydrogen sulfide. The in silico-calculated G+C content of the genomic DNA of strain 1633T was 55.64 mol%. 16S rRNA gene sequence analysis placed strain 1633T together with the non-validly published ‘Thermogladius shockii’ strain WB1 in a separate genus-level cluster within the family Desulfurococcaceae. Average nucleotide identity (ANI) results revealed 75.72 % identity between strain 1633T and ‘Thermogladius shockii’ WB1. Based on these results we propose a novel genus and species with the name Thermogladius calderae gen. nov., sp. nov. The type strain of the type species is 1633T ( = DSM 22663T = VKM B-2946T).
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Methanosarcina flavescens sp. nov., a methanogenic archaeon isolated from a full-scale anaerobic digester
More LessA novel, strictly anaerobic, methanogenic archaeon, strain E03.2T, was isolated from a full-scale biogas plant in Germany. Cells were non-motile sarcina-like cocci, occurring in aggregates. Strain E03.2T grew autotrophically on H2 plus CO2, and additionally cells could utilize acetate, methanol, moni-, di- and trimethylamine as carbon and energy sources; however, growth or methanogenesis on formate was not observed. Yeast extract and vitamins stimulated growth but were not mandatory. The optimal growth temperature of strain E03.2T was approximately 45 °C; maximal growth rates were obtained at about pH 7.0 in the presence of approximately 6.8 mM NaCl. The DNA G+C content of strain E03.2T was 41.3 mol%. Phylogenetic analyses based on 16S rRNA gene and mcrA sequences placed strain E03.2T within the genus Methanosarcina. Based on 16S rRNA gene sequence similarity strain E03.2T was related to seven different species of the genus Methanosarcina, but most closely related to Methanosarcina thermophila TM-1T. Phenotypic, physiological and genomic characteristics indicated that strain E03.2T represents a novel species of the genus Methanosarcina, for which the name Methanosarcina flavescens sp. nov. is proposed. The type strain is E03.2T ( = DSM 100822T = JCM 30921T).
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- Actinobacteria
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Phycicoccus endophyticus sp. nov., an endophytic actinobacterium isolated from Bruguiera gymnorhiza
More LessA novel endophytic actinobacterium, designated strain IP6SC6T, was isolated from surface-sterilized bark of Bruguiera gymnorhiza collected from Zhanjiang Mangrove Forest National Nature Reserve in Guangdong, China. Cells of strain IP6SC6T were Gram-stain-positive, aerobic, non-spore-forming, non-motile rods. Strain IP6SC6T grew at 20–42 °C (optimum, 37 °C), at pH 6.0–9.0 (optimum, pH 7.0) and in the presence of 0–8 % (w/v) NaCl (optimum, 0–2 %). Chemotaxonomic analyses showed that the isolate possessed meso-diaminopimelic acid as the diamino acid of the peptidoglycan, galactose and glucose as whole-cell sugars, and MK-8(H4) as the predominant menaquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylinositol and an unknown lipid. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The G+C content of the genomic DNA was 72.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain IP6SC6T belonged to the genus Phycicoccus and shared the highest sequence similarity with Phycicoccus jejuensis NRRL B-24460T (96.97 %). On the basis of phylogenetic analysis and phenotypic and chemotaxonomic characteristics, strain IP6SC6T represents a novel species of the genus Phycicoccus, for which the name Phycicoccus endophyticus sp. nov. is proposed. The type strain is IP6SC6T ( = DSM 100020T = CGMCC 4.7300T).
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Stackebrandtia cavernae sp. nov., a novel actinobacterium isolated from a karst cave sample
A novel actinobacterial strain, YIM ART06T, was isolated from a rock sample of karst cave located at Guizhou province, south-west China, and was characterized by a polyphasic taxonomic approach. The morphological and chemotaxonomic properties of strain YIM ART06T were in accordance with those of the genus Stackebrandtia. The 16S rRNA gene sequence of strain YIM ART06T showed highest similarity to Stackebrandtia nassauensis JCM 14905T (98.0 %). The DNA–DNA hybridization value between strains YIM ART06T and S. nassauensis JCM 14905T was, however, moderately high (62.9 %) but below the 70 % limit for species identification. Strain YIM ART06T contained meso-diaminopimelic acid as the diagnostic diamino acid, and mannose, ribose and xylose in the whole-cell hydrolysates. The predominant menaquinones detected were MK-10(H4), MK-10(H6), MK-11(H4) and MK-11(H6), while the cell membrane polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanolamine and three unidentified phospholipids. The genomic DNA G+C content of strain YIM ART06T was 71 mol%. The major fatty acids were anteiso-C17 : 0, iso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. Based on the taxonomic characteristics from the genotypic and phenotypic results, strain YIM ART06T merits recognition as a representative of a novel species of the genus Stackebrandtia, for which the name Stackebrandtia cavernae sp. nov. is proposed. The type strain is YIM ART06T ( = KCTC 39599T = CCTCC AA 2015021T = DSM 100594T).
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Streptomyces yangpuensis sp. nov., isolated from soil
More LessA novel Gram-stain-positive strain with sandy aerial mycelium and golden yellow substrate mycelium, designated fd2-tbT, was isolated from a soil sample collected in Shanghai, China, and its taxonomic status was established by phylogenetic analysis. 16S rRNA gene sequence analysis showed that strain fd2-tbT belonged to the genus Streptomyces and was related to Streptomyces amritsarensis JCM 19660T (99.9 % 16S rRNA gene sequence similarity), Streptomyces flavotricini NBRC 12770T (99.9 %), Streptomyces polychromogenes NBRC 13072T (99.8 %), Streptomyces racemochromogenes NRRL B-5430T (99.7 %), Streptomyces globosus LMG 19896T (99.5 %), Streptomyces toxytricini NBRC 12823T (99.5 %) and Streptomyces katrae NBRC 13447T (99.3 %). The cell wall of strain fd2-tbT contained ll-diaminopimelic acid, and whole-cell sugars were identified as glucose and ribose. The menaquinones MK-9(H4), MK-9(H6) and MK-9(H8) were also detected. In addition, the polar lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, as well as five unidentified phospholipids, were detected. Major cellular fatty acids were identified as anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0, iso-C15 : 0 and C16 : 0. DNA–DNA hybridization experiments showed that strain fd2-tbT exhibited 36.5 ± 0.6 %, 43.5 ± 2.0 %, 11.1 ± 1.3 %, 10.3 ± 3.1 %, 9.8 ± 1.9 %, 48.9 ± 3.9 % and 16.3 ± 1.7 % relatedness to S. amritsarensis JCM 40119660T, S. flavotricini NBRC 12770T, S. polychromogenes NBRC 13072T, S. racemochromogenes NRRL B-5430T, S. globosus LMG 19896T, S. toxytricini NBRC 12823T and S. katrae NBRC 13447T, respectively. Based on these analyses as well as some phenotypic differences, strain fd2-tbT is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces yangpuensis sp. nov. is proposed. The type strain is fd2-tbT ( = DSM 100336T = CGMCC 4.7256T).
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Kineococcus mangrovi sp. nov., isolated from mangrove sediment
An aerobic, Gram-stain-positive, motile, coccus-shaped actinobacterium, designated strain L2-1-L1T, was isolated from mangrove sediment in Thailand. The organism was deep orange, oxidase-negative and catalase-positive. Growth occurred at temperatures between 17 and 32 °C and with NaCl concentrations up to 10 %. Chemotaxonomic characteristics of strain L2-1-L1T were typical of the genus Kineococcus. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. Whole-cell hydrolysates contained arabinose, galactose, glucose, mannose and ribose. The menaquinone was MK-9(H2). Mycolic acids were not detected. Anteiso-C15 : 0 and iso-C14 : 0 were detected as the major cellular fatty acids. The major polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol and an unidentified phosphoglycolipid. The G+C content of the DNA was 74.7 mol%. A phylogenetic tree, based on 16S rRNA gene sequences, revealed that strain L2-1-L1T represents a novel member of the genus Kineococcus. The most closely related species were Kineococcus endophytica KLBMP 1274T, Kineococcus aurantiacus NBRC 15268T and Kineococcus rhizosphaerae RP-B16T, with 98.9, 98.6 and 98.5 % 16S rRNA gene sequence similarity, respectively. On the basis of phylogenetic analysis, DNA–DNA relatedness data, phenotypic characteristics and chemotaxonomic data, a novel species of the genus Kineococcus is proposed: Kineococcus magrovi sp. nov. The type strain is strain L2-1-L1T ( = BCC 75409T = NBRC 110933T).
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Bifidobacterium aquikefiri sp. nov., isolated from water kefir
More LessA novel Bifidobacterium, strain LMG 28769T, was isolated from a household water kefir fermentation process. Cells were Gram-stain-positive, non-motile, non-spore-forming, catalase-negative, oxidase-negative and facultatively anaerobic short rods. Analysis of its 16S rRNA gene sequence revealed Bifidobacterium crudilactis and Bifidobacterium psychraerophilum (97.4 and 97.1 % similarity towards the respective type strain sequences) as nearest phylogenetic neighbours. Its assignment to the genus Bifidobacterium was confirmed by the presence of fructose 6-phosphate phosphoketolase activity. Analysis of the hsp60 gene sequence revealed very low similarity with nucleotide sequences in the NCBI nucleotide database. The genotypic and phenotypic analyses allowed the differentiation of strain LMG 28769T from all recognized Bifidobacterium species. Strain LMG 28769T ( = CCUG 67145T = R 54638T) therefore represents a novel species, for which the name Bifidobacterium aquikefiri sp. nov. is proposed.
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Pseudoclavibacter endophyticus sp. nov., isolated from roots of Glycyrrhiza uralensis
A Gram-stain-positive, aerobic, rod-shaped, non-motile actinomycete strain, designated EGI 60007T, was isolated from healthy roots of Glycyrrhiza uralensis F. collected from Yili County, Xinjiang Province, north-west China. A polyphasic approach was applied to study the taxonomic position of the new isolate. The 16S rRNA gene sequence of strain EGI 60007T had highest similarities with members of the genus Pseudoclavibacter, including Pseudoclavibacter chungangensis CAU 59T (96.98 % 16S rRNA gene sequence similarity), Pseudoclavibacter helvolus DSM 20419T (96.43 %) and Pseudoclavibacter terrae THG-MD12T (96.14 %). The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain EGI 60007T clustered with members of the genus Pseudoclavibacter, and formed a distinct clade with P. chungangensis CAU 59T. The polar lipids detected for strain EGI 60007T were phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid and one unidentified lipid. The DNA G+C content was determined to be 63.3 mol%. The chemotaxonomic features of strain EGI 60007T showed typical characteristics of the genus Pseudoclavibacter, with MK-9 as the respiratory quinone, 2,4-diaminobutyric acid as the diamino acid in the peptidoglycan, and anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 as the major fatty acids. The sugars of whole-cell hydrolysates were mainly mannose, rhamnose, ribose and glucose, and a minor amount of xylose. Based on the results of the phylogentic analysis supported by morphological, physiological, chemotaxonomic and other differentiating phenotypic characteristics, strain EGI 60007T is considered to represent a novel species of the genus Pseudoclavibacter, for which the name Pseudoclavibacter endophyticus sp. nov. is proposed. The type strain is EGI 60007T ( = CGMCC 1.15081T = KCTC 39112T = DSM 29943T).
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Mariniluteicoccus endophyticus sp. nov., an endophytic actinobacterium isolated from root of Ocimum basilicum
Two strains of Gram-stain-positive, aerobic, non-motile, irregular coccus-shaped bacteria, designated YIM 2617T and YIM 2617-2, were isolated from the root of Ocimum basilicum. Phylogenetic analysis on the basis of 16S rRNA gene sequence comparison revealed that the two strains were closely related to Mariniluteicoccus flavus YIM M13146T (98.1 and 98.0 % similarities, respectively) and formed a robust clade with M. flavus in the neighbour-joining tree. Optimum growth of the strains was observed at 28–32 °C, at pH 7.0–8.0 and in the presence of 0–2 % (w/v) NaCl. The chemotaxonomic profiles of the strains comprised anteiso-C15 : 0 as the major cellular fatty acid, MK-9(H4) as the predominant menaquinone, alanine, glycine, glutamic acid and ll-diaminopimelic acid as peptidoglycan components, and phosphatidylcholine and diphosphatidylglycerol as the major polar lipids. The G+C contents of the genomic DNA of strains YIM 2617T and YIM 2617-2 were 66.4 and 66.6 mol%, respectively. DNA–DNA hybridizations of the two strains with M. flavus YIM M13146T gave mean relatedness values of 47.6 ± 2.0 and 43.2 ± 1.5 %, respectively, while the relatedness value between them was 92.1 ± 2.2 %. On the basis of the data recorded from the present study, strains YIM 2617T and YIM 2617-2 represent a novel species of the genus Mariniluteicoccus, for which the name Mariniluteicoccus endophyticus sp. nov. is proposed. The type strain is YIM 2617T ( = KCTC 29482T = DSM 28728T = JCM 30097T).
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Promicromonospora alba sp. nov., an actinomycete isolated from the cuticle of Camponotus japonicas Mayr
A novel actinomycete, designated strain 1C-HV12T, was isolated from the cuticle of Camponotus japonicas Mayr and characterized using a polyphasic approach. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the organism should be assigned to the genus Promicromonospora and that it forms a monophyletic clade with the closest relatives Promicromonospora umidemergens JCM 17975T(99.17 % 16S rRNA gene sequence similarity), Promicromonospora vindobonensis V45T (98.88 %) and Promicromonospora iranensis HM 792T (98.85 %). Moreover, morphological and chemotaxonomic properties of strain 1C-HV12T also confirmed the affiliation of the isolate to the genus Promicromonospora. The peptidoglycan hydrolysates contained alanine, glutamic acid and lysine, and whole-cell sugars were galactose, glucose, rhamnose and ribose. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified phosphoglycolipid, an unidentified phospholipid and an unidentified glycolipid. The major menaquinones were MK-9(H4) and MK-9(H2). The predominant cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The DNA G+C content was 71.6 mol%. However, the low level of DNA–DNA relatedness and some phenotypic characteristics allowed the isolate to be differentiated from closely related species. Therefore, it is concluded that strain 1C-HV12T represents a novel species of the genus Promicromonospora, for which the name Promicromonospora alba sp. nov. is proposed. The type strain is 1C-HV12T ( = CGMCC 4.7283T = DSM 100490T).
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Streptomyces daqingensis sp. nov., isolated from saline–alkaline soil
A novel strain of actinobacteria, designated strain NEAU-ZJC8T, was isolated from a saline–alkaline soil collected from Heilongjiang Province, north-east China and characterized using a polyphasic approach. Strain NEAU-ZJC8T exhibited morphological, cultural and chemotaxonomic features consistent with its classification as representing a member of the genus Streptomyces. Growth occurred at 16–35 °C, pH 5.0–11.0 and in the presence of 0–11 % (w/v) NaCl. The cell-wall peptidoglycan contained ll-diaminopimelic acid and glycine. Whole-cell hydrolysates mainly contained glucose, galactose and ribose. Predominant menaquinones were MK-9(H6), MK-9(H4) and MK-9(H8). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and two unidentified phospholipids. The major cellular fatty acids (>10 %) were iso-C16 : 0, iso-C15 : 0, anteiso-C17 : 0 and C16 : 0. The G+C content of the DNA was 72.7 mol%. A phylogenetic tree based on 16S rRNA sequences showed that strain NEAU-ZJC8T formed a distinct clade within the genus Streptomyces and was closely related to Streptomyces haliclonae DSM 41970T (98.56 % similarity) and Streptomyces marinus NBRC 105047T (97.96 % similarity). A combination of DNA–DNA hybridization results and some phenotypic characteristics demonstrated that strain NEAU-ZJC8T could be distinguished from its closest phylogenetic relatives. Therefore, strain NEAU-ZJC8T represents a novel species of the genus Streptomyces, for which the name Streptomyces daqingensis sp. nov. is proposed. The type strain is NEAU-ZJC8T ( = CGMCC 4.7178T = JCM 30057T).
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Streptosporangium saharense sp. nov., an actinobacterium isolated from Saharan soil
A novel actinobacterium, designated strain SG20T, was isolated from a Saharan soil sample collected from Béni-isguen (Mzab), Ghardaïa province, southern Algeria. The micro-organism developed small roundish sporangia on aerial mycelium that were sessile or carried by very short sporangiophores. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the whole-cell sugars comprised glucose, ribose and mannose, but madurose was not detected. The predominant menaquinones were MK-9(H4), MK-9(H6) and MK-9(H2). The major fatty acids were iso-C16 : 0 and C16 : 0. The phospholipids detected were diphosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine and unknown lipids. The phenotypic and chemotaxonomic characteristics of the novel strain resembled those of recognized members of the genus Streptosporangium. Moreover, phylogenetic analysis based on a 16S rRNA gene sequence generated from the strain identified its closest relative as Streptosporangium jomthongense BCC 53154T (98.5 % similarity), which produces single spores on aerial mycelium, but no sporangia. In hybridization experiments, the DNA–DNA relatedness values recorded between strain SG20T and S. jomthongense DSM 46822T fell well below 70 %. On the basis of phenotypic and genotypic data, strain SG20T can be distinguished as representing a novel species of the genus Streptosporangium, for which the name Streptosporangium saharense sp. nov. is proposed. The type strain is SG20T ( = DSM 46743T = CECT 8840T).
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Asanoa endophytica sp. nov., an endophytic actinomycete isolated from the rhizome of Boesenbergia rotunda
More LessA novel Gram-stain-positive, non-motile, endophytic actinomycete, designated strain BR3-1T, which produced spore chains borne on the tips of short sporophores, was isolated from the rhizome of Boesenbergia rotunda collected from Udon Thani province, Thailand. This strain was investigated for its taxonomic position using a polyphasic approach. The strain contained 3-hydroxydiaminopimelic acid and meso-diaminopimelic acid in the cell-wall peptidoglycan. The whole-cell sugars comprised glucose, mannose, rhamnose, ribose and xylose. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides were found as the characteristic phospholipids. The predominant menaquinones were MK-10(H8) and MK-10(H6). The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and anteiso-C15 : 0. The G+C content of the genomic DNA was 71.4 mol%. 16S rRNA gene sequence analysis revealed that strain BR3-1T belonged to the genus Asanoa and was most closely related to Asanoa ishikariensis (99.39 %), Asanoa iriomotensis (99.31 %), Asanoa siamensis (99.17 %), Asanoa ferruginea (98.84 %) and Asanoa hainanensis (98.71 %). The DNA–DNA relatedness value between strain BR3-1T and its phylogenetically closest relatives was in the range of 15.4 % ± 1.2 to 45.8 % ± 2.6. In addition, some physiological and biochemical properties indicated that strain BR3-1T could be readily distinguished from all type strains in the genus Asanoa. Thus, strain BR3-1T should be classified as a representative of a novel species, for which the name Asanoa endophytica sp. nov. is proposed. The type strain is BR3-1T ( = BCC 66355T = NBRC 110002T).
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Streptomyces arcticus sp. nov., isolated from frozen soil
More LessActinomycete strain ZLN234T was isolated from a frozen soil sample, which was collected from a glacier front in the Arctic. Chemotaxonomic and morphological characteristics were found to be typical of members of the genus Streptomyces. The strain formed a distinct phyletic line in the 16S rRNA gene tree and was closely related to Streptomyces olivochromogenes ATCC 3336T (98.63 % similarity) and Streptomyces aureus B7319T (98.56 %). Phylogenetic analysis based on the gyrB gene also showed clearly that strain ZLN234T was different from all recognized Streptomyces species. The whole-cell sugars were galactose, glucose, ribose and rhamnose. The whole-cell-wall amino acids included alanine, glutamine, glycine and meso-diaminopimelic acid with a minor amount of ll-diaminopimelic acid. The characteristic polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and unknown phospholipids. The major menaquinones were MK-9(H10), MK-9(H8) and MK-9(H4). The major cellular fatty acids comprised anteiso-C15 : 0, iso-C16 : 0 and C16 : 0 with a small amount of iso-C16 : 1ω7 and anteiso-C14 : 0. The DNA G+C content of strain ZLN234T was 77.5 mol%. On the basis of these phenotypic, phylogenetic and chemotaxonomic characteristics, strain ZLN234T ( = CCTCC AA 2015005T = DSM 100713T) is the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces arcticus sp. nov. is proposed.
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Streptomyces polygonati sp. nov., an endophytic actinomycete isolated from a root of Polygonatum odoratum (Mill.)
A novel actinomycete, designated strain NEAU-G9T, was isolated from the root of Polygonatum odoratum (Mill.) collected from Harbin, Heilongjiang province, north China, and was characterized using a polyphasic approach. Key morphological and chemotaxonomic properties confirmed the affiliation of strain NEAU-G9T to the genus Streptomyces. Strain NEAU-G9T contained ll-diaminopimelic acid as the diamino acid. The predominant menaquinones were MK-9(H8), MK-9(H6) and MK-9(H4). The phospholipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The predominant fatty acids were iso-C16 : 0, anteiso-C15 : 0 and C16 : 0.16S rRNA gene sequence similarity studies showed that strain NEAU-G9T belongs to the genus Streptomyces and exhibits the highest sequence similarity to Streptomyces yanglinensis JCM 13275T (97.75 %). However, phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain NEAU-G9T is most closely related to Streptomyces misakiensis JCM 4062T (97.12 % sequence similarity). A combination of DNA–DNA hybridization results and some phenotypic characteristics indicated that strain NEAU-G9T can be clearly distinguished from S. yanglinensis JCM 13275T and S. misakiensis JCM 4062T. Consequently, strain NEAU-G9T represents a novel species of the genus Streptomyces, for which the name Streptomyces polygonati sp. nov. is proposed. The type strain is NEAU-G9T ( = CGMCC 4.7237T = DSM 100521T).
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Sediminivirga luteola gen. nov., sp. nov., a member of the family Brevibacteriaceae, isolated from marine sediment
More LessA Gram-stain-positive actinobacterial strain, designated F23T, was isolated from marine sediment collected from the western Pacific. Strain F23T showed less than 94.5 % 16S rRNA gene sequence similarity with type strains of species with validly published names. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that the novel isolate formed a distinct monophyletic clade within the family Brevibacteriaceae and clustered distantly with the genera Brevibacterium and Spelaeicoccus. Cells of strain F23T were non-motile, rod-shaped and aerobic to microaerophilic. Optimal growth occurred at 35–37 °C, at pH 8.0–9.0 and in the presence of 1 % NaCl (w/v). The isolate contained meso-diaminopimelic acid as the characteristic cell-wall diamino acid, MK-8(H2) and MK-7(H2) as the predominant menaquinones and anteiso-C15 : 0 and anteiso-C17 : 0 as the major fatty acids. The DNA G+C content of strain F23T was 69.0 mol%. On the basis of phylogenetic analysis, phenotypic and chemotaxonomic characteristics and 16S rRNA gene signature nucleotide patterns, strain F23T represents a novel species in a novel genus in the family Brevibacteriaceae, for which the name Sediminivirga luteola gen. nov., sp. nov. is proposed. The type strain is F23T ( = JCM 19771T = CGMCC 1.12785T = MCCC 1A09945T).
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Tenggerimyces flavus sp. nov., isolated from soil in a karst cave, and emended description of the genus Tenggerimyces
More LessA novel actinomycete, designated strain S6R2A4-9T, was isolated from a soil sample collected from a karst cave in Henan Province, China, and subjected to a polyphasic taxonomic study. This isolate grew optimally at 25–28 °C, pH 6.5–8.0 and in the absence of NaCl. The substrate mycelium of the isolate was well developed with irregular branches. Aerial mycelium fragmented into long, rod-shaped elements. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain S6R2A4-9T resided in the cluster of the genus Tenggerimyces within the family Nocardioidaceae and shared the highest 16S rRNA gene sequence similarity (98.98 %) with Tenggerimyces mesophilus I12A-02601T. The G+C content of the genomic DNA was 67.0 mol%. The strain contained glucose, ribose and xylose in its whole-cell hydrolysates. Strain S6R2A4-9T possessed a novel variation of peptidoglycan derived from the type A1γ meso-Dpm-direct. The polar lipids consisted of diphosphatidylglycerol, N-acetylglucosamine-containing phospholipid, phosphatidylinositol mannoside, phosphatidylglycerol, phosphoglycolipids and glycolipids. The predominant menaquinones were MK-10(H6) and MK-10(H8). The major fatty acids were C16 : 0, iso-C16 : 0 and 10-methyl C17 : 0. The level of DNA–DNA relatedness between strain S6R2A4-9T and T. mesophilus I12A-02601T was 27.6 ± 3.0 %, which was low enough to indicate that the strain represents a distinct species of the genus Tenggerimyces. On the basis of the polyphasic taxonomic evidence, a novel species, Tenggerimyces flavus sp. nov., is proposed. The type strain of the novel species is S6R2A4-9T ( = DSM 28944T = CGMCC 4.7241T).
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Nesterenkonia aurantiaca sp. nov., an alkaliphilic actinobacterium isolated from Antarctica
More LessA Gram-stain-positive, non-endospore-forming, haloalkaliphilic actinobacterium, strain CK5T, was isolated from a soil sample, collected at Cape King (Antarctica), and its taxonomic position was investigated by using a polyphasic approach. Cells were cocci with orange pigmentation, non-motile and grew optimally at 25 °C and pH 9.0–9.5 in the presence of 2 % (w/v) NaCl. Cellular membrane contained MK-7 (72 %) and MK-8 (28 %), and anteiso-C15 : 0 (64.8 %), iso-C16 : 0 (13.3 %), n-C17 : 0 (9.9 %), n-C16 : 0 (4.0 %), n-C14 : 0 (3.7 %) as major cellular fatty acids. The DNA G+C content was 64.8 mol%. Strain CK5T, based on the 16S rRNA gene sequence similarity, was most closely related to Nesterenkonia jeotgali JG-241T (99.5 %), Nesterenkonia sandarakina YIM 70009T (99.4 %), Nesterenkonia lutea YIM 70081T (99.4 %), Nesterenkonia halotolerans YIM 70084T (99.3 %), Nesterenkonia xinjiangensis YIM 70097T (97.2 %), Nesterenkonia flava CAAS 251T (97.1 %) and Nesterekonia aethiopica CCUG 48939T (97.1 %). Strain CK5T revealed 31 % DNA–DNA relatedness with respect to N. sandarakina DSM 15664T, 29 % with respect to N. jeotgali DSM 19081T, 10 % with respect to N. lutea DSM 15666T and 1 % with respect to N. halotolerans, DSM 15474T, N. xinjiangensis DSM 15475T, N. aethiopica DSM 17733T and N. flava DSM 19422T. On the basis of 16S rRNA gene sequences, DNA–DNA hybridization and chemotaxonomic characteristics, strain CK5T represents a novel species of the genus Nesterenkonia, for which the name Nesterenkonia aurantiaca sp. nov. is proposed. The type strain is CK5T ( = DSM 27373T = JCM 19723T).
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Bifidobacterium eulemuris sp. nov., isolated from faeces of black lemurs (Eulemur macaco)
Forty-three strains of bifidobacteria were isolated from the faeces of two adult black lemurs, Eulemur macaco. Thirty-four were identified as Bifidobacterium lemurum, recently described in Lemur catta. The nine remaining isolates were Gram-positive-staining, non-spore-forming, fructose-6-phosphate phosphoketolase-positive, microaerophilic, irregular rod-shaped bacteria that often presented Y- or V-shaped cells. Typing techniques revealed that these isolates were nearly identical, and strain LMM_E3T was chosen as a representative and characterized further. Phylogenetic analysis based on 16S rRNA gene sequences clustered this isolate inside the genus Bifidobacterium and showed the highest levels of sequence similarity with B. lemurum DSM 28807T (99.3 %), with Bifidobacterium pullorum LMG 21816T and Bifidobacterium longum subsp. infantis ATCC 15697T (96.4 and 96.3 %, respectively) as the next most similar strains. The hsp60 gene sequence of strain LMM_E3T showed the highest similarity to that of Bifidobacterium stellenboschense DSM 23968T (93.3 %), and 91.0 % similarity to that of the type strain of B. lemurum. DNA–DNA reassociation with the closest neighbour B. lemurum DSM 28807T was found to be 65.4 %. The DNA G+C content was 62.3 mol%. Strain LMM_E3T showed a peptidoglycan structure that has not been detected in bifidobacteria so far: A3α l-Lys–l-Ser–l-Thr–l-Ala. Based on the phylogenetic, genotypic and phenotypic data, strain LMM_E3T represents a novel species within the genus Bifidobacterium, for which the name Bifidobacterium eulemuris sp. nov. is proposed; the type strain is LMM_E3T ( = DSM 100216T = JCM 30801T).
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Nakamurella endophytica sp. nov., a novel endophytic actinobacterium isolated from the bark of Kandelia candel
A Gram-stain-positive, aerobic, coccus-shaped, non-spore-forming actinobacterium, designated strain 2Q3S-4-2T, was isolated from the surface-sterilized bark of Kandelia candel, collected from Cotai Ecological Zones in Macao, PR China. It was tested using a polyphasic approach to determine its taxonomic position. Strain 2Q3S-4-2T grew optimally without NaCl at 28–30 °C and at pH 7.0. Substrate mycelia and aerial mycelia were not formed and no diffusible pigments were observed on the media tested. Phylogenetic analysis, based on 16S rRNA gene sequences, suggested that strain 2Q3S-4-2T belonged to the genus Nakamurella, sharing highest 16S rRNA gene sequence similarity with Nakamurella flavida DS-52T (96.76 %). The DNA G+C content of strain 2Q3S-4-2T was 67.8 mol%. The cell-wall peptidoglycan contained meso-diaminopimelic acid and MK-8(H4) was the predominant menaquinone. The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, unidentified aminophospholipids and phosphatidylinositol. The major fatty acids were iso-C16 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and C16 : 0. On the basis of the phylogenetic, phenotypic and chemotaxonomic analysis, strain 2Q3S-4-2T represents a novel species of the genus Nakamurella, for which the name Nakamurella endophytica sp. nov. is proposed. The type strain is 2Q3S-4-2T ( = DSM 100722T = CGMCC 4.7308T).
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- Firmicutes and Related Organisms
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Virgibacillus flavescens sp. nov., isolated from marine sediment
More LessA Gram-stain-variable, rod-shaped, motile bacterial strain, designated S1-20T, was isolated from marine sediment of the Yellow Sea in China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S1-20T was related to the genus Virgibacillus and had highest 16S rRNA gene sequence similarities with the type strains of Virgibacillus necropolis (98.1 %), Virgibacillus arcticus (97.7 %) and Virgibacillus carmonensis (97.3 %). The predominant cellular fatty acids of strain S1-20T were anteiso-C15 : 0 and anteiso-C17 : 0. The main menaquinone was MK-7. The genomic DNA G+C content of strain S1-20T was 38.3 mol%. The polar lipids profile contained diphosphatidylglycerol, phosphatidylglycerol, five unidentified phospholipids, one unknown aminophospholipid and an aminolipid. Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain S1-20T is a representative of a novel species of the genus Virgibacillus, for which the name Virgibacillus flavescens sp. nov. is proposed. The type strain is S1-20T ( = LMG 28381T = DSM 29015T).
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Bacillus piscicola sp. nov., isolated from Thai fish sauce (Nam-pla)
More LessA Gram-reaction-positive, spore-forming, rod-shaped bacterium, designated NR1-3-2T, was isolated from fish sauce collected from a factory in Chonburi province, Thailand. Strain NR1-3-2T grew at pH 5–10 (optimum 7.5), at 21–48 °C (optimum 37 °C) and with 0–15 % (w/v) NaCl (optimum 1–3 %). The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Menaquinone with seven isoprene units (MK-7) was the major isoprenoid quinone. The strain contained anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0 as major cellular fatty acids. Diphosphatidylglycerol, phosphatidyl glycerol and one unknown glycolipid were detected as major polar lipids. On the basis of 16S rRNA gene sequence analysis, strain NR1-3-2T belonged to the genus Bacillus and was closely related to Bacillus iranensis DSM 23995T (97.4 % similarity). Strain NR1-3-2T exhibited low DNA–DNA relatedness (31.2–39.8 %) with B. iranensis DSM 23995T. The DNA G+C content was 44.2 mol%. On the basis of phenotypic characteristics, DNA–DNA relatedness and phylogenetic analyses, the strain is considered to represent a novel species of the genus Bacillus and the name Bacillus piscicola sp. nov. is proposed. The type strain is NR1-3-2T ( = JCM 19598T = LMG 28281T = PCU 340T = TISTR 2295T).
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Paenibacillus cathormii sp. nov., isolated from tree bark
A Gram-stain-positive, facultatively anaerobic, rod-shaped and endospore-forming bacterium, strain BK114-2T isolated from tree bark in Thailand was characterized taxonomically using a polyphasic approach. Analysis based on comparison of 16S rRNA gene sequences indicated that strain BK114-2T was affiliated to the genus Paenibacillus, and was closely related to Paenibacillus timonensis 2301032T (96.7 % 16S rRNA gene sequence similarity), Paenibacillus phoenicis 3PO2SAT (96.6 %) and Paenibacillus barengoltzii SAFN-016T (96.4 %). Strain BK114-2T contained meso-diaminopimelic acid in its cell-wall peptidoglycan. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unknown phospholipids, five unknown aminophospholipids and six unknown lipids. The only menaquinone detected was MK-7 and the dominant cellular fatty acids were C16 : 0 (22.9 %), anteiso-C15 : 0 (22.6 %), iso-C16 : 0 (19.4 %) and anteiso-C17 : 0 (14.7 %). The DNA G+C content was 52.0 mol%. Based on these results, strain BK114-2T repreesents a novel species of the genus Paenibacillus, for which the name Paenibacillus cathormii sp. nov. is proposed. The type strain is BK114-2T ( = KCTC 33251T = TISTR 2282T).
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Bacillus zhangzhouensis sp. nov. and Bacillus australimaris sp. nov.
More LessTwo strains, designated DW5-4T and NH7I_1T, were isolated from aquaculture water of a shrimp farm of Zhangzhou city in China and from surface sediment of the South China Sea, respectively. Cells of the strains were Gram-stain-positive, oxidase- and catalase-positive, rod-shaped and motile. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains belonged to the Bacillus pumilus clade. 16S rRNA gene sequence similarity between strains DW5-4T and NH7I_1T was 99.8 %, and between each of the two strains and four type strains, B. pumilus ATCC 7061T, Bacillus safensis FO-36bT, Bacillus altitudinis 41KF2bT and Bacillus xiamenensis HYC-10T, were above 99.4 %. The digital DNA–DNA hybridization value between the two novel strains was 41.6 %, and between each of the two strains and the four above-mentioned type strains were below 53.0 %. In both strains, the principal fatty acids were iso-C15 : 0 and anteiso-C15 : 0, and the isoprenoid quinone was identified as MK-7 (100 %). The DNA G+C contents of strains DW5-4T and NH7I_1T were 41.4 and 41.3 mol%, respectively. Based on phenotypic and genotypic characteristics, two novel species of the genus Bacillus are proposed: Bacillus zhangzhouensis sp. nov., with DW5-4T ( = MCCC 1A08372T = LMG 27144T = KCTC 33531T) as the type strain, and Bacillus australimaris sp. nov., with NH7I_1T ( = MCCC 1A05787T = LMG 27697T = KCTC 33532T) as the type strain.
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Bacillus velezensis is not a later heterotypic synonym of Bacillus amyloliquefaciens; Bacillus methylotrophicus, Bacillus amyloliquefaciens subsp. plantarum and ‘Bacillus oryzicola’ are later heterotypic synonyms of Bacillus velezensis based on phylogenomics
More LessBacillus velezensis was previously reported to be a later heterotypic synonym of Bacillus amyloliquefaciens, based primarily on DNA–DNA relatedness values. We have sequenced a draft genome of B. velezensis NRRL B-41580T. Comparative genomics and DNA–DNA relatedness calculations show that it is not a synonym of B. amyloliquefaciens. It was instead synonymous with Bacillus methylotrophicus. ‘Bacillus oryzicola’ is a recently described species that was isolated as an endophyte of rice (Oryza sativa). The strain was demonstrated to have plant-pathogen antagonist activity in greenhouse assays, and the 16S rRNA gene was reported to have 99.7 % sequence similarity with Bacillus siamensis and B. methylotrophicus, which are both known for their plant pathogen antagonism. To better understand the phylogenetics of these closely related strains, we sequenced the genome of ‘B. oryzicola’ KACC 18228. Comparative genomic analysis showed only minor differences between this strain and the genomes of B. velezensis NRRL B-41580T, B. methylotrophicus KACC 13015T and Bacillus amyloliquefaciens subsp. plantarum FZB42T. The pairwise in silico DNA–DNA hybridization values calculated in comparisons between the strains were all greater than 84 %, which is well above the standard species threshold of 70 %. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the strains share phenotype and genotype coherence. Therefore, we propose that B. methylotrophicus KACC 13015T, B. amyloliquefaciens subsp. plantarum FZB42T, and ‘B. oryzicola’ KACC 18228 should be reclassified as later heterotypic synonyms of B. velezensis NRRL B-41580T, since the valid publication date of B. velezensis precedes the other three strains.
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Paraclostridium benzoelyticum gen. nov., sp. nov., isolated from marine sediment and reclassification of Clostridium bifermentans as Paraclostridium bifermentans comb. nov. Proposal of a new genus Paeniclostridium gen. nov. to accommodate Clostridium sordellii and Clostridium ghonii
More LessTwenty-three rod-shaped, endospore-forming, Gram-stain-positive, obligately anaerobic bacteria were isolated from different marine sediment samples of Gujarat. All 23 strains shared 16S rRNA gene sequence similarity of ∼100 %. Strain JC272T was designated the type strain and shared highest sequence similarity with Clostridium bifermentans ATCC 638T (99.8 %), Clostridium ghonii JCM 1400T (98.0 %), Clostridium sordellii ATCC 9714T (97.9 %) and other members of the genus Clostridium ( < 96.4 %). C16 : 0, C18 : 0, C17 : 0, C16 : 1ω9c and iso-C16 : 0 were the major (>5 %) fatty acids. Strain JC272T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unidentified amino lipids. Genome-based analysis of average nucleotide identity (ANI) and in silico DNA–DNA hybridization (DDH) of strain JC272T with C. bifermentans ATCC 638T yielded values of 94.35 and 58.5 ± 2.8 %, respectively. The DNA G+C content of strain JC272T was 28.3 mol%. Strain JC272T together with C. bifermentans were found to fall outside Clostridium rRNA cluster I considered as Clostridium senso stricto. Based on ANI value, in-silico DDH, and distinct morphological and physiological differences from the previously described taxa, we suggest that strain JC272T represents a novel species of a new genus in the family Clostridiaceae, for which the name Paraclostridium benzoelyticum gen. nov., sp. nov. is proposed. The type strain is JC272T ( = KCTC 15476T = LMG 28745T). It is also proposed to transfer C. bifermentans to this new genus, as Paraclostridium bifermentans comb. nov. (type strain ATCC 638T = DSM 14991T = JCM 1386T). The genus Paeniclostridium gen. nov. is proposed to accommodate C. sordellii and C. ghonii as Paeniclostridium sordellii comb. nov. (type strain ATCC 9714T = LMG 15708T = JCM 3814T) and Paeniclostridium ghonii comb. nov. (type strain ATCC 25757T = DSM 15049T = JCM 1400T).
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Sedimentibacter acidaminivorans sp. nov., an anaerobic, amino-acid-utilizing bacterium isolated from marine subsurface sediment
More LessA novel, anaerobic bacterium, strain MO-SEDIT, was isolated from a methanogenic microbial community, which was originally obtained from marine subsurface sediments collected from off the Shimokita Peninsula of Japan. Cells were Gram-stain-negative, non-motile, non-spore-forming rods, 0.4–1.4 μm long by 0.4–0.6 μm wide. The cells also formed long filaments of up to about 11 μm. The strain grew on amino acids (i.e. valine, leucine, isoleucine, methionine, glycine, phenylalanine, tryptophan, lysine and arginine), pyruvate and melezitose in the presence of yeast extract. Growth was observed at 4–37 °C (optimally at 30 °C), at pH 6.0 and 8.5 (optimally at 7.0–7.5) and in 0–60 g l− 1 NaCl (optimally 20 g NaCl l− 1). The G+C content of the DNA was 32.0 mol%. The polar lipids of strain MO-SEDIT were phosphatidylglycerol, phosphatidyl lipids and unknown lipids. The major cellular fatty acids (>10 % of the total) were C14 : 0, C16 : 1ω9 and C16 : 0 dimethyl aldehyde. Comparative sequence analysis of the 16S rRNA gene showed that strain MO-SEDIT was affiliated with the genus Sedimentibacter within the phylum Firmicutes. It was related most closely to the type strain of Sedimentibacter saalensis (94 % sequence similarity). Based on the phenotypic and genetic characteristics, strain MO-SEDIT is considered to represent a novel species of the genus Sedimentibacter, for which the name Sedimentibacter acidaminivorans sp. nov. is proposed. The type strain is MO-SEDIT ( = JCM 17293T = DSM 24004T).
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Terrilactibacillus laevilacticus gen. nov., sp. nov., isolated from soil
More LessA Gram-stain-positive, catalase-positive, facultatively anaerobic, spore-forming, rod-shaped bacterium, strain NK26-11T, was isolated from soil in Thailand. This strain produced d-lactic acid from glucose homofermentatively, and grew at 20–45 °C and pH 5–8.5. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major respiratory quinone was menaquinone 7 (MK-7), the DNA G+C content was 42.6 mol%, and the major cellular fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. On the basis of 16S rRNA gene sequences analysis, strain NK26-11T was closely related to Bacillus solimangrovi JCM 18994T (93.89 % 16S rRNA gene sequence similarity), Pullulanibacillus naganoensis LMG 12887T (93.32 %), Sporolactobacillus inulinus NRIC 1133T (92.99 %), Tuberibacillus calidus JCM 13397T (92.98 %) and Thalassobacillus devorans DSM 16966T ( < 90.93 %). Strain NK26-11T could be clearly distinguished from the closely related genera based on phenotypic characteristics and DNA G+C content, and thus represents a novel species of a new genus between the Bacillus and Sporolactobacillus cluster, for which the name Terrilactibacillus laevilacticus gen. nov., sp. nov. is proposed. The type strain of the type species is NK26-11T ( = LMG 27803T = TISTR 2241T = PCU 335T).
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Oceanobacillus halophilus sp. nov., a novel moderately halophilic bacterium from a hypersaline lake
A moderately halophilic bacterium was isolated from a brine sample of a hypersaline lake, Aran-Bidgol, in Iran. The strain, designated J8BT, was Gram-stain-positive, endospore-forming, rod-shaped, strictly aerobic, motile and produced cream colonies. Strain J8BT grew in NaCl at between 3.0–15.0 % (w/v) (optimally at 7.5 % NaCl, w/v), between pH 6.5–9.0 (optimally at pH 8.0) and between 20–45 °C (optimally at 35 °C). Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain J8BT is a member of the genus Oceanobacillus and most closely related to Oceanobacillus profundus CL-MP28T, Oceanobacillus polygoni SA9T and Oceanobacillus oncorhynchi R-2T (96.9 %, 96.3 % and 96.2 % similarities, respectively). The level of DNA–DNA relatedness between the novel isolate and O. profundus IBRC-M 10567T was 10 %. The major cellular fatty acids of the isolate were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The polar lipid pattern of strain J8BT consisted of phosphatidylglycerol, diphosphatidylglycerol, five phospholipids, two aminolipids and two glycoaminolipids. It contained MK-7 as the predominant menaquinone and meso-diaminopimelic acid in the cell-wall peptidoglycan. The G+C content of the genomic DNA of this strain was 39.2 mol%. Phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data suggest that this strain represents a novel species of the genus Oceanobacillus, for which the name Oceanobacillus halophilus sp. nov. is proposed. The type strain is strain J8BT ( = IBRC-M 10444T = DSM 23996T).
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Mobilisporobacter senegalensis gen. nov., sp. nov., an anaerobic bacterium isolated from tropical shea cake
A Gram-stain positive, endospore-forming, strictly anaerobic bacterium, designated strain Gal1T, was isolated from shea cake, a waste material from the production of shea butter, originating from Saraya, Senegal. The cells were rod-shaped, slightly curved, and motile with peritrichous flagella. The strain was oxidase-negative and catalase-negative. Growth was observed at temperatures ranging from 15 to 45 °C (optimum 30 °C) and at pH 6.5–9.3 (optimum pH 7.8). The salinity range for growth was 0–3.5 % NaCl (optimum 1 %). Yeast extract was required for growth. Strain Gal1T fermented various carbohydrates such as mannose, mannitol, arabinose, cellobiose, fructose, glucose, maltose, sucrose, trehalose and lactose and the major end-products were ethanol and acetate. The only major cellular fatty acid was C16 : 0 (19.6 %). The DNA base G+C content of strain Gal1T was 33.8 mol%. Analysis of the 16S rRNA gene sequence of the isolate indicated that this strain was related to Mobilitalea sibirica DSM 26468T with 94.27 % similarity, Clostridium populeti ATTC 35295T with 93.94 % similarity, and Clostridium aminovalericum DSM 1283T and Anaerosporobacter mobilis DSM 15930T with 93.63 % similarity. On the basis of phenotypic characteristics, phylogenetic analysis and the results of biochemical and physiological tests, strain Gal1T was clearly distinguished from closely related genera, and strain Gal1T can be assigned to a novel species of a new genus for which the name Mobilisporobacter senegalensis gen. nov., sp. nov. is proposed. The type strain is Gal1T ( = DSM 26537T = JCM 18753T).
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Paenibacillus bovis sp. nov., isolated from raw yak (Bos grunniens) milk
More LessStrain BD3526T, isolated from raw yak milk collected in Tibet, China, was studied to determine its taxonomic status. The strain was Gram-reaction positive, motile, catalase-positive, aerobic or facultatively anaerobic. The DNA G+C content of the strain was 47.5 mol% and its peptidoglycan contained meso-diaminopimelic acid. The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and C16 : 0. Based on 16S rRNA gene sequence analysis, similarities among strain BD3526T and its most closely related species, Paenibacillus shenyangensis A9T, ‘Paenibacillus dauci’ H9, ‘Paenibacillus wulumuqiensis’ Y24 and Paenibacillus hunanensis DSM 22170T were 99.0, 98.5, 97.3 and 96.7 %, respectively. Levels of DNA–DNA relatedness among strain BD3526T and P. hunanensis DSM 22170T and Paenibacillus polymyxa ATCC 842T ( = DSM 36T), the type species of the genus, were 41.2 and 45.6 %, respectively. In silico genome-to-genome comparison showed that the DNA–DNA hybridization values among strain BD3526T and P. shenyangensis A9T, ‘P. dauci’ H9 and ‘P. wulumuqiensis’ Y24 were lower than 70 %. Based on its molecular and physiological properties, strain BD3526T ( = DSM 28815T = CGMCC 8333T) is identified as the type strain of a novel species within the genus Paenibacillus, for which the name Paenibacillus bovis is proposed.
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- Proteobacteria
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Stenotrophomonas tumulicola sp. nov., a major contaminant of the stone chamber interior in the Takamatsuzuka Tumulus
During investigation of the biological contamination of the 1300-year-old mural paintings and plaster walls inside the stone chambers of the Takamatsuzuka and Kitora Tumuli (TT and KT) in Asuka-mura, Nara Prefecture, Japan, the identity of 17 bacterial isolates from blackish mouldy spots and viscous gels (biofilms) collected from both tumuli (16 isolates from TT and one from KT) during our 2005–2007 microbiological survey was systematically elucidated. One cluster of the major bacterial isolates was assigned to the genus Stenotrophomonas (class Gammaproteobacteria) by phylogenetic analysis of the 16S rRNA gene sequences. These isolates were divided into two groups A and B. Group A comprised 15 TT isolates that took a phylogenetic position near Stenotrophomonas chelatiphaga LPM-5T. Based on our analysis of the phenotypic (cultural, morphological, physiological and chemotaxonomic) characteristics and genotypic/molecular characteristics (DNA base composition, DNA–DNA relatedness, and 16S rRNA and gyrB gene sequences), the novel species name Stenotrophomonas tumulicola sp. nov. is proposed for the group A isolates with the type strain T5916-2-1bT ( = JCM 30961T = NCIMB 15009T). Group B, which contained only one TT and one KT isolate, was closely related to [Pseudomonas] geniculata, [P.] hibiscicola, [P.] beteli, Stenotrophomonas maltophilia and Stenotrophomonas pavanii. The two isolates were genotypically and phenotypically assignable to S. maltophilia.
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Brevundimonas albigilva sp. nov., isolated from forest soil
V. H. T. Pham, S. Jeong, S. Chung and J. KimStrain NHI-13T, a Gram-stain-negative, aerobic and short rod-shaped bacterium, was isolated from forest soil at Kyonggi University in Suwon, South Korea. It grew optimally in R2A medium, at 20–30 °C, in the presence of 0–4 % NaCl. Colonies resulting from incubation of the strain on agar plates for 2 days were circular, raised, translucent, viscous and whitish-yellow, with entire margins. This strain exhibited high catalase activity but was negative for oxidase. 16S rRNA gene sequence analysis showed that strain NHI-13T formed a coherent cluster with members of the genus Brevundimonas. Its similarities were 98.0 % with Brevundimonas aurantiaca DSM 4731T, 97.9 % with Brevundimonas vesicularis LMG 2350T, 97.6 % with Brevundimonas intermedia ATCC 15262T, 97.5 % with Brevundimonas nasdae GTC 1043T, 97.1 % with ‘Brevundimonas olei’ MJ15, 97.1 % with Brevundimonas mediterranea V4.BO.10T and 97.0 % with Brevundimonas poindexterae FWC40T. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), C16 : 0 and 11-methyl C18 : 1ω7c. The DNA G+C content was 63 mol%. The predominant quinone was ubiquinone Q-10. The polar lipid profile contained 1,2-di-O-acyl-3-O-α-d-glycopyranuronosyl glycerol, 1,2-di-O-acyl-3-O-α-d-glycopyranosyl glycerol, 1,2-di-O-acyl-3-O-[d-glycopyranosyl (1 → 4)-α-d-glucopyranuronosyl] glycerols, phosphatidylglycerol, 1,2-diacyl-3- O-(6′-phosphatidyl-α-d-glucopyranosyl) glycerol and other unknown lipids. The DNA relatedness of strain NHI-13T with its reference strains was in the range of 43–56 %. On the basis of its phenotypic, genotypic, chemotaxonomic and phylogenetic distinctiveness, strain NHI-13T is suggested to be a representative of a novel species, belonging to the genus Brevundimonas. Therefore, the name Brevundimonas albigilva. sp. nov. is proposed, with the type strain being NHI-13T ( = KEME 9005-016T = KACC 18249T = JCM 30385T).
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Lampropedia cohaerens sp. nov., a biofilm-forming bacterium isolated from microbial mats of a hot water spring, and emended description of the genus Lampropedia
More LessA biofilm-forming, Gram-stain-negative, aerobic, catalase-positive but oxidase-negative strain, designated CT6T, was isolated from the microbial mats (∼45 °C) of a hot water spring, located within the Himalayan ranges at Manikaran, Himachal Pradesh, India. Strain CT6T formed white, smooth colonies with irregular margins. Transmission electron microscopy revealed coccoid, non-flagellated cells with wavy boundaries. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CT6T belongs to the genus Lampropedia with a sequence similarity value of 95.4 % to the sole member of this genus, Lampropedia hyalina ATCC 11041T. Strain CT6T was found to have phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The major cellular fatty acids were C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C14 : 0, C19 : 0ω8c cyclo and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The major respiratory quinone was ubiquinone-8. The major polyamines were putrescine, spermidine and the betaproteobacterial-specific 2-hydroxyputrescine. The DNA G+C content was 63.5 mol%. Based on the genotypic, phenotypic, physiological and biochemical data, strain CT6T is considered to represent a novel species of the genus Lampropedia, for which the name Lampropedia cohaerens sp. nov. is proposed ( = DSM 100029T = KCTC 42939T = MCC 2711T).
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Pseudomonas helleri sp. nov. and Pseudomonas weihenstephanensis sp. nov., isolated from raw cow's milk
Analysis of the microbiota of raw cow's milk and semi-finished milk products yielded seven isolates assigned to the genus Pseudomonas that formed two individual groups in a phylogenetic analysis based on partial rpoD and 16S rRNA gene sequences. The two groups could be differentiated from each other and also from their closest relatives as well as from the type species Pseudomonas aeruginosa by phenotypic and chemotaxonomic characterization and average nucleotide identity (ANIb) values calculated from draft genome assemblies. ANIb values within the groups were higher than 97.3 %, whereas similarity values to the closest relatives were 85 % or less. The major cellular lipids of strains WS4917T and WS4993T were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol; the major quinone was Q-9 in both strains, with small amounts of Q-8 in strain WS4917T. The DNA G+C contents of strains WS4917T and WS4993T were 58.08 and 57.30 mol%, respectively. Based on these data, strains WS4917T, WS4995 ( = DSM 29141 = LMG 28434), WS4999, WS5001 and WS5002 should be considered as representatives of a novel species of the genus Pseudomonas, for which the name Pseudomonas helleri sp. nov. is proposed. The type strain of Pseudomonas helleri is strain WS4917T ( = DSM 29165T = LMG 28433T). Strains WS4993T and WS4994 ( = DSM 29140 = LMG 28438) should be recognized as representing a second novel species of the genus Pseudomonas, for which the name Pseudomonas weihenstephanensis sp. nov. is proposed. The type strain of Pseudomonas weihenstephanensis is strain WS4993T ( = DSM 29166T = LMG 28437T).
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Reclassification of Wolbachia persica as Francisella persica comb. nov. and emended description of the family Francisellaceae
The taxonomic status of the bacterium Wolbachia persica is described, and based on the evidence presented, transfer of this species to the genus Francisella as Francisella persica comb. nov. is proposed. This reclassification is supported by data generated from genomic comparisons of W. persica ATCC VR-331T ( = FSC845T = DSM 101678T) to other near neighbours, including Francisella tularensis subsp. novicida. The full-length 16S rRNA gene sequence of strain ATCC VR-331T had 98.5 % nucleotide identity to the cognate gene in F. tularensis, with the highest similarity to subspecies novicida. Phylogenetic trees of full-length 16S rRNA gene, gyrA and recA sequences from species of the genera Wolbachia (class Alphaproteobacteria) and Francisella (class Gammaproteobacteria) indicated that W. persica ATCC VR-331T was most closely related to members of the genus Francisella and not Wolbachia. Local collinear blocks within the chromosome of strain ATCC VR-331T had considerable similarity with F. tularensis subsp. novicida, but not with any Wolbachia strain. The genomes of strain ATCC VR-331T and F. tularensis subsp. novicida Utah 112T ( = ATCC 15482T) contained an average nucleotide identity mean of 88.72 % and median of 89.18 %. Importantly, the genome of strain ATCC VR-331T contained one Francisella Pathogenicity Island, similar to F. tularensis subsp. novicida, as well as the Francisella-specific gene fopA1 and F. tularensis-specific genes fopA2 and lpnA (also referred to as tul4). In contrast to the obligate intracellular genus Wolbachia, strain ATCC VR-331T and facultative intracellular Francisella can replicate in specialized cell-free media. Collectively, these results demonstrate that Wolbachia persica should be reclassified in the genus Francisella as Francisella persica comb. nov. The type strain of Francisella persica comb. nov. is ATCC VR-331T ( = FSC845T = DSM 101678T). An emended description of the family Francisellaceae is also provided.
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Roseomonas arctica sp. nov., isolated from arctic glacial foreland soil
A novel psychrotolerant bacterium, designed strain M6-79T, was isolated from an arctic glacial foreland soil sample collected from Ny-Ålesund in the Svalbard Archipelago, Norway. Cells of strain M6-79T were Gram-stain-negative, rod-shaped and produced a red-pigment. Strain M6-79T was strictly aerobic, non-motile, non-endospore-forming, oxidase-negative and catalase-positive. Based on 16S rRNA gene sequence analysis, strain M6-79T was phylogenetically related to Roseomonas aquatica TR53T (95.2 % 16S rRNA gene sequence similarity), Roseomonas lacus TH-G33T (94.3 %), ‘Roseomonas sediminicola’ FW-3 (94.3 %), Roseomonas terrae DS-48T (94.1 %) and Roseomonas soli 5N26T (94.1 %). The unique isoprenoid quinone detected in strain M6-79T was Q-9. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unknown aminolipid and one unknown lipid. Strain M6-79T possessed C18 : 1ω7c, C16 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) as the predominant fatty acids, and the DNA G+C content was 71.2 mol%. Combined data from phylogenetic, phenotypic and chemotaxonomic studies revealed that strain M6-79T represents a novel species of the genus Roseomonas, for which the name Roseomonas arctica sp. nov. is proposed. The type strain is strain M6-79T ( = CCTCC AB 2013101T = LMG 28251T).
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Rhizobium puerariae sp. nov., an endophytic bacterium from the root nodules of the medicinal plant Pueraria candollei var. candollei
More LessA Gram-stain-negative, rod-shaped, motile bacterium, PC004T, was isolated from root nodules of the Thai medicinal plant Pueraria candollei var. candollei. 16S rRNA gene sequence analysis indicated that the strain is phylogenetically related to species in the genus Rhizobium, showing highest similarity (96.6 %) with Rhizobium mesosinicum HAMBI 3194T. The phylogenetic tree reconstructed based on 16S rRNA gene sequences showed that strain PC004T forms a cluster with Rhizobium petrolearium KCTC 23288T. Based on atpD, gyrB and recA gene sequences, strain PC004T also showed low similarity ( < 90 %) to reference strains. These phylogenetic data indicate that PC004T may represent a novel species. Strain PC004T also exhibited low DNA–DNA relatedness with R. mesosinicum HAMBI 3194T (8.2 %) and R. petrolearium KCTC 23288T (26.3 %). The DNA G+C content of strain PC004T was 64 mol%, which is within the range reported for the genus Rhizobium. The major fatty acid of PC004T was C18 : 1ω7c with minor amounts of C16 : 0, C16 : 0 3-OH, C18 : 0 3-OH, C18 : 1 2-OH, C19 : 0 cyclo ω8c and summed feature 2. The strain was able to grow at pH 12 and with up to 2 % (w/v) NaCl. Strain PC004T did not nodulate five tested legumes and the nifH and nodC genes were not detected by PCR. Based on the physiological, chemotaxonomic and phenotypic data from this study, strain PC004T represents a novel species of the genus Rhizobium, for which the name Rhizobium puerariae sp. nov. is proposed; the type strain is PC004T ( = BCC 73740T = NBRC 110722T).
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Dethiosulfatarculus sandiegensis gen. nov., sp. nov., isolated from a methanogenic paraffin-degrading enrichment culture and emended description of the family Desulfarculaceae
A mesophilic deltaproteobacterium, designated strain SPRT, was isolated from a methanogenic consortium capable of degrading long-chain paraffins. Cells were motile, vibrio-shaped, and occurred singly, in pairs or in clusters. Strain SPRT did not metabolize hydrocarbons but grew fermentatively on pyruvate and oxaloacetate and autotrophically with H2 and CO2. Thiosulfate served as a terminal electron acceptor, but sulfate or sulfite did not. The organism required at least 10 g NaCl l− 1 and a small amount of yeast extract (0.001%) for growth. Optimal growth was observed between 30 and 37 °C and a pH range from 6.0 to 7.2. The DNA G+C content of SPRT's genome was 52.02 mol%. Based on 16S rRNA gene sequence analysis, strain SPRT was distinct from previously described Deltaproteobacteria, exhibiting the closest affiliation to Desulfarculus baarsii DSM 2075T and Desulfocarbo indianensis SCBMT, with only 91% similarity between their respective 16S gene sequences. In silico genome comparison supported the distinctiveness between strain SPRT and both Desulfocarbo indianensis SCBMT and Desulfarculus baarsii DSM 2075T. Based on physiological differences, as well as phylogenetic and genomic comparisons, we propose to classify SPRT as the type strain ( = DSM 100305T = JCM 30857T) of a novel species of a new genus with the name Dethiosulfatarculus sandiegensis gen. nov., sp. nov.
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Desulfurella amilsii sp. nov., a novel acidotolerant sulfur-respiring bacterium isolated from acidic river sediments
More LessA novel acidotolerant and moderately thermophilic sulfur-reducing bacterium was isolated from sediments of the Tinto River (Spain), an extremely acidic environment. Strain TR1T stained Gram-negative, and was obligately anaerobic, non-spore-forming and motile. Cells were short rods (1.5–2 × 0.5–0.7 μm), appearing singly or in pairs. Strain TR1T was catalase-negative and slightly oxidase-positive. Urease activity and indole formation were absent, but gelatin hydrolysis was present. Growth was observed at 20–52 °C with an optimum close to 50 °C, and a pH range of 3–7 with optimum between pH 6 and 6.5. Yeast extract was essential for growth, but extra vitamins were not required. In the presence of sulfur, strain TR1T grew with acetate, formate, lactate, pyruvate, stearate, arginine and H2/CO2. All substrates were completely oxidized and H2S and CO2 were the only metabolic products detected. Besides elemental sulfur, thiosulfate was used as an electron acceptor. The isolate also grew by disproportionation of elemental sulfur. The predominant cellular fatty acids were saturated components: C16 : 0, anteiso-C17 : 0 and C18 : 0. The only quinone component detected was menaquinone MK-7(H2). The G+C content of the genomic DNA was 34 mol%. The isolate is affiliated to the genus Desulfurella of the class Deltaproteobacteria, sharing 97 % 16S rRNA gene sequence similarity with the four species described in the genus Desulfurella. Considering the distinct physiological and phylogenetic characteristics, strain TR1T represents a novel species within the genus Desulfurella, for which the name Desulfurella amilsii sp. nov. is proposed. The type strain is TR1T ( = DSM 29984T = JCM 30680T).
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Nitrincola alkalisediminis sp. nov., an alkaliphilic bacterium isolated from an alkaline lake
Two Gram-stain-negative, aerobic, alkaliphilic bacteria (strains MEB087T and MEB142) were isolated from sediment and water samples, respectively, collected from the alkaline Lonar Lake in Maharashtra, India. Strains MEB087T and MEB142 shared 99.8 % 16S rRNA gene sequence similarity and were 85 % related on the basis of DNA–DNA hybridization. The 16S rRNA gene sequences of both strains showed close relationship with the genus Nitrincola, and their closest neighbour was Nitrincola lacisaponensis 4CAT with 97.7 % sequence similarity. MEB087T and MEB142 exhibited only 45 % and 54 % DNA–DNA relatedness, respectively, with Nitrincola lacisaponensis DSM 16316T. Both strains were asporogenous, short, non-motile rods capable of utilizing a limited range of organic acids as sole carbon and energy sources. They were oxidase- and catalase-positive, able to reduce nitrate and nitrite; but unable to degrade DNA, urea, gelatin, casein or starch. They grew optimally at pH 9.5 (tolerating up to pH 11) and could withstand up to 0.6 M NaCl. The predominant cellular fatty acids were summed feature 8 comprising C18 : 1ω7c/C18 : 1ω6c (47–49 %) followed by summed feature 3 comprising C16 : 1ω7c/C16 : 1ω6c (28–32 %). The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The DNA G+C content was 49.3–49.7 mol%. On the basis of the phylogenetic analysis and chemotaxonomic characteristics, strains MEB087T and MEB142 represent a novel species in the genus Nitrincola, for which the name Nitrincola alkalisediminis sp. nov. is proposed. The type strain is MEB087T ( = KCTC 42948T = JCM 19317T) with MEB142 ( = KCTC 42949 = JCM 19318) as an additional strain.
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Burkholderia jirisanensis sp. nov., isolated from forest soil
More LessA Gram-negative, catalase-positive, mesophilic, obligately aerobic bacterium designated JRM2-1T was isolated from forest soil of Jirisan Mountain, Republic of Korea, and its taxonomic position was investigated based on a polyphasic taxonomic approach. Cells of strain JRM2-1T grew optimally at pH 5.0–7.0 and at 25 °C. Strain JRM2-1T was susceptible to chloramphenicol, gentamicin, kanamycin, nalidixic acid, rifampicin, streptomycin and tetracycline. On the basis of 16S rRNA gene sequence similarity, the closest neighbour of strain JRM2-1T was Burkholderia rhizosphaerae WR43T (98.1 %). On the basis of our phylogenetic analysis, strain JRM2-1T is clearly distinguished from related species of the genus Burkholderia and is clustered with plant-associated members of the genus. The major cellular fatty acids were C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c. The polar lipid profile of strain JRM2-1T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, several unidentified aminolipids and an unidentified aminophospholipid. The isoprenoid quinone of strain JRM2-1T was Q-8 and the DNA G+C content was 63.7 mol%. On the basis of our polyphasic taxonomic investigation, strain JRM2-1T is considered to represent a novel species in the genus Burkholderia, for which the name Burkholderia jirisanensis sp. nov. is proposed. The type strain is JRM2-1T ( = AIM 0373T = KCTC 42072T = JCM 19985T).
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Lysobacter aestuarii sp. nov., isolated from estuary sediment
More LessA Gram-stain-negative, strictly aerobic, non-motile bacterium, designated strain S2-CT, was isolated from an estuary sediment in South Korea and subjected to a polyphasic taxonomic investigation. Cells were catalase- and oxidase-positive rods without gliding motility. Growth of strain S2-CT was observed at 15–40 °C (optimum, 30 °C), at pH 5.5–9.0 (optimum, pH 6.5–7.5) and in the presence of 0–7.0 % (w/v) NaCl (optimum, 0–2 %). Only ubiquinone-8 (Q-8) was detected as the isoprenoid quinone and iso-C16 : 0, iso-C15 : 0, summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl), iso-C11 : 0, iso-C11 : 0 3-OH and iso-C14 : 0 were found to be the major cellular fatty acids. Strain S2-CT contained phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the major polar lipids. The G+C content of the genomic DNA was 63.8 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain S2-CT formed a distinct phyletic lineage within the genus Lysobacter. Strain S2-CT was most closely related to Lysobacter daejeonensis GH1-9T with 97.1 % 16S rRNA gene sequence similarity and the DNA–DNA relatedness value between strain S2-CT and the type strain of L. daejeonensis was 45.7 ± 2.2 %. On the basis of the phenotypic, chemotaxonomic and molecular features, strain S2-CT clearly represents a novel species of the genus Lysobacter, for which the name Lysobacter aestuarii sp. nov. is proposed. The type strain is S2-CT ( = KACC 18502T = JCM 31130T).
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Izhakiella capsodis gen. nov., sp. nov., in the family Enterobacteriaceae, isolated from the mirid bug Capsodes infuscatus
More LessGram-stain-negative, oxidase-negative, facultatively anaerobic, motile, rod-shaped, non-pigmented bacterial strains (N6PO6T, N8PO1 and N8PI1) were isolated from the mirid bug Capsodes infuscatus captured on Asphodelus aestivus plants. The 16S rRNA gene sequences of the strains shared 94.7–95.7 % similarity with species of the genus Pantoea and 95.6 % or less with species from other genera in the family Enterobacteriaceae. A polyphasic approach that included determination of phenotypic properties and phylogenetic analysis based on 16S rRNA, rpoB, gyrB and atpD gene sequences supported the classification of strains N6PO6T, N8PO1 and N8PI1 as representing a novel species of a new genus in the family Enterobacteriaceae. Strain N6PO6T, and the two reference strains of the novel species, grew at 1–37 °C, and in the presence of NaCl (up to 7.5 %, w/v) and sucrose (up to 60 %). Their major cellular fatty acids were C16 : 0, C17 : 0 cyclo, C18 : 1ω7c, summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I) and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain N6PO6T was 49.9 mol%. On the basis of phenotypic properties and phylogenetic distinctiveness, the mirid bug isolates are classified as representing a novel species in a new genus Izhakiella, in the family Enterobacteriaceae, for which the name Izhakiella capsodis gen. nov., sp. nov. is proposed. The type strain of Izhakiella capsodis is N6PO6T ( = LMG 28430T = DSM 29293T).
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Pseudahrensia todarodis sp. nov., isolated from the gut of a Japanese flying squid, Todarodes pacificus
A novel Gram-stain-negative, non-motile, non-spore-forming, non-flagellated, aerobic, beige-coloured and rod-shaped bacterium, designated strain KHS02T, was isolated from the intestinal tract of a Japanese flying squid, Todarodes pacificus, which was collected from the East Sea, Korea. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain KHS02T formed a monophyletic clade with Pseudahrensia aquimaris HDW-32T, with which it had the highest sequence similarity (98.67 %). Strain KHS02T grew optimally at pH 7 with 2 % (w/v) NaCl at 25 °C on marine broth 2216, but could not grow without Na+. The predominant isoprenoid quinone was ubiquinone-10 (Q-10). The major fatty acids (>10 % of the total) were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and 11-methyl C18 : 1ω7c. The polar lipids of strain KHS02T comprised phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid and an unidentified lipid. The genomic DNA G+C content was 58.6 mol%. DNA–DNA hybridization showed that the isolate shared 16.2 ± 1.3 % (reciprocal, 15.7 ± 2.8 %) genomic relatedness with the type strain of the closest species. In conclusion, this isolate is suggested to represent a novel species of the genus Pseudahrensia, for which the name Pseudahrensia todarodis is proposed. The type strain is KHS02T ( = KACC 18257T = JCM 30419T).
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Lysobacter terricola sp. nov., isolated from greenhouse soil
Strain 5GH22-11T, which was isolated from greenhouse soil in the Yangpyeong region, Gyeonggi province, Republic of Korea, was characterized to be an aerobic, Gram-stain-negative, flagellated, rod-shaped bacterium. It could grow at temperatures from 10 to 33 °C (optimum of 28–30 °C), in the pH range of 6.0–10.0 (optimum of pH 7.0) and without NaCl. 16S rRNA gene sequence analysis showed that strain 5GH18-14T showed the highest sequence similarities with Lysobacter niabensis GH34-4T (98.6 %), Lysobacter yangpyeongensis GH19-3T (98.1 %), ‘Lysobacter fragariae’ THG-DN8.7 (97.9 %), Lysobacter terrae THG-A13T (97.3 %), ‘Lysobacter rhizosphaerae’ THG-DN8.3 (97.2 %), ‘Lysobacter tyrosinelyticus’ THG-DN8.2 (97.2 %) and Lysobacter oryzae YC6269T (97.2 %), revealing less than 95.5 % sequence similarities with all other species with validly published names. Phylogenetic trees also indicated that strain 5GH18-14T formed a compact subcluster with L. niabensis GH34-4T, L. yangpyeongensis GH19-3T, L. terrae THG-A13T and L. oryzae YC6269T within the genus Lysobacter. The predominant quinone of strain 5GH18-14T was Q-8. The polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylmonomethylethanolamine in large amounts, and moderate or small amounts of three unknown phospholipids and two unknown aminophospholipids. DNA–DNA hybridization values with closely related species were below 70 %. The DNA G+C content was 65.9 mol%. Based on the phylogenetic, physiological and chemotaxonomic data, it has been demonstrated that strain 5GH18-14T represents a novel species of the genus Lysobacter, for which the name Lysobacter terricola sp. nov. is proposed. The type strain is 5GH18-14T ( = KACC 16954T = JCM 30862T).
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Pseudomonas populi sp. nov., an endophytic bacterium isolated from Populus euphratica
A Gram-stain negative, aerobic, non-motile, short-rod-shaped bacterium, designated KBL-4-9T, was isolated from the storage liquid in the stems of Populus euphratica trees in Xinjiang, PR China. Strain KBL-4-9T grew at 4–45 °C (optimum 37 °C), 1–3 % (w/v) NaCl (optimum 1 %, w/v) and pH 5.5–9.5 (optimum pH 7.5). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain KBL-4-9T belonged to the genus Pseudomonas and showed the highest 16S rRNA gene sequence similarity of 97.36 % to Pseudomonas pelagia CL-AP6T, followed by Pseudomonas xinjiangensis S3-3T (97.16 %), Pseudomonas sabulinigri J64T (97.15 %) and Pseudomonas xiamenensis C10-2T (96.47 %). Analysis of strain KBL-4-9T based on the three housekeeping genes, rpoB, rpoD and gyrB, further confirmed the phylogenetic assignment of the isolates. The DNA G+C content was 61.6 mol% (sd = 2.19). DNA–DNA hybridization with P. pelagia CL-AP6T, P. xinjiangensis S3-3T and P. sabulinigri J64T revealed 49.3 % (sd = 3.04), 41.2 % and 52.5 % (sd = 4.45) relatedness, respectively. The major cellular fatty acids of strain KBL-4-9T were C16 : 0, C12 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C17 : 0 cyclo. The major isoprenoid quinone was Q-9. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. On the basis of phenotypic, chemotaxonomic and phylogenetic properties, strain KBL-4-9T is considered to represents a novel species of the genus Pseudomonas, for which the name Pseudomonas populi sp. nov. is proposed. The type strain is KBL-4-9T ( = JCM 19138T = CCTCC AB 2013069T = NRRL B-59988T).
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Ehrlichia minasensis sp. nov., isolated from the tick Rhipicephalus microplus
Recently, we obtained a rickettsial isolate (Ehrlichia sp. UFMG-EVT) from the haemolymph of engorged Rhipicephalus microplus tick females. On the basis of maximum-likelihood phylogenetic analysis using 16S rRNA gene, groEL, dsb, gltA and trp36 sequences we showed that Ehrlichia sp. UFMG-EVT belongs to the α-Proteobacteria, family Anaplasmataceae, genus Ehrlichia. Ehrlichia sp. UFMG-EVT is a sister taxon of Ehrlichia canis with 16S rRNA gene, groEL, dsb, gltA and trp36 sequence similarities of 98.3 %, 97.2 %, 94.7 %, 94.3 % and 49.1 %, respectively. Ehrlichia sp. UFMG-EVT has been maintained in the laboratory by continuous passage in the IDE8 tick cell line where the ultrastructure was characterized using electron microscopy and was found to resemble that of E. canis, Ehrlichia muris and Ehrlichia chaffeensis, but not Ehrlichia ruminantium and Ehrlichia ewingii. We propose the name Ehrlichia minasensis sp. nov. for this bacterium to acknowledge the place from where it was initially isolated, Minas Gerais, Brazil. The type strain is strain Ehrlichia sp. UFMG-EVT ( = DSM 100393T = TCB-TBB-0018T).
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Azospirillum agricola sp. nov., a nitrogen-fixing species isolated from cultivated soil
More LessA polyphasic approach was used to characterize a novel nitrogen-fixing bacterial strain, designated CC-HIH038T, isolated from cultivated soil in Taiwan. Cells of strain CC-HIH038T were Gram-stain-negative, facultatively aerobic and spiral-shaped, with motility provided by a single polar flagellum. The 16S rRNA gene sequence analysis of strain CC-HIH038T showed highest sequence similarity to Azospirillum doebereinerae (98.0 %), Azospirillum thiophilum (97.5 %), Azospirillum rugosum (97.4 %) and Azospirillum zeae (97.2 %) and lower sequence similarity ( < 97.0 %) to all other species of the genus Azospirillum. According to DNA–DNA association, the relatedness values of strain CC-HIH038T with A. doebereinerae, A. thiophilum, A. rugosum and A. zeae were 51.8 %, 41.2 %, 56.5 % and 37.5 %, respectively. Strain CC-HIH038T was able to grow at 20–37 °C and pH 7.0–8.0. Strain CC-HIH038T gave positive amplification for dinitrogen reductase (nifH gene); the activity was recorded as 8.4 nmol ethylene h− 1. The predominant quinone system was ubiquinone Q-10 and the DNA G+C content was 68.8 mol%. The major fatty acids found in strain CC-HIH038T were C16 : 0, iso-C18 : 0, C16 : 0 3-OH, C14 : 0 3-OH/iso-C16 : 1 and C18 : 1ω7c/C18 : 1ω6c. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain CC-HIH038T is considered to represent a novel species in the genus Azospirillum, for which the name Azospirillum agricola sp. nov. is proposed. The type strain is CC-HIH038T ( = BCRC 80909T = JCM 30827T).
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Ampullimonas aquatilis gen. nov., sp. nov. isolated from bottled mineral water
More LessTwo isolates, designated B15.09-116T and B15.09-124, were recovered from bottled mineral water in Portugal. Based on 16S rRNA gene sequence analysis, these strains were related most closely to species of the genus Derxia (belonging to the family Alcaligenaceae) with pairwise sequence similarities of 93.0–93.6 %. The isolates were not pigmented and formed Gram-stain-negative, short, motile rod-shaped cells. The organisms were strictly aerobic, oxidase-positive and catalase-negative. These organisms also fixed N2. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. Ubiquinone 8 was the major respiratory quinone. The DNA G+C content of strain B15.09-116T was 49.8 mol%. Based on phylogenetic, physiological and biochemical characteristics the two strains are considered to represent a novel species of a new genus, for which the name Ampullimonas aquatilis gen. nov., sp. nov. is proposed. The type strain of Ampullimonas aquatilis is B15.09-116T ( = CECT 8581T = LMG 28208T).
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Xuhuaishuia manganoxidans gen. nov., sp. nov., a manganese-oxidizing bacterium isolated from deep-sea sediments from the Pacific Polymetallic Nodule Province
More LessA Gram-stain-negative, strictly aerobic, non-motile, rod-shaped, manganese-oxidizing bacterial strain, designated DY6-4T, was isolated from the surface sediment of the Pacific Clarion-Clipperton Fracture Zone. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain DY6-4T formed a lineage within the family Rhodobacteraceae and was distinct from the most closely related genera Sulfitobacter, Aliiroseovarius and Loktanella (94.0–96.0 %, 93.4–96.0 % and 91.9–95.9 % 16S rRNA gene sequence similarity, repectively). Optimal growth occurred in the presence of 1 % (w/v) NaCl, at pH 7.0 and at 28 °C. Strain DY6-4T contained ubiquinone-10 (Q-10) as the major ubiquinone, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and one unidentified aminolipid as the predominant polar lipids, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the main fatty acids (>10 % of the total). The DNA G+C content of strain DY6-4T was 66.6 mol%. On the basis of the polyphasic analyses, strain DY6-4T is considered to represent a novel species of a novel genus in the Roseobacter clade of the family Rhodobacteraceae, for which the name Xuhuaishuia manganoxidans gen. nov., sp. nov. is proposed. The type strain is DY6-4T ( = KCTC 42421T = MCCC 1K00502T).
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Arenimonas aestuarii sp. nov., isolated from estuary sediment
More LessA novel species of the genus Arenimonas, represented by strain S2-21T, was isolated from an estuary of Asan in South Korea. Cells of strain S2-21T were Gram-stain-negative, aerobic, non-motile rods that were oxidase- and catalase-positive. Growth of strain S2-21T was observed at 15–40 °C (optimum, 25–30 °C), at pH 7.0–8.0 (optimum, pH 7.0) and in the presence of 0–2.0 % (w/v) NaCl (optimum, 0 %). The major cellular fatty acids were iso-C15 : 0, C11 : 0 3-OH, iso-C16 : 0, summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl), anteiso-C17 : 0 and iso-C11 : 0. The only respiratory quinone detected was ubiquinone-8 (Q-8) and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanol and two unknown phospholipids. The G+C content of the genomic DNA was 62.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S2-21T formed a tight phyletic lineage with Arenimonas donghaensis HO3-R19T within the genus Arenimonas. Strain S2-21T was related most closely to A. donghaensis HO3-R19T at 98.1 % 16S rRNA gene sequence similarity and the mean DNA–DNA relatedness value between strain S2-21T and the type strain of A. donghaensis was 23.6 ± 2.2 %. On the basis of phenotypic, chemotaxonomic and molecular features, strain S2-21T is considered to represent a novel species of the genus Arenimonas, for which the name Arenimonas aestuarii sp. nov. is proposed. The type strain is S2-21T ( = KACC 18504T = JCM 31129T).
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Novosphingobium piscinae sp. nov., isolated from a fish culture pond
More LessA bacterial strain designated SLH-16T was isolated from a fish culture pond in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain SLH-16T were Gram-stain-negative, aerobic, motile rods that were covered by large capsules and formed yellow colonies. Growth occurred at 20–40 °C (optimum, 37–40 °C), at pH 4.0–9.0 (optimum, pH 5.0–6.0) and with 0–0.5 % (w/v) NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SLH-16T belonged to the genus Novosphingobium and was related most closely to Novosphingobium taihuense T3-B9T with sequence similarity of 97.3 %. The major fatty acids (>10 %) of strain SLH-16T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major 2-hydroxy fatty acid was C14 : 0 2-OH. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, phosphatidylcholine and several uncharacterized lipids. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 65.2 mol%. The DNA–DNA hybridization value for strain SLH-16T and the type strain of N. taihuense was less than 43.2 %. Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus Novosphingobium. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain SLH-16T represents a novel species in the genus Novosphingobium, for which the name Novosphingobium piscinae sp. nov. is proposed. The type strain is SLH-16T ( = BCRC 80888T = LMG 28418T = KCTC 42194T).
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Marinobacterium profundum sp. nov., a marine bacterium from deep-sea sediment
A Gram-stain-negative, rod-shaped and motile strain, designated PAMC 27536T, was isolated from deep-sea sediment in the East Sea, Korea. Analysis of the 16S rRNA gene sequence of the strain showed an affiliation with the genus Marinobacterium. Phylogenetic analyses revealed that strain PAMC 27536T was related most closely to Marinobacterium rhizophilum CL-YJ9T with a 16S rRNA gene sequence similarity of 98.5 % and to other members of the genus Marinobacterium (94.0–91.7 %). Genomic relatedness analyses between strain PAMC 27536T and M. rhizophilum KCCM 42386T gave an average nucleotide identity of 85.6 % and an estimated DNA–DNA hybridization of 24.6 % using the genome-to-genome distance calculator, indicating that they represent genomically distinct species. Cells of strain PAMC 27536T grew optimally at 25–30 °C and pH 7.0–7.5 in the presence of 3 % (w/v) sea salts. The major cellular fatty acids were C16 : 1ω6c and/or C16 : 1ω7c, C18 : 1ω6c and/or C18 : 1ω7c, and C16 : 0. The major isoprenoid quinone was Q-8. The genomic DNA G+C content was 56.1–57.2 mol%. Based on the phylogenetic, chemotaxonomic, genomic and phenotypic data presented, a novel species with the name Marinobacterium profundum sp. nov. is proposed, with PAMC 27536T ( = KCCM 43095T = JCM 30410T) as the type strain.
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Erwinia gerundensis sp. nov., a cosmopolitan epiphyte originally isolated from pome fruit trees
A survey to obtain potential antagonists of pome fruit tree diseases yielded two yellow epiphytic bacterial isolates morphologically similar to Pantoea agglomerans, but showing no biocontrol activity. Whole-cell MALDI-TOF mass spectrometry and analysis of 16S rRNA gene and gyrB sequences suggested the possibility of a novel species with a phylogenetic position in either the genus Pantoea or the genus Erwinia. Multi-locus sequence analysis (MLSA) placed the two strains in the genus Erwinia and supported their classification as a novel species. The strains showed general phenotypic characteristics typical of this genus and results of DNA–DNA hybridizations confirmed that they represent a single novel species. Both strains showed a DNA G+C content, as determined by HPLC, of 54.5 mol% and could be discriminated from phylogenetically related species of the genus Erwinia by their ability to utilize potassium gluconate, potassium 2-ketogluconate, maltose, melibiose and raffinose. Whole-genome sequencing of strain EM595T revealed the presence of a chromosomal carotenoid biosynthesis gene cluster similar to those found in species of the genera Cronobacter and Pantoea that explains the pigmentation of the strain, which is atypical for the genus Erwinia. Additional strains belonging to the same species were recovered from different plant hosts in three different continents, revealing the cosmopolitan nature of this epiphyte. The name Erwinia gerundensis sp. nov. is proposed, with EM595T ( = LMG 28990T = CCOS 903T) as the designated type strain.
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Marinagarivorans algicola gen. nov., sp. nov., isolated from marine algae
More LessTwo novel agar-degrading, Gram-stain-negative, motile, heterotrophic, facultatively anaerobic and pale yellow-pigmented bacterial strains, designated Z1T and JL1, were isolated from marine algae Gelidium amansii (Lamouroux) and Gracilaria verrucosa, respectively. Growth of the isolates was optimal at 28–30 °C, pH 7.0–7.5 and with 2–3 % (w/v) NaCl. Both strains contained Q-8 as the sole respiratory quinone. The major cellular fatty acids in strain Z1T were C18 : 1ω7c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The predominant polar lipids in strain Z1T were phosphatidylethanolamine, phosphatidylglycerol and an aminolipid. The genomic DNA G+C content of both strains was 45.1 mol%. Strains Z1T and JL1 were closely related, with 99.9 % 16S rRNA gene sequence similarity. The average nucleotide identity (ANI) value between strains Z1T and JL1 was 99.3 %. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains Z1T and JL1 form a distinct phyletic line within the class Gammaproteobacteria, with less than 92.3 % similarity to their closest relatives. Based on data from the current polyphasic study, the isolates are proposed to belong to a novel species of a new genus designated Marinagarivorans algicola gen. nov., sp. nov. The type strain of the type species is Z1T ( = ATCC BAA-2617T = CICC 10859T).
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- Bacteroidetes
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Mucilaginibacter roseus sp. nov., isolated from a freshwater river
More LessA bacterial strain, designated TTM-1T, was isolated from a water sample taken from the Caohu River in Taiwan and characterized in a taxonomic study using a polyphasic approach. Cells of strain TTM-1T were Gram-stain-negative, aerobic, non-motile, rod-shaped and covered by large capsules, and formed pink-coloured colonies. Growth occurred at 10–37 °C (optimum 30–37 °C), at pH 6–8 (optimum pH 6–7) and with 0–2 % NaCl (optimum 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TTM-1T belonged to the genus Mucilaginibacter and was most closely related to Mucilaginibacter defluvii A5T with a 16S rRNA gene sequence similarity of 97.3 %. The predominant fatty acids of strain TTM-1T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 37.1 %) and iso-C15 : 0 (30.7 %). The polar lipid profile consisted of phosphatidylethanolamine and several uncharacterized aminophospholipids and phospholipids. The major isoprenoid quinone was MK-7. The DNA G+C content of the genomic DNA was 45.1 mol%. The DNA–DNA relatedness of strain TTM-1T with respect to recognized species of the genus Mucilaginibacter was less than 70 %. On the basis of the phylogenetic inference and phenotypic data, strain TTM-1T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter roseus sp. nov. is proposed. The type strain is TTM-1T ( = LMG 28454T = KCTC 42273T).
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Anseongella ginsenosidimutans gen. nov., sp. nov., isolated from soil cultivating ginseng
More LessA Gram-stain-negative, rod-shaped, non-spore-forming, oxidase and catalase-positive, strictly aerobic bacterium, designated strain Gsoil 524T, was isolated from the soil of a ginseng field and subjected to polyphasic taxonomic analysis. Phylogenetic analysis, based on the 16S rRNA gene sequence, placed Gsoil 524T in a distinct lineage in the family Sphingobacteriaceae, sharing 87.2–88.0 % sequence similarity with members of the closely related genera Pedobacter, Mucilaginibacter and Solitalea. Strain Gsoil 524T contained MK-7 as the predominant quinone, and iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 1ω5c as the major fatty acids. Strain Gsoil 524T could be distinguished from the other members of the family Sphingobacteriaceae by a number of chemotaxonomic and phenotypic characteristics. The major polar lipids in strain Gsoil 524T were phosphatidylethanolamine and two unidentified polar lipids. Compared with the standard and reference strains unidentified sphingolipid was also found. Based on this polyphasic taxonomic analysis, strain Gsoil 524T represents a novel species within a novel genus, for which the name Anseongella ginsenosidimutans gen. nov., sp. nov. is proposed. The type strain of Anseongella ginsenosidimutans is Gsoil 524T ( = KACC 14636T = KCTC 22261T = LMG 24494T).
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Gaetbulibacter aquiaggeris sp. nov., a member of the Flavobacteriaceae isolated from seawater
More LessA Gram-stain-negative, non-flagellated, non-gliding and rod-shaped bacterial strain, designated KEM-8T, was isolated from seawater in the Korean peninsula. Strain KEM-8T was found to grow optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain KEM-8T falls within the clade comprising species of the genus Gaetbulibacter, clustering with the type strains of Gaetbulibacter marinus and Gaetbulibacter lutimaris with which it exhibits 98.4 and 97.2 % 16S rRNA gene sequence similarity, respectively. Sequence similarities to Gaetbulibacter saemankumensis SMK-12T and Gaetbulibacter aestuarii KCTC 23303T were 95.4 and 95.2 %, respectively. Strain KEM-8T was found to contain MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 0 3-OH, iso-C16 : 0 3-OH and iso-C15 : 1 G as the major fatty acids. The major polar lipids were identified as phosphatidylethanolamine and an unidentified lipid. The DNA G+C content of strain KEM-8T was 36.0 mol% and mean DNA–DNA relatedness values with G. marinus KCTC 23046T and G. lutimaris D1-y4T were 27.6 ± 0.9 and 10.3 ± 1.4 %, respectively. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain KEM-8T is distinguishable from species of the genus Gaetbulibacter with validly published names. On the basis of the data presented, strain KEM-8T represents a novel species of the genus Gaetbulibacter, for which the name Gaetbulibacter aquiaggeris sp. nov. is proposed. The type strain is KEM-8T ( = KCTC 42198T = NBRC 110553T).
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Tenacibaculum ascidiaceicola sp. nov., isolated from the golden sea squirt Halocynthia aurantium
More LessA Gram-stain-negative, non-flagellated, non-spore-forming bacterial strain motile by gliding, designated RSS1-6T, was isolated from a golden sea squirt Halocynthia aurantium and its taxonomic position was investigated by using a polyphasic approach. Strain RSS1-6T grew optimally at 30–37 °C and in the presence of 1.0–4.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain RSS1-6T fell within the clade comprising species of the genus Tenacibaculum, clustering with the type strains of Tenacibaculum discolor, Tenacibaculum litoreum and Tenacibaculum gallaicum with which it exhibited 16S rRNA gene sequence similarity values of 98.5–99.5 %. Strain RSS1-6T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acids. The major polar lipids of strain RSS1-6T were phosphatidylethanolamine, two unidentified lipids, one unidentified aminophospholipid and one unidentified glycolipid. The DNA G+C content was 32.5 mol% and the mean DNA–DNA relatedness values with the type strains of T. discolor, T. litoreum and T. gallaicum were 17.3–25.2 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain RSS1-6T is separated from other recognized species of the genus Tenacibaculum. On the basis of the data presented, strain RSS1-6T is considered to represent a novel species of the genus Tenacibaculum, for which the name Tenacibaculum ascidiaceicola sp. nov. is proposed. The type strain is RSS1-6T ( = KCTC 42702T = NBRC 111225T).
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Membranicola marinus gen. nov., sp. nov., a new member of the family Saprospiraceae isolated from a biofilter in a recirculating aquaculture system
More LessA Gram-staining-negative bacterial strain (termed CZ-AZ5T) was isolated from a biological filter in a marine recirculating aquaculture system in Tianjin, China. Its taxonomic status was determined using a polyphasic approach. CZ-AZ5T cells were non-spore-forming, non-motile rods, 0.6–0.7 μm wide and 3.0–3.7 μm long. CZ-AZ5T was strictly heterotrophic, aerobic, oxidase-negative and catalase-positive. Growth occurred in the temperature range 20–40 °C (optimal: 30 °C), pH range 6.0–8.5 (optimal: pH 7.5) and salinity range 0–5 % (w/v) NaCl (optimal: 1 %). In phylogenetic analyses based on 16S rRNA gene sequences, CZ-AZ5T was assigned to the family Saprospiraceae (phylum Bacteroidetes) and was clustered with the genera Saprospira and Aureispira within this family. It showed highest sequence similarity to ‘Candidatus Haliscomenobacter calcifugiens’ (86.2 %), followed by Saprospira grandis ATCC 23119T (85.7 %) and Lewinella persica T-3T (85.6 %). DNA G+C content was 40.1 mol%, the major menaquinone was MK-7, and the major cellular fatty acids (>10 %) were C16 : 1ω7c and iso-C15 : 0. Our phenotypic, chemotaxonomic and phylogenetic observations, taken together, led us to conclude that strain CZ-AZ5T represents a novel species and genus of the family Saprospiraceae, for which the name Membranicola marinus gen. nov., sp. nov. is proposed. The type strain is CZ-AZ5T ( = CGMCC 1.13179T = JCM 18886T).
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Pseudofulvibacter marinus sp. nov., isolated from seawater
A novel Gram-stain-negative, rod-shaped, non-spore-forming, non-flagellated, strictly aerobic strain, designated RZW2-1T, was isolated from coastal seawater of the Yellow Sea in China (35.475° N 119.613° E). The organism grew optimally at 24 °C, at pH 7.0 and in the presence of 3.0 % (w/v) NaCl. The strain requires seawater or artificial seawater for growth and NaCl alone does not support growth. Strain RZW2-1T contained MK-6 as the only respiratory quinone and iso-C15 : 0, iso-C15 : 1 G and 10-methyl C16 : 0 and/or iso-C17 : 1ω9c as the dominant fatty acids. The polar lipids of strain RZW2-1T were four unidentified phospholipids (PL1–PL4), two unknown lipids (L1, L2) and one unidentified aminolipid (AL1). The DNA G+C content of strain RZW2-1T was 32 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was most closely related to the type strain of the only described species of genus Pseudofulvibacter, Pseudofulvibacter geojedonensis YCS-9T, with 95.1 % 16S rRNA gene sequence similarity. On the basis of polyphasic analyses, strain RZW2-1T represents a novel species of the genus Pseudofulvibacter, for which the name Pseudofulvibacter marinus sp. nov. is proposed. The type strain is RZW2-1T ( = JCM 30826T = MCCC 1K00695T).
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Apibacter adventoris gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from honey bees
More LessHoney bees and bumble bees harbour a small, defined set of gut bacterial associates. Strains matching sequences from 16S rRNA gene surveys of bee gut microbiotas were isolated from two honey bee species from East Asia. These isolates were mesophlic, non-pigmented, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0 and C16 : 0 3-OH. The DNA G+C content was 29–31 mol%. They had ∼87 % 16S rRNA gene sequence identity to the closest relatives described. Phylogenetic reconstruction using 20 protein-coding genes showed that these bee-derived strains formed a highly supported monophyletic clade, sister to the clade containing species of the genera Chryseobacterium and Elizabethkingia within the family Flavobacteriaceae of the phylum Bacteroidetes. On the basis of phenotypic and genotypic characteristics, we propose placing these strains in a novel genus and species: Apibacter adventoris gen. nov., sp. nov. The type strain of Apibacter adventoris is wkB301T ( = NRRL B-65307T = NCIMB 14986T).
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Leeuwenhoekiella nanhaiensis sp. nov., isolated from deep-sea water
More LessA novel heterotrophic, aerobic, Gram-stain-negative, rod-shaped and yellow bacterium, designated strain G18T, was isolated from a water sample collected from the deep South China Sea. Strain G18T grew at 4–40 °C (optimum 28–32 °C), at pH 6.0–8.0 (optimum pH 6.5–7.5) and with 0–12 % (w/v) NaCl (optimum 3–4 %). The organism was mesophilic and piezotolerant, its optimal growth pressure was 0.1 MPa, which was lower than that at the depth from which it was isolated. Its optimal growth temperature was higher than that at the depth of its isolation. The predominant cellular fatty acids were C15 : 0iso, C17 : 0iso 3-OH and C15 : 1iso. The major polar lipids were composed of phosphatidylethanolamine, one unknown aminolipid and one unknown polar lipid. The major respiratory quinone was menaquinone 6. The G+C content of the genomic DNA was 35 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain G18T clustered with species of the genus Leeuwenhoekiella with validly published names within the family Flavobacteriaceae with 95.9–98.2 % sequence similarity. DNA–DNA reassociation values ranged from 9 to 42 %. Differential phenotypic properties, together with the phylogenetic distinctiveness, suggest that strain G18T differs from species of the genus Leeuwenhoekiella with validly published names. On the basis of the polyphasic evidence, strain G18T represents a novel species, isolated from deep-sea, of the genus Leeuwenhoekiella for which the name Leeuwenhoekiella nanhaiensis sp. nov. is proposed. The type strain is G18T ( = CCTCC AB 2015204T = KCTC 42729T).
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Flavobacterium lutivivi sp. nov., isolated from activated sludge
More LessA Gram-stain-negative, strictly aerobic, yellow, rod-shaped bacterium, designated strain HQQT, was isolated from a municipal wastewater treatment plant in Hebei Province, PR China. Comparative 16S rRNA gene sequence analyses showed that strain HQQT is a member of the genus Flavobacterium and is closely related to ‘Flavobacterium shanxiense’ CCTCC AB 2014079T (94.8 %) and Flavobacterium macrobrachii DSM 22219T (94.7 %). Phylogenetic analysis showed that strain HQQT clustered with Flavobacterium fontis JCM 18212T and Flavobacterium squillarum KCTC 23915T. The polar lipid profile of strain HQQT revealed the presence of phosphatidylethanolamine, six unknown aminolipids, one unknown glycolipid and one unknown lipid and the only isoprenoid quinone was MK-6. The dominant fatty acids of strain HQQT were iso-C15 : 0, C15 : 0 and C16 : 1ω7c. The DNA G+C content of strain HQQT is 32 mol%. On the basis of the phylogenetic and phenotypic data, strain HQQT represents a novel species of the genus Flavobacterium, for which the name Flavobacterium lutivivi sp. nov. is proposed. The type strain is HQQT ( = CGMCC 1.15347T = KCTC 42935T).
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Bacteroides caecicola sp. nov. and Bacteroides gallinaceum sp. nov., isolated from the caecum of an Indonesian chicken
Six strains of anaerobic bacteria, C13EG70T, C13EG118, C13EG186T, C13GAMG5, C13GAMG28 and C13GAMG40, were isolated from the caecum of a healthy chicken bred in Bogor, Indonesia. Phylogenetic analysis showed the isolates were separated into two groups. Group I (C13EG70T and C13EG118) showed nearly identical 16S rRNA gene sequences (99.9 % sequence similarity). Group II (C13EG186T, C13GAMG5, C13GAMG28 and C13GAMG40) showed nearly identical 16S rRNA gene sequences (>99.4 % sequence similarity). The isolates showed low 16S rRNA gene sequence similarities to recognized species of the genus Bacteroides. High gene sequence similarities were found between type strains (C13EG70T and C13EG186T) and Bacteroides salanitronis JCM 13657T (87.9, 91.5 %, respectively). Physiological, biochemical and genotypic characteristics demonstrated that these strains could be separated from the type strain of B. salanitronis. It is concluded that Group I and Group II represent novel species. Two novel species of the genus Bacteroides are proposed as Bacteroides caecicola sp. nov. (type strain C13EG70T = LIPI12-4-Ck732T = JSAT12-4-Ck732T = InaCC B449T = NBRC 110958T) and Bacteroides gallinaceum sp. nov. (type strain C13EG186T = LIPI12-4-Ck844T = JSAT12-4-Ck884T = InaCC B451T = NBRC 110963T).
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Description of Proteiniphilum saccharofermentans sp. nov., Petrimonas mucosa sp. nov. and Fermentimonas caenicola gen. nov., sp. nov., isolated from mesophilic laboratory-scale biogas reactors, and emended description of the genus Proteiniphilum
More LessThree novel, facultatively anaerobic bacteria of the family Porphyromonadaceae (phylum Bacteroidetes) were isolated from mesophilic laboratory-scale biogas reactors. The strains were Gram-negative rods. Optimal growth occurred between 35 and 45 °C and at pH 7.1–7.8. The main fermentation products were acetic and propionic acids. The predominant fatty acid in all strains was anteiso-C15 : 0, and the only respiratory quinone detected was menaquinone MK-8. 16S rRNA gene sequence comparison indicated that strains M3/6T and ING2-E5BT were most closely related to the type strain of Proteiniphilum acetatigenes, with sequence similarities of 97.3 and 94.5 %. Strain ING2-E5AT showed the closest affiliation to the type strain of Petrimonas sulfuriphila, with 97 % sequence identity. DNA–DNA hybridization of strain M3/6T and ING2-E5AT with the most closely related type strains showed 43.3–45.6 and 23.8–25.7 % relatedness, respectively, which supports the conclusion that both isolates represent novel species. Phylogenetic analysis and comparison of cellular fatty acid patterns indicated that strain ING2-E5BT cannot be classified as a member of any previously described genus. Therefore, because of the physiological, genotypic and chemotaxonomic differences, it is proposed to designate novel species within the genera Proteiniphilum and Petrimonas, Proteiniphilum saccharofermentans sp. nov. (type strain M3/6T = DSM 28694T = CECT 8610T = LMG 28299T) and Petrimonas mucosa sp. nov. (type strain ING2-E5AT = DSM 28695T = CECT 8611T), and a novel species of a new genus, Fermentimonas caenicola gen. nov., sp. nov. (type strain of Fermentimonas caenicola is ING2-E5BT = DSM 28696T = CECT 8609T = LMG 28429T). In addition, an emended description of the genus Proteiniphilum is provided.
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Hymenobacter paludis sp. nov., isolated from a marsh
More LessA bacterial strain, designated KBP-30T, was isolated from a water sample taken from the Banping Lake Wetland Park in Taiwan and characterized taxonomically using a polyphasic approach. Cells of strain KBP-30T were Gram-stain-negative, aerobic, motile by gliding rods that were covered by large capsules and formed red colonies. Growth occurred at 10–37 °C (optimum 20 °C), at pH 6–8 (optimum pH 6) and with 0–1 % NaCl (optimum 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KBP-30T belonged to the genus Hymenobacter and was most closely related to Hymenobacter ocellatus Myx 2105T with a sequence similarity of 97.7 %; 16S rRNA gene sequence similarities were less than 95.1 % with other members of the genus. Strain KBP-30T contained iso-C15 : 0, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), anteiso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the predominant fatty acids. The major isoprenoid quinone was MK-7. The polar lipid profile consisted of phosphatidylethanolamine, three unidentified aminophospholipids, an unidentified aminolipid, an unidentified glycolipid and eight unidentified lipids. The major polyamine was homospermidine. The DNA G+C content of the genomic DNA was 60.3 mol%. The DNA–DNA relatedness of strain KBP-30T with respect to Hymenobacter ocellatus Myx 2105T was less than 42 %. On the basis of the phylogenetic inference and phenotypic data, strain KBP-30T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter paludis sp. nov. is proposed. The type strain is KBP-30T ( = LMG 27293T = KCTC 32237T).
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- Other Bacteria
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Multigene characterization of a new ‘Candidatus Phytoplasma rubi’-related strain associated with blackberry witches’ broom
A new phytoplasma was identified in naturally infected blackberry plants exhibiting witches’ broom symptoms in Portugal. The 16S rRNA gene sequence revealed that it is related to ‘Candidatus Phytoplasma rubi’ (16SrV-E ribosomal subgroup) and RFLP analysis revealed a unique profile following MseI endonuclease digestion of R16F2n/R2 amplicons that distinguished it from the strains belonging to previously established 16SrV phytoplasma subgroups. The in silico restriction analyses confirmed that the phytoplasma strain from blackberry is different from all the other strains reported in group 16SrV. Phylogeny of the 16S rRNA gene sequences, sequence analyses of 16S–23S, tuf, rplV-rpsC, rplF-rplR, rplO-SecY-map and uvrB-degV genetic loci, as well as the variability of unique oligonucleotide sequences defined for ‘Candidatus Phytoplasma rubi’ confirmed the uniqueness of this phytoplasma strain from Portugal for which a novel ribosomal subgroup, 16SrV-I, is proposed. The representative of this new subgroup was named blackPort phytoplasma (Portuguese blackberry phytoplasma).
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Borrelia bissettiae sp. nov. and Borrelia californiensis sp. nov. prevail in diverse enzootic transmission cycles
Two species of the genus Borrelia, Borrelia bissettiae sp. nov. and Borrelia californiensis sp. nov., were first described by Postic and co-workers on the basis of genetic analyses of several loci. Multilocus sequence analysis of eight housekeeping loci confirmed that these two Borrelia genomospecies are distinct members of the Borrelia burgdorferi sensu lato complex. B. bissettiae sp. nov. was initially described in transmission cycles involving Neotoma fuscipes wood rats and Ixodes pacificus ticks in California, and Neotoma mexicana and Ixodes spinipalpis in Colorado. The preferred host of B. californiensis sp. nov. appears to be the California kangaroo rat, Dipodomys californicus; Ixodes jellisoni, I. spinipalipis and I. pacificus ticks are naturally infected with it. Thus, the ecological associations of the two genomospecies and their genetic distance from all other known Borrelia genomospecies species justify their description as separate genomospecies: B. bissettiae sp. nov. (type strain DN127T = DSM 17990T = CIP 109136T) and B. californiensis (type strain CA446T = DSM 17989T = ATCC BAA-2689T).
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Reclassification of Anaerobaculum mobile, Anaerobaculum thermoterrenum, Anaerobaculum hydrogeniformans as Acetomicrobium mobile comb. nov., Acetomicrobium thermoterrenum comb. nov. and Acetomicrobium hydrogeniformans comb. nov., respectively, and emendation of the genus Acetomicrobium
More LessTaking into account their 16S rRNA gene sequences, it appears that Acetomicrobium flavidum and the three species of the genus Anaerobaculum described so far belong to the same phylogenetic clade with high levels (>95 %) of similarity. In this respect, these three Anaerobaculum species should be reclassified within the genus Acetomicrobium, which has priority over the genus Anaerobaculum, which was validated since the genus Acetomicrobium. The DNA G+C content of Acetomicrobium flavidum is 47.1 mol%, which is of the same order as that of the three Anaerobaculum species. All these bacteria have in common iso-C15 : 0 as their main fatty acid. Based on further phylogenetic, genetic and chemotaxonomic studies, we propose that Anaerobaculum mobile ( = DSM 13181T = JCM 12221T), Anaerobaculum thermoterrenum ( = DSM 13490T = ACM 5076T) and Anaerobaculum hydrogeniformans ( = DSM 22491T = ATCC BAA-1850T) be reclassified as Acetomicrobium mobile comb. nov., Acetomicrobium thermoterrenum comb. nov. and Acetomicrobium hydrogeniformans comb. nov., respectively. The four bacterial species belong to the phylum Synergistetes.
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- Eukaryotic micro-organisms
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Trichosporon heliocopridis sp. nov., a urease-negative basidiomycetous yeast associated with dung beetles (Heliocopris bucephalus Fabricius)
Ninety-six yeast isolates associated with dung beetles (Heliocopris bucephalus Fabricius) were examined based on a culture-dependent method. A comparison of the colony morphology and PCR-fingerprints obtained by (GTG)5 microsatellite-primed PCR indicated that 84 of these isolates belonged to one group. Five strains (DD1-1T, DD2-33, DD4-11, DD5-15 and DD6-1) were selected as the representatives of this main group, where each of the five selected strains had been derived from a different dung beetle collected in northern Thailand. A comparison of the D1/D2 domain sequence of the large subunit rRNA gene (LSU D1/D2) and the internal transcribed spacer (ITS) sequences revealed that these five strains were the same and were related to the genus Trichosporon. Phylogenetic analysis based on the LSU D1/D2 plus ITS sequences placed this group within the Trichosporon brassicae clade, but it was clearly separated from any known species. In addition, physiological tests showed that this group had the unusual property of the inability to hydrolyse urea, which was distinctly different from the related taxon. Therefore a novel yeast species named Trichosporon heliocopridis sp. nov. (ex-type strain DD1-1T = TISTR 5946T = JCM 30786T = CBS 14168T) is proposed. The MycoBank number is MB812098.
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Starmerella orientalis f.a., sp. nov., an ascomycetous yeast species isolated from flowers
Four strains of a novel ascomycetous yeast species were isolated from flowers in Iran and China. Phylogenetic analysis of the sequences of the ITS region (including 5.8S rRNA gene) and the LSU rRNA gene D1/D2 domains indicated that these strains belong to the Starmerella clade and show divergence from previously described species in this clade. Growth reactions on carbon and nitrogen sources were similar to those observed in related species of the Starmerella clade. Sexual reproduction was not observed after mating tests on different sporulation media. Based on physiological characteristics and phylogeny of rRNA gene sequences, the novel species is most closely related to Candida (iter. nom. Starmerella) powellii and Candida (iter. nom. Starmerella) floricola. It is therefore assigned to the genus Starmerella and described as Starmerella orientalis f.a., sp. nov. The type strain is SAM09T ( = IBRC-M 30204T = CBS 14142T). The MycoBank accession number is MB 814379.
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Prototheca miyajii sp. nov., isolated from a patient with systemic protothecosis
More LessSpecies of the genus Prototheca are achlorophyllous algae and ubiquitous in nature, and so far, six species have been listed in this genus: Prototheca wickerhamii, Prototheca zopfii, Prototheca blaschkeae, Prototheca cutis, Prototheca stagnora and Prototheca ulmea. A strain of the genus Prototheca, IFM 53848T, was isolated in Japan from a patient with systemic protothecosis and had been designated P. wickerhamii. Our previous study, by using PCR analysis, revealed that its SSU rRNA gene (rDNA) was distinctively larger than that of P. wickerhamii and other species of the genus Prototheca. In this study, molecular analysis showed that the exceptionally large SSU rDNA of IFM 53848T contains four group I introns. The morphology of IFM 53848T was indistinguishable from those of P. wickerhamii or P. cutis, and phylogenetic analyses, based on the sequences of the SSU rDNA exons and the D1/D2 region of the large subunit rDNA, indicated that IFM 53848T was closely related to P. cutis. On the other hand, unlike P. cutis, IFM 53848T failed to assimilate fructose or lysine and grew well at higher temperatures of up to 42 °C. In addition, the nucleotide sequence of the ribosomal internal transcribed spacer and the matrix assisted laser desorption ionization time-of-flight mass spectrometry profile of IFM 53848T were clearly distinct from those of P. cutis. The results strongly suggest that IFM 53848T represents a novel species, and so the seventh member of the genus Prototheca, which we have named Prototheca miyajii sp. nov. The unique characteristics of the strain may provide useful insights into the systematic taxonomy of the genus Prototheca.
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- EVOLUTION, PHYLOGENY AND BIODIVERSITY
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Complete genome sequence and cell structure of Limnochorda pilosa, a Gram-negative spore-former within the phylum Firmicutes
More LessLimnochorda pilosa is a pleomorphic facultative anaerobe and the sole species in the class Limnochordia, which has tentatively been placed in the phylum Firmicutes. In the present study, the complete genome sequence of L. pilosa HC45T was obtained and analysed. The genome size was 3.82 Mbp and the DNA G+C content was 69.73 %. Phylogenetic analyses based on the 30S-50S ribosomal proteins and 23S rRNA gene consistently indicated that L. pilosa is phylogenetically isolated from the other members of the phylum Firmicutes. Ultrastructural observation revealed that L. pilosa possesses a Gram-negative-type cell wall and the capacity to form endospores. Accordingly, the L. pilosa genome has characteristics that are specific to Gram-negative bacteria and contains many genes that are involved in sporulation. On the other hand, several sporulation genes were absent from the L. pilosa genome although they have been regarded as essential for the endospore-forming system of members of the phylum Firmicutes. The gyrB gene of L. pilosa possesses an intein sequence. The genome has a high percentage of GTG start codons and lacks several conserved genes related to cell division.
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Volumes and issues
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Volume 74 (2024)
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