- Volume 68, Issue 4, 2018
Volume 68, Issue 4, 2018
- Editorial
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- Notification List
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- New Taxa
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- Actinobacteria
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Actinorectispora metalli sp. nov., a novel actinomycete isolated from a mine and emended description of the genus Actinorectispora
More LessA novel actinomycete, designated strain KC 198T, was isolated from rare earth mine. The results of analysis of the 16S rRNA gene sequence indicated that KC 198T was most closely related to Actinorectispora indica YIM 75728T (98.4 %). Aerial hyphae differentiated into long, straight chains of cylindrical spores. Growth was observed at 10–45 °C (optimum 28 °C), with 0–10 % (w/v) NaCl (optimum, in the absence of NaCl) and at pH 6.0–8.0 (optimum pH 7.0). KC 198T possessed MK-9(H4) as the predominant respiratory quinone and a minor amount of MK-10(H4). Polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. Three unidentified lipids were also detected. The main cellular fatty acids were iso-C16 : 0 (30.9 %), iso-C16 : 1H (22.9 %) and iso-C15 : 0 (14.8 %). The genomic DNA G+C content was 66.8 mol%. On the basis of the phenotypic and genotypic characteristics, we propose that strain KC 198T represents a novel species of the genus Actinorectispora . The name Actinorectispora metalli sp. nov. is, therefore, proposed for the novel species with the type strain KC 198T (=CCTCC AA 2015043T=KCTC 39718T). The description of the genus Actinorectispora has also been emended.
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Microbacterium telephonicum sp. nov., isolated from the screen of a cellular phone
A cultivation-based study of the microbial diversity of cellular phone screens led to the isolation of a Gram-stain-positive, aerobic, rod-shaped and non-endospore-forming bacterium, designated S2T63T, exhibiting phenotypic and genotypic characteristics unique to the type strains of closely related species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain is a member of Microbacterium , and most closely related to Microbacterium aurantiacum IFO 15234T and Microbacterium kitamiense Kitami C2T. The DNA–DNA relatedness values of the strain S2T63T to M. aurantiacum KACC 20510T, M. kitamiense KACC 20514Tand Microbacterium laevaniformans KACC 14463T were 65 % (±4), 29.5 % (±3) and 55.9 % (±4), respectively. The genomic DNA G+C content was 71.8 mol%. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified polar lipids. The peptidoglycan contained the amino acids glycine, lysine, alanine and glutamic acid, with substantial amounts of hydroxy glutamic acid detected, which is characteristic of peptidoglycan type B1α. The predominant menaquinones were MK-12 and MK-13. Rhamnose, fucose and galactose were the whole-cell sugars detected. The strain also showed biofilm production, estimated by using crystal violet assay. Based on the results of the phenotypic and genotypic characterizations, it was concluded that the new strain represents a novel species of the genus Microbacterium , for which the name Microbacteriumtelephonicum is proposed, with S2T63T (=MCC 2967T=KACC 18715T=LMG 29293T) as the type strain.
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Tessaracoccus aquimaris sp. nov., isolated from the intestine of a Korean rockfish, Sebastes schlegelii, from a marine aquaculture pond
A novel coccus-shaped, Gram-stain-positive, non-motile and aerobic bacterium, designated strain NSG39T, was isolated from the intestine of a Korean rockfish, Sebastes schlegelii. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the newly isolated strain NSG39T was closely related to Tessaracoccus flavus RP1T (98.0 %). The isolate grew at 15–37 °C, pH 7–9 and 0–4 % (w/v) salinity, with optimal growth at 30 °C, pH 8 and 0 % (w/v) salinity. The cell wall of the organism contained ll-diaminopimelic acid as a diagnostic diamino acid, and ribose, mannose, glucose and galactose as diagnostic sugars. The polar lipid comprised diphosphatidylglycerol, phosphatidylglycerol, three glycolipids and four unidentified polar lipids. The major cellular fatty acid was anteiso-C15 : 0 (47.2 %). The major menaquinone was MK-9 (H4). The DNA G+C content of the isolate was 68.8 mol%. The genome-based orthologous average nucleotide identity value for strain NSG39T and T. flavus RP1T was 76.6 %. Based on the phylogenetic analysis and its biological characteristics, strain NSG39T is considered to represent a novel species of the genus Tessaracoccus , for which the name Tessaracoccus aquimaris is proposed. The type strain is NSG39T (=KACC 17540T=JCM 19289T).
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Micromonospora globbae sp. nov., an endophytic actinomycete isolated from roots of Globba winitii C. H. Wright
More LessA novel endophytic actinomycete, strain WPS1-2T, isolated from a root of Globba winitii C. H. Wright, was characterized taxonomically by using a polyphasic approach. Strain WPS1-2T exhibited identical characteristics to the members of the genus Micromonospora . Single spores were observed directly on substrate mycelia. The cell-wall peptidoglycan of the strain contained meso-diaminopimelic acid and 3-OH-meso-diaminopimelic acid. Whole-cell hydrolysates contained glucose, ribose, arabinose and xylose. The predominant menaquinones were MK-10(H8) and MK-10(H10). The major cellular fatty acids consisted of iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0. According to the 16S rRNA gene sequence of the strain, WPS1-2T showed highest similarity to Micromonospora costi CS1-12T (99.02 %). Phylogenetic analysis of the gyrase subunit B (gyrB) gene indicated that the strain was related to M. costi CS1-12T. The DNA G+C content was 73.7 mol%. The strain could be distinguished from closely related type strains by using a combination of morphological, chemotaxonomic, physiological and biochemical data together with DNA–DNA relatedness values. Based on these observations, strain WPS1-2T is considered to represent a novel species of the genus Micromonospora , for which the name Micromonospora globbae sp. nov. is proposed. The type strain is WPS1-2T (=KCTC 39787T=NBRC 112325T=TISTR 2405T).
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Frankia saprophytica sp. nov., an atypical, non-infective (Nod–) and non-nitrogen fixing (Fix–) actinobacterium isolated from Coriaria nepalensis root nodules
More LessStrain CN3T, a Coriaria nepalensis isolate, appears to form hyphae and sporangia typical of members fo the genus Frankia . However, it failed to form vesicles, to reduce acetylene and to induce nodules on its original host plant. A polyphasic approach was used here to determine the taxonomic status of strain CN3T. The 16S rRNA gene sequence of strain CN3T showed the highest sequence identity with Frankia asymbiotica type strain M16386T (99.4 %). Digital DNA–DNA hybridization between strains CN3T and M16386T was 25.7 %, which is clearly below the accepted cut-off point of 70 %. The G+C content of DNA was 71.8 mol%. Whole-cell hydrolysates of strain CN3T were rich in meso-diaminopimelic acid. Cell-wall sugars were composed of galactose, glucose, mannose, rhamnose and traces of ribose. The polar lipid profile contained phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, phosphoglycolipids, phospholipid, six uncharacterized glycolipids and two uncharacterized lipids. The predominant menaquinone (>25 %) was MK-9(H6). Major fatty acids (>15 %) of strain CN3T consisted of iso-C16 : 0, C17 : 1ω8c and C15 : 0. Based on 16S rRNA gene phylogeny, genome sequence analysis and phenotypic results, strain CN3T (=DSM 105290T=CECT 9314T) is proposed to represent the type strain of a novel species, Frankia saprophytica sp. nov.
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Jatrophihabitans telluris sp. nov., isolated from sediment soil of lava forest wetlands and the emended description of the genus Jatrophihabitans
A novel actinobacterial strain, designated N237T, was isolated from sediment soil of wetlands at Meonmulkkak, Dongbaek-Dongsan, the lava forest, Gotjawal, Jeju, Republic of Korea. Cells of strain N237T were Gram-stain-positive, non-motile rods and formed pale yellow colonies on ten-fold diluted Reasoner’s 2A agar. Strain N237T contained iso-C16 : 0 and C17 : 1 ω8c as the major fatty acids, MK-9(H4) as the predominant isoprenoid quinone and meso-DAP as the diamino acid in the peptidoglycan. It contained diphosphatidylglycerol, phosphatidylinositol polymannosides, an unidentified phospholipid, an unidentified aminophospholipid, an unidentified aminolipid, two unidentified glycophospholipids, three unidentified glycolipids and two unidentified lipids as polar lipids. The DNA G+C content was 68.1 mol%. Strain N237T formed a separate lineage in the genus Jatrophihabitans , as demonstrated by phylogenetic analysis based on 16S rRNA sequencing. It was most closely related to Jatrophihabitans soli KIS75-12T (95.6 % sequence similarity). The combined phenotypic, chemotaxonomic and phylogenetic characteristics supported the conclusion that strain N237T represents a novel species in the genus Jatrophihabitans , for which the name Jatrophihabitans telluris sp. nov. is proposed. The type strain is N237T (=KCTC 39922T=NRRL B-65477T).
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Georgenia deserti sp. nov., a halotolerant actinobacterium isolated from a desert sample
Strain SYSU D8004T was isolated from a sample collected from an arid area in Saudi Arabia. The isolate was Gram-stain-positive, non-motile, aerobic and non-spore-forming. It could grow at 4–45 °C, at pH 6.0–10.0 and in the presence of up to 17 % (w/v) NaCl. Pairwise comparison of the 16S rRNA gene sequences indicated that strain SYSU D8004T shared highest sequence similarity with Georgenia halophila YIM 93316T (96.5 %). Menaquinone MK-8(H4) was detected as the respiratory quinone. The polar lipid profile of strain SYSU D8004T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two phosphatidylinositol mannosides, two unidentified phospholipids and an unidentified glycolipid. Strain SYSU D8004T contained anteiso-C15 : 0, iso-C15 : 0 and C14 : 0 as the predominant fatty acids (>10 %). Galactose, glucose and rhamnose were detected as whole-cell sugars. Based on analyses of the phenotypic, genotypic and phylogenetic characteristics, it was determined that strain SYSU D8004T could be differentiated from other closely related members of the genus Georgenia . Strain SYSU D8004T is therefore considered to represent a novel species of the genus Georgenia , for which the name Georgenia deserti sp. nov. is proposed. The type strain is SYSU D8004T (=CGMCC 1.15793T=KCTC 39987T).
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Parolsenella catena gen. nov., sp. nov., isolated from human faeces
More LessStrain 2CBEGH3T, which is an obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-stain-positive coccobacillus, was isolated from a faecal sample of a healthy Japanese man. The 16S rRNA gene sequence analysis showed that strain 2CBEGH3T represented a member of the family Atopobiaceae and formed a monophyletic cluster with Olsenella uli DSM 7084T (93.6 % sequence similarity), Olsenella umbonata strain lac31T (93.0 %), Olsenella profusa JCM 14553T (92.7 %) and Olsenella scatoligenes strain SK9K4T (92.7 %) as closest neighbours and Atopobium species. The hsp60 gene sequence analysis supported the phylogenetic relationships based on the 16S rRNA gene sequences, with sequence similarity values of 82.1–84.7 % to the four species described above. A unique three-base (one amino acid residue) insertion was found in the alignment regions of the hsp60 gene sequence of strain 2CBEGH3T. The major end products from d-glucose were d- and l-lactic acids produced at the ratio of 75 : 25, while four species of the genus Olsenella produced d- and l-lactic acids at ratios of 94–98 : 2–6. The isolate formed characteristic crater-like colonies on Eggerth–Gagnon agar plates. The major cellular fatty acids were C18 : 1ω9c, C18 : 1ω9c dimethyl acetal (DMA) and C16 : 0 DMA. The G+C content of the genomic DNA was 68.4 mol%. On the basis of these data, strain 2CBEGH3T represents a novel species in a novel genus of the family Atopobiaceae, for which the name Parolsenella catena gen. nov., sp. nov. is proposed. The type strain of P. catena is 2CBEGH3T (=JCM 31932T=DSM 105194T).
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Cryobacterium aureum sp. nov., a psychrophilic bacterium isolated from glacier ice collected from the ice tongue surface
More LessA psychrophilic, Gram-stain-positive, rod-shaped bacterium, designated strain Hh31T, was isolated from Xinjiang No. 1 Glacier in China. Strain Hh31T was catalase-positive, oxidase-negative and able to grow at between 0–18 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Hh31T belonged to the genus Cryobacterium and was most closely related to the type strains of Cryobacterium levicorallinum , Cryobacterium luteum and Cryobacterium flavum . DNA–DNA hybridization, calculation of average nucleotide identity and digital DNA–DNA hybridization revealed that strain Hh31T was distinct from its closest phylogenetic neighbours. The major cellular fatty acids of strain Hh31T were anteiso-C15 : 0, anteiso-C15 : 1, iso-C15:0, iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinones of strain Hh31T were MK-9 and MK-10. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, one unidentified phospholipid, one unidentified glycolipid and another unidentified lipid. Physiological tests such as carbon source utilization, showed phenotypic differentiation of strain Hh31T from the closest related phylogenetic neighbours. Based on a polyphasic approach, a novel species, Cryobacterium aureum sp. nov., is proposed, with Hh31T (=NBRC 107882T=CGMCC 1.11213T) as the type strain.
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Blastococcus xanthinilyticus sp. nov., isolated from monument
A novel, non-motile, coccoid, Gram-stain-positive actinobacterium, designated BMG 862T, was isolated from a marble sample collected from the Bulla Regia monument, Northern Tunisia. Its taxonomic position was determined using a polyphasic approach. Results from chemotaxonomic analyses showed MK-9(H4), MK-8(H4) and MK-9(H2) as the predominant menaquinones. The major polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, hydroxy-phosphatidylethanolamine and three unidentified phospholipids. The fatty acids consisted of significant amounts (≥10 %) of iso-C16 : 0, C17 : 1ω8c, iso-C15 : 0 and C16 : 1ω7c. Phylogenetic analysis on the basis of 16S rRNA gene sequence comparisons showed that strain BMG 862T belongs to the genus Blastococcus , being most closely related to Blastococcus saxobsidens (=DSM 44509T) (99.5 %) and Blastococcus capsensis (=DSM 46835T=CECT 8876T) (99.3 %). The genomic DNA G+C content of the organism was 74.7 mol%. Results of DNA–DNA hybridization and physiological tests allowed differentiation of strain BMG 862T from related species. The strain was also characterized by its ability to hydrolyse xanthine. On the basis of phenotypic and molecular characteristics, strain BMG 862T (=DSM 46842T=CECT 8884T) represents the type strain of a novel species of the genus Blastococcus , for which the name Blastococcus xanthinilyticus sp. nov. is proposed.
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Stackebrandtia soli sp. nov., a novel actinobacterium isolated from a soil sample
An aerobic actinobacterium, strain AN130378T, was isolated from a soil sample collected in Korea and subjected to taxonomic investigation using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain AN130378T is a member of the genus Stackebrandtia , with sequence similarities of 97.3 % to Stackebrandtia albiflava YIM 45751T and 97.1 % to Stackebrandtia endophytica YIM 64602T. The whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid, and galactose, glucose and xylose. The major menaquinones were MK-11(H4), MK-10(H4) and MK-11(H6), while the major fatty acids were identified as iso-C15 : 0, anteiso-C17 : 0, anteiso-C15 : 0, iso-C17 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanolamine, an unidentified aminophospholipid, four unidentified glycolipids, three unidentified phospholipids and two unidentified polar lipids. The G+C content of the genomic DNA was determined to be 67.7 mol%. All chemotaxonomic and genotypic data indicated that the strain belongs to the genus Stackebrandtia . On the basis of morphological, chemotaxonomic data and phylogenetic analysis, strain AN130378T is considered to represent a novel species within the genus Stackebrandtia , for which the name Stackebrandtia soli sp. nov. is proposed. The type strain is AN130378T (=DSM 103573T=KCTC 39809T).
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Glycomyces anabasis sp. nov., a novel endophytic actinobacterium isolated from roots of Anabasis aphylla L.
A novel endophytic actinobacterium, designated strain EGI 6500139T, was isolated from the surface-sterilized roots of Anabasis aphylla L., collected from Xinjiang, northwest PR China, and subjected to polyphasic taxonomic characterization. Strain EGI 6500139T formed sparse aerial mycelium with rod-like spores. Whole-cell hydrolysates of the isolate contained meso-diaminopimelic acid as the cell-wall diamino acid, glucose as major sugar, and mannose, galactose, xylose and ribose as minor sugars. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified glycolipid, one unidentified phospholipid and four unidentified polar lipids. The major fatty acids identified were anteiso-C17 : 0, anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0. The predominant menaquinones detected were MK-11 and MK-11(H2). The G+C content of the genomic DNA of strain EGI 6500139T was 70.4 mol%. Strain EGI 6500139T showed the highest 16S rRNA gene sequence similarity to Glycomyces lacisalsi XHU 5089T (96.3 %). Phylogenetic analysis showed that strain EGI 6500139T fell within the clade of the genus Glycomyces , and formed a clade with G. lacisalsi XHU 5089T and G. albus CCTCC AA 2013004T. Based on phenotypic, chemotaxonomic and phylogenetic data, strain EGI 6500139T represents a novel species of the genus Glycomyces , for which the name Glycomyces anabasis sp. nov. (type strain EGI 6500139T=JCM 30088T=KCTC 29495T) is proposed.
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Pseudonocardia soli sp. nov., isolated from mountain soil
More LessA novel actinomycete, designated strain NW8-21T, was isolated from mountain soil in Mae-Wong National Park, Nakornsawan province, Thailand, and was taxonomically characterized by using a polyphasic approach. Based on 16S rRNA gene sequence analysis, the strain was revealed to have the closest similarity to Pseudonocardia endophytica YIM 56035T with the highest 16S rRNA gene sequence similarity value of 98.7 %, followed by Pseudonocardia nantongensis KLBMP 1282T (98.0 %). The chemotaxonomic properties, i.e. arabinose and galactose as the diagnostic reducing sugar in cells, MK-8 (H4) as a major menaquinone, iso-C16 : 0 as the main cellular fatty acid component and phosphatidylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol, phosphatidylcholine as the characteristic phospholipids, confirmed a taxonomic affiliation of the strain that was consistent with those of the genus Pseudonocardia . Several phenotypic differences and the DNA–DNA hybridization results (less than 40 % relatedness value) indicated that strain NW8-21T shoud be considered to represent a novel species of the genus Pseudonocardia , for which the name Pseudonocardia soli is proposed. The type strain is strain NW8-21T (=BCC 58125T=NBRC 109519T).
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Marmoricola silvestris sp. nov., a novel actinobacterium isolated from alpine forest soil
More LessA Gram-stain-positive, flagellated, catalase- and cytochrome c oxidase-positive bacterial strain, designated S20-100T, was isolated from alpine forest soil. Growth occurred at a temperature range of 0–30 °C, at pH 6–9 and in the presence of 0–1 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain S20-100T was related to the genus Marmoricola and had the highest 16S rRNA gene sequence similarity to Marmoricola ginsengisoli Gsoil 097T (98.4 %) and Marmoricola solisilvae KIS18-7T (98.3 %). The cell-wall peptidoglycan of strain S20-100T contained ll-diaminopimelic acid (ll-Dpm) as the diagnostic diamino acid and was of the type A3γ ll-Dpm – Gly. The strain contained MK-8(H4) as the predominant isoprenoid quinone and diphosphatidylglycerol, phosphatidylglycerol, four unidentified phospholipids and three unidentified lipids in lower amounts. The major cellular fatty acids (>10 %) were iso-C16 : 0, C17 : 1ω6c and C18 : 1ω9c. The genomic DNA G+C content was 66.2 mol%. Combined data of phylogenetic, phenotypic and chemotaxonomic analyses demonstrated that strain S20-100T represents a novel species of the genus Marmoricola , for which the name Marmoricola silvestris sp. nov. is proposed. The type strain is S20-100T (=DSM 104694T=LMG 30008T).
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Amnibacterium endophyticum sp. nov., an endophytic actinobacterium isolated from Aegiceras corniculatum
A Gram-stain-positive, aerobic, non-motile, non-spore-forming and short-rod-shaped actinobacterium, designated strain 1T4Z-3T, was isolated from a piece of surface-sterilized branch of Aegiceras corniculatum collected from the Cotai Ecological Zones in Macao, China. Comparative 16S rRNA gene sequence analysis showed that strain 1T4Z-3T was clearly affiliated to the genus Amnibacterium and exhibited 97.9 % gene sequence similarity to Amnibacterium kyonggiense JCM 16463T, 97.3 % gene sequence similarity to Amnibacterium soli JCM 19015T and less than 96.4 % gene sequence similarities to other genera of the family Microbacteriaceae. Strain 1T4Z-3T had L-2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid. The major fatty acids (>10 % of total fatty acids) were iso-C16 : 0 (46.6 %) and anteiso-C15 : 0 (27.3 %). The predominant menaquinones of strain 1T4Z-3T were MK-11 (81.4 %) and MK-12 (14.1 %). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, six unidentified glycolipids, four unidentified phospholipids and two unidentified lipids. The DNA G+C content of strain 1T4Z-3T was 71.4 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic features, strain 1T4Z-3T is considered to represent a novel species of the genus Amnibacterium , for which the name Amnibacterium endophyticum sp. nov. is proposed. The type strain of Amnibacterium endophyticum is 1T4Z-3T (=KCTC 39983T=CGMCC 1.16066T).
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Reclassification of Arthrobacter nasiphocae (Collins et al. 2002) as Falsarthrobacter nasiphocae gen. nov., comb. nov.
More LessThe original description of Arthrobacter nasiphocae M597/99/10T demonstrated that it is distantly related to the type species of the genus Arthrobacter, Arthrobacter globiformis, and that this phylogenetic relationship is reflected by the distinct peptidoglycan type [Lys-Ala2-Gly2-3-Ala(Gly)] and the features of the quinone system, which is composed of menaquinones MK-9(H2) and MK-8(H2). Here, we report a re-evaluation of the taxonomic status of A. nasiphocae. Phylogenetically, it was observed to be only distantly related to the genus Arthrobacter and to the type species of related genera. Re-analysis confirmed the quinone system menaquinones MK-9(H2) and MK-8(H2) in A. nasiphocae. Analysis of cell polar lipids showed a profile consisting of the predominant lipids diphosphatidylglycerol, phosphatidylglycerol, dimannosylglyceride, an unidentified phospholipid and an unidentified aminophosphoglycolipid, and several minor unidentified lipids. This profile clearly is different from that of Arthrobacter species. The cell fatty acid profile also showed characteristics that distinguished A. nasiphocae from Arthrobacter species. The phylogenetic distance of A. nasiphocae from any type species of genera within the family Micrococcaceae and the distinct chemotaxonomic traits warrant the reclassification of A. nasiphocae within a novel genus, for which we propose the name Falsarthrobacter nasiphocae gen. nov., comb. nov. The type strain is M597/99/10T (=CCUG 42953T=CIP 107054T=DSM 13988T=JCM 11677T).
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- Archaea
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Saccharolobus caldissimus gen. nov., sp. nov., a facultatively anaerobic iron-reducing hyperthermophilic archaeon isolated from an acidic terrestrial hot spring, and reclassification of Sulfolobus solfataricus as Saccharolobus solfataricus comb. nov. and Sulfolobus shibatae as Saccharolobus shibatae comb. nov.
More LessA novel hyperthermophilic archaeon of strain HS-3T, belonging to the family Sulfolobaceae , was isolated from an acidic terrestrial hot spring in Hakone Ohwaku-dani, Japan. Based on 16S rRNA gene sequence analysis, the closest phylogenetic relatives of strain HS-3T were, first, Sulfolobus solfataricus (96.4 %) and, second, Sulfolobus shibatae (96.2 %), indicating that the strain belongs to the genus Sulfolobus . However, the sequence similarity to the type species of the genus Sulfolobus ( Sulfolobus acidocaldarius ) was remarkably low (91.8 %). In order to determine whether strain HS-3T belongs to the genus Sulfolobus , its morphological, biochemical and physiological characteristics were examined in parallel with those of S. solfataricus and S. shibatae . Although there were some differences in chemolithotrophic growth between strain HS-3T, S. solfataricus and S. shibatae , their temperature, pH and facultatively anaerobic characteristics of growth, and their utilization of various sugars were almost identical. In contrast, the utilization of various sugars by S. acidocaldarius was quite different from that of HS-3T, S. solfataricus and S. shibatae . Phylogenetic evidence based on the 16S and the 23S rRNA gene sequences also clearly distinguished the monophyletic clade composed of strain HS-3T, S. solfataricus , and S. shibatae from S. acidocaldarius . Based on these results, we propose a new genus and species, Saccharolobus caldissimus gen. nov., sp. nov., for strain HS-3T, as well as two reclassifications, Saccharolobus solfataricus comb. nov. and Saccharolobus shibatae comb. nov. The type strain of Saccharolobus caldissimus is HS-3T (=JCM 32116T and InaCC Ar80T). The type species of the genus is Saccharolobus solfataricus.
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Methanolobus psychrotolerans sp. nov., a psychrotolerant methanoarchaeon isolated from a saline meromictic lake in Siberia
A psychrotolerant, methylotrophic methanogen, strain YSF-03T, was isolated from the saline meromictic Lake Shira in Siberia. Cells of strain YSF-03T were non-motile, irregular cocci and 0.8–1.2 µm in diameter. The methanogenic substrates utilized by strain YSF-03T were methanol and trimethylamine. The temperature range of growth for strain YSF-03T was from 0 to 37 °C. The optimum growth conditions were 30–37 °C, pH 7.0–7.4 and 0.17 M NaCl. The G+C content of the genome of strain YSF-03T was 41.3 mol%. Phylogenetic analysis revealed that strain YSF-03T was most closely related to Methanolobus profundi MobMT (98.15 % similarity in 16S rRNA gene sequence). Genome relatedness between strain YSF-03T and MobMT was computed using the Genome-to-Genome Distance Calculator and average nucleotide identity, which gave values of 23.5 and 79.3 %, respectively. Based on the morphological, phenotypic, phylogenetic and genomic relatedness data presented here, it is evident that strain YSF-03T represents a novel species of the genus Methanolobus , for which the name Methanolobus psychrotolerans sp. nov. is proposed. The type strain is YSF-03T (=BCRC AR10049T=DSM 104044T=NBRC 112514T).
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- Bacteroidetes
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Raineya orbicola gen. nov., sp. nov. a slightly thermophilic bacterium of the phylum Bacteroidetes and the description of Raineyaceae fam. nov.
An isolate, designated SPSPC-11T, with an optimum growth temperature of about 50 °C and an optimum pH for growth between 7.5 and 8.0, was recovered from a hot spring in central Portugal. Based on phylogenetic analysis of its 16S rRNA sequence, the new organism is most closely related to the species of the genus Thermonema but with a pairwise sequence similarity of <85 %. The isolate was orange-pigmented, formed non-motile long filaments and rod-shaped cells that stain Gram-negative. The organism was strictly aerobic, oxidase-positive and catalase-positive. The major fatty acids were iso-C15:0, iso-C15 : 0 2-OH and iso-C17 : 0 3-OH. The major polar lipids were one aminophospholipid, two aminolipids and three unidentified lipids. Menaquinone 7 was the major respiratory quinone. The DNA G+C content of strain SPSPC-11T was 37.6 mol% (draft genome sequence). The high quality draft genome sequence corroborated many of the phenotypic characteristics of strain SPSPC-11T. Based on genotypic, phylogenetic, physiological and biochemical characterization we describe a new species of a novel genus represented by strain SPSPC-11T (=CECT 9012T=LMG 29233T) for which we propose the name Raineya orbicola gen. nov., sp. nov. We also describe the family Raineyaceae to accommodate this new genus and species.
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Aquimarina spongiicola sp. nov., isolated from spongin
More LessA Gram-reaction-negative, aerobic, motile by gliding, non-spore-forming, rod-shaped bacterial strain, designated 122CH820-2T, was isolated from spongin. This bacterium was characterized to determine its taxonomic position by using a polyphasic approach. Strain 122CH820-2T grew well at 25–30 °C on marine agar. On the basis of 16S rRNA gene sequence similarity, strain 122CH820-2T belonged to the family Flavobacteriaceae and was closely related to Aquimarina mytili PSC33T (96.8 % sequence similarity) and A. penaei P3-1T (96.7 %). Lower sequence similarities (<96.5 %) were found with all of the other recognized members of the genus Aquimarina . The G+C content of the genomic DNA was 35.2 mol%. The major respiratory quinone was menaquinone MK-6 and the major fatty acids were C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G and iso-C15 : 0 3-OH. The polar lipids were phosphatidylethanolamine, one aminophospholipid and five unidentified polar lipids. Strain 122CH820-2T could be differentiated genotypically and phenotypically from recognized species of the genus Aquimarina . The isolate therefore represents a novel species, for which the name Aquimarina spongiicola sp. nov. is proposed, with the type strain 122CH820-2T (=KACC 19274T=LMG 30078T).
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Sphingobacterium solani sp. nov., isolated from potato stems
More LessA Gram-stain-negative, non-motile, non-spore-forming bacterium, designated MLS-26-JM13-11T, was isolated from potato stems, collected in Guyuan County, Hebei Province, China. Strain MLS-26-JM13-11T could grow at 10–39 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.2) and in the presence of 0–4.0 % (w/v) NaCl (optimum, 1.0 % w/v). Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain MLS-26-JM13-11T formed a stable clade with Sphingobacterium bambusae IBFC2009T and Sphingobacterium griseoflavum SCU-B140T, with the 16S rRNA gene sequence similarities ranging from 95.9 % to 97.0 %. The major cellular fatty acids comprised iso-C15 : 0 (36.9 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 34.0 %), C16 : 0 (3.0 %) and iso-C17 : 0 3-OH (13.4 %). Strain MLS-26-JM13-11T contained sphingoglycolipid, phosphatidyl ethanolamine, six unknown lipids, one unknown aminolipid, four unknown polarlipids and two unknown aminophospholipids. The isoprenoid quinone was MK-7. The DNA G+C content was 42.6 mol%. Furthermore, the average nucleotide identity and in silico estimated DNA–DNA reassociation values among MLS-26-JM13-11T and S. bambusae KCTC 22814T were in all cases below the respective threshold for species differentiation. On the basis of phenotypic, genotypic and phylogenetic evidence, strain MLS-26-JM13-11T (=ACCC 60057T=JCM 32274T) represents a novel species within the genus Sphingobacterium , for which the name Sphingobacterium solani sp. nov. is proposed.
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Adhaeribacter swui sp. nov., isolated from wet mud
More LessStrain 17mud1-7T, a pink, aerobic, catalase-positive, oxidase-positive and Gram-reaction-negative bacterium, was isolated from wet mud. The isolate grew aerobically at 18–37 °C (optimum 28 °C), at pH 6.0–8.0 (optimum pH 7.0) and in the presence of 0–1 % (w/v) NaCl (optimum 0 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 17mud1-7T belonged to the genus Adhaeribacter with highest sequence similarity of 96.4 % to Adhaeribacter aerophilus 6424S-25T. The strain showed the typical chemotaxonomic characteristics of the genus Adhaeribacter , with the presence of menaquinone MK-7 as the respiratory quinone, and summed feature 4 (composed of iso-C17 : 1 I/anteiso-C17 : 1 B), iso-C15 : 0 and C16 : 1 ω5c as the major fatty acids are. The polar lipid profile contained two aminophosphoglycolipids, two glycolipids and three unidentified lipids. The DNA G+C content of strain 17mud1-7T was 45.9 mol%. Strain 17mud1-7T should thus be classified as representing a novel species in the genus Adhaeribacter , for which the name Adhaeribacter swui sp. nov. is proposed. The type strain is 17mud1-7T (=KCTC 52873T=NBRC 112824T).
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Pedobacter mongoliensis sp. nov., isolated from grassland soil
Kai Yuan, Min Cao, Jingxin Li and Gejiao WangA Gram-stain-negative, rod-shaped, motile by gliding and strictly aerobic bacterial strain, named 1-32T, was isolated from soil of the Ordos grassland in Inner Mongolia, PR China. Strain 1-32T showed highest 16S rRNA gene sequence similarities to Pedobacter luteus N7d-4T (95.4 %), Pedobacter oryzae DSM 19973T (95.3 %), ‘ Pedobacter xinjiangensis ' 12157T (95.2 %) and Pedobacter tournemirensis TF5-37.2-LB10T (95.1 %). Phylogenetic analyses clustered strain 1-32T with ‘P. xinjiangensis' 12157T and P. tournemirensis TF5-37.2-LB10T. The DNA G+C content was 43.4 mol%. Menaquinone 7 was the main respiratory quinone. The predominant fatty acids (>5 %) were iso-C15 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and C16 : 1 ω5c. The polar lipids of strain 1-32T comprised phosphatidylethanolamine, two unidentified polar lipids, one unidentified glycolipid and two unidentified phospholipids. Strain 1-32T could be distinguished from the other members of the genus Pedobacter based on its phylogenetic distance and physiological and biochemical characteristics such as being negative for the assimilation of rhamnose and the activity of α-glucosidase. Therefore, strain 1-32T represents a novel species of the genus Pedobacter , for which the name Pedobacter mongoliensis sp. nov. is proposed. The type strain is 1-32T (=KCTC 52859T=CCTCC AB 2017084T).
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Hymenobacter rivuli sp. nov., isolated from a freshwater creek
More LessA bright-red bacterial strain, TAPP3T, was isolated from a freshwater sample taken from the Wanan Creek in Taiwan. Phylogenetic analyses based on 16S rRNA gene sequences revealed that TAPP3T represented a member of the genus Hymenobacter and showed the highest levels of sequence similarity to Hymenobacter ginsengisoli DCY57T (97.0 %) and Hymenobacter marinus KJ035T (96.5 %) and less than 96.2 % with other members of the genus. Cells of TAPP3T were Gram-stain-negative, aerobic, motile by gliding, rods that were surrounded by a thick capsule. Growth occurred at 20–35 °C (optimum, 25–30 °C), at pH 6.5–7.5 (optimum, pH 7) and with 0–1 % NaCl (optimum, 0 %). TAPP3T contained iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 1ω5c as the predominant fatty acids. The major isoprenoid quinone was MK-7. The polar lipid profile consisted of phosphatidylethanolamine, six uncharacterized aminophospholipids and four uncharacterized lipids. The major polyamine was homospermidine. The DNA G+C content of the genomic DNA was 62.8 mol%. The DNA–DNA relatedness of TAPP3T with respect to Hymenobacter ginsengisoli DCY57T was less than 40 %. On the basis of the phylogenetic inference and phenotypic data, TAPP3T should be classified as representing a novel species, for which the name Hymenobacter rivuli sp. nov. is proposed. The type strain is TAPP3T (=BCRC 80979T=LMG 29559T=KCTC 52236T).
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Bizionia berychis sp. nov., isolated from intestinal tract of a splendid alfonsino (Beryx splendens)
A Gram-stain-negative, non-motile, aerobic and rod-shaped bacterial strain, designated RA3-3-1T, was isolated from splendid alfonsino (Beryxsplendens) collected from the North Pacific Ocean. Strain RA3-3-1T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 1.0–3.0 % (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain RA3-3-1T belonged to the genus Bizionia , clustering with the type strain of Bizionia fulviae . Strain RA3-3-1T exhibited 16S rRNA gene sequence similarities of 98.7, 97.6 and 97.3 % to the type strains of B. fulviae , Bizionia paragorgiae and Bizionia saleffrena , respectively, and of 95.5–96.4 % to the type strains of the other Bizionia species. Strain RA3-3-1T contained MK-6 as the predominant menaquinone and anteiso-C15 : 0, iso-C16 : 0 3-OH, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C17 : 0 3-OH, iso-C15 : 0 and C17 : 0 2-OH as the major fatty acids. The major polar lipids detected in strain RA3-3-1T were phosphatidylethanolamine, one unidentified lipid and one unidentified aminolipid. The DNA G+C content of strain RA3-3-1T was 34.1 mol% and its DNA–DNA relatedness values with the type strains of B. fulviae , B. paragorgiae and B. saleffrena were 12–29 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain RA3-3-1T is separate from recognized species of the genus Bizionia . On the basis of the data presented, strain RA3-3-1T is considered to represent a novel species of the genus Bizionia , for which the name Bizionia berychis sp. nov. is proposed. The type strain is RA3-3-1T (=KCTC 62140T=NBRC 113024T).
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Vitellibacter todarodis sp. nov., isolated from intestinal tract of a squid (Todarodes pacificus)
A Gram-stain-negative, non-motile, aerobic and rod-shaped or ovoid bacterial strain, designated MYP2-2T, was isolated from the intestinal tract of a squid (Todarodes pacificus) collected from the East Sea, South Korea, and subjected to a polyphasic taxonomic study. Strain MYP2-2T grew optimally at 30–35 °C and in the presence of 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain MYP2-2T belonged to the genus Vitellibacter . Strain MYP2-2T exhibited 16S rRNA gene sequence similarities of 95.4–96.6 % to the type strains of Vitellibacter species and of less than 94.5 % to the type strains of other recognized species examined. Strain MYP2-2T contained menaquinone MK-6 as the predominant respiratory quinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain MYP2-2T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain MYP2-2T was 41.6 mol%. Differential phenotypic properties, together with its phylogenetic distinctiveness, revealed that strain MYP2-2T is separated from recognized species of the genus Vitellibacter . On the basis of the data presented, strain MYP2-2T is considered to represent a novel species of the genus Vitellibacter , for which the name Vitellibacter todarodis sp. nov. is proposed. The type strain is MYP2-2T (=KCTC 62141T=NBRC 113025T).
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Flavobacterium fluviatile sp. nov., isolated from a freshwater creek
More LessA yellowish-pink-coloured bacterial strain, TAPY14T, was isolated from a freshwater creek in Taiwan. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TAPY14T belonged to the genus Flavobacterium and showed the highest similarity (97.3 %) with respect to Flavobacterium reichenbachii WB 3.2-61T, Flavobacterium ginsengisoli DCY54T and Flavobacterium defluvii EMB117T and less than 97 % with other members of the genus. Cells of strain TAPY14T were Gram-stain-negative, strictly aerobic, motile by gliding and rod-shaped. Optimal growth occurred at 20–30 °C, pH 6 and in the presence of 0.5 % NaCl. Strain TAPY14T contained iso-C15 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids, one uncharacterized phospholipid and one uncharacterized lipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6. The DNA G+C content of the genomic DNA was 38.1 mol%. The DNA–DNA hybridization values for strain TAPY14T with F. reichenbachii DSM 21791T, F. ginsengisoli JCM 17336T and F. defluvii DSM 17963T were less than 30 %. On the basis of the phylogenetic inference and phenotypic data, strain TAPY14T should be classified as a novel species, for which the name Flavobacterium fluviatile sp. nov. is proposed. The type strain is TAPY14T (=BCRC 81012T=LMG 29733T=KCTC 52446T).
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Flavobacterium cyanobacteriorum sp. nov., isolated from cyanobacterial aggregates in a eutrophic lake
More LessA Gram-reaction-negative, aerobic, non-flagellated, non-gliding, rod-shaped and yellow-pigmented bacterium, designated strain TH021T, was isolated from cyanobacterial aggregates in a eutrophic lake, Taihu Lake, China. Optimal growth occurred at pH 7.0 (range: 5.0–10.0), 28 °C (range, 4–32 °C) and 0 % (w/v) NaCl (range, 0–1.0 %) in Reasoner’s 2A broth. No growth was observed at 37 °C. The cells were found to be positive for oxidase and catalase activities. The major respiratory quinone was menaquinone-6. The major fatty acids (>10 %) were identified as iso-C15 : 0 and C16 : 1ω7c/C16 : 1ω6c. The major polar lipid was phosphatidylethanolamine. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was affiliated with the genus Flavobacterium , with the highest sequence similarity found to Flavobacterium hauense BX12T (94.92 %), followed by Flavobacterium suzhouense XIN-1T (94.85 %), Flavobacterium arcticum SM1502T (94.79 %) and Flavobacterium beibuense F44-8T (94.30 %). The genomic G+C content of strain TH021T was 41.9 mol% based on total genome calculations. Average nucleotide identities and digital DNA–DNA hybridizations values for complete genomes ranged from 69.4 to 72.8 and 18.0 to 23.8 % between strain TH021T and strains within the genus Flavobacterium . The phenotypic, chemotaxonomic and phylogenetic properties, and genome analysis suggested that strain TH021T represents a novel species within the genus Flavobacterium , for which the name Flavobacterium cyanobacteriorum sp. nov. is proposed. The type strain is TH021T (=LMG 29720T=CGMCC 1.16325T).
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Proposal of Nemorincola gen. nov. to replace the illegitimate prokaryotic genus name Nemorella Chaudhary et al. 2018
More LessThe prokaryotic genus name Nemorella Chaudhary et al. 2018 is illegitimate because it is a later homonym of the plant genus name Nemorella Ehrhart 1789 [Principle 2 of the Prokaryotic Code (2008 Revision)]. This name is therefore not a correct name (Principle 6). Based on Rule 54 we propose the replacement name Nemorincola with Nemorincola caseinilytica as the type species.
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Aestuariimonas insulae gen. nov., sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, aerobic, non-motile and ovoid or rod-shaped bacterial strain, designated OITF-44T, was isolated from a tidal flat in Oido, an island of the Republic of Korea. Strain OITF-44T grew optimally at 25 °C and in the presence of 2.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain OITF-44T formed an independent lineage within the clade comprising the genera Lutimonas , Taeania , Actibacter and Namhaeicola . The novel strain exhibited 16S rRNA gene sequence similarity values of 93.9–95.7 % to the type strains of the species of the genera Lutimonas , Taeania , Actibacter and Namhaeicola , and of less than 93.5 % to the type strains of other recognized species. Strain OITF-44T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 G, iso-C16 : 1 H and iso-C16 : 0 3-OH as the major fatty acids. The major polar lipids of strain OITF-44T were phosphatidylethanolamine, one unidentified lipid and one unidentified phospholipid. The DNA G+C content of strain OITF-44T was 33.9 mol%. The chemotaxonomic data and other differential phenotypic properties made it reasonable to distinguish strain OITF-44T from the type strains of the type species of the genera Lutimonas , Taeania , Actibacter and Namhaeicola . On the basis of the data presented here, strain OITF-44T is considered to constitute a new genus and species within the family Flavobacteriaceae , for which the name Aestuariimonas insulae gen. nov., sp. nov. is proposed. The type strain of Aestuariimonas insulae is OITF-44T (=KACC 19569T=KCTC 62197T=DSM 105891T=NBRC 113118T).
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- Firmicutes and Related Organisms
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Marinicrinis lubricantis sp. nov., isolated from a coolant lubricant
More LessA Gram-stain-positive, aerobic, endospore-forming bacterium isolated from a coolant lubricant was studied for its taxonomic allocation. On the basis of 16S rRNA gene sequences, strain KSS164-79T shared highest similarity (92.3–92.4 %) to type strains of the species Marinicrinis sediminis, Paenibacillus dongdonensis , Paenibacillus abyssi and Paenibacillus motobuensis . In phylogenetic trees based on the 16S rRNA gene, strain KSS164-79T always formed a distinct cluster with the type strain of M. sediminis . The fatty acid profile supported the grouping of the strain to the genus Marinicrinis . As major fatty acids, anteiso-C15 : 0, iso-C15 : 0 and iso-C16 : 0 were detected. The polar lipid profile contained the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and two unidentified glycolipids. The major quinone was menaquinone MK-7. In addition, physiological and biochemical test results allowed the clear phenotypic differentiation of strain KSS164-79T from M. sediminis . Hence, KSS164-79T represents a novel species of the genus Marinicrinis , for which the name Marinicrinis lubricantis sp. nov. is proposed, with KSS164-79T (=DSM 104943T=LMG 30062T=CCM 8749T=CIP 111345T) as the type strain.
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Blautia hominis sp. nov., isolated from human faeces
A strictly anaerobic, Gram-stain-positive, non-motile and coccoid- or oval-shaped bacterium, designated strain KB1T, was isolated from a faecal sample of a patient with diverticulitis in South Korea. Degeneracies in the 16S rRNA gene sequence of strain KB1T were resolved by cloning, which yielded five different sequences with heterogeneity. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain KB1T formed a monophyletic branch with species in the genus Blautia , with highest sequence similarity to the type strain of Blautia producta (97.7–98.9 %), followed by Blautia coccoides (97.5–98.1 %). Strain KB1T was able to grow at temperatures of between 15 and 42 °C, with optimal growth at 37 °C, and in the presence of 20 % dehydrated bile. Acetic acid, succinic acid, lactic acid and fumaric acid were produced by strain KB1T from Gifu anaerobic medium broth as metabolic fermentation end-products. The major cellular fatty acids of strain KB1T were C14 : 0, C16 : 0 and C16 : 0 dimethyl aldehyde. The DNA G+C content was 46.3 mol%. The average nucleotide identity value between strain KB1T and the type strain of B. producta was 84.1 %. On the basis of polyphasic analysis, strain KB1T represents a novel species in the genus Blautia , for which the name Blautia hominis sp. nov. is proposed. The type strain is KB1T (=KCTC 15618T=JCM 32276T).
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Veillonella infantium sp. nov., an anaerobic, Gram-stain-negative coccus isolated from tongue biofilm of a Thai child
A strain of a novel anaerobic, Gram-stain-negative coccus was isolated from the tongue biofilm of a Thai child. This strain was shown, at the phenotypic level and based on 16S rRNA gene sequencing, to be a member of the genus Veillonella . Comparative analysis of the 16S rRNA, dnaK and rpoB gene sequences indicated that phylogenetically the strain comprised a distinct novel branch within the genus Veillonella . The novel strain showed 99.8, 95.1 and 95.9 % similarity to partial 16S rRNA, dnaK and rpoB gene sequences, respectively, to the type strains of the two most closely related species, Veillonella dispar ATCC 17748T and Veillonella tobetsuensis ATCC BAA-2400T. The novel strain could be discriminated from previously reported species of the genus Veillonella based on partial dnaK and rpoB gene sequencing and average nucleotide identity values. The major acid end-product produced by this strain was acetic acid under anaerobic conditions in trypticase-yeast extract-haemin with 1 % (w/v) glucose or fructose medium. Lactate was fermented to acetic acid and propionic acid. Based on these observations, this strain represents a novel species, for which the name Veillonella infantium sp. nov. is proposed. The type strain is T11011-4T (=JCM 31738T=TSD-88T).
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Methylomusa anaerophila gen. nov., sp. nov., an anaerobic methanol-utilizing bacterium isolated from a microbial fuel cell
More LessAbacterial strain, designated MMFC1T, was isolated from a methanol-fed microbial fuel cell that had been inoculated with sludge obtained from a wastewater-treatment facility in a chemical plant. The strain grows by fermenting methanol to produce acetate under anaerobic conditions, while homoacetogenic growth is not observed. MMFC1T also grows on pyruvate and lactate but not on sugars and other organic acids. Cells are curved rods and motile, have peritrichous flagella, and form endospores. The genome sequence of strain MMFC1T supports the physiological data. Phylogenetic analysis based on the 16S rRNA gene sequence shows that strain MMFC1T is affiliated with the family Sporomusaceae , while the closest relative is S poromusa ovata with nucleotide-sequencesimilarity of 93.5 %. Major fatty acids are iso-C13 : 0 3-OH, C16 : 1 ω9 and iso-C17 : 0. On the basis of its physiological, genomic and phylogenetic features, a novel genus and species are proposed to accommodate strain MMFC1T, with the name Methylomusa anaerophila gen. nov., sp. nov. The type strain of Methylomusa anaerophila is MMFC1T (=JCM 31821T = KCTC 15592T).
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Bacillus fermenti sp. nov., an indigo-reducing obligate alkaliphile isolated from indigo fermentation liquor for dyeing
More LessThe indigo-reducing, facultatively anaerobic and obligately alkaliphilic strains Bf-1T, Bf-2 and Bf-4 were isolated from an indigo fermentation liquor used for dyeing, which uses sukumo [composted Polygonum indigo (Polygonum tinctorium Lour.) leaves] as a basic ingredient and was obtained from a craft centre in Date City, Hokkaido, Japan. The 16S rRNA gene sequence analyses indicated that the closest neighbours of strain Bf-1T are Bacillus maritimus DSM 100413T (98.3 % 16S rRNA gene sequence similarity), Bacillus persicus DSM 25386T (98.2 %) and Bacillus rigiliprofundi LMG 28275T (97.7 %). The 16S rRNA gene sequence of strain Bf-1T was almost identical to the sequences of strains Bf-2 and Bf-4 (99.9 %). Cells of strain Bf-1T stained Gram-positive and formed straight rods that achieved motility through a pair of subpolar flagella. Strain Bf-1T grew at temperatures of between 15 and 45 °C with optimum growth at 33‒40 °C. The strain grew in the pH range of pH 8‒12, with optimum growth at pH 10. The isoprenoid quinone detected was menaquinone-7 (MK-7), and the DNA G+C content was 41.7 %. The whole-cell fatty acid profile mainly (>10 %) consisted of iso-C15 : 0 and iso-C16 : 0. Phylogenetically related neighbours, although demonstrating high 16S rRNA gene sequence similarity (>97.6 %) with strain Bf-1T, exhibited less than 9 % relatedness in DNA–DNA hybridization experiments. Based on evidence from this polyphasic study, the isolates represent a novel species, for which the name Bacillus fermenti sp. nov. is proposed. The type strain of this species is Bf-1T (=JCM 31807T=NCIMB 15079T).
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Paenibacillus mobilis sp. nov., a Gram-stain-negative bacterium isolated from soil
More LessA novel Gram-stain-negative bacterium, designated strain S8T, was isolated from a soil sample obtained in Gyeonggi Province, Republic of Korea. Cells of strain S8T were endospore-forming, motile by means of peritrichous flagella, and rod-shaped. S8T colonies were round, convex, wavy and white. Strain S8T grew optimally at 37 °C, pH 6–8, and up to 2.0 % (w/v) NaCl. Based on 16S rRNA gene sequence similarity, strain S8T was affiliated with the genus Paenibacillus in the family Paenibacillaceae and was most closely related to Paenibacillus yonginensis DCY84T and Paenibacillus physcomitrellae XBT (98.8 and 97.1 % sequence similarity). The DNA G+C content of the novel strain was 53.1±0.3 mol%. Strain S8T contained diphosphatidylglycerol, phosphatidylglycerol, two phospholipids, four aminophospholipids, an aminolipid and three unidentified lipids. The major fatty acid was anteiso-branched C15 : 0. The quinone was menaquinone MK-7. The peptidoglycan of strain S8T contained meso-diaminopimelic acid. The DNA–DNA hybridization values of strain S8T with P. yonginensis KCTC 33428T and P. physcomitrellae DSM 29851T were 44 % and 32 %, respectively. Data from the DNA–DNA hybridization, biochemical, phylogenetic and physiological analyses indicate that strain S8T (=KCTC 33848T=JCM 31672T) represents a novel species of the genus Paenibacillus , for which the name Paenibacillus mobilis sp. nov. is proposed.
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Bacillus alkalitolerans sp. nov., isolated from marine sediment near a hydrothermal vent
Yan Liu, Min Yu and Xiao-Hua ZhangA Gram-stain-positive, endospore-forming, rod-shaped, motile and strictly aerobic strain, designated T3-209T, was isolated from sediment sampled at a water depth of 1206 m of the southern Okinawa Trough at station T1 (25.07° N, 122.58° E) near the Tangyin hydrothermal vent during an expedition on the R/V Kexue in May 2014. The strain was able to grow at a temperature range of 10–42 °C (optimum 28 °C). Growth was observed at NaCl concentrations (w/v) of 0–6 % (optimum 0 %). The pH range for growth was 7.0–9.0 (optimum 8.0). The 16S rRNA gene sequence analysis indicated that strain T3-209T belonged to the genus Bacillus within the family Bacillaceae and was most closely related to Bacillus drentensis LMG 21831T and Bacillus bataviensis LMG 21833T, with the same sequence similarity (97.0 %), but shared relatively low levels of similarity (92.6–96.9 %) to the type strains of other Bacillus species. The peptidoglycan type of strain T3-209T was meso-diaminopimelic acid. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and alcohol-C16 : 1 ω7c. The respiratory quinone was menaquinone-7. The polar lipids of strain T3-209T comprised phosphatidylglycerol, two unidentified phospholipids and one unidentified aminolipid. The DNA G+C content was 41.8 mol%. Combining results of phylogenetic analysis, phenotypic characterization and chemotaxonomic studies, strain T3-209T represents a novel species of the genus Bacillus , for which the name Bacillus alkalitolerans sp. nov. is proposed. The type strain is T3-209T (=KCTC 33631T=DSM 29135T=MCCC 1K00503T).
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Virgibacillus phasianinus sp. nov., a halophilic bacterium isolated from faeces of a Swinhoe's pheasant, Lophura swinhoii
A rod-shaped, Gram-stain-positive, motile and aerobic bacterium, designated LM2416T, was isolated from faeces of Lophuras winhoii living in Seoul Grand Park, Gyeonggi-do, Republic of Korea. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain LM2416T belonged to the genus Virgibacillus , sharing high 16S rRNA gene sequence similarities to Virgibacillus necropolis LMG 19488T (99.0 %), Virgibacillus carmonensis LMG 20964T (98.4 %), Virgibacillus arcticus Hal 1T (98.3 %) and Virgibacillus flavescens S1-20T (97.9 %). The isolate grew at 10–30 °C, pH 6–7 and 0–20 % (w/v) NaCl. Optimal growth was observed at 30 °C, pH 6–7 and 10 % (w/v) NaCl. The major fatty acid was anteiso-C15 : 0. Polar lipids were composed of phosphatidylglycerol, diphosphatidylglycerol, three unknown phospholipids and two unknown aminophospholipids. The main menaquinone was MK-7. Strain LM2416T had alanine, lysine, glutamic acid, glycine and aspartic acid as cell-wall amino acids and ribose as a cell-wall sugar. The whole genome sequences of strain LM2416T and V. necropolis KCTC 3820T were sequenced by PacBio RS II sequencing. The genome sequence-based G+C content of strain LM2416T was 39.5 mol%. The orthologous average nucleotide identity value, showing genetic relatedness between strain LM2416T and V. necropolis KCTC 3820T, was 78.3 %. Based on the phylogenetic, biochemical, chemotaxonomic and genotypic data presented in this study, strain LM2416T is considered to represent a novel species of the genus Virgibacillus , for which the name Virgibacillus phasianinus is proposed. The type strain is LM2416T (=KCTC 33927T=JCM 32144T).
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- Other Bacteria
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Roseisolibacter agri gen. nov., sp. nov., a novel slow-growing member of the under-represented phylum Gemmatimonadetes
A novel slow-growing bacterium, designated strain AW1220T, was isolated from agricultural floodplain soil sampled at Mashare (Kavango region, Namibia) by using a high-throughput cultivation approach. Strain AW1220T was characterized as a Gram-negative, non-motile, rod-shaped bacterium. Occasionally, some cells attained an unusual length of up to 35 µm. The strain showed positive responses for catalase and cytochrome-c oxidase and divided by binary fission and/or budding. The strain had an aerobic chemoorganoheterotrophic metabolism and was also able to grow under micro-oxic conditions. Colonies were small and pink pigmented. Strain AW1220T was found to be a mesophilic, neutrophilic and non-halophilic bacterium. Cells accumulated polyphosphate intracellularly and mainly utilized complex protein substrates for growth. 16S rRNA gene sequence comparisons revealed that strain AW1220T belonged to the class Gemmatimonadetes (=group 1). Its closest relatives were found to be Gemmatimonas aurantiaca T-27T (90.9 % gene sequence similarity), Gemmatimonas phototrophica AP64T (90.8 %) and Longimicrobium terrae CB-286315T (84.2 %). The genomic G+C content was 73.3 mol%. The major fatty acids were iso-C15 : 0, C16 : 1ω7c and/or iso-C15 : 0 2-OH, iso-C17 : 1ω9c, iso-C15 : 0 3-OH and C16 : 0. The predominant respiratory quinone was MK-9, albeit minor amounts of MK-8 and MK-10 are also present. The polar lipids comprised major amounts of phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and one unidentified phosphoglycolipid. On the basis of its polyphasic characterization, strain AW1220T represents a novel genus and species of the class Gemmatimonadetes for which the name Roseisolibacter agri gen. nov., sp. nov. is proposed, with the type strain AW1220T (=DSM 104292T=LMG 29977T).
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Oleiharenicola alkalitolerans gen. nov., sp. nov., a new member of the phylum Verrucomicrobia isolated from an oilsands tailings pond
A novel member of the phylum Verrucomicrobia was isolated from an oilsands tailings pond in Alberta, Canada. Cells of isolate NVTT are Gram-negative, strictly aerobic, non-pigmented, non-motile cocci to diplococci 0.5–1.0 µm in diameter. The bacterium is neutrophilic (optimum pH 6.0–8.0) but alkalitolerant, capable of growth between pH 5.5 and 11.0. The temperature range for growth is 15–40 °C (optimum 25–37 °C). Carbon and energy sources include sugars and organic acids. Nitrogen sources include nitrate, urea, l-glycine, l-alanine, l-proline and l-serine. Does not fix atmospheric nitrogen. Does not require NaCl and is inhibited at NaCl concentrations above 3.0 % (w/v). The DNA G+C content of strain NVTT, based on a draft genome sequence, is 66.1 mol%. MK-6 and MK-7 are the major respiratory quinones. Major cellular fatty acids are anteiso-C15 : 0 and iso-C15 : 0. Phylogenetic analysis of 16S rRNA gene sequences revealed that the strain belongs to the family Opitutaceae of the phylum Verrucomicrobia . The most closely related validated species is Opitutus terrae (93.7 % 16S rRNA gene sequence identity to its type strain PB90-1T). Based on genotypic, phenotypic and chemotaxonomic characteristics, it was concluded that this strain represents a novel genus and species, for which the name Oleiharenicola alkalitolerans gen. nov., sp. nov. is proposed. The type strain of this novel species is NVTT (=ATCC BAA-2697T;=DSM 29249T).
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Edaphobacter lichenicola sp. nov., a member of the family Acidobacteriaceae from lichen-dominated forested tundra
An isolate of aerobic, Gram-stain-negative, rod-shaped, non-motile and light-pink pigmented bacteria, designated SBC68T, was obtained from slightly decomposed thalli of the lichen Cladonia sp. collected from the forested tundra of north-western Siberia. Cells of this isolate occurred singly, in pairs or in rosettes. These bacteria were acidophilic (optimum growth at pH 4.3–5.6) and mesophilic (optimum growth at 20–30 °C) but were also capable of growth at low temperatures, down to 7 °C. The preferred growth substrates were sugars, some organic acids and lichenan. The major fatty acids were iso-C15 : 0, C16 : 1ω7c, C16 : 0, C16 : 1ω7t, and 13,16-dimethyl octacosanedioic acid. The only quinone was MK-8, and the G+C content of the DNA was 54.7 mol%. SBC68T represented a member of the family Acidobactericeae; the closest taxonomically described relatives were Edaphobacter dinghuensis DHF9T and Granulicella aggregans TPB6028T (97.2 and 97.1 % 16S rRNA gene sequence similarity, respectively). In 16S rRNA gene-based trees, SBC68T clustered together with species of the genus Edaphobacter . However, this isolate differed from all previously described species of the genus Edaphobacter with respect to the pink pigmentation, formation of cell rosettes and substrate utilization pattern. On the basis of these data, strain SBC68T should be considered to represent a novel species of acidobacteria, for which the name Edaphobacter lichenicola sp. nov. is proposed. The type strain is SBC68T (=DSM 104462T=VKM B-3208T).
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Deinococcus lacus sp. nov., a gamma radiation-resistant bacterium isolated from an artificial freshwater pond
More LessA Gram-stain-negative, pink-coloured, non-motile and gamma radiation-resistant bacterium, designated strain IMCC1711T, was isolated from a freshwater sample collected from an artificial pond (Inkyong Pond). The 16S rRNA gene sequence analysis showed that strain IMCC1711T was most closely related to Deinococcus piscis 3axT (94.2 %) and formed a robust phylogenetic clade with other species of the genus Deinococcus . Optimal growth of strain MCC1711T was observed at 25 °C and pH 7.0 without NaCl. Strain IMCC1711T exhibited high resistance to gamma radiation. The DNA G+C content of strain IMCC1711T was 59.1 mol% and MK-8 was the predominant isoprenoid quinone. Major fatty acid constituents of the strain were C17 : 1ω8c, C16 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and C15 : 1 ω6c. The major polar lipids constituted phosphatidylethanolamine, one unidentified phosphoglycolipid and two unidentified glycolipids. On the basis of taxonomic data obtained in this study, it was concluded that strain IMCC1711T represented a novel species of the genus Deinococcus , for which the name Deinococcus lacus sp. nov. is proposed. The type strain of Deinococcus lacus is IMCC1711T (KCTC 52494T=KACC 18979T=NBRC 112440T).
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Rubritalea profundi sp. nov., isolated from deep-seawater and emended description of the genus Rubritalea in the phylum Verrucomicrobia
More LessA Gram-stain-negative, short-rod, facultatively anaerobic, non-motile and red-pigmented bacterium, designated SAORIC-165T, was isolated from a deep-seawater sample collected from the Pacific Ocean. The 16S rRNA gene sequence analysis showed that strain SAORIC-165T was most closely related to Rubritalea marina Pol012T (95.7 % sequence similarity) and formed a robust phylogenetic clade with other species of the genus Rubritalea in the phylum Verrucomicrobia . Optimal growth of strain SAORIC-165T was observed at 10 °C, pH 7.0 and in the presence of 2.0–3.5 % (w/v) NaCl. The DNA G+C content of strain SAORIC-165T was 50.7 mol% and MK-9 was the predominant isoprenoid quinone. The major cellular fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C14 : 0, anteiso-C15 : 0, C16 : 0 and C14 : 0. The major polar lipids constituted phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified phospholipids and aminolipids. On the basis of the taxonomic data obtained in this study, it was concluded that strain SAORIC-165T represented a novel species of the genus Rubritalea , for which the name Rubritalea profundi sp. nov. is proposed. The type strain of Rubritalea profundi is SAORIC-165T (=NBRC 110691T=KCTC 52460T).
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- Proteobacteria
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Halomonas malpeensis sp. nov., isolated from rhizosphere sand of a coastal sand dune plant
More LessA Gram-stain-negative, aerobic, non-endospore-forming organism, isolated from the rhizosphere sand of a coastal sand dune plant was studied for its taxonomic position. On the basis of 16S rRNA gene sequence similarity comparisons, strain YU-PRIM-29T was grouped within the genus Halomonas and was most closely related to Halomonas johnsoniae (97.5 %). The 16S rRNA gene sequence similarity to other Halomonas species was <97.5 %. Strain YU-PRIM-29T grew optimally at 28 °C (growth range, 10–36 °C), at a pH of 7–9 (growth range, pH 5.5–12.0) and in the presence of 0.5 to 5 % (w/v) NaCl (growth up to 20 % NaCl). The fatty acid profile from whole-cell hydrolysates supported the allocation of the strain to the genus Halomonas . The fatty acids C18 : 1ω7c and C16 : 0 were found as major compounds, followed by the hydroxylated fatty acid C12 : 0 3-OH. The quinone system consisted predominantly of ubiquinone Q-9. The polar lipid profile was composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. In the polyamine pattern, spermidine was the predominant compound. The DNA G+C content was 64.8 mol%. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain YU-PRIM-29T from its closest-related species. Hence, YU-PRIM-29T represents a new species of the genus Halomonas , for which we propose the name Halomonas malpeensis sp. nov., with YU-PRIM-29T (=LMG 28855T=CCM 8737T) as the type strain.
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Reclassification of Mameliella phaeodactyli, Mameliella atlantica, Ponticoccus lacteus and Alkalimicrobium pacificum as later heterotypic synonyms of Mameliella alba and an emended description of Mameliella alba
More LessThe aim of the study was to reclarify the taxonomic status of four species, Mameliella phaeodactyli , Mameliella atlantica , Ponticoccus lacteus and Alkalimicrobium pacificum , by using a polyphasic taxonomic approach. A combination of physiological properties of the four type strains, KD53T, L6M1-5T, JL351T and F15T, was consistent with those of the closest type strain JLT354-WT of Mameliella alba . The 16S rRNA gene sequences of the five type strains shared 100 % identity. The close relationship between the five strains was underpinned by the results of chemotaxonomic characteristics, including the fatty acids, quinone and polar lipids. The pairwise digital DNA–DNA hybridization values among the five strains were well above 70 %, considered the threshold value for species definition. In this case a further statement of Rule 24a applies, in which priority of names is determined by the date of the original publication. Hence, we propose that that Mameliella phaeodactyli , Mameliella atlantica , Ponticoccus lacteus and Alkalimicrobium pacificum should be regarded as later heterotypic synonyms of Mameliella alba .
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Phyllobacterium salinisoli sp. nov., isolated from a Lotus lancerottensis root nodule in saline soil from Lanzarote
A Gram-negative rod, designated strain LLAN61T, was isolated from a root nodule of Lotus lancerottensis growing in a saline soil sample from Lanzarote (Canary Islands). The strain grew optimally at 0.5 % (w/v) NaCl and tolerated up to 3.5 %. The 16S rRNA gene sequence analysis showed that strain LLAN61T belonged to genus Phyllobacterium and that Phyllobacterium leguminum ORS 1419T and Phyllobacterium myrsinacearum IAM 13584T are the closest related species with 97.93 and 97.86% similarity values, respectively. In the atpD phylogeny, P. leguminum ORS 1419T and P. myrsinacearum ATCC 43591T, sharing similarities of 87.6 and 85.8% respectively, were also the closest species to strain LLAN61T. DNA–DNA hybridization showed an average value of 21 % between strain LLAN61T and P. leguminum LMG 22833T, and 6 % with P. myrsinacearum ATCC 43590T. The predominant fatty acids were C19 : 0 cyclo ω8c and C18 : 1ω6c/C18 : 1ω7c (summed feature 8). The DNA G+C content was 58.0 mol%. Strain LLAN61T differed from its closest relatives in some culture conditions and in assimilation of several carbon sources. Based upon the results of phylogeny, DNA–DNA hybridization, phenotypic tests and fatty acid analysis, this strain should be classified as a novel species of Phyllobacterium for which the name Phyllobacterium salinisoli sp. nov. is proposed (type strain LLAN61T=LMG 30173T = CECT 9417T).
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Salinisphaera aquimarina sp. nov., isolated from seawater
More LessA Gram-stain-negative, aerobic, rod-shaped, motile bacterium with a subpolar flagellum, designated strain CCMM005T, was isolated from offshore seawater at Qingdao, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CCMM005T belonged to the genus Salinisphaera and exhibited highest 16S rRNA gene sequence similarity to Salinisphaera dokdonensis CL-ES53T (96.9 %). It showed lower sequence similarities (94.9–96.4 %) with all other representatives of the genus Salinisphaera . Optimal growth occurred in the presence of 4 % (w/v) NaCl, at 30 °C and at pH 7.0. The polar lipids of strain CCMM005T consisted of phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, one unidentified phosphoglycolipid and one unidentified phospholipid. The predominant isoprenoid quinone was Q-8. The major fatty acids were C19 : 0cyclo ω8c, C18 : 0 and C18 : 1ω7c. The DNA G+C content of strain CCMM005T was 65.3 mol%. On the basis of data from this polyphasic study, strain CCMM005T is considered to represent a novel species of the genus Salinisphaera , for which the name Salinisphaera aquimarina sp. nov. is proposed. The type strain is CCMM005T (=MCCC 1K03246T=KCTC 52640T).
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Vibrio fujianensis sp. nov., isolated from aquaculture water
More LessA Gram-stain-negative, facultatively anaerobic strain, designated FJ201301T, was isolated from aquaculture water collected from Fujian province, China. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain FJ201301T belonged to the genus Vibrio , formed a distinct cluster with Vibrio cincinnatiensis ATCC 35912T and shared the highest similarity with Vibrio salilacus CGMCC 1.12427T. A 15 bp insertion found in the 16S rRNA gene was a significant marker that distinguished strain FJ201301T from several phylogenetic neighbours (e.g. V. cincinnatiensis ). Multilocus sequence analysis of eight genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA and topA; concatenated 4135 bp sequence) showed that, forming a long and independent phylogenetic branch, strain FJ201301T clustered with V. cincinnatiensis ATCC 35912T, V ibrio injenensis KCTC 32233T and Vibrio metschnikovii CIP 69.14T clearly separated from V. salilacus CGMCC 1.12427T. Furthermore, the highest in silico DNA–DNA hybridization and average nucleotide identity values between strain FJ201301T and the closest related species were 26.3 and 83.1 % with V. cincinnatiensis ATCC 35912T, less than the proposed cutoff levels for species delineation, i.e. 70 and 95 %, respectively. Biochemical, sequence and genomic analysis suggested the designation of strain FJ201301T representing a novel species of the genus Vibrio , for which the name Vibrio fujianensis sp. nov. is proposed. The type strain is FJ201301T (=DSM 104687T=CGMCC 1.16099T).
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Halomonas saliphila sp. nov., a moderately halophilic bacterium isolated from a saline soil
More LessA novel, Gram-stain-negative, aerobic, rod-shaped, motile and moderately halophilic bacterium, designated strain LCB169T, was isolated from a saline soil sample from Gansu Province, PR China. The cells of LCB169T grew at 10–52 °C (optimum 30 °C), at pH 6.0–10.0 (optimum pH 8.0) and in the presence of 0–17 % (w/v) NaCl (optimum 10–15 %). Phylogenetic analysis based on 16S rRNA gene sequences and concatenated 16S rRNA, gyrB and rpoD genes sequences revealed that LCB169T represented a member of the genus Halomonas in the class Gammaproteobacteria . The most closely related species were Halomonas daqingensis DQD2-30T (98.0 % 16S rRNA gene sequence similarity), Halomonas kenyensis AIR-2T (97.8 %) and Halomonas desiderata FB2T (97.5 %). DNA–DNA relatedness values between LCB169T and H. daqingensis CGMCC 1.6443T, H. desiderata DSM 9502T and H. kenyensis DSM 17331T were 33, 35 and 38 %, respectively. The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and three unidentified phospholipids. The major fatty acids were C18 : 1ω7c, C16 : 0, C16 : 1ω7c and C12 : 0 3-OH. The genomic DNA G+C content was 66.1 mol% and the predominant respiratory quinone was Q-9. On the basis of the results of phenotypic, phylogenetic and chemotaxonomic analyses and DNA–DNA hybridization relatedness values, LCB169T is considered to represent a novel species of the genus Halomonas, for which the name Halomonas saliphila sp. nov. is proposed. The type strain is LCB169T (=CGMCC 1.15818T=KCTC 52618T).
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Luteimonas rhizosphaerae sp. nov., isolated from the rhizosphere of Triticum aestivum L.
More LessA Gram-stain-negative, rod-shaped bacterium, strain 4-12T, was isolated from the rhizosphere of Triticum aestivum L. from the Xiaokai River irrigation area, China. The isolate grew optimally at 30 °C, pH 7.5–8.0 and with 1.0 % (w/v) NaCl. Based on the 16S rRNA gene sequence and phylogenetic analysis, strain 4-12T belonged to the genus Luteimonas with the highest degree of 16S rRNA gene sequence similarity to Luteimonas tolerans UM1T (97.68 %), followed by Luteimonas terrae THG-MD21T (97.67 %), Lysobacter panaciterrae Gsoil 068T (97.21 %) and Luteimonas aestuarii B9T (97.16 %). However, the DNA–DNA relatedness values between strain 4-12T and closely related Luteimonas strains were well below 40 %. The average nucleotide identity and the Genome-to-Genome Distance Calculator also showed low relatedness (below 95 and 70 %, respectively) between strain 4-12T and the type strains in genus Luteimonas . Ubiquinone-8 was the predominant quinone. The major fatty acids were iso-C15 : 0, iso-C11 : 0, iso-C17 : 0 and iso-C17 : 1ω9c. Polar lipids were dominated by diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unidentified phospholipids. The DNA G+C content was 69.5 %. According to the phenotypic, genetic and chemotaxonomic data, strain 4-12T is considered to represent a novel species in the genus Luteimonas , for which the name >Luteimonas rhizosphaerae sp. nov. is proposed, with strain 4-12T (=CCTCC AB 2016261T=KCTC 52585T) as the type strain.
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Roseovarius nitratireducens sp. nov., a halotolerant bacterium isolated from a saline lake
More LessA Gram-stain-negative, aerobic, non-motile and ovoid- to rod-shaped bacterial strain, designated TFZT, was isolated from a water sample of a saline lake in Xinjiang, China and subjected to polyphasic taxonomic investigation. Strain TFZT grew at 4–42 °C and pH 6.5–10.0 (optimum, 30 °C and pH 7.0) and with 0.5–18.0 % (w/v) NaCl (optimum, 1.5 %). According to phylogenetic analysis based on 16S rRNA gene sequences, strain TFZT was assigned to the genus Roseovarius with highest 16S rRNA gene sequence similarity of 97.5 % to Roseovarius tolerans EL-172T, followed by Roseovarius azorensis SSW084T (96.6 %) and Roseovarius mucosus DSM 17069T (95.5 %). Digital DNA–DNA hybridization (DDH) and average nucleotide identity (ANI) were determined to evaluate the genomic relationship between strain TFZT and R. tolerans EL-172T. Digital DDH estimation (22.80±2.35 %) as well as ANI (80.1 %) proved the dissimilarity of strain TFZT. Chemotaxonomic analysis showed that strain TFZT contained ubiquinone-10 as the predominant respiratory quinone and possessed summed feature 8 (comprising C18 : 1 ω7c and/or ω6c) and C16 : 0 as the predominant form of fatty acid. The polar lipids of strain TFZT consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and five unidentified lipids. The DNA G+C content was 65.4 mol% (by genome sequencing). Based on the polyphasic taxonomic characterization, strain TFZT is considered to represent a novel species of the genus Roseovarius , for which the name Roseovarius nitratireducens sp. nov. is proposed (type strain TFZT=MCCC 1K03339T=KCTC 52967T).
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Comamonas aquatilis sp. nov., isolated from a garden pond
More LessA beige-pigmented bacterial strain, SB30-Chr27-3T, isolated from a garden pond, was studied for its taxonomic position. Cells of the isolate were rod-shaped and stained Gram-negative. A comparison of the 16S rRNA gene sequence with the sequences of the type strains of the most closely related species showed that the strain belongs to the genus Comamonas and showed highest sequence similarities to the type strains of Comamonas jiangduensis (97.5 %), Comamonas aquatica (97.4 %) and Comamonas phosphati (97.3 %). The 16S rRNA gene sequence similarities to all other Comamonas species were below 97.0 %. The fatty acid profile of strain SB30-Chr27-3T consisted of the major fatty acids C16 : 0, C15 : 0iso 2-OH/ C16 : 1ω7c, C18 : 1ω7c/C18 : 1 ω9c and, in a minor amount, C10 : 0 3-OH. Major compounds in the polar lipid profile were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine and diphosphatidylglycerol. The quinone system was exclusively composed of ubiquinone Q-8. The polyamine pattern contained the major compounds putrescine, cadaverine and 2-hydroxyputrescine. These data and the differentiating biochemical properties indicated that isolate SB30-CHR27-3T represents a novel species of the genus Comamonas , for which we propose the name >Comamonas aquatilis sp. nov. with the type strain SB30-Chr27-3T (=CIP 111491T=CCM 8815T).
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Paracoccus alimentarius sp. nov., isolated from a Korean foodstuff, salted pollack
More LessA Gram-stain-negative, aerobic, non-motile and coccoid or ovoid bacterial strain, designated LB2T, was isolated from a Korean foodstuff, salted pollack. Strain LB2T grew optimally at 25–30 °C, at pH 7.0–8.0 and in the presence of 0–2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain LB2T belonged to the genus Paracoccus , coherently clustering with the type strain of Paracoccus sulfuroxidans . Strain LB2T exhibited 16S rRNA gene sequence similarity values of 98.0 and 97.0 % to the type strains of P. sulfuroxidans and Paracoccus halophilus , respectively, and of less than 96.9 % to the type strains of other Paracoccus species. Strain LB2T contained Q-10 as the predominant ubiquinone. Major fatty acids of strain LB2T were cyclo C19 : 0 ω8c, C18 : 1 ω7c and C16 : 0 (when grown on MA) or C18 : 1 ω7c and C16 : 0 (on TSA). The major polar lipids detected in strain LB2T were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid and one unidentified glycolipid. The DNA G+C content of strain LB2T was 61.4 mol% and its DNA–DNA relatedness values with the type strains of P. sulfuroxidans and P. halophilus were 26 and 18 %, respectively. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain LB2T is separated from recognized Paracoccus species. On the basis of the data presented, strain LB2T is considered to represent a novel species of the genus Paracoccus , for which the name Paracoccus alimentarius sp. nov. is proposed. The type strain is LB2T (=KCTC 62138T=NBRC 113023T).
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Paraburkholderia aromaticivorans sp. nov., an aromatic hydrocarbon-degrading bacterium, isolated from gasoline-contaminated soil
Yunho Lee and Che Ok JeonA Gram-stain-negative, facultatively aerobic, aromatic hydrocarbon-degrading bacterium, designated strain BN5T, was isolated from gasoline-contaminated soil. Cells were motile and slightly curved rods with a single flagellum showing catalase and oxidase activities. Growth was observed at 20–37 °C (optimum, 25–30 °C), pH 3–7 (optimum, pH 5–6) and 0–2 % NaCl (optimum, 0 %). Ubiquinone-8 was the predominant respiratory quinone. The major fatty acids were C16 : 0, cyclo-C19 : 0 ω8c and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phosphoamino lipid, three unidentified amino lipids and eight unidentified lipids were the identified polar lipids. The DNA G+C content was 62.93 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BN5T formed a phylogenic lineage with members of the genus Paraburkholderia and showed the highest 16S rRNA gene sequence similarities to Paraburkholderia phytofirmans PsJNT (99.4 %), Paraburkholderia dipogonis DL7T (98.8 %) and Paraburkholderia insulsa PNG-AprilT (98.8 %). The average nucleotide identity and in silico DNA–DNA hybridization (DDH) values between strain BN5T and P. phytofirmans PsJNT were 88.5 and 36.5 %, respectively. The DDH values for strain BN5T with P. dipogonis LMG 28415T and P. insulsa DSM 28142T were 41.0±4.9 % (reciprocal, 33.0±4.3 %) and 47.1±6.6 % (reciprocal, 51.7±5.4 %), respectively. Based on its physiological, chemotaxonomic and phylogenetic features, we conclude that strain BN5T is a novel species of the genus Paraburkholderia , for which the name Paraburkholderia aromaticivorans sp. nov. is proposed. The type strain is BN5T (=KACC 19419T=JCM 32303T).
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Arcobacter canalis sp. nov., isolated from a water canal contaminated with urban sewage
More LessFour bacterial strains recovered from shellfish (n=3) and from the water (n=1) of a canal contaminated with urban sewage were recognized as belonging to a novel species of the genus Arcobacter (represented by strain F138-33T) by using a polyphasic characterization. All the new isolates required 2 % NaCl to grow. Phylogenetic analyses based on 16S rRNA gene sequences indicated that all strains clustered together, with the most closely related species being Arcobacter marinus and Arcobacter molluscorum . However, phylogenetic analyses using the concatenated sequences of housekeeping genes (atpA, gyrB, hsp60, gyrA and rpoB) showed that all the novel strains formed a distinct lineage within the genus Arcobacter . Results of in silico DNA–DNA hybridization and the average nucleotide identity between the genome of strain F138-33T and those of the closely related species A. marinus and other relatively closely related species such as A. molluscorum and Arcobacter halophilus were all below 70 and 96 %, respectively. All the above results, together with the 15 physiological and biochemical tests that could distinguish the newly isolated strains from the closely related species, confirmed that these strains represent a novel species for which the name Arcobacter canalis sp. nov. is proposed, with the type strain F138-33T (=CECT 8984T=LMG 29148T).
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Parvibium lacunae gen. nov., sp. nov., a new member of the family Alcaligenaceae isolated from a freshwater pond
More LessA bacterial strain designated KMB9T was isolated from a freshwater pond in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain KMB9T were Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, motile by means of a monopolar flagellum, non-spore-forming and rods surrounded by a thick capsule and forming white-coloured colonies. Growth occurred at 20–40 °C (optimum, 25–37 °C), at pH 6.5–7.5 (optimum, pH 7.0) and with 0–0.5 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene and four housekeeping gene sequences (recA, rpoA, rpoB and atpD) showed that strain KMB9T forms a distinct phyletic line within the family Alcaligenaceae , and the levels of 16S rRNA gene sequence similarity to its closest relatives with validly published names were less than 93.3 %. The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8. The major polyamine was putrescine. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol and several uncharacterized aminophospholipids, aminolipids, phospholipids and lipids. The genomic DNA G+C content of strain KMB9T was 54.5 mol%. On the basis of the genotypic and phenotypic data, strain KMB9T represents a novel species of a new genus in the family Alcaligenaceae , for which the name Parvibium lacunae gen. nov., sp. nov. is proposed. The type strain is KMB9T (=BCRC 81053T=LMG 30055T=KCTC 52814T).
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Herbaspirillum robiniae sp. nov., isolated from root nodules of Robinia pseudoacacia in a lead–zinc mine
More LessA novel endophytic bacterium, designated strain HZ10T, was isolated from root nodules of Robinia pseudoacacia growing in a lead–zinc mine in Mianxian County, Shaanxi Province, China. The bacterium was Gram-stain-negative, aerobic, motile, slightly curved- and rod-shaped, methyl red-negative, catalase-positive, and did not produce H2S. Strain HZ10T grew at 4–45 °C (optimum, 25–30 °C), pH 5–9 (optimum, pH 7–8) and 0–1 % (w/v) NaCl. The major fatty acids were identified as C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), and the quinone type was Q-8. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The DNA G+C content of the genomic DNA was 64.9 mol% based on the whole genome sequence. According to the 16S rRNA gene sequence analysis, the closest phylogenetic relative to strain HZ10T is Herbaspirillum chlorophenolicum CPW301T (98.72 % sequence identity). Genome relatedness of the type strains H. chlorophenolicum CPW301T, Herbaspirillum seropedicae Z67T and Herbaspirillum aquaticum IEH 4430T, was quantified by using the average nucleotide identity (86.9–88.0 %) and a genome-to-genome distance analysis (26.6 %–29.3 %), with both strongly supporting the notion that strain HZ10T belongs to the genus Herbaspirillum as a novel species. Based on the results from phylogenetic, chemotaxonomic and physiological analyses, strain HZ10T represents a novel Herbaspirillum species, for which the name Herbaspirillum robiniae sp. nov. is proposed. The type strain is HZ10T (=JCM 31754T=CCTCC AB 2014352T).
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Thalassotalea insulae sp. nov., isolated from tidal flat sediment
More LessA Gram-stain-negative, aerobic, motile and rod-shaped or ovoid bacterial strain, designated JDTF-40T, was isolated from a tidal flat in Jindo, an island of the Republic of South Korea. Strain JDTF-40T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain JDTF-40T fell within the cluster comprising the type strains of Thalassotalea species. Strain JDTF-40T exhibited 16S rRNA gene sequence similarity values of 93.8–95.7 % to the type strains of Thalassotalea species. Strain JDTF-40T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0 as the major fatty acids. The major polar lipids of strain JDTF-40T were phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid, one unidentified glycolipid and three unidentified lipids. The DNA G+C content of strain JDTF-40T was 41.3 mol%. Differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain JDTF-40T is distinct from recognized species of the genus Thalassotalea . On the basis of the data presented here, strain JDTF-40T is considered to represent a novel species of the genus Thalassotalea , for which the name Thalassotalea insulae sp. nov. is proposed. The type strain is JDTF-40T (=KACC 19433T=KCTC 62186T=NBRC 113040T).
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Pseudomaribius aestuariivivens gen. nov., sp. nov., isolated from a tidal flat sediment
More LessA Gram-stain-negative, non-motile and ovoid or rod-shaped bacterial strain, DBTF-15T, was isolated from a tidal flat sediment on the Yellow Sea in South Korea. Strain DBTF-15T grew optimally at 25–30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain DBTF-15T joined the cluster comprising the type strains of species of the genus Palleronia . Strain DBTF-15T exhibited higher 16S rRNA gene sequence similarity values to the type strains (96.5–96.7 %) of Maribius pelagius and Maribius salinus than to those (94.6–96.1 %) of the three species of the genus Palleronia . It exhibited 16S rRNA gene sequence similarity values of less than 93.9 % to the type strains of the other recognized species. Strain DBTF-15T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids of strain DBTF-15T were phosphatidylcholine, phosphatidylglycerol and one unidentified aminolipid. The DNA G+C content of strain DBTF-15T was 68.7 mol%. The chemotaxonomic data and other differential phenotypic properties made it possible to distinguish strain DBTF-15T from the genera Maribius and Palleronia . On the basis of the data presented, strain DBTF-15T constitutes a novel genus and species within the class Alphaproteobacteria , for which the name Pseudomaribius aestuariivivens gen. nov., sp. nov. is proposed. The type strain is DBTF-15T (=KACC 19431T=NBRC 113039T).
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Aestuariibius insulae gen. nov., sp. nov., isolated from a tidal flat sediment
More LessA Gram-stain-negative, non-motile and ovoid or rod-shaped bacterial strain, DBTF-13T, which was isolated from a tidal flat sediment of the Yellow Sea in South Korea, was characterized taxonomically. Strain DBTF-13T grew optimally at 25–30 °C and pH 7.0–8.0, and in the presence of 2.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences revealed that strain DBTF-13T formed an evolutionary lineage independent of other genera, including the genera Pseudooctadecabacter and Octadecabacter . Strain DBTF-13T exhibited 16S rRNA gene sequence similarity values of 96.9 % to the type strain of Pseudooctadecabacter jejudonensis , and of 95.8–96.5 % to the type strains of Octadecabacter species. Strain DBTF-13T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c and C16 : 0 as the major fatty acids. The major polar lipids of strain DBTF-13T were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain DBTF-13T was 61.6 mol%. The chemotaxonomic data and other differential phenotypic properties made it reasonable to differentiate strain DBTF-13T from the genera Pseudooctadecabacter and Octadecabacter . On the basis of the data presented, strain DBTF-13T constitutes a new genus and species within the class Alphaproteobacteria , for which the name Aestuariibius insulae gen. nov., sp. nov. is proposed. The type strain is DBTF-13T (=KACC 19432T=NBRC 113038T).
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Whole-genome sequencing reveals that Shewanella haliotis Kim et al. 2007 can be considered a later heterotypic synonym of Shewanella algae Simidu et al. 1990
More LessPreviously, experimental DNA–DNA hybridization (DDH) between Shewanella haliotis JCM 14758T and Shewanella algae JCM 21037T had suggested that the two strains could be considered different species, despite minimal phenotypic differences. The recent isolation of Shewanella sp. MN-01, with 99 % 16S rRNA gene identity to S. algae and S. haliotis , revealed a potential taxonomic problem between these two species. In this study, we reassessed the nomenclature of S. haliotis and S. algae using available whole-genome sequences. The whole-genome sequence of S. haliotis JCM 14758T and ten S. algae strains showed ≥97.7 % average nucleotide identity and >78.9 % digital DDH, clearly above the recommended species thresholds. According to the rules of priority and in view of the results obtained, S. haliotis is to be considered a later heterotypic synonym of S. algae . Because the whole-genome sequence of Shewanella sp. strain MN-01 shares >99 % ANI with S. algae JCM 14758T, it can be confidently identified as S. algae .
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Proteus alimentorum sp. nov., isolated from pork and lobster in Ma’anshan city, China
More LessTwo strains of Gram-stain-negative, facultatively anaerobic short-rod bacteria were recovered from two different food samples in Ma’anshan city, Anhui province, China in 2008. The bacteria were characterized in a polyphasic taxonomic study that included phenotypic, phylogenetic and genotypic methodologies. Phylogenetic analysis of the 16S rRNA gene demonstrated that the two strains belonged to the genus Proteus and were most similar to Proteus vulgaris ATCC 29905T with a score of 99.7 %. Phylogenetic analysis of the rpoB gene placed the two strains into a cluster with a distinctly interspecies phylogenetic branch that was clearly separated from six type strains of the genus Proteus , with the most closely related species being Proteus mirabilis ATCC 29906T. In silico genomic comparisons, including in silico DNA–DNA hybridization (isDDH) and average nucleotide identity (ANI) analysis showed that the representative strain, 08MAS0041T, and all six Proteus species share less than 70 % isDDH and have a 95 % ANI cutoff level, supporting the designation of the two strains as a novel species of the genus Proteus . The predominant cellular fatty acids of strain 08MAS0041T were C16 : 0 (24.8 %), C16 : 1ω7c/16 : 1ω6c (16.5 %), C18 : 1ω6c/C18 : 1 ω7c (14.5 %), C17 : 0 cyclo (12.6 %) and C16 : 1iso I/C14 : 0 3-OH (10.6 %). The analysis of biochemical, phylogenetic and genomic data confirmed that the two strains were clearly different from all recognized species of the genus Proteus and represent a novel Proteus species, for which the name Proteus alimentorum sp. nov. is proposed. The type strain is 08MAS0041T (=DSM 104685T=CGMCC 1.15939T).
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- Eukaryotic Micro-Organisms
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Polyphasic data support the splitting of Aspergillus candidus into two species; proposal of Aspergillus dobrogensis sp. nov.
Aspergillus candidus is a species frequently isolated from stored grain, food, indoor environments, soil and occasionally also from clinical material. Recent bioprospecting studies highlighted the potential of using A. candidus and its relatives in various industrial sectors as a result of their significant production of enzymes and bioactive compounds. A high genetic variability was observed among A. candidus isolates originating from various European countries and the USA, that were mostly isolated from indoor environments, caves and clinical material. The A. candidus sensu lato isolates were characterized by DNA sequencing of four genetic loci, and agreement between molecular species delimitation results, morphological characters and exometabolite spectra were studied. Classical phylogenetic methods (maximum likelihood, Bayesian inference) and species delimitation methods based on the multispecies coalescent model supported recognition of up to three species in A. candidus sensu lato. After evaluation of phenotypic data, a broader species concept was adopted, and only one new species, Aspergillus dobrogensis, was proposed. This species is represented by 22 strains originating from seven countries (ex-type strain CCF 4651T=NRRL 62821T=IBT 32697T=CBS 143370T) and its differentiation from A. candidus is relevant for bioprospecting studies because these species have different exometabolite profiles. Evaluation of the antifungal susceptibility of section Candidi members to six antifungals using the reference EUCAST method showed that all species have low minimum inhibitory concentrations for all tested antifungals. These results suggest applicability of a wide spectrum of antifungal agents for treatment of infections caused by species from section Candidi.
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Saturnispora kantuleensis f.a., sp. nov., a novel yeast species isolated from peat in a tropical peat swamp forest in Thailand
More LessTwo strains (DMKU-PPS4-5T and DMKU-EPS3-4) representing a single novel anamorphic yeast species were isolated from two peat samples collected in Kan Tulee peat swamp forest, Surat Thani Province, Thailand. The strains differed by two nucleotide substitutions in the sequences of the D1/D2 region of the large subunit (LSU) rRNA gene and only one nucleotide substitution in the internal transcribed spacer (ITS) region. Phylogenetic analysis based on the D1/D2 regions showed that the two strains represented a single species in the genus Saturnispora and were clearly distinct from other related species. Saturnispora sekii was the most closely related species, but with 1.7–2.1 % nucleotide substitutions in the D1/D2 region of the LSU rRNA gene, and 3.1–3.3 % nucleotide substitutions in the ITS region. They therefore represent a novel species of the genus Saturnispora, although the formation of ascospores was not observed. The name Saturnispora kantuleensis f.a., sp. nov. is proposed. The type strain is DMKU-PPS4-5T (=CBS 15217T=TBRC 7762T).
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Starmerella camargoi f.a., sp. nov., Starmerella ilheusensis f.a., sp. nov., Starmerella litoralis f.a., sp. nov., Starmerella opuntiae f.a., sp. nov., Starmerella roubikii f.a., sp. nov. and Starmerella vitae f.a., sp. nov., isolated from flowers and bees, and transfer of related Candida species to the genus Starmerella as new combinations
Six novel yeast species, Starmerella camargoi f.a., sp. nov., Starmerella ilheusensis f.a., sp. nov., Starmerella litoralis f.a., Starmerella opuntiae f.a., sp. nov., sp. nov., Starmerella roubikii f.a., sp. nov. and Starmerella vitae f.a, sp. nov. are proposed to accommodate 19 isolates recovered from ephemeral flowers or bees in Brazil, Costa Rica and Belize. Sequence analysis of the ITS-5.8S region (when available) and the D1/D2 domains of the large subunit of the rRNA gene showed that the six novel yeasts are phylogenetically related to several species of the Starmerella clade. The type strains are Starmerella camargoi f.a., sp. nov. UFMG-CM-Y595T (=CBS 14130T; Mycobank number MB 822640), Starmerella ilheusensis f.a., sp. nov. UFMG-CM-Y596T (=CBS CBS14131T; MB 822641), Starmerella litoralis f.a., sp. nov. UFMG-CM-Y603T (=CBS14104T; MB 822642), Starmerella opuntiae f.a., sp. nov. UFMG-CM-Y286T (=CBS 13466T; MB 822643), Starmerella roubikii f.a., sp. nov. UWOPS 01–191.1 (=CBS 15148; MB 822645) and Starmerella vitae f.a., sp. nov. UWOPS 00–107.2 (=CBS 15147T; MB 822646). In addition, 25 species currently assigned to the genus Candida are reassigned formally to the genus Starmerella.
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- Evolution, Phylogeny and Biodiversity
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Mixta gen. nov., a new genus in the Erwiniaceae
The Erwiniaceae contain many species of agricultural and clinical importance. Although relationships among most of the genera in this family are relatively well resolved, the phylogenetic placement of several taxa remains ambiguous. In this study, we aimed to address these uncertainties by using a combination of phylogenetic and genomic approaches. Our multilocus sequence analysis and genome-based maximum-likelihood phylogenies revealed that the arsenate-reducing strain IMH and plant-associated strain ATCC 700886, both previously presumptively identified as members of Pantoea , represent novel species of Erwinia . Our data also showed that the taxonomy of Erwinia teleogrylli requires revision as it is clearly excluded from Erwinia and the other genera of the family. Most strikingly, however, five species of Pantoea formed a distinct clade within the Erwiniaceae , where it had a sister group relationship with the Pantoea + Tatumella clade. By making use of gene content comparisons, this new clade is further predicted to encode a range of characters that it shares with or distinguishes it from related genera. We thus propose recognition of this clade as a distinct genus and suggest the name Mixta in reference to the diverse habitats from which its species were obtained, including plants, humans and food products. Accordingly, a description for Mixta gen. nov. is provided to accommodate the four species Mixta calida comb. nov., M. gaviniae comb. nov., M. intestinalis comb. nov. and M. theicola comb. nov., with M. calida as the type species for the genus.
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- Corrigendum
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Volumes and issues
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Volume 74 (2024)
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