- Volume 66, Issue 12, 2016
Volume 66, Issue 12, 2016
- Notification List
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- Review
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Paraphyly and (yeast) classification
More LessYeast systematics has wholeheartedly embraced the phylogenetic approach. Central to this has been the unspoken convention that taxa at all ranks be strictly monophyletic. This can result in a proliferation of small genera and instances of nomenclatural instability, counter to the expected benefit of phylogenetic systematics. But the literature abounds with examples, at all taxonomic levels, where paraphyly is a reality that can no longer be ignored. The very concepts of Bacteria or Archaea, under the constraint of monophyly, are in peril. It is therefore desirable to effect a shift in practices that will recognize the existence of paraphyletic taxa.
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- New taxa
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- Actinobacteria
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Streptomyces lacrimifluminis sp. nov., a novel actinobacterium that produces antibacterial compounds, isolated from soil
A novel actinobacterial strain, designated Z1027T, was isolated from a soil sample collected near the Tuotuo River, Qinghai–Tibet Plateau (China). The strain exhibited antibacterial activity against Escherichia coli and Staphylococcus aureus . The taxonomic position of strain Z1027T was determined using a polyphasic approach. The organism had chemotaxonomic and morphological properties consistent with its classification in the genus Streptomyces and formed a distinct phyletic line in the 16S rRNA gene tree, together with Streptomyces turgidiscabies ATCC 700248T (99.19 % similarity), Streptomyces graminilatus JL-6T (98.84 %) and Streptomyces reticuliscabiei CFBP 4531T (98.36 %). The genomic DNA G+C content of strain Z1027T was 74±1 mol%. The DNA–DNA relatedness values between strain Z1027T and Streptomyces turgidiscabies ATCC 700248T and Streptomyces reticuliscabiei CFBP 4531T were 38.5±0.4 and 26.2±1.2 %, respectively, both of them significantly lower than 70 %. Chemotaxonomic data revealed that strain Z1027T possessed MK-9(H6) and MK-9(H8) as the major menaquinones, ll-diaminopimelic acid as the diagnostic diamino acid and galactose as a whole-cell sugar. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatydilinositol and seven other unknown polar lipids were detected; iso-C16 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0 were the major fatty acids. On the basis of these genotypic and phenotypic data, it is proposed that isolate Z1027T (=CGMCC 4.7272T=JCM 31054T) should be classified as the type strain of a novel species of the genus Streptomyces , Streptomyces lacrimifluminis sp. nov.
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Nonomuraea purpurea sp. nov., an actinomycete isolated from mangrove sediment
A polyphasic approach was used to verify the novel actinomycete, strain 1SM4-01T, isolated from mangrove sediment collected from Ranong Province, Thailand. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the organism was a member of the genus Nonomuraea and was most closely related to Nonomuraea syzygii GKU 164T (98.7 % sequence similarity), Nonomuraea rhizophila YIM 67092T (98.4 %), Nonomuraea solani NEAU-Z6T (98.4 %), Nonomuraea monospora PT708T (98.3 %) and Nonomuraea thailandensis KC-061T (98.2 %). The strain produced branching aerial mycelium which differentiated into straight chains of rough-surfaced spores borne at the end of a short sporophore. The whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid, with madurose, mannose and ribose as the main sugars. MK-9(H4) was a major menaquinone of this strain. The acyl type of peptidoglycan was N-acetyl. The predominant cellular fatty acids were C17 : 1 ω8c and iso-C16 : 0. Phospholipids consisted of diphosphatidylglycerol, hydroxy-phosphatidylethanolamine, hydroxy-phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, aminophospholipids and unidentified lipids. The G+C content of the genomic DNA was 70.4 mol%. On the basis of phenotypic characteristics, DNA–DNA relatedness and phylogenetic distinctiveness, strain 1SM4-01T represents a novel species of the genus Nonomuraea , for which the name Nonomuraea purpurea sp. nov. is proposed. The type strain is 1SM4-01T (=BCC 60397T=NBRC 109647T).
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Nocardiopsis akesuensis sp. nov., an actinomycete isolated from a salt water beach
More LessThe taxonomic position of a novel actinomycete, strain TRM 46250T, isolated from the sediment of a salt water beach at Baicheng, Xinjiang, China, was determined by a polyphasic approach. Strain TRM 46250T grew optimally in the presence of 2 % (w/v) NaCl and an optimum temperature range for growth of 28–37 °C. The whole-cell sugars of strain TRM 46250T were ribose, xylose, mannose and galactose. The diagnostic diamino acid was meso-diaminopimelic acid. The polar lipids were phosphatidylinositol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmethyl ethanolamine and six unidentified phospholipids. The predominant menaquinones were MK-10, MK-10(H6) and MK-10(H8). The major fatty acids were 10-methyl C18 : 0, iso-C16 : 0, C16 : 0, iso-G C16 : 1 and C18 : 1 ω9c. Based on morphological and chemotaxonomic characteristics the isolate was determined to belong to the genus Nocardiopsis . The phylogenetic tree based on its nearly complete 16S rRNA gene sequence (1493 nt) with those of representative strains showed that the strain consistently falls into a distinct phyletic line together with Nocardiopsis gilva YIM 90087T (97.68 % similarity) and a subclade consisting of Nocardiopsis composta KS9T (97.52 %), Nocardiopsis rosea YIM 90094T (97.44 %) and Nocardiopsis rhodophaea YIM 90096T (97.16 %). However, DNA–DNA hybridization studies between strain TRM 46250T and N. gilva YIM 90087T showed only 36.94 % relatedness. On the basis of these data, strain TRM 46250T should be designated as a representative of a novel species of the genus Nocardiopsis , for which the name Nocardiopsis akesuensis sp. nov. is proposed. The type strain is TRM 46250T (=CCTCC AA 2015027T=KCTC 39725T).
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Streptomyces tremellae sp. nov., isolated from a culture of the mushroom Tremella fuciformis
A novel actinomycete strain, designated Js-1T, was isolated from Tremella fuciformis collected from Gutian, Fujian Province, in southeastern China. The taxonomic status of this strain was determined by a polyphasic approach, which demonstrated that the novel strain was a member of the genus Streptomyces . The cell walls of this strain were found to contain ll-diaminopimelic acid, muramic acid and glycine. An analysis of whole-cell hydrolysates revealed that no characteristic sugar was present. The key identified menaquinones were MK-9 (H6) and MK-9 (H8), while the diagnostic polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylmethylethanolamine and phosphatidylglycerol. The main cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and iso-C16 : 0. An analysis of an almost complete 16S rRNA gene sequence showed that the strain shared the highest levels of sequence similarity with Streptomyces sannanensis KC-7038T (97.87 %), Streptomyces hebeiensis YIM 001T (97.84 %), Streptomyces pathocidini NBRC 13812T (97.80 %), Streptomyces cocklensis BK168T (97.25 %), Streptomyces coerulescens NBRC 12758T (97.12 %), Streptomyces aurantiogriseus NBRC 12842T (97.06 %) and Streptomyces rimosus subsp. rimosus ATCC 10970T (97.04 %). The DNA G+C content of the genomic DNA of strain Js-1T was 70.1 mol%. Furthermore, DNA–DNA hybridization tests revealed that the relatedness values between strain Js-1T and the most closely related species ranged from 15.10 to 47.20 %. Based on its phenotypic and genotypic characteristics, strain Js-1T (=CCTCC M 2011365T=JCM 30846T) is considered to represent a novel species within the genus Streptomyces , which we classified as Streptomyces tremellae sp. nov.
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Streptomyces litoralis sp. nov., isolated from a salt water beach
More LessA novel actinomycete strain, designated TRM 46515T, was isolated from a salt water beach at Awat, Xinjiang, Northwest China, and characterized using polyphasic taxonomy. Comparison of 16S rRNA gene sequences showed that strain TRM 46515T is a member of the genus Streptomyces , exhibiting highest similarity with Streptomyces qinglanensis 172205T (98.32 %). However, DNA–DNA relatedness and phenotypic data readily distinguished strain TRM 46515T from phylogenetically related type strains. The G+C content of the DNA was 70.40 mol%. Whole-cell hydrolysates of strain TRM 46515T were found to contain ll-diaminopimelic acid as the diagnostic diamino acid and ribose was the major whole-cell sugar. The major fatty acids identified were anteiso-C17 : 0, anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0. The main menaquinone was MK-9(H8) and the polar lipids were identified as diphosphatidylglycerol, phosphatidyl ethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and one unknown glycolipid. On the basis of these phenotypic, chemotaxonomic and phylogenetic data, strain TRM 46515T should be designated as a representative of a novel species of the genus Streptomyces , for which the name Streptomyces litoralis sp. nov. is proposed. The type strain is TRM 46515T (=CCTCC AA 2015040T=KCTC 39729T).
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Patulibacter brassicae sp. nov., isolated from rhizosphere soil of Chinese cabbage (Brassica campestris)
A novel actinobacterial strain, designated SDT, was isolated from rhizosphere soil of Chinese cabbage in Shandong province, China. The cells were aerobic, Gram-staining-positive, oxidase- and catalase-positive, short rods and formed white colonies on trypticase soy agar. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid and alanine, glutamic acid and leucine. Diphosphatidylglycerol was the predominant polar lipid. The predominant cellular fatty acid was C18 : 1 ω9c; minor components were anteiso-C15 : 0 and anteiso-C17 : 0. The only isoprenoid quinone was demethylmenaquinone 7 (DMK-7), and the DNA G+C content was 72.7 mol%. Based on the full-length 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain SDT were Patulibacter medicamentivorans DSM 25962T (96.9 %), Patulibacter minatonensis DSM 18081T (96.7 %), Patulibacter americanus DSM 16676T (96.2 %) and Patulibacter ginsengiterrae DSM 25990T (95.9 %). Considering combined phenotypic and genotypic characteristics, it is proposed that strain SDT represents a novel species of the genus Patulibacter , for which the name Patulibacter brassicae sp. nov. is proposed. The type strain is SDT (=CICC 24108T=KCTC 39817T).
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Tersicoccus solisilvae sp., nov., a bacterium isolated from forest soil
A Gram-stain-positive, aerobic, non-motile, coccoid bacterial strain, 36AT, was isolated from Munnar, in India. Based on the results of 16S rRNA gene sequence analysis, this strain was identified as representing a member of the genus Tersicoccus and was most closely related to the type strain of Tersicoccus phoenicis (98.9 %, sequence similarity), the only other member of the genus, and to members of the related genus Arthrobacter (<96.1 %, sequence similarity). However, the DNA–DNA relatedness of strain 36AT with T. phoenicis DSM 30849T was only 31.9±0.8. The DNA G+C content of strain 36AT was 70.9 mol%. Strain 36AT was an aerobic microbe with optimal growth at 37 °C, pH 6.0–8.0 and NaCl 0.5-3 % (w/v). Cell-wall peptidoglycan of strain 36AT was of type A11.20 (Lys–Ser–Ala2). Polar lipids present were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, two phospholipids, a glycolipid and four unknown lipids. The major isoprenoid quinones were MK-9 (H2) and MK-8 (H2). Major fatty acids of strain 36AT were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. The results of phylogenetic, chemotaxonomic and biochemical tests allowed a clear differentiation of strain 36AT, which represents a novel member of the genus Tersicoccus , for which the name Tersicoccus solisilvae sp. nov., is proposed. The type strain is 36AT (=KCTC 33776T=CGMCC 1.15480T).
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Nocardiopsis rhizosphaerae sp. nov., isolated from rhizosphere soil of Halocnermum strobilaceum (Pall.) Bieb
An alkalitolerant actinomycete strain, designated EGI 80674T, was isolated from a rhizosphere soil of Halocnermumstrobilaceum (Pall.) Bieb in Xinjiang, north-west China and subjected to a taxonomic characterization using a polyphasic approach. Strain EGI 80674T formed white aerial hyphae with long spore chains. Whole-cell hydrolysates of the isolate contained meso-diaminopimelic acid as the diagnostic diamino acid with no diagnostic sugars. The major fatty acids identified were iso-C16 : 0, anteiso-C17 : 0 and 10-methyl-C18 : 0TBSA. The predominant menaquinones detected were MK-10(H8) and MK-10(H6). The G+C content of the genomic DNA of strain EGI 80674T was 70.9 mol%. Strain EGI 80674T showed the highest 16S rRNA gene sequence similarity (97.24 %) to Nocardiopsis nikkonensis NBRC 102170T. The DNA–DNA relatedness value of strain EGI 80674T and N. nikkonensis NBRC 102170T was 18.4±1.3 %. Phenotypical, chemotaxonomic and phylogenetic characteristics and DNA–DNA hybridization data suggest that strain EGI 80674T represents a novel species of the genus Nocardiopsis , for which the name Nocardiopsis rhizosphaerae sp. nov. is proposed. The type strain is EGI 80674T (=CGMCC 4.7228T=KCTC 39673T).
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Saccharomonospora xiaoerkulensis sp. nov., isolated from lake sediment
More LessA novel actinomycete, strain TRM 41495T, was isolated from lake sediment of Xiaoerkule lake in Xinjiang province, China, and was examined using a polyphasic approach. Strain TRM 41495T was aerobic, Gram-stain-positive, growing best on ISP medium 7 with abundant white aerial mycelium formed and brown soluble pigments produced. The optimum NaCl concentration for growth was 3.0 % (w/v), and the optimum temperature for growth was 37 °C. On the basis of 16S rRNA gene sequence analysis, strain TRM 41495T was shown to belong to the genus Saccharomonospora with a sequence similarity of 97.50 % with the most closely related species, Saccharomonospora xinjiangensis . The organism had chemical and morphological features typical of the genus Saccharomonospora . The cell wall of strain TRM 41495T contained meso-diaminopimelic acid, and galactose, arabinose, ribose and mannose were the major whole-cell sugars. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and an unknown phosphoglycolipid. The predominant menaquinones were MK-9(H4) and MK-9(H2). The major fatty acids were iso-C16 : 0, C16 : 0, C17 : 1ω6c, anteiso-C17 : 0 and iso-C16 : 1H. The G+C content of the DNA was 72.9 mol%. However, DNA–DNA hybridization studies between strain TRM 41495T and Saccharomonospora xinjiangensis showed only 43.9 % relatedness. Whole-cell sugars, menaquinones and fatty acids differentiate strain TRM 41495T from Saccharomonospora xinjiangensis . On the basis of the polyphasic evidence, strain TRM 41495T represents a novel species of the genus Saccharomonospora , for which the name Saccharomonospora xiaoerkulensis sp. nov. is proposed. The type strain is TRM 41495T (=CCTCC AA 2015038T=KCTC 39727T).
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Proposal of a type strain for Frankia alni (Woronin 1866) Von Tubeuf 1895, emended description of Frankia alni, and recognition of Frankia casuarinae sp. nov. and Frankia elaeagni sp. nov.
Before the establishment of pure cultures, the species Frankia alni , ‘ Frankia casuarinae ’ and ‘ Frankia elaeagni ’ were proposed to encompass all causal agents of the nitrogen-fixing root nodules of dicotyledonous plants from the genera Alnus, Casuarina or Elaeagnus. The sole Frankia species with a validly published name, the type species F. alni , was described by Woronin (1866) as present in the root of alder. Until now no type strain has been designated for F. alni , even though the absence of a type strain has seriously inhibited the application of modern taxonomic methods to the genus Frankia . Thus, we propose that strain ACN14aT, isolated in pure culture from Alnus viridis ssp. crispa with morphological properties matching the original description of F. alni , be recognized as the type strain of this species according to Rule 18f of the International Code of Nomenclature of Bacteria. We compared ACN14aT to two strains, CcI3T and BMG5.12T, isolated from Casuarina cunninghamiana and Elaeagnus angustifolia, respectively, based on chemotaxonomy, phenotype microarray data and molecular data retrieved from genome sequences. All three tested strains grew as branched hyphae, produced vesicles and multilocular sporangia containing non-motile spores and metabolized short fatty acids, TCA-cycle intermediates and carbohydrates. Chemotaxonomically, the three strains were indistinguishable with respect to phospholipids (phosphatidylinositol, diphosphatidylglycerol, glycophospholipids and phosphatidylglycerol) and cell-sugar composition (glucose, mannose, ribose, rhamnose, galactose and xylose, with the latter two being diagnostic for the genus). The major fatty acids identified in all three strains were iso-C16 : 0, C17 : 1 ω8c, C15 : 0, C17 : 0 and C16 : 0. ACN14aT and BMG5.12T also shared C15 : 1 ω6c, while C18 : 1 ω9c was found to be unique to BMG5.12T. The major menaquinones identified in all three novel type strains were MK-9(H8), MK-9(H6) and MK-9(H4). MK-9(H2) was shared by ACN14aT and BMG5.12T, while MK-10(H4) and MK-8(H4) were only found in BMG5.12T. Analysis of 16S rRNA gene sequences showed 98.1–98.9 % identity between strains ACN14aT, CcI3T and BMG5.12T. Digital DNA–DNA hybridization values between the three type strains were well below 70 %. These results confirm the separation of the strains into three distinct species, Frankia alni , Frankia casuarinae sp. nov. and Frankia elaeagni sp. nov. Thus, we propose ACN14aT (=DSM 45986T=CECT 9034T), CcI3T (=DSM 45818T=CECT 9043T) and BMG5.12T (=DSM 46783T=CECT 9031T) as the respective type strains.
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Frigoribacterium salinisoli sp. nov., isolated from saline soil, transfer of Frigoribacterium mesophilum to Parafrigoribacterium gen. nov. as Parafrigoribacterium mesophilum comb. nov.
A Gram-stain-positive, short-rod, aerobic bacterium, designated as strain LAM9155T, was isolated from saline soil sample collected from Lingxian County, Shandong Province, PR China. The strain grew optimally at 25–30 °C, pH 7.0 and 0.5 % (w/v) NaCl. The 16S rRNA gene sequence analysis revealed that strain LAM9155T belonged to the genus Frigoribacterium and was closely related to Frigoribacterium endophyticum EGI 6500707T (99.4 %), Frigoribacterium faeni 801T (98.6 %) and Frigoribacterium mesophilum MSL-08T (96.2 %). The DNA–DNA hybridization values between strain LAM9155T and F. endophyticum JCM 30093T and between strain LAM9155T and F. faeni DSM 10309T were 40.2±2.1 and 32.8±1.6 %, respectively. The major fatty acids of LAM9155T were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The cell-wall analysis showed the B-type peptidoglycan containing alanine, glutamate, glycine, serine and lysine and that the cell wall contained the sugars galactose and ribose. The genomic DNA G+C content of strain LAM9155T was 68.2 mol%. The predominant menaquinone was MK-9. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unknown glycolipid and four unknown lipids. Based on the DNA–DNA hybridization and phenotypic, phylogenetic and chemotaxonomic properties, strain LAM9155T could be distinguished from the recognized species of the genus Frigoribacterium and was suggested to represent a novel species, for which the name Frigoribacterium salinisoli sp. nov. is proposed. The type strain is LAM9155T (=ACCC 19902T=JCM 30848T). Moreover, the transfer of F . mesophilum Dastager et al. 2008 to Parafrigoribacterium gen. nov. as Parafrigoribacterium mesophilum comb. nov. (type strain MSL-08T=DSM 19442T=KCTC 19311T) is also proposed.
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Brevibacterium sediminis sp. nov., isolated from deep-sea sediments from the Carlsberg and Southwest Indian Ridges
More LessThree actinobacterial strains, FXJ8.128, FXJ8.269T and FXJ8.309, were isolated from deep-sea sediments collected from the Carlsberg Ridge and Southwest Indian Ridge at depths of 3690, 1800 and 2461 m, respectively. The three strains had highly similar 16S rRNA gene sequences (99.8–99.9 % identities) and formed a monophyletic clade within the Brevibacterium 16S rRNA gene tree, showing 98.2–98.9 % 16S rRNA gene sequence identities with type strains Brevibacterium epidermidis NCIMB 702286T, Brevibacterium iodinum DSM 20626T, Brevibacterium linens DSM 20425T, Brevibacterium oceani BBH7T and Brevibacterium permense VKM Ac-2280T. All three isolates showed activity towards the breakdown of pectin and fluoranthene. They contained MK-8(H2) as the most predominant menaquinone, diphosphatidylglycerol, phosphatidylglycerol and a glycolipd as the main polar lipids, and anteiso-C15 : 0 and anteiso-C17 : 0 as the major cellular fatty acids. Moreover, the three isolates were distinguished readily from the phylogenetically related type strains by DNA–DNA hybridization values, by random amplified polymorphic DNA fingerprint profiles and by a range of physiological and biochemical characteristics. On the basis of the above polyphasic taxonomic data, strains FXJ8.128, FXJ8.269T and FXJ8.309 represent a novel species of the genus Brevibacterium , for which the name Brevibacterium sediminis sp. nov. is proposed. The type strain is FXJ8.269T (=CGMCC 1.15472T=DSM 102229T).
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Nocardioides flavus sp. nov., isolated from marine sediment
More LessA Gram-stain-positive, aerobic, non-motile, non-spore-forming and short rod-shaped actinomycete strain, Y4T, was isolated from a sediment sample collected from the Western Pacific. This isolate grew in the presence of 0–10 % (w/v) NaCl and at pH 6.0–9.0 and 4–40 °C; optimum growth was observed with 1 % (w/v) NaCl and at pH 7.0 and 35–37 °C. Phylogenetic analyses based on 16S rRNA gene sequence showed that strain Y4T belonged to the genus Nocardioides and was most closely related to the type strains Nocardioides ganghwensis JC2055T (98.0 %) and Nocardioides exalbidus RC825T (98.0 %), followed by Nocardioides alpinus Cr7-14T (97.9 %), Nocardioides oleivorans DSM 16090T (97.9 %), Nocardioides furvisabuli SBS-26T (97.4 %) and Nocardioides hwasunensis HFW-21T (97.4 %). Sequence similarities between strain Y4T and the other related species of the genus Nocardioides were less than 96.3 %. Strain Y4T had MK-8(H4) and MK-7(H4) as the predominant respiratory quinones and C17 : 1ω8c, iso-C16 : 0 and C17 : 0 as major fatty acids. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown phospholipid, two unknown glycolipids and one unknown lipid. The DNA G+C content was 70.4 mol%. The diagnostic diamino acid in the cell-wall peptidoglycan was ll-diaminopimelic acid. Strain Y4T could be differentiated from recognized Nocardioides species based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA–DNA hybridization data. Thus, strain Y4T is considered to represent a novel species of the genus Nocardioides , for which the name Nocardioides flavus sp. nov. is proposed. The type strain is Y4T (=MCCC 1A09944T=LMG 28100T=JCM 19770T=CGMCC 1.12791T).
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Corynebacterium crudilactis sp. nov., isolated from raw cow's milk
More LessA Gram-stain-positive, rod-shaped bacterium (strain JZ16T) was isolated from raw cow's milk from the bulk tank of a dairy farm in Germany. The 16S rRNA gene sequence of the isolate showed a similarity of 98.3 % to the nearest related type strain Corynebacterium glutamicum ATCC 13032T, a similarity of 97.6 % to Corynebacterium deserti GIMN1.010T and a similarity of 97.4 % to Corynebacterium callunae DSM 20147T. Determination of chemotaxonomic characteristics revealed oleic acid (18 : 1 cis 9) as the predominant fatty acid, major amounts of hexadecanoic acid (16 : 0) and minor amounts of heptadecanoic acid (17 : 0). The isolate showed an acetyl type of peptidoglycan and corynemycolic acids. The menaquinones MK-8(H2) and MK-9(H2) and the phospholipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside were detected, which was in agreement with the description of the genus Corynebacterium . Strain JZ16T was positive for reduction of nitrate to nitrite, pyrazinamidase, β-glucuronidase, β-glucosidase and urease activities. Acid was produced from d-glucose, d-ribose and d-mannitol, but not from d-xylose, maltose, lactose, sucrose and glycogen. The results of phylogenetic, phenotypic and chemotaxonomic analyses enabled the differentiation of the isolated strain from other closely related species of the genus Corynebacterium . Therefore, strain JZ16T represents a novel species of the genus Corynebacterium , for which the name Corynebacterium crudilactis sp. nov. is proposed. The type strain is JZ16T (=DSM 100882T=CCUG 69192T=LMG 29813T).
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Phycicoccus ginsengisoli sp. nov., isolated from cultivated ginseng soil
Ginseng-cultivated soil is an excellent habitat for soil-borne bacteria to proliferate. A novel strain, DCY87T, was isolated from ginseng-cultivated soil in Gochang County, Republic of Korea, and subsequently characterized by polyphasic approach. Cells were rod shaped, non-motile, aerobic, Gram-reaction-positive, oxidase-negative and catalase-positive. 16S rRNA gene sequence analysis showed that strain DCY87T shared the highest similarity to ‘ Phycicoccus ochangensis ’ L1b-b9 (98.7 %). Closely phylogenetic relatives of strain DCY87T were identified: Phycicoccus ginsenosidimutans BXN5-13T (97.9 %), Phycicoccus soli THG-a14T (97.8 %), Phycicoccus bigeumensis MSL-03T (97.3 %), Phycicoccus cremeus V2M29T (97.3 %), Phycicoccus aerophilus 5516T-20T (97.3 %), Phycicoccus dokdonensis DS-8T (97.3 %) and Phycicoccus jejuensis KSW2-15T (97.1 %). The major polar lipids were classified as phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were composed of iso-C15 : 0, anteiso-C15:0, C17 : 0 and C17 : 1 ω8c. The menaquinone was resolved as MK-8(H4). Strain DCY87T contained meso-diaminopimelic acid as diamino acid in the cell-wall peptidoglycan and glucose, xylose and rhamnose in the whole-cell sugar. The genomic DNA G+C content was calculated to be 72.7 mol%. DNA–DNA hybridization value between strain DCY87T and ‘ P. ochangensis ’ L1b-b9 was estimated to be 50 %. However, DNA–DNA hybridization value obtained between strain DCY87T and P. ginsenosidimutans BXN5-13T, P. soli THG-a14T and P. bigeumensis MSL-03T was well below 17 %. In general, polyphasic taxonomy demonstrated that DCY87T strain represented a novel species within the genus Phycicoccus . Accordingly, we propose the name Phycicoccus ginsengisoli sp. nov. The type strain is DCY87T (=KCTC 39635T=JCM 31016T).
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Streptomyces kronopolitis sp. nov., an actinomycete that produces phoslactomycins isolated from a millipede (Kronopolites svenhedind Verhoeff)
More LessA phoslactomycin-producing actinomycete, designated strain NEAU-ML8T, was isolated from a millipede (Kronopolites svenhedind Verhoeff) and characterized using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain NEAU-ML8T belongs to the genus Streptomyces with the highest sequence similarities to Streptomyces lydicus NBRC 13058T (99.39 %) and Streptomyces chattanoogensis DSM 40002T (99.25 %). The maximum-likelihood phylogenetic tree based on 16S rRNA gene sequences showed that the isolate formed a distinct phyletic line with NBRC 13058T and S. chattanoogensis DSM 40002T. This branching pattern was also supported by the tree rconstructed with the neighbour-joining method. A combination of DNA–DNA hybridization experiments and phenotypic tests were carried out between strain NEAU-ML8T and its phylogenetically closely related strains, which further clarified their relatedness and demonstrated that NEAU-ML8T could be distinguished from NBRC 13058T and S. chattanoogensis DSM 40002T. Therefore, it is concluded that strain NEAU-ML8T can be classified as representing a novel species of the genus Streptomyces , for which the name Streptomyces kronopolitis sp. nov. is proposed. The type strain is NEAU-ML8T (=DSM 101986T=CGMCC 4.7323T).
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Proposal to reclassify Propionibacterium acnes type I as Propionibacterium acnes subsp. acnes subsp. nov. and Propionibacterium acnes type II as Propionibacterium acnes subsp. defendens subsp. nov.
More LessRecently, it has been proposed that strains of Propionibacterium acnes from the type III genetic division should be classified as P. acnes subsp. elongatum subsp. nov., with strains from the type I and II divisions collectively classified as P. acnes subsp. acnes subsp. nov. Under such a taxonomic re-appraisal, we believe that types I and II should also have their own separate rank of subspecies. In support of this, we describe a polyphasic taxonomic study based on the analysis of publicly available multilocus and whole-genome sequence datasets, alongside a systematic review of previously published phylogenetic, genomic, phenotypic and clinical data. Strains of types I and II form highly distinct clades on the basis of multilocus sequence analysis (MLSA) and whole-genome phylogenetic reconstructions. In silico or digital DNA–DNA similarity values also fall within the 70–80 % boundary recommended for bacterial subspecies. Furthermore, we see important differences in genome content, including the presence of an active CRISPR/Cas system in type II strains, but not type I, and evidence for increasing linkage equilibrium within the separate divisions. Key biochemical differences include positive test results for β-haemolytic, neuraminidase and sorbitol fermentation activities with type I strains, but not type II. We now propose that type I strains should be classified as P. acnes subsp. acnes subsp. nov., and type II as P. acnes subsp. defendens subsp. nov. The type strain of P. acnes subsp. acnes subsp. nov. is NCTC 737T (=ATCC 6919T=JCM 6425T=DSM 1897T=CCUG 1794T), while the type strain of P. acnes subsp. defendens subsp. nov. is ATCC 11828 (=JCM 6473=CCUG 6369).
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Glycomyces lacisalsi sp. nov., an actinomycete isolated from a hypersaline habitat
More LessA novel actinomycete strain, designated XHU 5089T, was isolated from a hypersaline habitat in China. The strain was aerobic, Gram-stain-positive and the optimum NaCl concentration for growth was 1–3 % (w/v). Phylogenetic analysis based on the almost-complete 16S rRNA gene sequence of strain XHU 5089T showed that the organism was related most closely to Glycomyces albus TRM 49136T (97.7 % similarity). However, it had a relatively low mean DNA–DNA relatedness value with G. albus TRM 49136T (18.9±5.8 %). The whole-cell sugar pattern consisted of glucose and galactose. The predominant menaquinones were MK-10(H4) and MK-9(H4). The major fatty acids were anteiso-C15 : 0, iso-C16 : 0, iso-C16 : 1 and anteiso-C17 : 0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unidentified glycolipids and two unknown phospholipids. The G+C content of the genomic DNA was 68.6 mol%. A novel species, Glycomyces lacisalsi sp. nov., is proposed, with XHU 5089T (=CCTCC AA 2015034T=KCTC 39688T) as the type strain.
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Huakuichenia soli gen. nov., sp. nov., a new member of the family Microbacteriaceae, isolated from contaminated soil
More LessA novel Gram-stain-positive, non-motile, rod-shaped bacterial strain designated LIP-1T was isolated from the contaminated soil of a pesticide factory in Xinyi, China, was investigated for its taxonomic allocation by a polyphasic approach. Cell growth occurred at 16–37 °C (optimum, 30 °C), in the presence of 0–2.0 % (w/v) NaCl (optimum, 0 %) and at pH 6.0–9.0 (optimum, pH 7.0). The major fatty acids of strain LIP-1T were anteiso-C15 : 0 (50.8 %), iso-C16 : 0 (17.6 %) and anteiso-C17 : 0 (17.4 %). The cell-wall peptidoglycan type was B2δ with 2,4-diaminobutyric acid as the diagnostic diamino acid. The major polar lipids were diphosphatidylglycerol and two unidentified glycolipids. The major menaquinones were MK-12 and MK-11. The genomic DNA G+C content was approximately 63.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain LIP-1T formed a distinct clade within the radiation of the family Microbacteriaceae and had the highest sequence similarity with Microbacterium ginsengisoli Gsoil 259T (96.01 %) followed by Cryobacterium arcticum SK1T (94.94 %). On the basis of the phylogenetic analyses and distinct phenotypic characteristics, a new genus, namely Huakuichenia gen. nov., is proposed, harbouring the novel species Huakuichenia soli gen. nov., sp. nov. with the type strain LIP-1T (=CCTCC AB 2015422T=KCTC 39698T).
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Verrucosispora sonchi sp. nov., a novel endophytic actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.)
A novel actinobacterium, designated strain NEAU-QY3T, was isolated from the leaves of Sonchus oleraceus L. and examined using a polyphasic taxonomic approach. The organism formed single spores with smooth surface on substrate mycelia. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the strain had a close association with the genus Verrucosispora and shared the highest sequence similarity with Verrucosispora qiuiae RtIII47T (99.17 %), an association that was supported by a bootstrap value of 94 % in the neighbour-joining tree and also recovered with the maximum-likelihood algorithm. The strain also showed high 16S rRNA gene sequence similarities to Xiangella phaseoli NEAU-J5T (98.78 %), Jishengella endophytica 202201T (98.51 %), Micromonospora eburnea LK2-10T (98.28 %), Verrucosispora lutea YIM 013T (98.23 %) and Salinispora pacifica CNR-114T (98.23 %). Furthermore, phylogenetic analysis based on the gyrB gene sequences supported the conclusion that strain NEAU-QY3T should be assigned to the genus Verrucosispora . However, the DNA–DNA hybridization relatedness values between strain NEAU-QY3T and V. qiuiae RtIII47T and V. lutea YIM 013T were below 70 %. With reference to phenotypic characteristics, phylogenetic data and DNA–DNA hybridization results, strain NEAU-QY3T was readily distinguished from its most closely related strains and classified as a new species, for which the name Verrucosispora sonchi sp. nov. is proposed. The type strain is NEAU-QY3T (=CGMCC 4.7312T=DSM 101530T).
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Nakamurella silvestris sp. nov., an actinobacterium isolated from alpine forest soil
A Gram-stain-positive, non-motile, catalase-positive and cytochrome c oxidase-negative bacterium, designated strain S20-107T, was isolated from alpine forest soil. Growth occurred at 0–30 °C, at pH 6–9 and in the presence of 0–3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S20-107T was related to the genus Nakamurella and had the highest 16S rRNA gene sequence similarity with Nakamurella flavida DS-52T (96.1 %). Strain S20-107T showed <96.1% 16S rRNA gene sequence similarities to all other recognized members of the genus Nakamurella . The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major whole-cell sugars were glucose, galactose, mannose, arabinose, ribose and rhamnose. The strain contained MK-8(H4) as the predominant menaquinone and diphosphatidylglycerol, phosphatidylethanolamine and an unidentified aminophospholipid as the major polar lipids. The major cellular fatty acids were anteiso-C15 : 0, C16 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c and/or iso-C15 : 0 2-OH) and iso-C16 : 0. The genomic DNA G+C content was 70.5 mol%. Combined data of phylogenetic, phenotypic and chemotaxonomic analyses demonstrated that strain S20-107T represents a novel species of the genus Nakamurella , for which the name Nakamurella silvestris sp. nov. is proposed. The type strain is S20-107T (=DSM 102309T=LMG 29427T).
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Oceanitalea nanhaiensis Fu et al. 2012 is a later heterotypic synonym of Georgenia satyanarayanai Srinivas et al. 2012
More LessOceanitalea nanhaiensis JLT1488T was compared with Georgenia satyanarayanai KCTC 19802T to clarify the taxonomic relationship of both species because they are phylogenetically highly related. 16S rRNA gene sequence comparisons demonstrated that these species share 99.6 % sequence similarity. Investigation of fatty acid patterns and substrate utilization profiles displayed no striking differences of the type strains of both species. DNA–DNA hybridizations between both strains showed a 100 % similarity clearly demonstrating that both strains are members of a single species. Due to priority Oceanitalea nanhaiensis is reclassified as Georgenia satyanarayanai , based on the estimated phylogenetic position derived from 16S rRNA gene sequence data, fatty acid, polar lipid and biochemical data, and DNA–DNA hybridization results.
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Raineyella antarctica gen. nov., sp. nov., a psychrotolerant, d-amino-acid-utilizing anaerobe isolated from two geographic locations of the Southern Hemisphere
A Gram-stain-positive bacterium, strain LZ-22T, was isolated from a rhizosphere of moss Leptobryum sp. collected at the shore of Lake Zub in Antarctica. Cells were motile, straight or pleomorphic rods with sizes of 0.6–1.0×3.5–10 µm. The novel isolate was a facultatively anaerobic, catalase-positive, psychrotolerant mesophile. Growth was observed at 3–41 °C (optimum 24–28 °C), with 0–7 % (w/v) NaCl (optimum 0.25 %) and at pH 4.0–9.0 (optimum pH 7.8). The quinone system of strain LZ-22T possessed predominately menaquinone MK-9(H4). The genomic G+C content was 70.2 mol%. Strain 10J was isolated from a biofilm of sediment microbial fuel cell, in Uruguay and had 99 % 16S rRNA gene sequence similarity to strain LZ-22T. DNA–DNA-hybridization values of 84 % confirmed that both strains belonged to the same species. Both strains grew on sugars, proteinaceous compounds, and some amino- and organic acids. Strain LZ-22T uniquely grew on D-enantiomers of histidine and valine while neglecting growth on L-enantiomers. Both strains were sensitive to most of the tested antibiotics but resistant to tested nitrofurans and sulfanilamides. Phylogenetic analyses of the 16S rRNA gene sequences indicated that the strains were related to members of the family Propionibacteriaceae (~93–94 % 16S rRNA gene sequence similarity) with formation of a separate branch within the radiation of the genera Granulicoccus and Luteococcus . Based on phenotypic and genotypic characteristics, we propose the affiliation of both strains into a novel species of a new genus. The name Raineyella antarctica gen. nov., sp. nov. is proposed for the novel taxon with the type strain LZ-22T (=ATCC TSD-18T=DSM 100494T=JCM 30886T).
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Microbacterium sorbitolivorans sp. nov., a novel member of Microbacteriaceae isolated from fermentation bed in pigpen
More LessTwo bacterial strains SZDIS-1-1T and GZDIS-1-1 were isolated from fermentation bed of a pigpen in Fujian Province, China. Cells were Gram-stain-positive, facultatively anaerobic, short rods without flagellum. Their nearest phylogenetic neighbours were Microbacterium amylolyticum N5T (16S rRNA gene sequence similarity 98.2 %), Microbacterium indicum BBH6T (97.9 %) and Microbacterium gubbeenense DPC 5286T (97.8 %) with the DNA–DNA hybridization values to strain SZDIS-1-1T as 20.0±1.2, 14.3±5.8 and 19.1±1.6 %, respectively. The DNA G+C content of the new isolates was 67.6–71.1 mol% and anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 were their predominant cellular fatty acids. These results were consistent with classification into the genus Microbacterium . However, cell-wall sugars and characteristic amino acid were rhamnose, glucose, galactose and ornithine. Major menaquinones were MK-11 and MK-10. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, glycolipids, unknown phospholipid and unknown lipids. These characteristics constructed a distinct profile of the two isolates. Therefore, based on polyphasic taxonomic characteristics, strains SZDIS-1-1T and GZDIS-1-1 represented a novel species of genus Microbacterium , for which the name Microbacterium sorbitolivorans sp. nov. is proposed, with strain SZDIS-1-1T (=CGMCC 1.15228T=DSM 103422T) as the type strain.
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- Archaea
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Halopiger thermotolerans sp. nov., a thermo-tolerant haloarchaeon isolated from commercial salt
Three thermo-tolerant halophilic archaeal strains, SR-441T, SR-412 and SR-188, were isolated from commercial salt samples. Cells were non-motile pleomorphic rod-shaped, and stained Gram-negative. Colonies were pink-pigmented. The three strains were able to grow with 1.7–4.6 M NaCl (optimum, 2.5 M), at pH 6.5–9.0 (optimum, pH 8.0) and at 35–60 °C (optimum, 45 °C). The orthologous 16S rRNA gene sequence similarities amongst the three strains were 98.8–99.3 %, and the level of DNA–DNA relatedness was 71–74 and 72–75 % (reciprocally). The closest relative was Halopiger aswanensis JCM 11628T with 98.6 %–99.1 % similarity in the orthologous 16S rRNA gene sequences, followed by two more Halopiger species, Halopiger xanaduensis JCM 14033T (98.5 %–99.1 %) and Halopiger salifodinae JCM 9578T (95.5 %–95.6 %). DNA–DNA relatednesses between the three strains and H. aswanensis JCM 11628T and H. xanaduensis JCM 14033T were 61 and 54 %, respectively. The polar lipids of the three novel strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, and bis-sulfated diglycosyl archaeol-1. The most distinctive feature of the three strains was the ability to grow at 60 °C, while the maximum growth temperature of H. aswanensis is 55 °C. Based on phenotypic and phylogenetic analyses, the isolates are considered to represent a novel species of the genus Halopiger , for which the name Halopiger thermotolerans sp. nov. is proposed. The type strain is SR-441T (=JCM 19583T=KCTC 4248T) isolated from solar salt produced in Australia. SR-412 (=JCM 19582) and SR-188 (=JCM 19581) isolated from commercial salt samples are additional strains of the species.
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Haloparvum alkalitolerans sp. nov., alkali-tolerant haloarchaeon isolated from commercial salt
A Gram-stain-negative, rod-pleomorphic, aerobic, halophilic archaeon, strain MK62-1T, was isolated from commercial salt made from seawater in the Philippines. Strain MK62-1T was able to grow at 2.1–4.7 M NaCl (with optimum at 2.1–2.6 M NaCl), pH 6.5–9.5 (optimum, pH 7.0–7.5) and 20–55 °C (optimum, 45–50 °C). Based on the orthologous 16S rRNA gene sequence, the closest relative was Haloparvum sedimenti JCM 30891T with 99.2 % similarity. The RNA polymerase subunit B′ gene sequence also showed the highest similarity (97.4 %) to that of Haloparvum sedimenti DYS4T. The DNA G+C content of MK62-1T was 70.1 mol%, while that of Haloparvum sedimenti JCM 30891T was 69.5 mol% by the HPLC method. The levels of DNA–DNA relatedness between MK62-1T and Haloparvum sedimenti JCM 30891T were 60.6 and 60.8 % (reciprocally). The major polar lipids of the isolate were C20C20 archaeol derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate. Based on the phenotypic and phylogenetic analyses, it is proposed that the isolate represents species within the genus Haloparvum , for which the name Haloparvum alkalitolerans sp. nov. is proposed. The type strain is MK62-1T (=JCM 30442T =KCTC 4214T).
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- Bacteroidetes
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Pelobium manganitolerans gen. nov., sp. nov., isolated from sludge of a manganese mine
More LessA Gram-staining-negative, rod-shaped, motile by gliding and facultative anaerobic bacterial strain, YS-25T, was isolated from a sludge of a manganese mine. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YS-25T formed a single branch within the strains of the family Sphingobacteriaceae and showed low similarities to Pedobacter arcticus CCTCC AB 2010223T (91.7 %), ‘ Pedobacter zeaxanthinifaciens ’ TDMA-5 (91.5 %), Pedobacter terricola DS-45T (90.9 %), Pedobacter ureilyticus THG-T11T (90.9 %), Pseudopedobacter beijingensis MCCC 1A01299T (90.8 %) and Pedobacter heparinus CCTCC AB 209030T (88.5 %). Strain YS-25T had some unique physiological and biochemical characteristics: facultative anaerobic, able to hydrolyse Tween 40, positive for cystine arylamidase and negative for mannose assimilation and β-galactosidase. The polar lipids of strain YS-25T were phosphatidylethanolamine, aminolipid, two unknown lipids and two glycolipids. The presence of glycolipids and absence of sphingolipid were different from the Pedobacter and Pseudopedobacter strains. The major fatty acids (>5 %) were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c), unknown ECL 13.565, iso-C17 : 0 3-OH, iso-C17 : 1 ω9c and anteiso-C15 : 0. The genomic DNA G+C content was 42.0 mol%, and the only respiratory quinone was menaquinone 7. On the basis of polyphasic taxonomic analyses, strain YS-25T is considered to represent a novel genus and species, for which the name Pelobium manganitolerans gen. nov., sp. nov. is proposed. The type strain is YS-25T (=KCTC 52203T=CCTCC AB 2016051T).
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Sphingobacterium chuzhouense sp. nov., isolated from farmland soil
A novel Gram-staining-negative bacterium, designated DH-5T, was isolated from a farmland soil in Chuzhou, Anhui province, China. Cells of strain DH-5T were aerobic, non-motile, non-spore-forming and rod-shaped. The organism grew at 20–37 °C, pH 6.0–9.0 and with 0–5 % NaCl (w/v). The DNA G+C content was 42.8 mol%. The major fatty acids (>5 %) were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and C16 : 0. The respiratory quinone was MK-7, and the major polar lipids were phosphatidylethanolamine and phosphoglycolipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DH-5T was a member of the genus Sphingobacterium and shared the highest similarity with Sphingobacterium gobiense H7T (96.0 %), followed by Sphingobacterium arenae H-12T (94.5 %). Strain DH-5T exhibited low DNA–DNA relatedness with S. gobiense H7T (35.1±1.4 %) and S. arenae H-12T (21.4±1.0 %). On the basis of phenotypic, genotypic and phylogenetic evidence, DH-5T is considered to represent a novel species of the genus Sphingobacterium , for which the name Sphingobacterium chuzhouense sp. nov. is proposed. The type strain is DH-5T (=ACCC 19856T=KCTC 42746T).
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Pedobacter vanadiisoli sp. nov., isolated from soil of a vanadium mine
More LessA Gram-stain-negative, light pink, non-motile, rod-shaped, aerobic bacterium, designated strain XNV015T, was isolated from soil of a vanadium mine. Phylogenetic analyses based on 16S rRNA gene sequences indicated that it belongs to the genus Pedobacter and was closely related to Pedobacter suwonensis DSM 18130T (96.93 % sequence similarity), Pedobacter alluvionis NWER-II11T (96.66 %), Pedobacter terrae DS-57T (96.54 %), Pedobacter kyungheensis KACC 16221T (96.54 %) and Pedobacter soli KACC 14939T (96.47 %). This strain clearly differed from the closely related species in terms of acid production from rhamnose and ethanol. Menaquinone-7 was the predominant respiratory quinone. The predominant fatty acids included iso-C15 : 0, C16 : 1 ω5c, summed feature 3, iso-C17 : 0 3-OH and C17 : 0 2-OH. The major polar lipids were phosphatidylethanolamine, glycolipids, lipids and aminolipids. The genomic DNA G+C content was 43.8 mol%. The genotypic analysis, biochemical properties, and phenotypic and chemotaxonomic characteristics indicate that strain XNV015T represents a novel species of the genus Pedobacter , for which the name Pedobacter vanadiisoli sp. nov. is proposed. The type strain is XNV015T (=CCTCC AB 2015319T=KCTC 42866T).
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Psychroflexus saliphilus sp. nov., isolated from a marine solar saltern
More LessA Gram-stain-negative, non-motile, rod-shaped, orange-pigmented strain, WDS4A13T, was isolated from a marine solar saltern in Weihai, China. Strain WDS4A13T grew under optimal conditions of pH 7.0–8.0, 33 °C and with 6 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain WDS4A13T belonged to the genus Psychroflexus . The levels of similarity between the 16S rRNA gene sequence of strain WDS4A13T and those of the type strains of recognized species of the genus Psychroflexus were 92.0–97.3 %. The polar lipid profile of the novel isolate consisted of two unidentified phospholipids, diphosphatidylglycerol, phosphatidylethanolamine, a glycolipid and an unidentified lipid as the major polar lipids. The predominant menaquinone was MK-6, and iso-C15 : 1 G, iso-C15 : 0 and C15 : 0 were the major fatty acids. The DNA G+C content was 35.2 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain WDS4A13T represents a novel species within the genus Psychroflexus , for which the name Psychroflexus saliphilus sp. nov. is proposed. The type strain is WDS4A13T (=MCCC 1H00134T=KCTC 52043T).
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Mucilaginibacter antarcticus sp. nov., isolated from tundra soil
More LessThe novel, pale yellow bacterial strain, designated S14-88T, was isolated from a tundra soil near Antarctic Peninsula, South Shetland Islands, and its taxonomic position was investigated by a genotypic and phenotypic analysis. Cells were facultatively anaerobic, Gram-stain-negative, non-motile and rod-shaped. Growth occurred at 4–28 °C (optimum at 15 °C), at pH 7.0–8.0 (optimum at 7.0) and with 0–0.6 % (w/v) NaCl (optimum, no NaCl). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S14-88T formed a lineage within the genus Mucilaginibacter . The 16S rRNA gene sequence similarity between strain S14-88T and the type strains of related species ranged from 92.2 to 96.5 %, and the 16S rRNA gene sequence of S14-88T showed highest similarity of 96.5 % to Mucilaginibacter soyangensis HME6664T. The major cellular fatty acids of strain S14-88T were iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The major respiratory quinone was menaquinone MK-7, and the main polar lipid was phosphatidylethanolamine. The DNA G+C content of strain S14-88T was 42.3 mol%. On the basis of the evidence presented in this study, strain S14-88T is considered to represent a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter antarcticus sp. nov. is proposed. The type strain is S14-88T (=CCTCC AB 2015321T=KCTC 52232T).
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Rufibacter quisquiliarum sp. nov., a new member of the phylum Bacteroidetes isolated from a bioreactor treating landfill leachate
A novel bacterium, CAI-18bT, was isolated from a bioreactor that treated landfill leachate using an oligotrophic growth medium. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CAI-18bT is a member of the genus Rufibacter , showing 97.1 % pairwise similarity to Rufibacter roseus H359T, 96.4 % to Rufibacter tibetensis 1351T, 96.4 % to Rufibacter glacialis MDT1-10-3T and 96.0 % to Rufibacter immobilis MCC P1T. Strain CAI-18bT was rod-shaped, motile, oxidase- and catalase-positive. The predominant fatty acids were iso-C15 : 0 (24.1 %) and iso-C17 : 1 I (22.3 %), the major respiratory quinone was MK-7, and the predominant polar lipids were phosphatidylethanolamine and an unknown aminophospholipid. The G+C content of the genomic DNA of strain CAI-18bT was 50.7 mol%. The novel bacterium can be distinguished from related type strains based on its ability to assimilate N-acetylglucosamine and gentiobiose. On the basis of the phenotypic, chemotaxonomic and molecular data, strain CAI-18bT represents a novel species of the genus Rufibacter, for which the name Rufibacter quisquiliarum sp. nov. is proposed. The type strain is CAI-18bT (=DSM 29854T=NCAIM B.02614T).
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Emticicia fontis sp. nov., isolated from a freshwater pond
More LessA bacterial strain, designated IMCC1731T, was isolated from an eutrophic freshwater pond and characterized using a polyphasic taxonomic approach. Cellular growth occurred at pH 6–9 (optimum, pH 8.0), at 10–30 °C (optimum, 25 °C) and with 0–1 % (w/v) NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain IMCC1731T belonged to the genus Emticicia in the family Cytophagaceae and was most closely related to Emticicia ginsengisoli Gsoil 085T (98.1 %) followed by Emticicia paludis HMF3850T (95.0 %), Emticicia oligotrophica DSM 17448T (94.7 %), Emticicia aquatica HMF2925T (94.4 %) and Emticicia sediminis JBR12T (94.0 %). The DNA–DNA relatedness between strain IMCC1731T and E. ginsengisoli Gsoil 085T was 47±4 %. The DNA G+C content of strain IMCC1731T was 37.7 mol%. The predominant cellular fatty acids were summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and iso-C15 : 0. Based on the physiological and chemotaxonomic characteristics, DNA–DNA relatedness and 16S rRNA gene phylogeny, stain IMCC1731T is considered to represent a novel species of the genus Emticicia , for which the name Emticicia fontis sp. nov. is proposed. The type strain is IMCC1731T (=KCTC 52248T=JCM 31373T).
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Niastella hibisci sp. nov., isolated from rhizosphere soil of mugunghwa, the Korean national flower
More LessA Gram-stain-negative, aerobic, non-motile, long rods with no flagellum strain, designated THG-YS3.2.1T, was isolated from rhizosphere soil of mugunghwa, collected from Kyung Hee University, Yongin, South Korea. Growth occurred at 10−40 °C (optimum 28 °C), at pH 6.0−8.0 (optimum pH 7.0) and with 0−1.0 % NaCl (optimum 1.0 %). The predominant menaquinone was menaquinone-7 (MK-7). The major cellular fatty acids were anteiso-C12 : 0, iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1 G, anteiso-C15 : 1 A, C15 : 0 2-OH, C16 : 0, iso-C16 : 0, C16 : 0 3-OH, iso-C16 : 0 3-OH, iso-C16 : 1 G, C17 : 0 2-OH, iso-C17 : 0 3-OH, C17 : 1ω6c, C18 : 3ω6c (6, 9, 12), C18 : 0, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The major polar lipids were phosphatidylmethylethanolamine), phosphatidylethanolamine, five unidentified aminolipids and three unidentified lipids. The DNA G+C content of strain THG-YS3.2.1T was 45.3 mol%. Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-YS3.2.1T were Niastella populi KCTC 22560T (98.7 % 16S rRNA gene sequence similarity), Niastella gongjuensis KACC 17399T (96.9 %), Niastella vici KCTC 42474T (96.2 %), Niastella yeongjuensis KACC 11466T (95.5 %) and Niastella koreensis KACC 11465T (95.1 %). DNA–DNA hybridization values between strain THG-YS3.2.1T and N. populi KCTC 22560T, N. gongjuensis KACC 17399T, N . vici KCTC 42474T, N. yeongjuensis KACC 11466T and N. koreensis KACC 11465Twere 55.8±1.0, 39.5±0.5, 35.2±0.1, 17.6±0.3 and 12.5±1.2 %, respectively. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA−DNA hybridization data, strain THG-YS3.2.1T represents a novel species of the genus Niastella , for which the name Niastella hibisci sp. nov. is proposed. The type strain is THG-YS3.2.1T (=KCTC 52084T=CCTCC AB 2015356T).
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Description of Lunatimonas salinarum sp. nov.
More LessA Gram-stain-negative, crescent-shaped, non-motile, aerobic bacterium was isolated from a saltern at Nari along the Bhavnagar coast, Gujarat, India. The strain designated JC344T was oxidase- and catalase-positive. The 16S rRNA gene sequence analysis and sequence comparison data indicated that JC344T represented a member of the genus Lunatimonas and was closely related to the only species of the genus, Lunatimonas lonarensis AK24T (95.5 %). The DNA G+C content of JC344T was 43 mol%. JC344T has phosphatidylethanolamine (PE) and four unidentified polar lipids. MK-7 is the only respiratory quinone. The major (>10 %) fatty acids of strain JC344T are iso-C15 : 0, anteiso-C15 : 0 and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl). On the basis of physiological, genotypic, phylogenetic and chemotaxonomic analyses, we conclude that JC344T represents a novel species of the genus Lunatimonas , for which the name Lunatimonas salinarum sp. nov. is proposed. The type strain is JC344T (=KCTC 42988T=LMG 29259T).
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Sphingobacterium cibi sp. nov., isolated from the food-waste compost and emended descriptions of Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983 and Sphingobacterium thermophilum Yabe et al. 2013
More LessA novel, pale yellow-coloured, Gram-staining-negative, aerobic, rod-shaped and non-motile bacterium, designated as strain CC-YY411T, was isolated from the food-waste compost and subjected to polyphasic taxonomy. Strain CC-YY411T exhibited the highest pairwise 16S rRNA gene sequence similarity to Sphingobacterium thermophilum JCM 17858T (94.6 %) while sharing 94.1 to 89.7 % similarities with other Sphingobacterium species. Novel strain established a discrete phylogenetic lineage within the clade that accommodated validly established members of the genus Sphingobacterium . The polar lipid profile of strain CC-YY411T contained major amounts of phosphatidylethanolamine, one unidentified lipid and two unidentified aminolipids besides accommodating trace amounts of a sphingolipid, two phospholipids, an unidentified aminophospholipid and an unidentified glycolipid. The DNA G+C content of strain CC-YY411T was 34.5 mol%. The major and minor respiratory quinones were MK-7 (89.1 %) and MK-6 (10.9 %), respectively. The predominant fatty acids were iso-C15 : 0 (24.0 %), iso-C17 : 0 3-OH (11.9 %), iso-C15 : 0 3-OH (6.9 %), C15 : 1ω5c (5.5 %) and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (32.0 %). Based on the phylogenetic, phenotypic and chemotaxonomic distinctiveness, strain CC-YY411T represents a novel species of Sphingobacterium , for which the name Sphingobacterium cibi sp. nov. is proposed. The type strain is CC-YY411T (=BCRC 80430T=JCM 18407T). Amended species descriptions of Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983 and Sphingobacterium thermophilum Yabe et al. 2013 are also proposed based on new data obtained in this study.
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Pedobacter lycopersici sp. nov., isolated from the rhizosphere of tomato plant (Solanum lycopersicum L.)
More LessA Gram-stain-negative, rod-shaped, white bacterium, designated strain T16R-88T, was isolated from a rhizosphere soil sample collected in Buyeo-gun of Chungcheongnam-do, South Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain T16R-88T formed a lineage within the genus Pedobacter . It showed highest sequence similarities to Pedobacter ginsengisoli Gsoil 104T (97.4 %), Pedobacter nutrimenti J22T (97.2 %), Pedobacter nyackensis NWG-II14T (97.1 %), Pedobacter seoulensis THG-G12T (97.1 %) and Pedobacter panaciterrae Gsoil 042T (97.0 %). The predominant respiratory quinone was menaquinone MK-7. The major cellular fatty acids (>10 % of the total fatty acids) were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c), iso-C17 : 0 3-OH and iso-C15 : 0. The polar lipids consisted of phosphatidylethanolamine, sphingolipid, one unidentified aminophospholipid, three unidentified aminolipids, three unidentified lipids and one unidentified phospholipid. DNA–DNA hybridization values between strain T16R-88T and its most closely related species were below 70 %. The DNA G+C content was 35.6 mol%. On the basis of the evidence presented in this study, strain T16R-88T represents a novel species of the genus Pedobacter , for which the name Pedobacter lycopersici sp. nov. is proposed. The type strain is T16R-88T (=KACC 18652T=NBRC 111984T).
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Carboxylicivirga flava sp. nov., isolated from marine surface sediment
More LessA novel bacterial strain, designated Q15T, was isolated from sediments obtained from the Bohai Sea in China and subjected to a polyphasic taxonomic study. Cells of strain Q15T were Gram-stain-negative, strictly aerobic rods that produced circular, flat, orange colonies. Phylogenetic analysis based on 16S rRNA gene sequences revealed that Q15T was affiliated with the genus Carboxylicivirga in the family Marinilabiliaceae of the phylum Bacteroidetes . Strain Q15T differed genotypically from the type strains of the three recognized species of this genus ( Carboxylicivirga taeanensis MEBiC 08903T, C arboxylicivirga mesophila MEBiC 07026T and C arboxylicivirga linearis FB218T) and shared 94.0–95.2 % 16S rRNA gene sequence similarity with them. The DNA G+C content of strain Q15T was 44.7 mol%. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0 3-OH, and menaquinone MK-7 was the main respiratory quinone. Polar lipids contained phosphatidylethanolamine, an unidentified aminolipid, an unidentified phospholipid and other unknown lipids. Based on the data from the current polyphasic analysis, a novel species, Carboxylicivirga flava sp. nov., is hereby proposed with Q15T (=CICC 23923T=KCTC 42707T) as the type strain.
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Algoriphagus litorisediminis sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, non-flagellated, non-gliding, aerobic and rod-shaped bacterium, designated strain OITF-19T, was isolated from a tidal flat in Oido, an island of South Korea, and subjected to a polyphasic taxonomic study. Strain OITF-19T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain OITF-19T belonged to the genus Algoriphagus , clustering with the type strain of Algoriphagus namhaensis, with which it shared 96.5 % sequence similarity. Strain OITF-19T exhibited the highest 16S rRNA gene sequence similarity to Algoriphagus chungangensis CAU 1002T (97.0 %) and of 92.0–96.8 % to the type strains of other Algoriphagus species. Strain OITF-19T contained MK-7 as the predominant menaquinone and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain OITF-19T were phosphatidylcholine, phosphatidylethanolamine and three unidentified lipids. The DNA G+C content of strain OITF-19T was 38.3 mol%. Mean DNA–DNA relatedness between strain OITF-19T and the type strain of A. chungangensis was 26 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain OITF-19T is separated from recognized species of the genus Algoriphagus . On the basis of the data presented, strain OITF-19T is considered to represent a novel species of the genus Algoriphagus , for which the name Algoriphagus litorisediminis sp. nov. is proposed. The type strain is OITF-19T (=KCTC 52456T=NBRC 112418T).
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Pontibacter aydingkolensis sp. nov., isolated from soil of a salt lake
A Gram-stain-negative, short rod-shaped and light-red-pigmented bacterium, designated XAAS-1T, was isolated from the soil of Aydingkol Lake near the Turpan City, Xinjiang, China. The isolate was positive for oxidase, catalase and hydrolysis of starch, casein, gelatin and aesculin. The sole respiratory quinone was MK-7 and the principal cellular fatty acids were iso-C15 : 0 and C15 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, one unidentified phospholipid and two unidentified polar lipids. The polyamine pattern was found to contain mainly sym-homospermidine. 16S rRNA gene sequence analysis indicated that strain XAAS-1T belongs to the genus Pontibacter in the family Cytophagaceae , with sequence similarities ranging from 93.8 to 96.7 % with other type species of the genus Pontibacter . On the basis of phenotypic and genotypic data, strain XAAS-1T represents a novel species of the genus Pontibacter , for which the name Pontibacter aydingkolensis sp. nov. (type strain XAAS-1T=CCTCC AB 2016134T=JCM 31442T) is proposed.
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Proposal to reclassify Roseivirga ehrenbergii (Nedashkovskaya et al., 2008) as Roseivirga seohaensis comb. nov., description of Roseivirga seohaensis subsp. aquiponti subsp. nov. and emendation of the genus Roseivirga
More LessThe genus Roseivirga currently includes five species: Roseivirga ehrenbergii , R. echinicomitans , R. spongicola , R. marina and R. maritima . Marinicola seohaensis SW-152T was renamed as Roseivirga seohaensis SW-152T and then reclassified again as a later heterotypic synonym of R. ehrenbergii KMM 6017T. In this study, based on average nucleotide identity and digital DNA–DNA hybridization values obtained from in silico methods, together with fatty acid analyses and biochemical tests, we propose to reclassify R. ehrenbergii SW-152 as Roseivirga seohaensis comb. nov. (type strain SW-152T=KCTC 1231T=JCM 12600T). In this work, a Gram-negative, rod-shaped, aerobic and pink-pigmented strain designated as D-25T was isolated from seawater (Desaru Beach, Johor, Malaysia). The 16S rRNA gene analysis revealed that strain D-25T was related to the genus Roseivirga . Strain D-25T was found most closely related to R. seohaensis SW-152T based on average nucleotide identity and digital DNA–DNA hybridization values, phenotypic and chemotaxonomic analyses, indicating that these strains belong to the same species. Thus, it is proposed to split the species R.oseivirga seohaensis into two novel subspecies, Roseivirga seohaensis subsp. seohaensis subsp. nov. (type strain SW-152T=KCTC 12312T=JCM 12600T) and Roseivirga seohaensis subsp. aquiponti subsp. nov. (type strain D-25T=KCTC 42709T=DSM 101709T) and to emend the description of the genus Roseivirga .
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Polaribacter haliotis sp. nov., isolated from the gut of abalone Haliotis discus hannai
More LessA Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated RA4-7T, was isolated from the gut of an abalone (Haliotis discus hannai) collected from the sea around Jeju island, South Korea, and subjected to a polyphasic taxonomic study. RA4-7T grew optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2.0–3.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that RA4-7T represented a member of the genus Polaribacter . RA4-7T exhibited 16S rRNA gene sequence similarity values of 97.64 and 97.23 % to Polaribacter atrinae WP25T and Polaribacter dokdonensis DSW-5T, respectively, and of 93.83–96.99 % to the type strains of the other species of the genus Polaribacter . RA4-7T contained MK-6 as the predominant menaquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 3-OH and iso-C15 : 0as the major fatty acids. The major polar lipids detected in RA4-7T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of RA4-7T was 30.5 mol% and its DNA–DNA relatedness values with the type strains of P. atrinae and P. dokdonensis were 16 and 11 %, respectively. Differential phenotypic properties, in combination with its phylogenetic and genetic distinctiveness, revealed that RA4-7T is separated from species of the genus Polaribacter with validly published names. On the basis of the data presented, RA4-7T represented a novel species of the genus Polaribacter , for which the name Polaribacterhaliotis sp. nov. is proposed. The type strain is RA4-7T (=KCTC 52418T=NBRC 112383T).
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Spirosoma soli sp. nov., isolated from biological soil crusts
More LessA Gram-negative, aerobic, short rod-shaped, non-motile, pale-yellow bacterial strain was isolated from biological soil crusts collected in the desert of Kubuqi, Inner Mongolia of China, designated MIMBbqt12T. The G+C content of the genomic DNA of strain MIMBbqt12T was 49.5 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain MIMBbqt12T belongs to the genus Spirosoma with the highest sequence similarity of 93.5 % to Spirosoma arcticum R2-35T. The major fatty acids of strain MIMBbqt12T were C16 : 0, iso-C15 : 0, iso-C17 : 03-OH, C16 : 1ω5c and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The results of phenotypic properties and phylogenetic distinctiveness supported that strain MIMBbqt12T represents a novel species of the genus Spirosoma , for which the name Spirosoma soli sp. nov. is proposed. The type strain is MIMBbqt12T (=MCCC 1K01308T=KCTC 42805T).
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- Firmicutes and related organisms
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Paenibacillus sinopodophylli sp. nov., a siderophore-producing endophytic bacterium isolated from roots of Sinopodophyllum hexandrum (Royle) Ying
More LessA Gram-stain-positive, strictly aerobic, rod-shaped, motile and endospore-forming bacterial strain, designated TEGR-3T, was isolated from the roots of Sinopodophyllum hexandrum collected from the Qinling Mountains in Shaanxi Province, China. Strain TEGR-3T produced siderophores and hydrolysed aesculin, starch and CM-cellulose. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TEGR-3T was a member of the genus Paenibacillus , exhibiting the highest sequence similarity to Paenibacillus endophyticus LMG 27297T (97.3 %) and Paenibacillus castaneae DSM 19417T (97.3 %). MK-7 was the only menaquinone detected and anteiso-C15 : 0 and C16 : 0 were the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids and an unidentified lipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The DNA G+C content was 45.2 mol%. DNA–DNA relatedness values for strain TEGR-3T with respect to its closest phylogenetic relatives Paenibacillus endophyticus LMG 27297T and Paenibacillus castaneae DSM 19417T were lower than 40 %. Based on the phenotypic, phylogenetic and genotypic data, strain TEGR-3T is considered to represent a novel species of the genus Paenibacillus , for which the name Paenibacillus sinopodophylli sp. nov. is proposed. The type strain is TEGR-3T (=CCTCC AB 2016047T=KCTC 33807T).
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Paenibacillus oryzae sp. nov., isolated from rice roots
A novel endophytic bacterium, strain 1DrF-4T, isolated from rice roots, was characterized on the basis of its phenotypic characteristics and genotypic information. The novel strain was Gram-positive-staining, endospore-forming, facultatively anaerobic, motile and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 1DrF-4T formed a monophyletic clade within the genus Paenibacillus . The most phylogenetically related species was Paenibacillus pinesoli KACC 17472T, with which strain 1DrF-4T showed 16S rRNA gene sequence similarity of 95.2 %. 16S rRNA gene sequence similarities with type strains of other species of the genus Paenibacillus were less than 95 %. The predominant cellular fatty acids were anteiso-C15 : 0 (61.1 %) and C16 : 0 (11.1 %), which is one of the characteristic traits of the genus Paenibacillus . The quinone system contained exclusively menaquinone MK-7. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, glycolipid and an unknown phospholipid. The DNA G+C content was 50.16 mol%, which was within the range reported for species of the genus Paenibacillus . Characterization by genotypic, chemotaxonomic and phenotypic analysis indicated that strain 1DrF-4T (=ACCC 19927T=JCM 30486T) represents a novel species of the genus Paenibacillus , for which the name Paenibacillus oryzae sp. nov. is proposed.
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Saccharibacillus endophyticus sp. nov., an endophyte of cotton
More LessA Gram-positive-staining, facultatively aerobic, endospore-forming bacterial strain, isolated from the stem tissue of cotton (Gossypium hirsutum) was subjected to a detailed taxonomic study using a polyphasic approach. Based on 16S rRNA gene sequence similarity comparisons, strain JM-1350T grouped into the genus Saccharibacillus , and was most closely related to the type strain of Saccharibacillus sacchari (96.5 % 16S rRNA gene sequence similarity), followed by the type strains of Saccharibacillus kuerlensis (96.3 %) and Saccharibacillus deserti (95.1 %). The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The quinone system contained exclusively menaquinone MK-7. The polar lipid (L1) profile consisted of the major lipids diphosphatidylglycerol and phosphatidylglycerol and moderate amounts of three glycolipids and an aminophospholipid and a polar lipid (L1). The major fatty acids were iso- and anteiso-branched fatty acids. The genomic G+C content was 55.2 mol%. In addition, the results of physiological and biochemical tests allowed phenotypic differentiation of strain JM-1350T from all closely related species. Thus, strain JM-1350T represents a novel species of the genus Saccharibacillus , for which the name Saccharibacillus endophyticus sp. nov. is proposed. The type strain is JM-1350T (=LMG 29710T=CCM 8702T).
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Description of Jeotgalibacillus alkaliphilus sp. nov., isolated from a solar salt pan, and Jeotgalibacillus terrae sp. nov., a name to replace ‘Jeotgalibacillus soli’ Chen et al. 2010
More LessA Gram-stain-positive, non-motile, rod-shaped bacterium (strain JC303T) isolated from a salt pan was identified based on 16S rRNA gene sequence analysis as a member of the genus Jeotgalibacillus . It was related most closely to Jeotgalibacillus salarius ASL-1T (99.1 % similarity), J eotgalibacillus alimentarius YKJ-13T (97.9 %), J eotgalibacillus soli JSM 081008 (97.9 %), J eotgalibacillus malaysiensis D5T (97.8 %), J eotgalibacillus marinus DSM 1297T (96.3 %), J eotgalibacillus campisalis SF-57T (96.1 %) and J. soli P9T (94.9 %). Genomic relatedness based on DNA–DNA hybridization of strain JC303T with the type strains of the closest related species was less than 40 %. Diphosphatidylglycerol, three aminophospholipids, an unidentified aminoglycolipid, two unidentified phospholipids and an unidentified lipid were the polar lipids of strain JC303T. Major (>10 %) fatty acids were anteiso-C15 : 0, iso-C15 : 0 and iso-C14 : 0. Cell-wall amino acids contained peptidoglycan with l-lysine as the diagnostic diamino acid. Strain JC303T contained MK-7 as the predominant (96 %) menaquinone with the presence of a significant amount (4 %) of MK-8. The DNA G+C content was 43 mol%. On the basis of morphological, physiological, genotypic, phylogenetic and chemotaxonomic analyses, strain JC303T is considered to represent a novel species of the genus Jeotgalibacillus , for which the name Jeotgalibacillus alkaliphilus sp. nov. is proposed. The type strain is JC303T (=KCTC 33662T=LMG 28756T). In addition, we propose to rename J. soli (Chen et al., 2010), an illegitimate homonym of the validly published name Jeotgalibacillus soli (Cunha et al., 2012) as Jeotgalibacillus terrae sp. nov. with type strain JSM 081008T (=DSM 22174T=KCTC 13528T).
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Peptococcus simiae sp. nov., isolated from rhesus macaque faeces and emended description of the genus Peptococcus
A study of the faecal microbiome in three healthy female rhesus macaques revealed the presence of a novel obligately anaerobic, chemoorganoheterotrophic, non-sporing, coccoid, non-motile, Gram-stain-positive bacterial species. Three strains of this species, designated as M108T, M916-1/1, and M919-2/1, were non-haemolytic, H2S-positive, catalase-positive, bile- and NaCl-sensitive and required peptone for growth. Strains also were asaccharolytic, able to utilize sulfite, thiosulfate and elemental sulfur as electron acceptors, and produced acetic and butyric acids as metabolic end-products. Strain M108T is characterized by the prevalence of C14 : 0, C16 : 0 and C18 : 1ω9cis dimethyl acetal among the cellular fatty acids, and the presence of MK-10 menaquinone. The DNA G+C content was found to be 51 mol%. Phylogenetic analysis of partial 16S rRNA gene sequences of strains M108T, M916-1/1 and M919-2/1 placed these strains into the genus Peptococcus (family Peptococcaceae ). On the basis of phenotypic and genotypic properties we conclude that these strains represent a novel bacterial species for which the name Peptococcus simiae sp. nov. is proposed. The type strain is M108T (=DSM 100347T=VKM B-2932T).
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Lentibacillus populi sp. nov., a moderately halophilic, endophytic bacterium isolated from a poplar tree, and emended description of the genus Lentibacillus
More LessA Gram-staining-positive, moderately halophilic, aerobic, endospore-forming, rod-shaped bacterial strain, designated WD4L-1T was isolated from surface-sterilized stem tissue of a poplar tree planted in the Wudalianchi National Geopark of Heilongjiang province, PR China. This novel isolate grew in the presence of 0–15 % (w/v) NaCl, at pH 6.0–9.0 and 15–50 °C; optimum growth was observed with 7–8 % (w/v) NaCl, at pH 7.0 and 30 °C. The 16S rRNA gene sequence analysis indicated that the strain WD4L-1T belonged to the genus Lentibacillus , and was most closely related to Lentibacillus garicola SL-MJ1T with a sequence similarity of 96.1 %. The DNA G+C content of strain WD4L-1T was determined to be 36.9 mol%. The respiratory quinone was identified as menaquinone-7 (MK-7) and the major lipids were diphosphatidylglycerol and phosphatidylglycerol and one unidentified phospholipid. The major fatty acids of strain WD4L-1T were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The results of the physiological and biochemical tests and the minor differences in the fatty acid profiles allowed a clear phenotypic differentiation of strain WD4L-1T from the closely related Lentibacillus garicola JCM 30131T. Thus, strain WD4L-1T represents a novel species of the genus Lentibacillus , for which the name Lentibacillus populi sp. nov. is proposed. The type strain is WD4L-1T (=CGMCC 1.15454T=DSM 101738T). An emended description of the genus Lentibacillus is also provided.
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Paludifilum halophilum gen. nov., sp. nov., a thermoactinomycete isolated from superficial sediment of a solar saltern
A novel filamentous, halophilic, thermotolerant bacterium, strain SMBg3T was isolated from superficial sediment of a solar saltern in Sfax, Tunisia. The isolate is Gram-staining-positive, aerobic, catalase- and oxidase-positive. Optimum growth occurred at 40–45 °C, with 10 % (w/v) NaCl and at pH 8.0–9.0. Long and well developed aerial and substrate mycelia, with long chains of fluorescent and circular spores, were observed on all tested media. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SMBg3T belongs to an independent phylogenetic lineage of the family Thermoactinomycetaceae and shows a gene sequence similarity of 94 % with Desmospora activa DSM 45169T 94.2 % with Kroppenstedtia eburnea DSM 45196T, 94.3 % with Kroppenstedtia guangzhouensis KCTC 29149T, 94.3 % with Melghirimyces algeriensis DSM 45474T and 94.5 % with Salinithrix halophila CECT 8506T. The predominant menaquinone is MK-7, but MK-8 and some minor unidentified components are also present in trace amounts. The major cellular fatty acids are anteiso-C15 : 0, iso-C15 : 0 and iso-C17 : 0. In addition to four major polar lipids identified as phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylmethylethanolamine, five minor unknown lipids were detected in cell membranes. The DNA G+C content of strain SMBg3T is 51.2 mol%. Strain SMBg3T is distinct from recognized genera of the family Thermoactinomycetaceae by morphological, biochemical and chemotaxonomic characteristics. On the basis of physiological and phylogenetic data, strain SMBg3T represents a novel species of a new genus in the family Thermoactinomycetaceae for which the name Paludifilum halophilum gen. nov., sp. nov. is proposed. The type strain of the type species is SMBg3T (=DSM 102817T=CCUG 68698T).
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Lactobacillus ixorae sp. nov., isolated from a flower (West-Indian jasmine)
A Gram-stain-positive, lactic acid bacterium, strain Ru20-1T, was isolated from a flower (West-Indian jasmine) collected from Kalasin province, Thailand. A polyphasic approach was used to determine the taxonomic position of this strain. Studies of morphological and biochemical characteristics revealed that strain Ru20-1T belonged to the genus Lactobacillus . The strain was heterofermentative, non-spore-forming and rod-shaped. It produced dl-lactic acid. Based on 16S rRNA gene sequence similarity, this strain was closely related to Lactobacillus lindneri LMG 14528T (96.8 %), Lactobacillus sanfranciscensis NRIC 1548T (95.4 %) and Lactobacillus florum NRIC 0771T (95.2 %), respectively. In addition, the pheS gene sequence of strain Ru20-1T was closely related to those of L. sanfranciscensis NRIC 1548T (92.0 %), L. lindneri LMG 14528T (89.0 %) and L. florum NRIC 0771T(85.0 %). Phylogenetic analysis indicated that strain Ru20-1T was clearly separated from closely related species of the genus Lactobacillus . The DNA G+C content of strain Ru20-1T was 47.8 mol %. The cell-wall peptidoglycan type was l-Lys–d-Asp. The major cellular fatty acids were C18 : 1ω9c, C20 : 0, C20 : 1ω9c and summed feature 7 (unknown 18.846 and/or C19 : 1ω6c and/or C19 : 0 cyclo). On the basis of the data provided, strain Ru20-1T represents a novel species of the genus Lactobacillus , for which the name Lactobacillus ixorae sp. nov. is proposed. The type strain is Ru20-1T (=LMG 29008T=NBRC 111239T=PCU 346T=TISTR 2381T).
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Phylogenomic analysis of the family Peptostreptococcaceae (Clostridium cluster XI) and proposal for reclassification of Clostridium litorale (Fendrich et al. 1991) and Eubacterium acidaminophilum (Zindel et al. 1989) as Peptoclostridium litorale gen. nov. comb. nov. and Peptoclostridium acidaminophilum comb. nov.
More LessIn 1994, analyses of clostridial 16S rRNA gene sequences led to the assignment of 18 species to Clostridium cluster XI, separating them from Clostridium sensu stricto ( Clostridium cluster I). Subsequently, most cluster XI species have been assigned to the family Peptostreptococcaceae with some species being reassigned to new genera. However, several misclassified Clostridium species remained, creating a taxonomic conundrum and confusion regarding their status. Here, we have re-examined the phylogeny of cluster XI species by comparing the 16S rRNA gene-based trees with protein- and genome-based trees, where available. The resulting phylogeny of the Peptostreptococcaceae was consistent with the recent proposals on creating seven new genera within this family. This analysis also revealed a tight clustering of Clostridium litorale and Eubacterium acidaminophilum . Based on these data, we propose reassigning these two organisms to the new genus Peptoclostridium as Peptoclostridium litorale gen. nov. comb. nov. (the type species of the genus) and Peptoclostridium acidaminophilum comb. nov., respectively. As correctly noted in the original publications, the genera Acetoanaerobium and Proteocatella also fall within cluster XI, and can be assigned to the Peptostreptococcaceae . Clostridium sticklandii , which falls within radiation of genus Acetoanaerobium , is proposed to be reclassified as Acetoanaerobium sticklandii comb. nov. The remaining misnamed members of the Peptostreptococcaceae , [ Clostridium ] hiranonis, [ Clostridium ] paradoxum and [ Clostridium ] thermoalcaliphilum, still remain to be properly classified.
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- other bacteria
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Fervidobacterium thailandense sp. nov., an extremely thermophilic bacterium isolated from a hot spring
Strain FC2004T, a strictly anaerobic, extremely thermophilic heterotroph, was isolated from a hot spring in Thailand. Typical cells of strain FC2004T were rod shaped (0.5–0.6×1.1–2.5 µm) with an outer membrane swelling out over an end. Filaments (10–30 µm long) and membrane-bound spheroids containing two or more cells inside (3–8 µm in diameter) were observed. The temperature range for growth was 60–88°C (optimum 78–80°C), pH range was 6.5–8.5 (optimum pH 7.5) and NaCl concentration range was 0 to <5 g l−1 (optimum 0.5 g l−1). S0 stimulated growth yield. S2O3 2– and NO3 − did not influence growth. Glucose, maltose, sucrose, fructose, cellobiose, CM-cellulose and starch were utilized for growth. The membrane was composed mainly of the saturated fatty acids C16:0 and C18:0. The DNA G+C content was 45.8 mol%. The 16S rRNA gene sequence of strain FC2004T revealed highest similarity to species of the genus Fervidobacterium : F. pennivorans DSM 9078T (97–96 %), F. islandicum AW-1 (96 %), F. changbaicum CBS-1T (96 %), F. islandicum H21T (95 %), F. nodosum Rt17-B1T (95 %), F. riparium 1445tT (95 %) and F. gondwanense AB39T (93 %). Phylogenetic analysis of 16S rRNA gene sequences and average nucleotide identity analysis suggested that strain FC2004T represented a novel species within the genus Fervidobacterium , for which the name Fervidobacterium thailandense sp. nov. is proposed. The type strain is FC2004T (=JCM 18757T=ATCC BAA-2483T).
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Marinitoga arctica sp. nov., a thermophilic, anaerobic heterotroph isolated from a Mid-Ocean Ridge vent field
More LessA thermophilic, anaerobic, heterotrophic bacterium, designated 2PyrY55-1T, was isolated from the wall of an active hydrothermal white-smoker chimney in the Soria Moria vent field (71° N) at the Mohns Ridge in the Norwegian–Greenland Sea. Cells of the strain were Gram-negative, motile rods that possessed a polar flagellum and a sheath-like outer structure (‘toga’). Growth was observed at 45–70 °C (optimum 65 °C), at pH 5.0–7.5 (optimum pH 5.5) and in 1.5–5.5 % (w/v) NaCl (optimum 2.5 %). The strain grew on pyruvate, complex proteinaceous substrates and various sugars. Cystine and elemental sulfur were used as electron acceptors, and sulfide was then produced. The G+C content of the genomic DNA was 27 mol% (T m method). Cellular fatty acids included C16 : 0, C14 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH, C16 : 1 ω9c, C18 : 1 ω9c, C18 : 0, C18 : 1 ω7c and C12 : 0. Phylogenetic analyses of the 16S rRNA gene showed that the strain belonged to the genus Marinitoga in the family Petrotogaceae . Based on the phylogenetic and chemotaxonomic data, strain 2PyrY55-1T (=DSM 29778T=JCM 30566T) is the type strain of a novel species of the genus Marinitoga , for which the name Marinitoga arctica sp. nov. is proposed.
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Deinococcus persicinus sp. nov., a radiation-resistant bacterium from soil
Two Gram-stain-negative, oxidase-negative, catalase-positive, aerobic and coccus-shaped bacterial strains, KSY3-6T and JSH6-18, were isolated from soil in South Korea. Strains KSY3-6T and JSH6-18 showed high resistance to gamma-ray and UVC irradiation. The 16S rRNA gene sequences of strains KSY3-6T and JSH6-18 showed a novel subline within the genus Deinococcus in the family Deinococcaceae . They shared 94.8–86.4 % nucleotide similarities with other species of the genus Deinococcus. Strain KSY3-6T exhibited high DNA–DNA hybridization values with JSH6-18 (77±0.8 %). The two strains showed typical chemotaxonomic characteristics of the genus Deinococcus , including the presence of menaquinone 8 (MK-8) as predominant respiratory quinone and C16 : 0, C17 : 0cyclo and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) as major fatty acids. The G+C content of the DNA of strains KSY3-6T and JSH6-18 was 62.0 and 62.4 mol%, respectively. Polar lipids in strains KSY3-6T and JSH6-18 were mainly phosphoglycolipids. Based on their phenotypic and genotypic properties, strains KSY3-6T and JSH6-18 should be classified as representatives of a novel species in the genus Deinococcus , for which the name Deinococcus persicinus sp. nov. is proposed. The type strain is KSY3-6T (=KCTC 33787T=JCM 31313T). The reference strain is JSH6-18 (=KCTC 33788=JCM 31312).
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Deinococcus saudiensis sp. nov., isolated from desert
Two gamma- and UV-radiation-resistant, pink-coloured bacterial strains, designated YIM F302T and YIM F235, were isolated from the desert of Yanbu' al Bahr located in west of Saudi Arabia. Taxonomic positions of the two isolates were investigated by polyphasic taxonomic approaches. Cells of the two strains were Gram-stain-negative, aerobic and rod-shaped. They were able to grow at 15–45 °C and pH 6.0–8.0 and had a NaCl tolerance limit of 1 % (w/v). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains YIM F302T and YIM F235 represent members of the genus Deinococcus , sharing highest sequence similarities of 98.3 and 98.4 %, respectively, with Deinococcus grandis DSM 3963T. The strains were found to contain MK-8 as the respiratory menaquinone. Major fatty acids (>10 %) of the two strains were C15 : 1 ω6c, C16 : 0 and C16 : 1 ω7c. DNA–DNA hybridization values of the two isolates against the closely related type strains were significantly below the 70 % limit for species delineation. Genomic DNA G+C contents of strains YIM F302T and YIM F235 were 69.3 and 69.0 mol%, respectively. Based on the phenotypic and genotypic characteristics recorded, it is determined that the two isolates represent a novel species of the genus Deinococcus , for which the name Deinococcus saudiensis sp. nov. is proposed. The type strain is YIM F302T (=CGMCC 1.15089T=DSM 29933T).
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Description of ‘Candidatus Phytoplasma meliae’, a phytoplasma associated with Chinaberry (Melia azedarach L.) yellowing in South America
China tree yellows (ChTY) phytoplasma is associated with the yellowing disease of the China tree (Melia azedarach) in Argentina. According to partial 16S rRNA gene analysis, ChTY phytoplasma belongs to the 16Sr XIII group, subgroup G. Strains of species of ChTY have 98–99 % 16S rDNA gene sequence similarity with 16SrXIII-group phytoplasmas, and less than 97.5 % when compared to all ‘Candidatus Phytoplasma ’ described so far, except for the novel ‘Candidatus Phytoplasma hispanicum '. However, strains of species of ChTY are differentiated from the latter due to having additional molecular and biological attributes. The presence of unique features in the 16S rDNA sequence distinguishes ChTY from all species of ‘Candidatus Phytoplasma ’ currently described. The in silico RFLP profile of 16S rDNA (1.2 kb) and rpLV-rpsC (1.3 kb) genes distinguished ChTY, as in the 16SrXIII-G subgroup within the 16SrXIIII group. The phylogenetic analyses, based on 16S rDNA, rpLV-rpsC and secA gene sequences, in addition to the restricted host range, characteristic symptoms and geographical distribution, confirm that the collective strains of the species ChTY represent a distinct lineage within the phytoplasma clade and support the description of a novel species of ‘Candidatus Phytoplasma meliae ’ with the reference strain being ChTY-Mo3 (Montecarlo, Argentina).
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Isolation and characterization of Acidobacterium ailaaui sp. nov., a novel member of Acidobacteria subdivision 1, from a geothermally heated Hawaiian microbial mat
More LessA novel member of Acidobacteria was isolated from a microbial mat growing on a geothermally heated dead tree trunk in Hawai’i Volcanoes National Park (HI, USA). The rod-shaped, Gram-negative capsulated cells of strain PMMR2T were non-motile and catalase and oxidase negative. Growth occurred aerobically from 15 to 55 °C (optimum, 40 °C) and at pH values from 4.5 to 7.0 (optimum, 6.5). A limited range of sugars and organic acids supported growth. However, results of a genomic analysis suggested that various polysaccharides might be hydrolysed as carbon sources, and evidence for pectin degradation was observed in liquid cultures. A genomic analysis also revealed genes for a Group 1f uptake hydrogenase; assays with liquid cultures confirmed hydrogen consumption, including uptake at sub-atmospheric concentrations. Nitrate was not dissimilated to nitrite. Major membrane fatty acids included iso-C15 : 0 and iso-C17 : 0. The G+C content was 57.2mol%. A comparative genome analysis revealed an average nucleotide identity of 72.2 % between PMMR2T and its nearest cultured phylogenetic neighbour, Acidobacterium capsulatum ATCC 51196T (=JCM 7670T); analysis of the 16S rRNA gene revealed a 96.8 % sequence identity with Acidobacterium capsulatum ATCC 51196T. These results and other phenotypic differences indicated that strain PMMR2T represents a novel species in the genus Acidobacterium , for which the name Acidobacterium ailaaui sp. nov. is proposed. The type strain, PMMR2T (=DSM 27394T=LMG 28340T), is the second formal addition to the genus Acidobacterium .
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Deinococcus budaensis sp. nov., a mesophilic species isolated from a biofilm sample of a hydrothermal spring cave
Following the exposure of a biofilm sample from a hydrothermal spring cave (Gellért Hill, Budapest, Hungary) to gamma radiation, a strain designated FeSTC15-38T was isolated and studied by polyphasic taxonomic methods. The spherical-shaped cells stained Gram-negative, and were aerobic and non-motile. The pH range for growth was pH 6.0–9.0, with an optimum at pH 7.0. The temperature range for growth was 20–37 °C, with an optimum at 28 °C. Phylogenetic analysis based on the 16S rRNA gene sequence of the isolate indicated that the organism belongs to the genus Deinococcus. The highest sequence similarities appeared with Deinococcus hopiensis KR-140T (94.1 %), Deinococcus aquaticus PB314T (93.3 %) and Deinococcus aerophilus 5516T-11T (92.7 %). The DNA G+C content of the novel strain was 68.2 mol%. The predominant fatty acids (>10 %) were iso-C16 : 0 and C16 : 1ω7c, and the cell-wall peptidoglycan type was A3β l-Orn–Gly2-3, corroborating the assignment of the strain to the genus Deinococcus. Strain FeSTC15-38T contained MK-8 as the major menaquinone and several unidentified phospholipids, glycolipids and phosphoglycolipids. Resistance to gamma radiation (D10) of strain FeSTC15-38T was <3.0 kGy. According to phenotypic and genotypic data, strain FeSTC15-38T represents a novel species for which the name Deinococcus budaensis sp. nov. is proposed. The type strain is FeSTC15-38T (=NCAIM B.02630T=DSM 101791T).
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Description of ‘Candidatus Marispirochaeta associata’ and reclassification of Spirochaeta bajacaliforniensis, Spirochaeta smaragdinae and Spirochaeta sinaica to a new genus Sediminispirochaeta gen. nov. as Sediminispirochaeta bajacaliforniensis comb. nov., Sediminispirochaeta smaragdinae comb. nov. and Sediminispirochaeta sinaica comb. nov.
More LessStrain JC231 was isolated from a coastal saline habitat of Gujarat and was identified based on 16S rRNA gene sequence analysis as a member belonging to the genus Spirochaeta and showed highest sequence similarity (<91 %) with Spirochaeta bajacaliforniensis DSM 16054T and other members of the family Spirochaetaceae . Intensive attempts to culture strain JC231 in pure culture have failed and were associated with only one species of a Desulfovibrio . However, presence of fosmidomycin inhibited the growth of Desulfovibrio sp. and strain JC231 was characterized in its presence. Strain JC231 was an obligate anaerobe, helical shaped and Gram-stain-negative with catalase and oxidase negative. Draft genome sequence analysis of strain JC231 indicated the full complement of genes for both 2-C-methyl-d-erythritol 4-phosphate and 3-hydroxy-3-methylglutaryl-CoA pathways of terpenogenesis. C14 : 0, iso-C15 : 0, C16 : 0, iso-C15 : 1H/C13 : 0 3OH and iso-C14 : 0 are the major (>5 %) fatty acids. Strain JC231 contains diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and six unidentified lipids (L1–L6). G+C content of strain JC231 was 55.7 mol%. Distinct morphological, physiological and genotypic differences from the previously described taxa support the classification of strain JC231 as a representative of a new genus and species in the family Spirochaetaceae , for which the name ‘Candidatus Marispirochaeta associata’ is proposed. Strain JC231 is deposited as a defined co-culture with Desulfovibrio sp. JC271 to DSMZ (DSM 29857) and KCTC (KCTC 15472). Based on phenotypic, genotypic and phylogenetic analyses, we also propose the reclassification of Spirochaeta bajacaliforniensis as Sediminispirochaeta bajacaliforniensis gen. nov., comb. nov., Spirochaeta smaragdinae as Sediminispirochaeta smaragdinae comb. nov. and Spirochaeta sinaica as Sediminispirochaeta sinaica comb. nov.
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- Proteobacteria
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Sphingoaurantiacus capsulatus sp. nov., isolated from mountain soil, and emended description of the genus Sphingoaurantiacus
More LessA novel Gram-stain-negative, strictly aerobic, non-motile, rod-shaped, capsule-forming bacterium, designated strain YLT33T, that formed orange-red colonies was isolated from mountain cliff soil from Enshi Grand Canyon, southwest China. Growth occurred at 4–35 °C (optimum 28 °C) and at pH 6.0–10.0 (optimum 7.0). It showed maximum (99.3 %) 16S rRNA gene sequence similarity and formed a monophyletic clade with Sphingoaurantiacus polygranulatus MC 3718T (=CCTCC 2014274T). The DNA G+C content was 68.5 mol% and strain YLT33T showed a 50.5 % DNA–DNA relatedness value to S. polygranulatus MC 3718T. The major fatty acids (>5 %) were C17 : 1ω6c (40.7 %), C15 : 0 (10.4 %), C15 : 1ω6c (9.4 %), summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH; 8.6 %), C17 : 1ω8c (7.1 %), C18 : 1ω7c (6.1 %), and C15 : 0 2-OH (5.7 %). Ubiquinone-10 was the sole respiratory quinone. The polar lipids of strain YLT33T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, two unknown glycolipids and one unknown phospholipid. Carotenoids were present in cells. Homospermidine was the major polyamine. In addition, strain YLT33T showed obvious differences from the closely related strain S. polygranulatus MC 3718T with respect to major polar lipids, fatty acids and other morphological, physiological and biochemical characteristics. These results from polyphasic taxonomic studies reveal that strain YLT33T represents a novel species of the genus Sphingoaurantiacus , for which the name Sphingoaurantiacus capsulatus sp. nov. is proposed. The type strain is YLT33T (=CCTCC AB 2015150T=KCTC 42644T).
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Reclassification of strains MAFF 303099T and R7A into Mesorhizobium japonicum sp. nov.
In this work we revise the taxonomic status of the Lotus-nodulating strains MAFF 303099T and R7A isolated in Japan and New Zealand, respectively. Their 16S rRNA gene sequences are identical and show 98.0, 99.7, 99.8 and 99.9 % similarity values with respect to Mesorhizobium loti NZP 2213T, M. jarvisii ATCC 33669T, M. huakuii USDA 4779T (=CCBAU 2609T) and M. erdmanii USDA 3471T, respectively. The analysis of recA and glnII gene sequeces showed that M. jarvisii ATCC 33669T and M. huakuii USDA 4779T (=CCBAU 2609T) are the most closely related strains to MAFF 303099T and R7A, with similarity values suggesting that these two strains belong to a different species for which MAFF 303099T is selected as the type strain. The DNA–DNA relatedness values between strain MAFF 303099T and its closest phylogenetic relatives ranged from 53 to 60 % in average. Strains MAFF 303099T and R7A presented slight differences in the proportions of C18 : 1ω7c 11-methyl and C19 : 0 cyclo ω8c fatty acids with respect to M. jarvisii ATCC 33669T and M. huakuii USDA 4779T, and also in several phenotypic characteristics. Therefore, we propose the reclassification of these two strains into a novel species named Mesorhizobium japonicum sp. nov., with the type strain being MAFF 303099T (=LMG 29417T=CECT 9101T).
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Thalassospira indica sp. nov., isolated from deep seawater
More LessA taxonomic study using a polyphasic approach was carried out on strain PB8BT, which was isolated from the deep water of the Indian Ocean. Cells of the bacterium were Gram-stain-negative, oxidase- and catalase-positive, curved rods and motile. Growth was observed at salinities of 0–15 % and at temperatures of 10–41°C. The isolate could reduce nitrate to nitrite and degrade Tween 80, but not degrade gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PB8BT belonged to the genus Thalassospira , with the highest sequence similarity to the closely related type strain Thalassospira tepidiphila 1-1BT (99.7 %), followed by Thalassospira profundimaris WP0211T (99.6 %). Multilocus sequence analysis demonstrated low similarities of 94.1 and 93.7 % between strain PB8BT and the two reference type strains. Digital DNA–DNA hybridization values between strain PB8BT and the two above-mentioned type strains were, respectively, 56.3 and 55.3 %. The principal fatty acids of strain PB8BT were C18 : 1 ω6c/C18 : 1 ω7c, C19 : 0 cyclo ω8c and C16 : 0. The G+C content of the chromosomal DNA was 54.9 mol%. The quinone was determined to be Q-10 (100 %). Phosphatidylglycerol, phosphatidylethanolamine, and several unidentified phospholipids and lipids were present. Based on phenotypic and genotypic characteristics, strain PB8BT represents a novel species within the genus Thalassospira , for which the name Thalassospira indica sp. nov. is proposed. The type strain of the novel species is PB8BT (=MCCC 1A01103T=LMG 29620T).
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Shewanella inventionis sp. nov., isolated from deep-sea sediment
Ming-qing Wang and Li SunA novel Gram-stain-negative, rod-shaped bacterial strain, designated KX27T, was isolated from deep-sea sediment of the Okinawa Trough and characterized on the basis of a polyphasic taxonomic approach. The phenotypic features of strain KX27T were similar to those of members of the genus Shewanella . Strain KX27T exhibited highest 16S rRNA gene sequence similarity (98.37 %) to Shewanella basaltis JCM 14937T. Levels of gyrB gene sequence similarity between strain KX27T and its closest genetic neighbours were lower than 90 %, the species cut-off value for Shewanella . The DNA–DNA hybridization value between strain KX27T and S. basaltis JCM 14937T (54 %) was lower than the accepted species threshold. The predominant cellular fatty acids of strain KX27T were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C17 : 1 ω8c, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and iso-C15 : 0. The major polar lipids of strain KX27T were phosphatidylethanolamine and phosphatidylglycerol. On the basis of combined phenotypic, chemotaxonomic and phylogenetic analysis, strain KX27T represents a novel species of the genus Shewanella , for which the name Shewanella inventionis sp. nov. is proposed. The type strain is KX27T (=KCTC 42807T=CGMCC 1.15339T).
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The status of the genus Pseudoroseovarius Sun et al. 2015
More LessThe results of phylogenetic analyses of the genera Aliiroseovarius Park et al. 2015 and Pseudoroseovarius Sun et al. 2015 and comparison of the phenotypic features of their members showed that these genera should be united. Based on nomenclatural priority of the genus Aliiroseovarius , it is proposed to reclassify Pseudoroseovarius crassostreae as a later homotypic synonym of Aliiroseovarius crassostreae , Pseudoroseovarius halocynthiae as a later homotypic synonym of Aliiroseovarius halocynthiae , Pseudoroseovarius sediminilitoris as a later homotypic synonym of Aliiroseovarius sediminilitoris and Pseudoroseovarius zhejiangensis as Aliiroseovarius zhejiangensis comb. nov.
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Nitratireductor lacus sp. nov., isolated from Yuncheng Salt Lake, China
More LessThis is the taxonomic study of a novel bacterial strain, designated GSS14T, isolated from a sediment sample of Yuncheng Salt Lake, China. Cells were Gram-negative, ovoid to rod-shaped and motile by means of flagella. The isolate could grow at 10–45 °C, at pH 6.5–11.0 and in the presence of 0–12 % (w/v) NaCl. The dominant fatty acids were summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c; 76.7 %) and the DNA G+C content was 61 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GSS14T was affiliated with the genus Nitratireductor , and it was most closely related to Nitratireductor kimnyeongensis KY 101T (98.2 % 16S rRNA gene sequence similarity) and Nitratireductor aquibiodomus JCM 21793T (96.6 %). DNA–DNA hybridization between strains GSS14T and N. kimnyeongensis KY 101T revealed 52 % relatedness. Phenotypic, chemotaxonomic and phylogenetic data support assignment of this isolate to the genus Nitratireductor as a representative of a novel species. The name Nitratireductor lacus sp. nov. is proposed, with strain GSS14T (=KCTC 52186T=MCCC 1K02481) as the type strain.
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Bacterioplanoides pacificum gen. nov., sp. nov., isolated from seawater of South Pacific Gyre
More LessA Gram-staining-negative, strictly aerobic, transparent and smooth, curved-rod-shaped motile bacterium with a single polar flagellum, designated strain sw100T, was isolated from surface seawater of South Pacific Gyre during Integrated Ocean Drilling Program Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain sw100T was most closely related to the member of the family Oceanospirillaceae and was distinct from the most closely related genera Bacterioplanes , Thalassolituus and Oceanobacter (95.8, 94.5–95.3 and 94.4 % 16S rRNA gene sequence similarities, respectively). Growth occurred in the presence of 0–11 % NaCl (w/v, optimum 7 %), at 10–37 °C (optimum 28 °C) and pH 6.0–9.0 (optimum pH 7.0). The major fatty acids (>10 % of total fatty acids) are C16 : 0, C16 : 0 N alcohol and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). The major polar lipids were phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified polar lipids. The DNA G+C content of strain sw100T was 55.3 mol%. The major respiratory quinone was ubiquinone-10 (Q-10). On the basis of polyphasic analyses, strain sw100T is considered to represent a novel species in a novel genus of the family Oceanospirillaceae , for which the name Bacterioplanoides pacificum gen. nov., sp. nov. is proposed. The type strain is sw100T (=JCM 30597T=MCCC 1K00501T=KCTC 42424T).
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Iodidimonas muriae gen. nov., sp. nov., an aerobic iodide-oxidizing bacterium isolated from brine of a natural gas and iodine recovery facility, and proposals of Iodidimonadaceae fam. nov., Iodidimonadales ord. nov., Emcibacteraceae fam. nov. and Emcibacterales ord. nov.
More LessA chemo-organotrophic iodide (I−)-oxidizing bacterial strain, C-3T, isolated from natural gas brine of an iodine recovery facility in Kujukuri, Chiba, Japan, was characterized for representation of a novel species in the class Alphaproteobacteria . Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the nearest neighbours of strain C-3T were members of the genera Eilatimonas , Kordiimonas , Rhodothalassium and Temperatibacter with 88–91 % sequence similarity. Cells of strain C-3T were aerobic, Gram-staining-negative, non-sporulating and rod-shaped (1.3–3.6 µm in length). Strain C-3T grew optimally at 30 °C, pH 7.5 and with 3 % NaCl (w/v). Iodide oxidation to form molecular iodine (I2) was a unique trait for strain C-3T, whereas the strain did not utilize iodide as a sole electron donor for chemolithoautotrophic growth. The major isoprenoid quinone was Q-10. The major cellular fatty acids were C18 : 1 ω7c and C16 : 1 ω5c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified aminolipids. The G+C content of the genomic DNA was 58.5 mol%. Iodide oxidation and the major cellular fatty acids composition distinguished strain C-3T from phylogenetically related bacteria. On the basis of the phenotypic features and the phylogenetic position, a novel genus and species are proposed for strain C-3T (=JCM 17843T=LMG 28660T), to be named Iodidimonas muriae gen. nov., sp. nov. We also propose to place the distinct sublineages of the genera Iodidimonas gen. nov. and Emcibacter in the orders Iodidimonadales ord. nov. and Emcibacterales ord. nov., respectively, because these genera are located far apart from the order Kordiimonadales and form the distinct lineage in the class Alphaproteobacteria .
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Pseudoxanthomonas helianthi sp. nov., isolated from roots of Jerusalem artichoke (Helianthus tuberosus)
More LessA bacterium designated as strain roo10T was isolated from roots of Jerusalem artichoke (Helianthus tuberosus). Cells were Gram-stain-negative and non-motile rods. The phylogenetic analysis of the 16S rRNA gene indicated that it represented a member of the genus Pseudoxanthomonas , and its close relatives included Pseudoxanthomonas kalamensis JA40T (97.8 % 16S rRNA gene sequence similarity), Pseudoxanthomonas sangjuensis 5GH38-5T (97.7 %) and Pseudoxanthomonas daejeonensis TR6-08T (97.1 %). Growth of roo10T occurred at pH 7–9. The temperature for growth ranged from 20 to 37 °C. Tolerance to NaCl was observed from 0.005 to 5 % (w/v) concentration. Predominant fatty acids were iso-C15 : 0 (23.5 %), iso-C16 : 0 (18.9 %) and anteiso-C15 : 0 (11.5 %). Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidyl-N-methylethanolamine were the major polar lipids. The predominant quinone was ubiquinone 8 (Q-8). The DNA G+C content was 65.7 mol% [from melting temperature (Tm )]. Comparison of phenotypic and chemotaxonomic characteristics indicated that roo10T was distinguishable from its close relatives. Additionally, the DNA–DNA relatedness levels between roo10T and P. kalamensis DSM 18571T (22±0.5 %), P. sangjuensis 5GH38-5T (21±0.2 %) and P. daejeonensis DSM 17801T (3±1 %) were lower than 70 %. These results indicated that roo10T represented a novel species of the genus Pseudoxanthomonas , for which the name Pseudoxanthomonas helianthi sp. nov. is proposed. The type strain is roo10T (=BCC 70700T=NBRC 110414T).
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Thalassotalea euphylliae sp. nov., isolated from the torch coral Euphyllia glabrescens
More LessStrain Eup-16T, isolated from the torch coral Euphyllia glabrescens, was characterized using a polyphasic taxonomy approach. Cells of strain Eup-16T were Gram-staining-negative, aerobic, motile by means of a single polar flagellum, contained poly-β-hydroxybutyrate, rod-shaped and formed pale yellow colonies. Optimal growth occurred at 25–30 °C, pH 7.5–9 and in the presence of 1 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Eup-16T belonged to the genus Thalassotalea and was most closely related to Thalassotalea montiporae CL-22T with sequence similarity of 98.4 %. Strain Eup-16T contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c, C16 : 0 and C17 : 1ω8c as the predominant fatty acids. The predominant isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA G+C content of strain Eup-16T was 43.2 mol%. The DNA–DNA hybridization value for strain Eup-16T with T. montiporae CL-22T was less than 34 %. Differential phenotypic properties, together with the phylogenetic inference, demonstrate that strain Eup-16T should be classified as a representative of a novel species of the genus Thalassotalea , for which the name Thalassotalea euphylliae sp. nov. is presented. The type strain is Eup-16T (=BCRC 80910T=LMG 29001T=KCTC 42743T).
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Novosphingobium bradum sp. nov., isolated from a spring
More LessA bacterial strain designated STM-24T was isolated from a spring in Taiwan and characterized using the polyphasic taxonomic approach. Cells of strain STM-24T were Gram-staining- negative, aerobic, poly-β-hydroxybutyrate accumulating, non-motile, rod shaped and forming light yellow-coloured colonies. Growth occurred at 15–30 °C (optimum, 20 °C), at pH 5.0–9.0 (optimum, pH 6.0) and with 0–0.5 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain STM-24T belonged to the genus Novosphingobium and was most closely related to Novosphingobium piscinae SLH-16T with sequence similarity of 98.4 %. The major fatty acids (>10 %) of strain STM-24T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major 2-hydroxy fatty acid was C14 : 0 2-OH. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, phosphatidylcholine and several uncharacterized lipids. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 69.1mol%. The DNA–DNA hybridization value for strain STM-24T with N . piscinae SLH-16T, Novosphingobium taihuense JCM 12465T and Novosphingobium subterraneum DSM 12447T was less than 55 %. Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus Novosphingobium . On the basis of the genotypic, chemotaxonomic and phenotypic data, strain STM-24T represents a novel species in the genus Novosphingobium , for which the name Novosphingobium bradum sp. nov. is proposed. The type strain is STM-24T (=BCRC 80925T=LMG 29291T=KCTC 42984T).
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Psychrobacter pocilloporae sp. nov., isolated from a coral, Pocillopora eydouxi
More LessTwo closely related aerobic, Gram-stain-negative, rod-shaped bacteria (S6-60T and S6-67) were isolated from the mucus of the coral, Pocillopora eydouxi, from the Andaman Sea, India. Heterotrophic growth on marine agar was observed at 4–37 °C and at pH 6.5–10.0; optimum growth occurred at 25–30 °C and at pH 7–9. 16S rRNA gene sequence analysis confirmed that the isolates belong to the genus Psychrobacter ; the two isolates shared more than 99.5 % pairwise sequence similarity. Strain S6-60T showed a maximum 16S rRNA similarity of 98.92 % with Psychrobacter pacificensis DSM 23406T. DNA–DNA homology between the two isolates, S6-60T and S6-67, was above 90 %, whereas strain S6-60T showed less than 70 % homology with closely related type species. The DNA G+C content was 47.7 mol%. It contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phospholipid as the major polar lipids. C10 : 0, C12 : 0 3OH, C16 : 0, C18 : 1ω9c, C17 : 1ω8c and C16 : 1ω7c were found to be the predominant fatty acids. Based on a polyphasic analysis, the isolates (S6-60T and S6-67) represent a novel species of the genus Psychrobacter for which the name Psychrobacter pocilloporae sp. nov. is proposed with S6-60T(=JCM 31058T=LMG 29157T) as the type strain.
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Proposal of Verticiella gen. nov. as replacement for the illegitimate prokaryotic genus name Verticia Vandamme et al. 2015
More LessThe prokaryotic genus name Verticia Vandamme et al. 2015 is illegitimate because it is a later homonym of the insect genus name Verticia Malloch 1927 [Principle 2, Rule 51b(4) of the Prokaryotic Code (2008 Revision)]. This name is therefore not a correct name (Principle 6), and a replacement genus name must be proposed (Rule 54).
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Paracoccus contaminans sp. nov., isolated from a contaminated water microcosm
More LessA beige-pigmented, oxidase-positive bacterial strain (WPAn02T), isolated as a presumably airborne contaminant of an axenic bacterial microcosm, was studied using a polyphasic taxonomic approach. Cells of the isolate were coccoid and stained Gram-negative. A comparison of the 16S rRNA gene sequence of strain WPAn02T with sequences of type strains of the most closely related species of the genus Paracoccus showed highest sequence similarities to Paracoccus chinensis (97.7 %), Paracoccus marinus (97.1 %), Paracoccus niistensis (97.4 %) and ‘ Paracoccus zhejiangensis ' (97.0 %). 16S rRNA gene sequence similarities to all other species of the genus Paracoccus were below 97 %. The fatty acid profile of the strain consisted of the major fatty acids C18 : 1ω7c/ω9t/ω12t and C18 : 0. DNA–DNA hybridizations between WPAn02T and type strains of P. chinensis, P. marinus , P. niistensis , and ‘P. zhejiangensis’ resulted in similarity values of 49 % (reciprocal 22 %), 16 % (reciprocal 10 %), 30 % (reciprocal 32 %), and 18 % (reciprocal 7 %), respectively. DNA–DNA hybridization results together with the differentiating biochemical and chemotaxonomic properties indicated that WPAn02T represents a novel species of the genus Paracoccus , for which the name Paracoccus contaminans sp. nov. (type strain WPAn02T=RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T), is proposed.
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Uliginosibacterium paludis sp. nov., isolated from a marsh
More LessA novel bacterial strain, designated KBP-13T, was isolated from a water sample taken from the Banping Lake Wetland Park in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain KBP-13T were Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, motile rods that formed light yellow colonies. Growth occurred at 15–40 °C (optimum, 30–40 °C), at pH 6.0–8.0 (optimum, pH 6.0) and with 0–2 % (w/v) NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KBP-13T belonged to the genus Uliginosibacterium within the family Rhodocyclaceae of the class Betaproteobacteria and its most closely related neighbour was Uliginosibacterium gangwonense 5YN10-9T with sequence similarity of 96.0 %. Strain KBP-13T contained summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and C14 : 0 as predominant fatty acids. The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 65.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one uncharacterized aminophospholipid, one uncharacterized aminolipid, two uncharacterized phospholipids and three uncharacterized glycolipids. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain KBP-13T represents a novel species in the genus Uliginosibacterium , for which the name Uliginosibacterium paludis sp. nov. is proposed. The type strain is KBP-13T (=BCRC 80903T=LMG 28837T=KCTC 42655T).
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Pseudohongiella nitratireducens sp. nov., isolated from seawater, and emended description of the genus Pseudohongiella
More LessTwo Gram-stain-negative, aerobic, motile by a single polar flagellum and rod-shaped strains, designated SCS-49T and SCS-111, were isolated from seawater of the South China Sea. The two strains grew at 4–35 °C, with 0.5–7.5 % (w/v) NaCl and at pH 6.5–9.0 and were able to reduce nitrate. Q-8 was the sole ubiquinone. The major fatty acids of the two strains were C16 : 0, C18 : 1 ω7c and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phospoglycolipid, three unidentified glycolipids, five unidentified phospholipids and two to three unidentified lipids. The isolates formed a stable clade with Pseudohongiella acticola and Pseudohongiella spirulinae based on phylogenetic analysis of 16S rRNA gene sequences. Strains SCS-49T and SCS-111 exhibited 16S rRNA gene sequence similarity values of 97.2 and 96.0 % with respect to the type strains of P. acticola and P. spirulinae , respectively. The average nucleotide diversity and in silico DNA–DNA hybridization values between strain SCS-49T and P. acticola KCTC 42131T were 71.4 and 25.1 %, respectively and the values between strain SCS-49T and SCS-111 were 99.9 and 99.2 %, respectively. Based upon the phenotypic, chemotaxonomic and genetic data, strains SCS-49T and SCS-111 represent a novel species in the genus Pseudohongiella , for which the name Pseudohongiella nitratireducens sp. nov. is proposed. The type strain is SCS-49T (=CGMCC 1.15425T=KCTC 52155T=MCCC 1K03186T).
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Labrenzia salina sp. nov., isolated from the rhizosphere of the halophyte Arthrocnemum macrostachyum
A novel, halophilic, motile, rod-shaped, Gram-staining-negative and non-endospore forming bacterium, designated Cs25T, was isolated from the rhizosphere of the halophyte Arthrocnemum macrostachyum growing in a tidal flat. Strain Cs25T was observed to be catalase-negative and oxidase-positive, and to hydrolyse hypoxanthine. Growth occurred from 15 to 40 °C, at pH 7.0−10.0 and with 1−11 % (w/v) NaCl. Q-10 was identified as the dominant ubiquinone, and the major cellular fatty acids were C18 : 1 ω7c, 11-methyl C18 : 1ω7c, C20 : 1ω7c and C18 : 0. The polar lipids comprised phosphatidylmonomethylethanolamine, phosphatidylcholine, sulphoquinovosyldiacylglyceride, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The 16S rRNA gene showed 99.19, 98.6 and 98.59 % sequence identity with Labrenzia alba DSM 18320T, L. aggregata DSM 13394T and L. marina DSM 17023T, respectively. Based on the phenotypic and molecular features and DNA–DNA hybridization data, it is concluded that strain Cs25T represents a novel species for which the name Labrenzia salinasp. nov. is proposed. The type strain is Cs25T (=DSM 29163T=CECT 8816T).
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Coetzeea brasiliensis gen. nov., sp. nov. isolated from larvae of Anopheles darlingi
A Gram-stain-negative, rod-shaped strain, Braz8T, isolated from larvae of Anopheles darlingi was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Braz8T was related most closely to species of the genus Thorsellia , with 95.6, 96.5 and 96.6 % similarity to the type strains of Thorsellia anophelis , Thorsellia kandunguensis and Thorsellia kenyensis , respectively, and formed a separate branch in the phylogenetic tree next to the monophyletic cluster of the genus Thorsellia . Chemotaxonomic data supported the allocation of the strain to the family Thorselliaceae . The major fatty acids were C18 : 1 ω7c, C16 : 0 and C14 : 0. The quinone system was composed of ubiquinones Q-8 and Q-7 (1 : 0.3), the predominant polar lipids were diphosphatidylglycerol and phosphatidylglycerol, and the polyamine pattern showed the major compound putrescine. However, qualitative and quantitative differences in the major polyamine, polar lipid profile and fatty acid patterns distinguished strain Braz8T from species of the genus Thorsellia . Phylogenetic analysis based on 16S rRNA gene sequences, average nucleotide identity, DNA–DNA hybridization, multilocus sequence analysis as well as physiological and biochemical tests distinguished strain Braz8T both genotypically and phenotypically from the three Thorsellia species but also showed its placement in the family Thorselliaceae . Thus, strain Braz8T is considered to represent a novel species of a new genus most closely related to the genus Thorsellia, for which the name Coetzeea brasiliensis gen. nov., sp. nov. is proposed. The type strain of Coetzeea brasiliensis is Braz8T (=LMG 29552T=CIP 111088T).
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Isolation and characterization of a novel Gram-negative bacterium Chromobacterium alkanivorans sp. nov., strain IITR-71T degrading halogenated alkanes
The taxonomic position of a Gram-stain negative, non-violaceinpigmented bacterium isolated from an insecticide-contaminated site was characterized by a polyphasic approach. The bacterium was able to grow on three different halogenated compounds namely 1-hlorobutane, 1-hloropropane and 1,2-ichloroethane. As a critical step in the degradation of these haloalkanes, stoichiometric amounts of dechlorination were estimated. Based on selective enrichment method for three months, using a highly contaminated mixed chemical soil, a bacterium was obtained and designated as IITR-71T. Its versatility and novelty led us to further characterize it by polyphasic taxonomy. The 16S rRNA gene sequence (1446 bases) comparison showed highest similarity with those of members of the genus Chromobacterium with the most closely related species to strain IITR-71T being Chromobacterium aquaticum (99.3 %) followed by Chromobacterium haemolyticum (98.6 %) and Chromobacterium piscinae (97.1 %). The major ubiquinone was Q-8. Predominant polar lipids are phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG). The DNA G+C content of IITR-71T was estimated to be 61.2 mol%. The genotypic and phenotypic distinctiveness of IITR-71T and its phylogenetic relationships indicate that IITR-71T represents a novel species, for which the name Chromobacterium alkanivorans sp. nov. is proposed. The type strain is IITR-71T (=MTCC 11059T=JCM 30068T=KCTC 52433T).
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Rickettsia amblyommatis sp. nov., a spotted fever group Rickettsia associated with multiple species of Amblyomma ticks in North, Central and South America
In 1973, investigators isolated a rickettsial organism, designated strain WB-8-2T, from an adult Amblyomma americanum tick collected at Land Between the Lakes National Recreation Area, TN, USA. This organism is now recognized as highly prevalent in A. americanum, as well as several other Amblyomma species found throughout the Western hemisphere. It has been suggested that cross-reactivity to WB-8-2T and similar strains contributes to the increasing number of spotted fever cases reported in the USA. In 1995, investigators provided preliminary evidence that this strain, as well as another strain from Missouri, represented a distinct taxonomic unit within the genus Rickettsia by evaluating sequences of the 16S rRNA and 17 kDa protein genes. However, the bacterium was never formally named, despite the use of the designation ‘ Rickettsia amblyommii’ and later ‘Candidatus Rickettsia amblyommii’, for more than 20 years in the scientific literature. Herein, we provide additional molecular evidence to identify strain WB-8-2T as a representative strain of a unique rickettsial species and present a formal description for the species, with the proposed name modified to Rickettsia amblyommatis sp. nov. to conform to the International Code of Nomenclature of Prokaryotes. We also establish a pure culture of strain WB-8-2T and designate it as the type strain for the species. The type strain is WB-8-2T (=CRIRC RAM004T=CSURP2882T).
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Piscinibacterium candidicorallinum gen. nov., sp. nov., a member of the order Burkholderiales isolated from a fish pond
More LessA bacterial strain designated LYH-15T was isolated from a freshwater fish pond in Taiwan and characterized using a polyphasic taxonomy approach. Cells of LYH-15T were Gram-staining-negative, aerobic, motile by means of a single polar flagellum, poly-β-hydroxybutyrate-containing, non-spore forming, straight rods and formed light-coral-colored colonies. Growth occurred at 15–40 °C (optimum, 30 °C), at pH 5.0–9.0 (optimum, pH 7.0) and with 0–0.5 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that LYH-15T forms a distinct phyletic line within the order Burkholderiales , with less than 94 % sequence similarity to its closest relatives with validly published names. 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 and the DNA G+C content was 63.8 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized lipids. The major polyamines were 2-hydroxyputrescine and putrescine. On the basis of the genotypic and phenotypic data, LYH-15T represents a novel species of a new genus in the order Burkholderiales , for which the name Piscinibacterium candidicorallinum gen. nov., sp. nov. is proposed. The type strain is LYH-15T (=BCRC 80969T=LMG 29480T=KCTC 52168T).
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Ensifer alkalisoli sp. nov. isolated from root nodules of Sesbania cannabina grown in saline–alkaline soils
Yan Li, Jun Yan, Bing Yu, En Tao Wang, Xiangyue Li, Hui Yan, Wei Liu and Zhihong XieA group of Sesbania cannabina rhizobia belonging to four recA genotypes of a novel group was further characterized in comparison with the related Ensifer species. They showed 98.2 to 99.9 % similarities among themselves and 92.9 to 93.3 % similarities with the most related strain Ensifer sojae CCBAU 05684T in multilocus sequence analysis of recA, atpD and glnII. The genome average nucleotide identity values between representative strain YIC4027T and the type strains of its closely related species were 81.6 to 88.9 %. Identical symbiotic gene (nodA, nodC and nifH) sequences highly similar with those in other Sesbania-nodulating strains ( Rhizobium sp. SIN-1, Neorhizobium huautlense S02T, Ensifer saheli ORS609T and Rhizobium sp. IRBG74) were detected. The representative strain YIC4027T could form effective nodules on its original host Sesbania cannabina, but not on Sophora flavescens, Trifolium repens, Glycine max, Glycyrrhiza uralensis, Phaseolus vulgaris or Medicago sativa. The use of lactulose as sole carbon source, possession of C13 : 0 2-OH, C13 : 1 at 12–13, C15 : 1 iso ω9c, C17 : 0 anteiso and C18 : 0 iso and absence of C14 : 0 anteiso, C15 : 0 anteiso and C18 : 0 3-OH in fatty acids distinguished the strain YIC4027T from the type strains of its closely related species. Based on all the analyses mentioned above, we propose a novel species Ensifer alkalisoli sp. nov. and designate YIC4027T (=HAMBI 3655T=LMG 29286T) as the type strain. The genome size of YIC4027T is 5.97 Mbp, comprising 5588 predicted genes, and the DNA G+C content is 62.2 mol%.
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Sphingomonas piscinae sp. nov., isolated from a fish pond
More LessA bacterial strain designated LYH-20T was isolated from a fish pond in Taiwan and characterized using a polyphasic taxonomy approach. Cells of strain LYH-20T were aerobic, Gram-stain-negative, non-motile, poly-β-hydroxybutyrate containing, showing straight and rod shaped that were covered by large capsules and formed yellow-coloured colonies. Growth occurred at 15–40 °C (optimum, 30 °C), with 0–1.0 % NaCl (optimum, 0–0.1 %) and at pH 5.0–9.0 (optimum, pH 8.0–9.0). According to a phylogenetic tree based on 16S rRNA gene sequence analysis, strain LYH-20T belonged to the genus Sphingomonas and clustered with Sphingomonas fonticola TNR-2T, with which it shared the highest 16S rRNA gene sequence similarity (97.5 %). The major fatty acids (>10 %) of strain LYH-20T were C18 : 1ω7c and C16 : 0. The DNA G+C content was 67.5 mol%. The sole isoprenoid quinone was Q-10. The polyamines detected were spermidine, putrescine and homospermidine. The polar lipid profile consisted of a mixture of sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol and three uncharacterized phospholipids. The DNA–DNA hybridization value for strain LYH-20T with Sphingomonas fonticola TNR-2T was less than 35 %. Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus Sphingomonas . On the basis of the genotypic, chemotaxonomic and phenotypic data, strain LYH-20T represents a novel species in the genus Sphingomonas , for which the name Sphingomonas piscinae sp. nov. is proposed. The type strain is LYH-20T (=BCRC 80911T=LMG 29002T=KCTC 42741T).
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Microvirgula curvata sp. nov., isolated from hydrocarbon-contaminated soil, and emended description of the genus Microvirgula
More LessA novel Gram-stain-negative, small curved-rod-shaped, motile strain, designated L6T, was isolated from hydrocarbon-contaminated soils collected from Kuwait. Strain L6T was able to grow at 10–40 °C (optimum, 27–32 °C), pH 6.1–8.8 (optimum, 6.5–7.5) and 0–4.5 % (w/v) NaCl (optimum, 0–0.5). C18 : 1ω6c/C18 : 1ω7c, C16 : 0, C16 : 1ω6c/C16 : 1ω7c, C12 : 0 and C12 : 0 3-OH were predominant fatty acids with minor amounts of C14 : 0 and C17 : 0 cyclo. Phosphatidylglycerol and phosphatidylethanolamine were major polar lipids. The genomic G+C content was 61.2 mol%. 16S rRNA gene sequence comparisons indicated that strain L6T represents a member of the genus Microvirgula within the family Neisseriaceae of the class Betaproteobacteria . Strain L6T has a sequence similarity of 99.2 % with Microvirgula aerodenitrificans SGLY2T and <93.8 % with other members of the family Neisseriaceae . However, strain L6T showed only 56.5±2 % relatedness (based on DNA–DNA hybridization) with M. aerodenitrificans KACC 12055T (=SGLY2T). Distinct morphological, physiological and genotypic differences from the previously described taxa support the classification of strain L6T as a representative of a novel species in the genus Microvirgula , for which the name Microvirgula curvata sp. nov. is proposed. The type strain is L6T (=KEMB 2255-471T=JCM 31223T). An emended description of the genus Microvirgula is also proposed.
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Transfer of the potato plant isolates of Pectobacterium wasabiae to Pectobacterium parmentieri sp. nov.
Pectobacterium wasabiae was originally isolated from Japanese horseradish (Eutrema wasabi), but recently some Pectobacterium isolates collected from potato plants and tubers displaying blackleg and soft rot symptoms were also assigned to P. wasabiae . Here, combining genomic and phenotypical data, we re-evaluated their taxonomic position. PacBio and Illumina technologies were used to complete the genome sequences of P. wasabiae CFBP 3304T and RNS 08-42-1A. Multi-locus sequence analysis showed that the P. wasabiae strains RNS 08-42-1A, SCC3193, CFIA1002 and WPP163, which were collected from potato plant environment, constituted a separate clade from the original Japanese horseradish P. wasabiae . The taxonomic position of these strains was also supported by calculation of the in-silico DNA–DNA hybridization, genome average nucleotide indentity, alignment fraction and average nucleotide indentity values. In addition, they were phenotypically distinguished from P. wasabiae strains by producing acids from (+)-raffinose, α-d(+)-α-lactose, d(+)-galactose and (+)-melibiose but not from methyl α-d-glycopyranoside, (+)-maltose or malonic acid. The name Pectobacterium parmentieri sp. nov. is proposed for this taxon; the type strain is RNS 08-42-1AT (=CFBP 8475T=LMG 29774T).
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Idiomarina tyrosinivorans sp. nov., isolated from estuarine surface water
A tyrosine-metabolizing, Gram-stain-negative, strictly aerobic, non-spore-forming, curved-rod-shaped, motile (due to monopolar flagellum) marine bacterium, designated strain CC-PW-9T, was isolated from estuarine water off Pingtung, Taiwan. Strain CC-PW-9T not only shared highest 16S rRNA gene sequence similarities with Idiomarina representatives (96.4–93.4 %, n=26), but also formed a distinct phyletic lineage and coherent phylogenetic cluster associated with those species. Cells of strain CC-PW-9T grew with 6–12 % (w/v) NaCl, at 20–40 °C and at pH 6–9. It produced predominant amounts of phosphatidylethanolamine, plus diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, two unidentified phospholipids, an unidentified phosphoglycolipid, two unidentified lipids and an unidentified aminolipid in moderate to trace amounts. Fatty acids such as iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1 ω9c and/or C16 : 010-methyl (summed feature 9) were found in major amounts. The DNA G+C content was 51.1 mol%. Ubiquinone-8 (Q-8) was the sole respiratory quinone. Based on evidence from this polyphasic taxonomic study, strain CC-PW-9T is considered to represent a novel species of the genus Idiomarina , affiliated to the family Idiomarinaceae , for which the name Idiomarina tyrosinivorans sp. nov. is proposed. The type strain is CC-PW-9T (=JCM 19757T=BCRC 80745T).
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Acinetobacter celticus sp. nov., a psychrotolerant species widespread in natural soil and water ecosystems
More LessA novel, taxonomically unique group of six strains of the genus Acinetobacter was discovered during an exploratory study on strains culturable from soil and water natural ecosystems in the Bohemian part of the Czech Republic. Based on the comparative analyses of the 16S rRNA gene, gyrB and rpoB sequences, these strains formed strongly supported and internally coherent clusters (intracluster identities of ≥99.9, ≥96.1 and ≥97.3 %, respectively), which were clearly separated from all known species of the genus Acinetobacter (≤98.7, ≤83.2 and ≤88.9 %, respectively). The distinctness of the group at the species level was evidenced also by the results of the genus-wide analyses of the whole-cell mass fingerprints of the six strains generated by matrix-assisted laser desorption/ionization-time-of-flight MS and the whole-genome sequence of a group member, ANC 4603T. Compared with the known species of the genus Acinetobacter , all six strains exhibited a unique phenotype, characterized by psychrotolerance (growth at 1 °C through 28 °C), the inability to grow at 32 °C and the ability to assimilate l-aspartate and malonate but not 2,3-butanediol or citrate. Based on these results, the name Acinetobacter celticus sp. nov. is proposed for the taxon represented by the six strains. The type strain is ANC 4603T (=CCM 8700T=CCUG 69239T=CNCTC 7549T).
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Gilvimarinus japonicus sp. nov., a cellulolytic and agarolytic marine bacterium isolated from coastal debris
A cellulolytic and agarolytic bacterial strain, designated 12-2T, was isolated from a piece of cotton rope fragment washed ashore on a beach and was studied phenotypically, genotypically and phylogenetically. Analyses of 16S rRNA and gyrB gene sequences and DNA base composition suggested that the strain is a member of the genus Gilvimarinus . However, levels of 16S rRNA and gyrB gene sequence similarity between it and the type strains of Gilvimarinus species were no higher than 97.9 and 78.7 %, respectively, suggesting that the strain is distinct. Moreover, the results of DNA–DNA hybridization experiments and physiological characterization clearly differentiated the strain from its closest neighbours. The strain is therefore considered to represent a novel species of the genus Gilvimarinus , for which the name Gilvimarinus japonicus sp. nov. is proposed. The type strain is 12-2T (=NBRC 111987T=KCTC 52141T).
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Altererythrobacter sediminis sp. nov., isolated from lagoon sediments
More LessA Gram-stain-negative, non-motile, non-spore-forming, ovoid rod-shaped bacterium, designated strain CAU1172T, was isolated from lagoon sediments along the east coast of the Republic of Korea. Strain CAU1172T formed a yellow pigment on marine agar. Growth occurred at 20–37 °C (optimum, 30 °C), at pH 6.5–10 (optimum, 7.5) and in the presence of 0–4 % (w/v) NaCl (optimum, 1 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU1172T formed a separate lineage within the genus Altererythrobacter , and was most closely related to Altererythrobacter gangjinensis KJ7T (96.1 % similarity). Ubiquinone 10 (Q-10) was the predominant respiratory quinone. The dominant fatty acids were C18 : 1 ω7c, C17 : 1 ω6c and summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c). The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phospatidylcholine and four unidentified lipids. The DNA G+C content of strain CAU1172T was 63.2 mol%. On the basis of phenotypic and chemotaxonomic data, strain CAU1172T represents a novel species of the genus Altererythrobacter , for which the name Altererythrobacter sediminis sp. nov. is proposed. The type strain is CAU1172T (=KCTC 42453T=NBRC 110917T).
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Luteimonas padinae sp. nov., an epiphytic bacterium isolated from an intertidal macroalga
A Gram-stain-negative, rod-shaped bacterium, forming yellow colonies and designated CDR SL 15T, was isolated from the surface of Padina sp., a brown macroalga, which grows in the Western coastal regions of the state of Goa, India. The 16S rRNA gene sequence phylogeny placed the strain in the genus Luteimonas and it showed closest sequence similarity to Luteimonas terricola BZ92rT (97.6 %) and <97.0 % to other species of the genus Luteimonas . Chemotaxonomic features, such as having iso-C15 : 0 and summed feature 9 (C16 : 0 10-methyl/iso-C17 : 1ω9c) as the major fatty acids and Q-8 as the only ubiquinone further supported its placement within this genus. There were some critical differences in phenotypic properties between Luteimonas padinae sp. nov. CDR SL 15T and L. terricola DSM 22344T i.e. temperature range for growth and salinity range and optimum for growth ( L. terricola is a psychrotolerant bacterium with a lower optimum temperature for growth), acid production and assimilation of substrates, enzyme activities and resistance to certain antibiotics. The DNA–DNA relatedness value of the novel strain with its closest phylogenetic relative was only 40 %, below the 70 % threshold value recommended for species delineation. All these characteristics are consistent with strain CDR SL 15T representing a novel species of the genus Luteimonas , for which the name Luteimonas padinae sp. nov. is proposed. The type strain is CDR SL 15T (=DSM 101536T=KCTC 52403T).
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Identification and taxonomic characterization of Bordetella pseudohinzii sp. nov. isolated from laboratory-raised mice
Bordetella hinzii is known to cause respiratory disease in poultry and has been associated with a variety of infections in immunocompromised humans. In addition, there are several reports of B. hinzii infections in laboratory-raised mice. Here we sequenced and analysed the complete genome sequences of multiple B. hinzii -like isolates, obtained from vendor-supplied C57BL/6 mice in animal research facilities on different continents, and we determined their taxonomic relationship to other Bordetella species. The whole-genome based and 16S rRNA gene based phylogenies each identified two separate clades in B. hinzii , one was composed of strains isolated from poultry, humans and a rabbit whereas the other clade was restricted to isolates from mice. Distinctly different estimated DNA–DNA hybridization values, average nucleotide identity scores, gene content, metabolic profiles and host specificity all provide compelling evidence for delineation of the two species, B. hinzii – from poultry, humans and rabbit – and Bordetella pseudohinzii sp. nov. type strain 8-296-03T (=NRRL B-59942T=NCTC 13808T) that infect mice.
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Arsenicitalea aurantiaca gen. nov., sp. nov., a new member of the family Hyphomicrobiaceae, isolated from high-arsenic sediment
A novel arsenic-resistant bacterium, designated 42-50T, was isolated from the high-arsenic sediment of Jianghan Plain, Hubei Province, China. Phylogenetic and biochemical analysis indicated that this bacterium represents the first species of a novel genus belonging to the family Hyphomicrobiaceae . The 16S rRNA gene of strain 42-50T shares 96.3–94.2, 96.3, 96.2 and 94.9–93.8 % sequence identities to those of species from the genera Devosia , Youhaiella , Paradevosia and Pelagibacterium , respectively. The major cellular fatty acids are C16 : 0, C18 : 0, C18 : 1 ω7c 11-methyl and summed feature 8 (comprising C18 : 1 ω7c and C18 : 1 ω6c). The predominant polar lipids are diphosphatidylglycerol, phosphatidylglycerol and two unidentified glycolipids. The predominant respiratory quinone is ubiquinone-10 (Q-10). The DNA G+C content of strain 42-50T is 73.7 mol%. The distinct phylogenetic lineage and unique cellular fatty acids suggest that strain 42-50T represents a novel species of a new genus affiliated with the family Hyphomicrobiaceae , for which the name Arsenicitalea aurantiaca gen. nov., sp. nov. is proposed. The type strain is 42-50T (=CCTCC AB 2014325T=KCTC 42825T).
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Sphingomonas lutea sp. nov., isolated from freshwater of an artificial reservoir
More LessAn aerobic, Gram-stain-negative, gliding and yellow-pigmented bacterium, designated strain JS5T, was isolated from freshwater of Juam reservoir, Republic of Korea. Cells were catalase-positive and oxidase-negative. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain JS5T forms an independent lineage within the genus Sphingomonas . Strain JS5T was related distantly to ‘ Sphingomonas parvus ’ GP20-2 (98.2 % 16S rRNA gene sequence similarity), Sphingomonas sediminicola Dae 20T (96.8 %) and Sphingomonas daechungensis CH15-11T (96.7 %). The major fatty acids of strain JS5T were C16 : 0, summed feature 3 comprising C16 : 1 ω7c and/or C16 : 1 ω6c and summed feature 8 comprising C18 : 1 ω7c and/or C18 : 1 ω6c. The predominant isoprenoid quinone of the isolate was ubiquinone-10. The DNA G+C content of strain JS5T was 65 mol%. Phenotypic characteristics distinguished strain JS5T from related species of the genus Sphingomonas . On the basis of the evidence presented in this study, a novel species, Sphingomonas lutea sp. nov., is proposed to accommodate strain JS5T (=KCTC 23642T=JCM 18309T).
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Tropicimonas arenosa sp. nov., isolated from marine sand
More LessA Gram-staining-negative, aerobic, non-motile, rod-shaped bacterial strain, designated CAU 1062T, was isolated from marine sand in Jeju island, Republic of Korea and its taxonomic position was investigated using a polyphasic approach. CAU 1062T grew optimally at 30 °C and pH 8 in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that CAU 1062T formed a distinct lineage within the genus Tropicimonas and was the most closely related to Tropicimonas sediminicola M97T (similarity 96.11 %). The strain had ubiquinone-10 (Q-10) as the predominant respiratory quinone and C18 : 1ω7c as the major cellular fatty acid. The polar lipid pattern of CAU 1062T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, an aminolipid, six phospholipids and five lipids. The DNA G+C content was 65.7 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, CAU 1062T represents a novel species of the genus Tropicimonas , for which the name Tropicimonas arenosa sp. nov. is proposed. The type strain is CAU 1062T (=KCTC 52178T=NBRC 111995T).
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Marinomonas blandensis sp. nov., a novel marine gammaproteobacterium
A novel Gram-staining-negative, chemoorganotrophic, moderately halophilic, strictly aerobic bacterium, strain MED121T, was isolated from a seawater sample collected at the Blanes Bay Microbial Observatory in the north-western Mediterranean Sea. Analysis of its 16S rRNA gene sequence, retrieved from the whole-genome sequence, showed that this bacterium was most closely related to Marinomonas dokdonensis and other Marinomonas species (96.3 and 93.3–95.7 % sequence similarities, respectively), within the family Oceanospirillaceae . Strain MED121T was included into a whole-genome sequencing study and, subsequently, it was characterized using a polyphasic taxonomic approach. It was found to be oxidase and catalase positive, its cells are cocci to short rods, it does not ferment carbohydrates and does not reduce nitrate to nitrite or gas and it requires at least 2.5 % (w/v) marine salts and tolerates up to 7 % (w/v) salts. Its major cellular fatty acids in order of abundance are C16 : 1ω7c/C16 : 1ω6c, C18 : 1ω7c, C16 : 0 and C10 : 0 3-OH. Its genome had an approximate length of 5.1 million bases and a DNA G+C content equal to 40.9 mol%. Analysis of the annotated genes reveals the capacity for the synthesis of ubiquinone 8 (Q8) and the polar lipids phosphatidylglycerol and phosphatidylethanolamine, in agreement with other members of the genus. All the data collected supported the creation of a novel species to accommodate this bacterium, for which the name Marinomonas blandensis sp. nov. is proposed. The type strain is MED121T (=CECT 7076T=LMG 29722T).
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Primorskyibacter aestuariivivens sp. nov., isolated from a tidal flat, and emended description of the genus Primorskyibacter
More LessA Gram-stain-negative, aerobic, non-spore-forming, motile and coccoid, ovoid or rod-shaped bacterial strain, designated OITF-36T, was isolated from a tidal flat in Oido, an island of South Korea, and subjected to a polyphasic taxonomic study. Strain OITF-36T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0–3.0 % (w/v) NaCl. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain OITF-36T clustered with the type strains of Primorskyibacter sedentarius and Primorskyibacter insulae , showing 97.4–97.6 % sequence similarity. It exhibited sequence similarity values of less than 96.9 % to the type strains of the other recognized species. Strain OITF-36T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids detected in strain OITF-36T were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain OITF-36T was 61.8 mol%, and its mean DNA–DNA relatedness values with the type strains of P . sedentarius and P . insulae were 16–24 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain OITF-36T is separate from P . sedentarius and P . insulae . On the basis of the data presented, strain OITF-36T is considered to represent a novel species of the genus Primorskyibacter , for which the name Primorskyibacter aestuariivivens sp. nov. is proposed. The type strain is OITF-36T (=KCTC 52455T=NBRC 112419T).
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- Eukaryotic micro-organisms
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Apiotrichum terrigenum sp. nov., a soil-associated yeast found in both the UK and mainland Europe
Five arthroconidium-producing yeast strains representing a novel Trichosporon-like species were independently isolated from the UK, Hungary and Norway. Two strains (Bio4T and Bio21) were isolated from biogas reactors used for processing grass silage, with a third strain (S8) was isolated from soil collected at the same UK site. Two additional strains were isolated in mainland Europe, one from soil in Norway (NCAIM Y.02175) and the other from sewage in Hungary (NCAIM Y.02176). Sequence analyses of the D1/D2 domains of the LSU rRNA gene and internal transcribed spacer (ITS) region indicated that the novel species belongs to the recently reinstated genus Apiotrichum and is most closely related to Apiotrichum scarabaeorum, a beetle-associated species first found in South Africa. Despite having similar physiological characteristics, the two species can be readily distinguished from one another by ITS sequencing. The species name Apiotrichum terrigenum sp. nov. is proposed to accommodate these strains, with Bio4T (=CBS 11373T=NCYC 3540T) designated as the type strain. The Mycobank deposit number is MB817431.
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Kockovaella libkindii sp. nov., a yeast species isolated from water tanks of bromeliad
During a study of yeast community associated with water tanks (phytotelmata) of the bromeliad Vriesea minarum, two strains of a novel stalk-forming yeast species were found. The sequences of the region spanning the ITS and D1/D2 domains of the large subunit rRNA gene showed that this species belongs to the genus Kockovaella. The novel species differs by 14 or more nucleotide substitutions in the D1/D2 domains and by 26 or more substitutions in the ITS–5.8S region from all other Kockovaella species. We describe this species as Kockovaella libkindii sp. nov. The type strain of Kockovaella libkindii sp. nov. is UFMG-CM-Y6053T (=UFMG-BRO-488T=CBS 12685T). The MycoBank number is MB 817710.
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Volumes and issues
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