- Volume 68, Issue 9, 2018
Volume 68, Issue 9, 2018
- Validation List
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- Notification List
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- New Taxa
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- Actinobacteria
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Blastococcus atacamensis sp. nov., a novel strain adapted to life in the Yungay core region of the Atacama Desert
A polyphasic study was undertaken to establish the taxonomic status of a Blastococcus strain isolated from an extreme hyper-arid Atacama Desert soil. The isolate, strain P6T, was found to have chemotaxonomic and morphological properties consistent with its classification in the genus Blastococcus . It was shown to form a well-supported branch in the Blastococcus 16S rRNA gene tree together with the type strains of Blastococcus capsensis and Blastococcus saxobsidens and was distinguished from the latter, its close phylogenetic neighbour, by a broad range of phenotypic properties. The draft genome sequence of isolate P6T showed 84.6 % average nucleotide identity, 83.0 % average amino acid identity and a digital DNA–DNA hybridisation value of 27.8 % in comparison with the genome sequence of B. saxobsidens DSM 44509T, values consistent with its assignment to a separate species. Based on these data it is proposed that isolate P6T (NCIMB 15090T=NRRL B-65468T) be assigned to the genus Blastococcus as Blastococcus atacamensis sp. nov. Analysis of the whole genome sequence of B. atacamensis P6T, with 3778 open reading frames and a genome size of 3.9 Mb showed the presence of genes and gene clusters that encode for properties that reflect its adaptation to the extreme environmental conditions that prevail in Atacama Desert soils.
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Glycomyces xiaoerkulensis sp. nov., isolated from Xiaoerkule lake in Xinjiang, China
More LessA novel actinomycete, strain TRM 41368T, was isolated from a silt sample from Xiaoerkule lake in Xinjiang province, China, and was examined using a polyphasic approach. Strain TRM 41368T was aerobic, Gram-stain-positive, with an optimum NaCl concentration for growth of 5 % (w/v), and an optimum temperature for growth of 35–37 °C. On the basis of 16S rRNA gene sequence analysis, strain TRM 41368T was most closely related to Glycomycesfuscus TRM 49117T (98.46 % similarity). However, it had a relatively low DNA–DNA relatedness value with G. fuscus TRM 49117T (ANI=70.59 %). The organism had chemical and morphological features typical of the genus Glycomyces . The cell wall of TRM 41368T contained meso-diaminopimelic acid; xylose, ribose and glucose were the major whole-cell sugars. The diagnostic polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and phosphatidylinositolmannosides. The predominant menaquinone was MK-9(H6). The major fatty acids were C18 : 1ω9c, C16 : 0, iso-C16 : 0, anteiso-C17 : 0 and anteiso-C15 : 0. The G+C content of the DNA was 69.9 mol%. On the basis of the polyphasic evidence, strain TRM 41368T should be designated as a novel species of the genus Glycomyces , for which the name Glycomyces xiaoerkulensis sp. nov. is proposed. The type strain is TRM 41368T (=CCTCC AA 2017005T=KCTC 39932T).
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Brevibacterium hankyongi sp. nov., isolated from compost
A Gram-positive, strictly aerobic, non-motile, milky-white to creamy coloured and rod-shaped bacterium, designated BS05T, was isolated from compost. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that the strain formed a distinct lineage within the genus Brevibacterium and was most closely related to Brevibacterium avium NCFB 3055T (96.3 %), Brevibacterium oceani BBH7T (96.2 %) and Brevibacterium epidermidis NBRC 14811T (96.1 %). The DNA G+C content was 62.3 mol%. The predominant quinone was MK-8(H2). The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. The cell-wall peptidoglycan of strain BS05T contained meso-diaminopimelic acid. The major polar lipid was phosphatidylglycerol. Moreover, the low sequence similarity of the 16S rRNA gene sequencing, physiological, biochemical and chemotaxonomic analyses allowed the phenotypic and genotypic differentiation of strain BS05T from the recognized species of the genus Brevibacterium . Therefore, strain BS05T represents a novel species of the genus Brevibacterium , for which the name Brevibacterium hankyongi sp. nov. is proposed, with the type strain BS05T (=KACC 18875T=LMG 29562T).
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Sphaerisporangium rhizosphaerae sp. nov., an actinomycete isolated from the rhizosphere soil of a rubber tree (Hevea brasiliensis Muell. Arg)
A novel actinomycete, designated strain NEAU-mq3T, was isolated from the rhizosphere soil of a rubber tree (Hevea brasiliensis Muell. Arg) collected from Xianglu Mountain in Heilongjiang Province, north-east China, and characterized by using a polyphasic approach. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the organism should be assigned to the genus Sphaerisporangium and that it forms a monophyletic clade with its closest relatives ‘ Sphaerisporangium dianthi ’ NEAU-CY18T (99.2 % 16S rRNA gene sequence similarity) and Sphaerisporangium cinnabarinum JCM 3291T (98.8 %). Morphological and chemotaxonomic properties of strain NEAU-mq3T were also consistent with the description of the genus Sphaerisporangium . The whole-cell sugars were madurose, mannose, ribose and glucose. The menaquinones were MK-9(H2), MK-9(H4), MK-9(H0) and MK-9(H6). The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylinositol mannoside, an unidentified polar lipid and an unidentified phospholipid. The major fatty acids were identified as iso-C16 : 0, 10-methyl C17 : 0, C16 : 1ω7c and C17 : 1ω7c. DNA–DNA hybridization experiments and phenotypic tests were carried out between strain NEAU-mq3T and its most closely related strains, which further clarified their relatedness and demonstrated that NEAU-mq3T could be distinguished from these strains. Therefore, it is concluded that strain NEAU-mq3T represents a novel species of the genus Sphaerisporangium , for which the name Sphaerisporangium rhizosphaerae sp. nov. is proposed. The type strain is NEAU-mq3T (=CGMCC 4.7429T=JCM 32389T).
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Frankia irregularis sp. nov., an actinobacterium unable to nodulate its original host, Casuarina equisetifolia, but effectively nodulates members of the actinorhizal Rhamnales
More LessA red pigmented actinobacterium designated G2T, forming extremely branched vegetative hyphae, vesicles and mutilocular sporangia, was isolated from Casuarina equisetifolia nodules. The strain failed to nodulate its original host plant but effectively nodulated members of actinorhizal Rhamnales. The taxonomic position of G2T was determined using a polyphasic approach. The peptidoglycan of the strain contained meso-diaminopimelic acid as diagnostic diamino acid, galactose, glucose, mannose, rhamnose, ribose and xylose. The polar lipid pattern consisted of phosphatidylinositol (PI), diphosphatidylglycerol (DPG), glycophospholipids (GPL1–2), phosphatidylglycerol (PG), aminophospholipid (APL) and unknown lipids (L). The predominant menaquinones were MK-9 (H4) and MK-9 (H6) while the major fatty acids were iso-C16 : 0, C17 : 1ω8c and C15 : 0. The size of the genome of G2T was 9.5 Mb and digital DNA G+C content was 70.9 %. The 16S rRNA gene showed 97.4–99.5 % sequence identity with the type strains of species of the genus Frankia . Digital DNA –DNA hybridisation (dDDH) values between G2T and its nearest phylogenetic neighbours Frankia elaeagni and Frankia discariae were below the threshold of 70 %. On the basis of these results, strain G2T (=DSM 45899T=CECT 9038T) is proposed to represent the type strain of a novel species Frankia irregularis sp. nov.
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Euzebya rosea sp. nov., a rare actinobacterium isolated from the East China Sea and analysis of two genome sequences in the genus Euzebya
Rare Actinobacteria , known as non- Streptomyces , hold great potential to produce new bioactive compounds for drug development. A strain designated DSW09T, which belongs those rare Actinobacteria , was isolated from surface seawater of the East China Sea. The cells were aerobic, Gram-positive, non-motile, non-spore-forming and rod-shaped (0.4 µm wide and 1.5–4.0 µm long). The closest relative was Euzebya tangerina F10T (96.46 % of 16S rRNA gene similarity). Cell growth occurred at 15–45 °C (optimum, 25–30 °C), at pH 6.0–9.0 (pH 6.0–7.0) and at NaCl concentrations of 0.5–5.0 % (w/v; 1.0–4.0 %). The major cellular fatty acids were summed feature 3 (comprising C16 : 1 ω7c and/or C15 : 0 iso 2OH), C17 : 1 ω8c and C16 : 0. The predominant polar lipid was diphosphatidylglycerol. The predominant menaquinone was MK-9(H4). The cell-wall peptidoglycan was A1 γ–type, containing meso-DPA. The major cell-wall sugars were rhamnose and ribose. The genome size was 5 509 297 bp with a 71.29 mol% G+C content for strain DSW09T, while 4 781 440 bp with a 68.87 mol% G+C content for E. tangerina F10T. The average nucleotide identity and digital DNA–DNA hybridization values between strain DSW09T and E. tangerina F10T were 73.44 % and 16.43 %, respectively. Based on phylogenetic, phenotypic, chemotaxonomic evidence and genomic analyses, strain DSW09T is a novel species of genus Euzebya , for which the name Euzebya rosea sp. nov. is proposed. The type strain is DSW09T (=DMS 104446T=MCCC 1K03290T).
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Actinomadura deserti sp. nov., isolated from desert soil
A Gram-positive, strictly aerobic actinobacterium, designated BMP B8004T, was isolated from desert soil collected in Xinjiang Province, Northwest China. It produced an extensively branched non-fragmenting substrate mycelium, and very scanty aerial mycelium that formed a short hooked chain of arthrospores with a smooth surface. Optimum growth occurred at 28 °C, pH 7.0 and 0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BMP B8004T formed a distinct phyletic lineage within the genus Actinomadura . It shared the highest 16S rRNA gene sequence similarity to Actinomadura apis IM17-1T (99.2 %) and Actinomadura rifamycini NBRC 14183T (98.6 %). However, it could be distinguished from the two closest strains based on the low levels of DNA–DNA relatedness (52.7±0.7 and 45±1.8 %, respectively). Chemotaxonomic characteristics, including the main phospholipids, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides, the major menaquinones MK-9(H6) and MK-9(H8), the predominant fatty acids iso-C16 : 0, C16 : 0, C18 : 0 10-methyl and C18 : 1ω9c, were also consistent with the properties of the genus Actinomadura . The DNA G+C content of strain BMP B8004T was 71.9 mol%. Based on phenotypic and genotypic features, strain BMP B8004T is considered to represent a novel species of the genus Actinomadura , for which the name Actinomadura deserti sp. nov. is proposed. The type strain is BMP B8004T (=CGMCC 4.7432T=KCTC 39998T).
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Pseudonocardia mangrovi sp. nov., isolated from soil
More LessA novel Gram-stain-positive, aerobic actinomycete, designated strain SMC 195T, was isolated from soil collected from a mangrove forest in Thailand. The strain produced extensively branched substrate and aerial mycelia. The substrate mycelium was fragmented into rod-shaped elements, and spore chains consisting of smooth and rod-shaped spores were formed on the aerial mycelium. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that SMC 195T represented a member of the genus Pseudonocardia , and the most closely phylogenetically related species were Pseudonocardia yuanmonensis JCM 18055T (99.2 % 16S rRNA gene sequence similarity), Pseudonocardia halophobica NRRL B-16514T (98.9 %) and Pseudonocardia kujensis NRRL B-24890T (98.7 %). However, the DNA–DNA relatedness values between SMC 195Tand the closest phylogenetically related species were significantly below 70 %. The G+C content of the genomic DNA was 74±0.8 mol%. The cell wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars consisted of arabinose, galactose, glucose, rhamnose and ribose. The menaquinone was MK-8(H4) only. The major cellular fatty acid was the branched fatty acid iso-C16 : 0 (33.6 %). The polar lipids detected were phosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxyphosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and unidentified glycolipids. On the basis of the results from phenotypic, chemotaxonomic and genotypic studies, it is concluded that SMC 195T represents a novel species of the genus Pseudonocardia , for which the name Pseudonocardia mangrovi sp. nov. is proposed. The type strain is SMC 195T (=TBRC 7778T=NBRC 113150T).
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Nocardioides currus sp. nov., isolated from a mobile car air-conditioning system
More LessA strictly aerobic Gram-stain-positive bacterial strain, designated IB-3T, was isolated from a car air-conditioning system in the Republic of Korea. Cells were non-motile rods showing catalase- and oxidase-positive reactions. Growth of IB-3T was observed at 20–40 °C (optimum, 25 °C), at pH 6.5–9.0 (optimum, pH 7.5) and in the presence of 0–1 % (w/v) NaCl (optimum, 0 %). Menaquinone-8 (H4) was detected as the predominant respiratory quinone and iso-C16 : 0, 10-methyl-C17 : 0, iso-C17 : 0, C18 : 1ω9c, C17 : 1ω8c, C18 : 0, 10-methyl-C18 : 0 (TBSA) and C17 : 0 were identified as the major cellular fatty acids. Phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and phosphatidylinositol were detected as the major polar lipids. The major cell wall peptidoglycan type was ll-2,6-diaminopimelic acid. The G+C content of the genomic DNA was 71.5 mol%. IB-3T was most closely related to Nocardioides terrigena DS-17T with a 98.0 % 16S rRNA gene sequence similarity. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that IB-3T formed a distinct phylogenetic lineage within the genus Nocardioides of the family Nocardioidaceae . On the basis of the phenotypic, chemotaxonomic and molecular features, IB-3T represents a novel species of the genus Nocardioides , for which the name Nocardioides currus sp. nov. is proposed. The type strain is IB-3T (=KACC 19522T=JCM 32672T).
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Frankia canadensis sp. nov., isolated from root nodules of Alnus incana subspecies rugosa
Strain ARgP5T, an actinobacterium isolated from a root nodule present on an Alnus incana subspecies rugosa shrub growing in Quebec City, Canada, was the subject of polyphasic taxonomic studies to clarify its status within the genus Frankia . 16S rRNA gene sequence similarities and ANI values between ARgP5T and type strains of species of the genus Frankia with validly published names were 98.8 and 82 % or less, respectively. The in silico DNA G+C content was 72.4 mol%. ARgP5T is characterised by the presence of meso-A2pm, galactose, glucose, mannose, rhamnose (trace), ribose and xylose as whole-organism hydrolysates; MK-9(H8) as predominant menaquinone; diphosphatidylglycerol, phosphatidylinositol and phosphatidylglycerol as polar lipids and iso-C16 : 0 and C17 : 1ω8c as major fatty acids. The proteomic results confirmed the distinct position of ARgP5T from its closest neighbours in Frankia cluster 1. ARgP5T was found to be infective on two alder (Alnus glutinosa and Alnusalnobetula subsp. crispa) and on one bayberry (Morella pensylvanica) species and to fix nitrogen in symbiosis and in pure culture. On the basis of phylogenetic (16S rRNA gene sequence), genomic, proteomic and phenotypic results, strain ARgP5T (=DSM 45898=CECT 9033) is considered to represent a novel species within the genus Frankia for which the name Frankia canadensis sp. nov., is proposed.
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Actinomadura rhizosphaerae sp. nov., isolated from rhizosphere soil of the plant Azadirachta indica
More LessA novel actinomycete, strain SDA37T, belonging to the genus Actinomadura , was isolated from rhizosphere soil collected from Udon Thani Province, Thailand. The taxonomic position of the strain was characterized using a polyphasic approach. Meso-diaminopimelic acid, glucose, ribose, galactose and madurose were detected in cell-wall and whole-cell hydrolysates. The N-acyl type of muramic acid was acetyl. Menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The predominant cellular fatty acids were iso-C16 : 0, C16 : 0, 10-methyl C18 : 0 and iso-C14 : 0. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol. blast analysis of the almost-complete 16S rRNA gene sequence showed 98.8 % similarity to Actinomadura oligospora NBRC 104149T, 98.7 % similarity to Actinomadura gamaensis DSM 100815T and 97.2 % similarity to Actinomadura rupiterrae KCTC 19559T. The DNA G+C content was 73.1 mol%. Strain SDA37T showed low DNA–DNA relatedness (44.3±7.3 to 58.5±8.7 %) to A. oligospora NBRC 104149T, Actinomadura gamaensis DSM 100815T and Actinomadura rupiterrae KCTC 19559T. The new strain could also be distinguished from its closely related strains by the differences in the phenotypic characteristics. The results of taxonomic analysis suggested that strain SDA37T represented a novel species of the genus Actinomadura for which the name Actinomadura rhizosphaerae sp. nov. is proposed. The type strain is SDA37T (=KCTC 39965T=NBRC 112909T=TISTR 2523T).
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Actinomycetospora endophytica sp. nov., isolated from wild orchid (Podochilus microphyllus Lindl.) in Thailand
A novel endophytic actinomycete, designated strain A-T 8314T, was isolated from a wild orchid, Podochilus microphyllus Lindl., collected from Trat Province, Thailand. The taxonomic position of strain A-T 8314T was established using a combination of genotypic and phenotypic analyses. The isolate was a Gram-positive bacterium that developed bud-like spore chains. Strain A-T 8314T grew aerobically at an optimum temperature of 20–25 °C and an optimal pH 6.0. The cell wall contained meso-diaminopimelic acid, and the whole-cell sugars were ribose, arabinose and galactose. The predominant menaquinone was MK-8 (H4). The polar lipid profile contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, phosphatidylmonomethylethanolamine, hydroxy-phosphatidylmonomethylethanolamine and hydroxyl phosphatidylethanolamine. The predominant cellular fatty acid was iso-C16 : 0. The DNA G+C content of the genomic DNA was 73.2±0.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain A-T 8314T belonged to the genus Actinomycetospora , and was most closely related to Actinomycetospora chiangmaiensis YIM 0006T (98.8 %) and Actinomycetospora corticicola 014-5T (98.6 %). The DNA–DNA relatedness values that distinguished A-T 8314T from its closest species were below 70 %. Following an evaluation of phenotypic, chemotaxonomic and genotypic studies, it was concluded that the new isolate represents as a novel species, for which the name Actinomycetospora endophytica sp. nov is proposed. The type strain is A-T 8314T (=TBRC 5722T=NBRC 113235T).
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Saccharopolyspora maritima sp. nov., an actinomycete isolated from mangrove sediment
More LessA novel Saccharopolyspora strain, designated 3SS5-12T, isolated from mangrove sediment collected from Ranong Province is described. The strain was characterized by pale yellow branching aerial mycelium which differentiated into flexuous chains of spores covered with tufts of short curved hairs. The whole-cell hydrolysates of the strain contained meso-diaminopimelic acid as the diagnostic diamino acid, with arabinose, galactose and ribose as the main sugars. A major menaquinone of this strain was MK-9(H4). Mycolic acids were absent. The DNA G+C content of the genomic DNA was 69.4 mol%. The predominant cellular fatty acids were iso-C16 : 0 and anteiso-C17 : 0. Polar lipids consisted of diphosphatidylglycerol, hydroxy-phosphatidylethanolamine, hydroxy-phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, unidentified phospholipids and unidentified lipids. Phylogenetic determination based on 16S rRNA gene sequences indicated that the organism was classified in the genus Saccharopolyspora and highly similar to Saccharopolyspora jiangxiensis W12T (98.8 % sequence similarity), Saccharopolyspora hirsuta subsp. kobensis JCM 9109T (98.8 %), Saccharopolyspora antimicrobica I05-00074T (98.2 %) and Saccharopolyspora indica VRC122T (98.1 %). Evidence from the chemotaxonomic, phenotypic and molecular systematic data indicated that strain 3SS5-12T should be classified as a representing novel species of the genus Saccharopolyspora , for which the name Saccharopolyspora maritima sp. nov. is proposed. The type strain is 3SS5-12T (=TBRC 7048T=NBRC 112863T).
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Glycomyces dulcitolivorans sp. nov., isolated from rhizosphere soil of wheat (Triticum aestivum L.)
A novel actinomycete, designated strain SJ-25T, was isolated from rhizosphere soil of wheat (Triticumaestivum L.) and characterized using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain SJ-25T belonged to the genus Glycomyces and was closely related to Glycomyces scopariae YIM 56256T (99.0 % 16S rRNA gene sequence similarity), Glycomyces artemisiae IXS4T (98.8 %), Glycomyces sambucus E71T (98.7 %) and Glycomyces mayteni YIM 61331T (98.4 %). Moreover, key morphological and chemotaxonomic properties also confirmed the affiliation of strain SJ-25T to the genus Glycomyces . The cell wall contained meso-diaminopimelic acid and the whole-cell hydrolysates contained galactose, glucose and xylose. The phospholipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannoside, glycolipid and two unidentified polar lipids. The menaquinones were MK-11, MK-10(H4) and MK-10(H2). Major fatty acids were iso-C16 : 0, anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C14 : 0. The DNA G+C content was 72.2 mol%. The combination of DNA–DNA hybridization results and some phenotypic characteristics demonstrated that strain SJ-25T could be distinguished from its closely related strains. Therefore, it is proposed that strain SJ-25T represents a novel species of the genus Glycomyces , for which the name Glycomyces dulcitolivorans sp. nov. is proposed. The type strain is SJ-25T (=CGMCC 4.7414T=DSM 105121T).
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- Bacteroidetes
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Hymenobacter bucti sp. nov., isolated from subsurface sandstone sediment
More LessA Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming bacterial strain, designated DK6-66T, was isolated from subsurface sandstone sediment located in the Qilian Mountains in Qinghai Province, Northwest China. Strain DK6-66T was found to grow optimally at pH 7.0 and 22 °C. The 16S rRNA gene sequence analysis indicated that strain DK6-66T belonged to the genus Hymenobacter and clustered with the type strain of Hymenobacter arcticus , with which it exhibited a 16S rRNA gene sequence similarity value of 98.2 %. The DNA G+C content was 60.4 mol%. The major respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. The major fatty acids were C16 : 1ω7c and/or C16 : 1ω6c, anteiso-C17 : 1 B and/or iso-C17 : 1 I, iso-C15 : 0, anteiso-C15 : 0 and C16 : 1ω5c. On the basis of phylogenetic and phenotypic data, strain DK6-66T was classified in the genus Hymenobacter as a member of a novel species, for which the name Hymenobacter bucti sp. nov. is proposed. The type strain is DK6-66T (=CGMCC 1.15795T=KCTC 52629T).
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Solitalea longa sp. nov., isolated from freshwater and emended description of the genus Solitalea
Yunho Lee and Che Ok JeonA Gram-negative, strictly aerobic, oxidase-positive, catalase-negative and yellow-pigmented bacterium, designated strain HR-AVT, was isolated from a water sample of the Han River. Cells were elongated rods with gliding motility without flagellum. Growth was observed at 5–30 °C (optimum, 20 °C), pH 7–8 and 0–0.5 % NaCl. The major respiratory quinone was menaquinone-7. The major fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and anteiso-C15 : 0. The polar lipids comprised phosphatidylethanolamine, an unidentified amino lipid and five unidentified lipids. The DNA G+C content of strain HR-AVT was 38.4 mol%. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HR-AVTbelonged to the family Sphingobacteriaceae in the phylum Bacteroidetes and formed a phylogenic lineage with Solitalea canadensis DSM 3403T and Solitalea koreensis R2A36-4T. Strain HR-AVT was most closely related to S. canadensis DSM 3403T and S. koreensis R2A36-4T with 97.3 and 94.0 % 16S rRNA gene sequence similarities, respectively, and then had low similarities (below 90.9 %) with other bacteria with validly published names. Average nucleotide identity and in silico DNA–DNA hybridization values between strain HR-AVT and S. canadensis were 74.0 and 19.7 %, respectively. Based on these results, strain HR-AVT represents a novel species of the genus Solitalea , for which the name Solitalea longa sp. nov. is proposed. The type strain is HR-AVT (=KACC 19411T=JCM 32259T). An emended description of the genus Solitalea is also proposed.
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Winogradskyella tangerina sp. nov., a member of the Flavobacteriaceae isolated from coastal sediment
More LessA Gram-stain-negative, rod-shaped bacterium (designated strain M1309T), with slow gliding motility, was isolated from marine sediment obtained off the coast of Weihai, PR China. The growth of M1309T was observed at 16–42 °C (optimum, 37 °C) and pH 6.5–8.0 (optimum, 7.0–7.5) in the presence of 2.0–6.0 % (w/v) NaCl (optimum, 2.0–3.0 %). Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the strain represented a member of the genus Winogradskyella . M1309T exhibited the highest 16S rRNA gene sequence similarity, of 95.5 %, to Winogradskyella poriferorum JCM 12885T. Chemotaxonomic analysis revealed that the sole respiratory quinone was menaquinone 6 (MK-6) and the major fatty acids included iso-C15 : 0, iso-C15 : 1G and iso-C17 : 0 3-OH. The major polar lipids included phosphatidylethanolamine, two aminolipids, and three unidentified lipids. The DNA G+C content of the strain was 36.1 mol%. On the basis of phenotypic distinctiveness and phylogenetic divergence, strain M1309T is considered to represent a novel species of the genus Winogradskyella , for which the name Winogradskyella tangerina sp. nov. is proposed. The type strain is M1309T (=KCTC 52896T=MCCC 1K03310T).
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Hymenobacter rufus sp. nov., a bacterium isolated from soil
More LessA bacterial strain, S1-2-2-6T, was isolated from a soil sample collected in Jeollabuk-do province, Republic of Korea. Cells of this strain were observed to be Gram-stain-negative, short and rod-shaped, and colonies were red to pink in colour. Analysis of 16S rRNA gene sequences identified this strain as representing a member of the genus Hymenobacter in the family Cytophagaceae , with the highest levels of sequence similarity being observed in relation to Hymenobacter terrae DG7AT (98.2 %), Hymenobacter rubidus DG7BT (97.9 %), Hymenobacter soli PB17T (97.7 %), and Hymenobacter daeguensis 16F3Y-2T (97.3 %). Growth of S1-2-2-6T was observed at 4–30 °C, pH 6–8 and in the presence of 0–0.5 % NaCl. The predominant respiratory quinone of this strain was menaquinone-7, the major fatty acids were C15 : 0 iso, C15 : 0 anteiso, and Summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), and the major polar lipid was phosphatidylethanolamine. The genomic DNA G+C content of S1-2-2-6T was 60.7 mol%. DNA–DNA hybridization experiments with H. terrae , H. rubidus , H. soli and H. daeguensis resulted in relatedness values of 35.9 and 38.4 %, 34.2 and 30.4 %, 28.3 and 33.1 %, and 23.5 and 27.9 %, respectively. These DNA–DNA hybridization results, in addition to some differentiating phenotypic properties, clearly indicate that S1-2-2-6T is a representative of a novel species of the genus Hymenobacter , for which the name Hymenobacter rufus sp. nov. is proposed. The type strain is S1-2-2-6T (=KCTC 52736T=JCM 32196T).
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- Firmicutes and Related Organisms
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Clostridium beihaiense sp. nov., an anaerobic bacterium isolated from activated sludge
More LessA Gram-positive, strictly anaerobic, rod-shaped bacterium, designated YB-7T, was isolated from activated sludge of an anaerobic baffled reactor pond in Weizhou terminal wastewater treatment plant, Beihai, Guangxi, China. Strain YB-7T grew at pH 5.0–12.0 (optimum, pH 7.0), 20–45 °C (37 °C) and NaCl concentration of 0–5 % w/v (optimum, 5 %). 16S rRNA gene sequence analysis results showed that strain YB-7T belonged to the genus Clostridium and it was most closely related to Clostridium tetanomorphum DSM 4474T (96.9 % similarity). The DNA–DNA relatedness of strain YB-7T to Clostridium tetanomorphum DSM 4474T was 47.4 %. The DNA G+C content of strain YB-7T was determined to be 32.3 mol%, and the predominant cellar fatty acid (>10 %) was C16 : 0. Polar lipids of strain YB-7T included diphosphatidylglycerol, phosphatidylethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two unidentified aminophospholipids, two unidentified phospholipids and unidentified lipids. The results of this study supported the conclusion that strain YB-7T should be assigned to a new member of the genus Clostridium , for which the name Clostridium beihaiense sp. nov. is proposed. The type strain is YB-7T (=CICC 24109T=KCTC 15555T).
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Pueribacillus theae gen. nov., sp. nov., isolated from Pu’er tea
More LessA novel bacterial strain, designated T8T, isolated from ripened Pu’er tea, was investigated by using a polyphasic taxonomic approach. Cells stained Gram-positive and were aerobic, sporogenous and rod-shaped with flagella. Phylogenetic analysis of 16S rRNA gene sequences revealed the strain belonged to the family Bacillaceae in the class Bacilli and represented an independent taxon separated from other genera. Strain T8T shared low levels of 16S rRNA gene sequence similarity (<94 %) to members of other genera in the family Bacillaceae and was most closely related to Bacillus composti SgZ-9T (93.3 % sequence similarity). The DNA G+C content of strain T8T was 40 mol%. The major fatty acids (>10 %) of strain T8T were iso-C15 : 0 and iso-C16 : 0. The strain had a cell-wall type A1γ peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. MK-7 (62 %), MK-6 (31 %) and MK-8 (7 %) were detected as the isoprenoid quinones. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine and six unidentified phospholipids. On the basis of the polyphasic evidence presented, strain T8T is considered to represent a novel genus and species in the family Bacillaceae , for which we propose the name Pueribacillus theae gen. nov., sp. nov. The type strain is T8T (=CGMCC 1.15924T=KCTC 333888T).
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Review of Desulfotomaculum species and proposal of the genera Desulfallas gen. nov., Desulfofundulus gen. nov., Desulfofarcimen gen. nov. and Desulfohalotomaculum gen. nov.
More LessThe genus Desulfotomaculum is a heterogeneous group of spore-forming sulfate-reducing bacteria. The type species of the genus is Desulfotomaculum nigrificans (Approved Lists 1980) emend. Visser et al. 2014. The results of phylogenetic analysis demonstrated that the genus Desulfotomaculum already has lost the clustering monophyly and was segregated into some distinct groups with low sequence similarity. Major features of the type strains in these groups were compared, and four novel genera, Desulfallas gen. nov., Desulfofundulus gen. nov., Desulfofarcimen gen. nov. and Desulfohalotomaculum gen. nov. were proposed to accommodate species transferred from the genus Desulfotomaculum .
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Lactobacillus terrae sp. nov., a novel species isolated from soil samples in the Republic of Korea
More LessA novel strain, designated NIBRBAC000499792T, was isolated from a soil sample collected at Jukgye, Dongnam, Cheonan, Republic of Korea. Cells were Gram-positive, non-motile, non-spore-forming, rod-shaped, oxidase-negative and catalase-negative. Colonies grown on de Man, Rogosa and Sharpe agar were white, circular, raised and entire. Analysis of the 16S rRNA gene sequence analysis revealed that strain NIBRBAC000499792T belongs to the genus Lactobacillus (family Lactobacillaceae ) and is most closely related to Lactobacillus nodensis DSM 19682T (96.1 % similarity) and Lactobacillus tucceti KCTC 21005T (96.7 %). The results of DNA–DNA hybridization experiments demonstrated that strain NIBRBAC000499792T represents a novel species. Major fatty acids are C18 : 1ω9c, C16 : 0 and unidentified 18.846 and/or C19 : 1ω6c and/or C19 : 0cyclo. The predominant respiratory quinones are menaquinone-8 and menaquinone-9. The major polar lipids are phosphatidylglycerol and diphosphatidylglycerol. The minor polar lipids are one unidentified aminophospholipid, one unidentified phospholipid, and four unidentified lipids. Next-generation sequencing analysis of strain NIBRBAC000499792T indicated that the total genome size was 1 548 794 bp with a G+C content of 33.1 mol%, 1586 coding sequences, 50 tRNAs and nine rRNAs. The most closely related genomes belonged to Lactobacillus species. Most metabolic pathways were related to carbon metabolism and carbon fixation. Based on this polyphasic analysis, strain NIBRBAC000499792T represents a novel species of the genus Lactobacillus , for which the name Lactobacillus terrae sp. nov. is proposed, with the type strain NIBRBAC000499792T (=KCTC 21093T=JCM 32269T).
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Cohnella kolymensis sp. nov., a novel bacillus isolated from Siberian permafrost
A facultative anaerobic, rod-shaped, endospore-forming and non-motile bacterium was isolated from permafrost sediment cores in the Kolyma lowland, Siberia, Russia. The permafrost isolate clustered with members of the genus Cohnella on the basis of 16S rRNA gene sequence analysis and showed the highest sequence similarity to Cohnella saccharovorans CJ22T (96.3 %), followed by Cohnella cellulosilytica FCN3-3T (96.0 %) and Cohnella panacarvi KCTC 13060T (96.0 %). The chemotaxonomic characteristics (quinone system, cellular fatty acids and polar lipid profile) of strain 20.16T were consistent with members of the genus Cohnella . The peptidoglycan diaminoacids included meso-diaminopimelic acid and a small amount of ll-diaminopimelic acid. The molar ratio and composition of major amino acids (meso-diaminopimelic acid, alanine, and glutamic acid) correspond to the peptydoglycan type A1γ. The estimated genome size of strain 20.16T is 4.34 Mb (lower than those in other Cohnella species). The genome has a G+C content of 50.5 mol% and encodes 4843 predicted genes, of these 4740 are protein-coding ones. The results of chemotaxonomic, physiological and biochemical characterization allowed clear differentiation of strain 20.16T from the closest Cohnella species. Based on data provided, a new species Cohnella kolymensis sp. nov. is proposed, with 20.16T (=VKM B-2846T=DSM 104983T) as the type strain.
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Clostridium bovifaecis sp. nov., a novel acetogenic bacterium isolated from cow manure
Hui Zhu, Bo Fu, Shuailing Lu, Hongbo Liu and He LiuA strictly anaerobic, Gram-staining-positive, spore-forming rod-shaped bacterium, and designated BXXT, was isolated from cow manure. Colonies on DSMZ medium 311c agar plates were cream, circular, opaque and lustrous. Growth occurred at 20–45 °C with a pH range of 5.0–10.0 and at NaCl concentrations of up to 2 % (w/v). The optimum temperature, pH and NaCl concentration for growth were 30 °C, pH 7 and 1 % (w/v), respectively. The major cellular fatty acids were C16 : 0 (26.8 %), C14 : 0 (22.8 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (16.4 %) and C16 : 1ω9c (10.7 %). The main polar lipids of BXXT were diphosphatidylglycerol, phosphatidylethanolamine, unidentified aminolipids, an unidentified phospholipid and unidentified lipids. Acetate was mainly produced from H2/CO2, H2/CO2/CO (4/3/3, v/v/v), formate, glycerol, 1,2-propanediol, pyruvate, d-fructose and 2-methoxyethanol. BXXT is most closely related to Clostridium thermobutyricum DSM 4928T, Clostridium homopropionicum DSM 5847T and Clostridium thermopalmarium DSM 5974T with 16S rRNA gene sequence similarities of 96.9, 96.6 and 96.5 %, respectively. The DNA G+C content of BXXT was 33.7 mol%, which was lower than that of C. thermobutyricum DSM 4928T (37.0 mol%) and C. thermopalmarium DSM 5974T (35.7 mol%). In addition, DSM 4928T and DSM 5974Tare thermophilic members of the genus Clostridium . The absence of C15 : 0 also distinguished BXXT from Clostridium thermobutyricum . On the basis of phylogenetic, phenotypic and chemotaxonomic evidence, the novel isolate represents a novel species within the genus Clostridium , for which the name Clostridium bovifaecis sp. nov is proposed. The type strain of the type species is BXXT (=JCM 32382T=CGMCC 1.5228T).
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Thalassorhabdus alkalitolerans gen. nov., sp. nov., a novel Bacillaceae member isolated from marine sediment
More LessA novel Gram-stain-variable, rod-shaped, non-motile and non-endospore-forming bacterium (strain G27T) was isolated from near Dhuvaran, Gujarat, India. Based on 16S rRNA gene sequence analysis, strain G27T was identified as a member of the class Firmibacteria and was most closely related to Bacillus populi FJAT-45347T (94.9 % sequence similarity), Salipaludibacillus aurantiacus S9T (94.9 %), Salipaludibacillus neizhouensis KCTC 13187T (94.7 %), Alteribacillus iranensis DSM 23995T (94.6 %) and other Firmibacteria (<94.6 %). The DNA G+C content of strain G27T was 43.4±0.6 mol%. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Polar lipids included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified phospholipid and five unidentified lipids. The predominant isoprenoid quinone was menaquinone MK-7. Major fatty acids (>5 %) included anteiso-C15:0, iso-C15 : 0, anteiso-C17:0, C16 : 0 and iso-C16 : 0. The results of phylogenetic, chemotaxonomic and biochemical tests allowed the clear differentiation of strain G27T from all other members of the family Bacillaceae . It is therefore considered to represent a novel species of a new genus, for which the name Thalassorhabdus alkalitolerans gen. nov., sp. nov., is proposed. The type strain of Thalassorhabdus alkalitolerans is G27T (=MCC 3411T=CGMCC 1.15772T=KCTC 33941T).
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Paludirhabdus telluriireducens gen. nov., sp. nov. and Paludirhabdus pumila sp. nov., isolated from soil of a mountain wetland and emended description of Gorillibacterium massiliense
More LessTwo strains of Gram-stain-positive, endospore-forming, motile by means of peritrichous flagella, aerobic or facultative anaerobic, and rod-shaped bacteria that were designated ON8T and ON6T were isolated from soil collected from a mountain wetland in Gwang-ju, Republic of Korea. The isolates were catalase-positive and oxidase-negative. Cells of ON8T and ON6T grew at 15–35 °C (optimal 30 °C) and 15–40 °C (optimal 30 °C), respectively. The major menaquinone was MK-7 and the major cellular fatty acids (>10 % of the total) were anteiso-C15 : 0, iso-C15 : 0, C14 : 0 and C16 : 0. The predominant polar lipids were diphosphatidylglycerol, aminophospholipid and phospholipid. Meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The DNA G+C contents of strains ON8T and ON6T were 50.6 and 53.5 mol%, respectively, and the 16S rRNA gene sequence analysis showed that the nearest phylogenetic neighbour of both strains was Gorillibacterium massiliense G5T (93.9 %), followed by the members of the genus Paenibacillus in the family Paenibacillaceae . The DNA–DNA hybridization relatedness value between ON8T and ON6T was 44.1 %, which indicated that they represented distinct species. Based on polyphasic characteristics, a novel genus is proposed with the name Paludirhabdus gen. nov., which consists of two species, Paludirhabdus telluriireducens sp. nov. (the type species; type strain ON8T=KACC 19267T=JCM 31958T) and Paludirhabdus pumila sp. nov. (type strain ON6T=KACC 19266T=JCM 31957T).
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Bacillus acanthi sp. nov., isolated from the rhizosphere soil of a mangrove plant Acanthus ilicifolius
Ke Ma, Qi Yin, Liying Chen, Qiliang Lai and Ying XuA novel bacterium, designated strain L28T, was isolated from the rhizosphere soil of a mangrove plant in Hong Kong. Cells of strain L28T are Gram-stain-positive, rod-shaped and endospore-forming. Optimum growth occurs at 37 °C (range, 20–45 °C), 0.5 % (w/v) NaCl (range, 0–5.0 %) and pH 7.5 (range, 6.5–9.0). The major fatty acids are iso-C15 : 0 and C16 : 1ω7c alcohol. The major respiratory quinone is MK-7. The polar lipid profile comprises phospholipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and two unidentified lipids. The 16S rRNA gene sequence analyses indicated that strain L28T exhibited the highest similarity of 96.7 % to Bacillus asahii MA001T. The genome size of strain L28T was 4 063 863 bp with a 36.9 mol% DNA G+C content. Based on the phenotypic and chemotaxonomic properties, along with the phylogenic distinctiveness, it was concluded that this strain represents a novel species of the genus Bacillus , for which the name Bacillus acanthi sp. nov. is proposed. The type strain of this novel species is L28T (=DSM 104296T=MCCC 1K03287T).
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- Other Bacteria
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Extending the ecological distribution of Desmonostoc genus: proposal of Desmonostoc salinum sp. nov., a novel Cyanobacteria from a saline–alkaline lake
Cyanobacteria is an ancient phylum of oxygenic photosynthetic microorganisms found in almost all environments of Earth. In recent years, the taxonomic placement of some cyanobacterial strains, including those belonging to the genus Nostoc sensu lato, have been reevaluated by means of a polyphasic approach. Thus, 16S rRNA gene phylogeny and 16S–23S internal transcribed spacer (ITS) secondary structures coupled with morphological, ecological and physiological data are considered powerful tools for a better taxonomic and systematics resolution, leading to the description of novel genera and species. Additionally, underexplored and harsh environments, such as saline–alkaline lakes, have received special attention given they can be a source of novel cyanobacterial taxa. Here, a filamentous heterocytous strain, Nostocaceae CCM-UFV059, isolated from Laguna Amarga, Chile, was characterized applying the polyphasic approach; its fatty acid profile and physiological responses to salt (NaCl) were also determined. Morphologically, this strain was related to morphotypes of the Nostoc sensu lato group, being phylogenetically placed into the typical cluster of the genus Desmonostoc. CCM-UFV059 showed identity of the 16S rRNA gene as well as 16S–23S secondary structures that did not match those from known described species of the genus Desmonostoc, as well as distinct ecological and physiological traits. Taken together, these data allowed the description of the first strain of a member of the genus Desmonostoc from a saline–alkaline lake, named Desmonostoc salinum sp. nov., under the provisions of the International Code of Nomenclature for algae, fungi and plants. This finding extends the ecological coverage of the genus Desmonostoc, contributing to a better understanding of cyanobacterial diversity and systematics.
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- Proteobacteria
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Review of the genus Methylobacterium and closely related organisms: a proposal that some Methylobacterium species be reclassified into a new genus, Methylorubrum gen. nov.
More LessThe genus Methylobacterium , when first proposed by Patt et al. in 1976, was a monospecific genus created to accommodate a single pink pigmented facultatively methylotrophic bacterium. The genus now has over 50 validly published species, however, the percentage 16S rRNA sequence divergence within Methylobacterium questions whether or not they can still be accommodated within one genus. Additionally, several strains are described as belonging to Methylobacterium , but nodulate legumes and in some cases are unable to utilize methanol as a sole carbon source. This study reviews and discusses the current taxonomic status of Methylobacterium . Based on 16S rRNA gene, multi-locus sequence analysis, genomic and phenotypic data, the 52 Methylobacterium species can no longer be retained in one genus. Consequently, a new genus, Methylorubrum gen. nov., is proposed to accommodate 11 species previously held in Methylobacterium . The reclassified species names are proposed as: Methylorubrum aminovorans comb. nov. (type strain TH-15T=NCIMB 13343T=DSM 8832T), Methylorubrum extorquens comb. nov. (type strain NCIMB 9399T=DSM 1337T), Methylorubrum podarium comb. nov. (type strain FM4T=NCIMB 14856T=DSM 15083T), Methylorubrum populi comb. nov. (type strain BJ001T=NCIMB 13946T=ATCC BAA-705T), Methylorubrum pseudosasae comb. nov. (type strain BL44T=ICMP 17622T=NBRC 105205T), Methylorubrum rhodesianum comb. nov. (type strain NCIMB 12249T=DSM 5687T), Methylorubrum rhodinum comb. nov. (type strain NCIMB 9421T=DSM 2163T), Methylorubrum salsuginis comb. nov. (type strain MRT=NCIMB 14847T=NCCB 100140T), Methylorubrum suomiense comb. nov. (type strain F20T=NCIMB 13778T=DSM 14458T), Methylorubrum thiocyanatum comb. nov. (type strain ALL/SCN-PT=NCIMB 13651T=DSM 11490T) and Methylorubrum zatmanii comb. nov. (type strain NCIMB 12243T=DSM 5688T). The taxonomic position of several remaining species is also discussed.
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Solimonas fluminis sp. nov., isolated from a freshwater river
More LessA strictly aerobic, catalase-negative and oxidase-positive bacterium (HR-BBT), isolated from a water sample of the Han River, was taxonomically studied using a polyphasic approach. Cells were Gram-stain-negative motile rods with a polar flagellum. The strain grew at 20–35 °C and pH 7–8 and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HR-BBT belonged to the family Nevskiaceae in the phylum Proteobacteria and formed a phylogenic lineage with members of the genus Solimonas . A comparison of the 16S rRNA gene sequences of strain HR-BBT and the type strains of closely related species of the genus Solimonas showed that it shared highest sequence similarity with Solimonas terrae KIS83-12T (94.9 %), Solimonas soli DCY12T (94.8 %), Solimonas variicoloris MN28T (94.4 %) and Solimonas flava CW-KD 4T (94.2 %). The fatty acids of the strain consisted of summed features 8 (comprising C18 : 1 ω6c and/or C18 : 1 ω7c) and 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c), C16 : 0 and C12 : 0 as major components. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unidentified phospholipids and an unidentified lipid. Ubiquinone-8 was detected as the sole respiratory quinone. The DNA G+C content of strain HR-BBT was 68.5 mol%. Based on the genotypic, chemotaxonomic and phenotypic analyses, strain HR-BBT represents a novel species of the genus Solimonas , for which the name Solimonas fluminis sp. nov. is proposed. The type strain is HR-BBT (=KACC 19410T=JCM 32268T).
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Pseudomonas tianjinensis sp. nov., isolated from domestic sewage
More LessA novel Gram-stain-negative bacterium, designated as type strain 68T, was isolated from domestic sewage in Tianjin, China. Cells of strain 68T were aerobic, motile and rod-shaped. The organism grew at 15–42 °C, pH 6.0–11.0 and with 0–4 % NaCl (w/v). The DNA G+C content was 61.9 mol%. The major fatty acids (>10 %) were summed feature 8 (C18 : 1ω7c), summed feature 3 (C16 : 1ω7c or C16 : 1ω6c), C16 : 0 and C12 : 0. The respiratory quinone was Q9. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified aminophospholipid. Phylogenetic analysis based on full 16S rRNA gene sequences showed that strain 68T was a member of the genus Pseudomonas and showed similarities to Pseudomonas toyotomiensis HT-3T (98.58 %), Pseudomonas chengduensis MBRT (98.53 %), Pseudomonas alcaliphila AL15-21T (98.44 %), Pseudomonas composti C2T (97.75 %) and Pseudomonas anguilliseptica NCIMB 1949T (97.66 %). Strain 68T exhibited low DNA–DNA hybridization homology with P. alcaliphila AL15-21T (35.40 %), P. toyotomiensis HT-3T (33.30 %), P. chengduensis MBRT (35.40 %), P. anguilliseptica NCIMB 1949T (14.40 %) and P. composti C2T (20.40 %). On the basis of phenotypic, genotypic and phylogenetic evidence, strain 68T is considered to represent a novel species of the genus Pseudomonas, for which the name Pseudomonas tainjinensis sp. nov. is proposed. The type strain is 68T (=CICC 24204T=KCTC 52977T).
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Sphingomonas turrisvirgatae sp. nov., an agar-degrading species isolated from freshwater
A yellow pigmented and agar-pitting colony was isolated from a water sample obtained from a drainage ditch within a disused system of constructed wetlands. The strain was purified and named MCT13T. This rod-shaped, Gram-negative, oxidase- and catalase-positive, aerobic, non-spore-forming, and non-motile strain formed round colonies and grew optimally at pH 7.5±0.2, at 28–30 °C on LB agar, with 0–0.5 % NaCl. The 16S rRNA gene sequence analysis placed the MCT13T isolate within the Sphingomonas (sensu stricto) cluster. The DNA G+C content was 65.3 %. The only observed ubiquinone was Q10. The major fatty acids included C17 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. The major polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major polyamine was spermidine. The 16S rRNA gene phylogenetic analysis performed on the whole sequence, showed the closest relative of MCT13T to be Sphingomonas koreensis (98.52 %); however, there are several genotypic and phenotypic differences between the novel isolate and the type strain JSS26T of S. koreensis . On the basis of these results, strain MCT13T represents a novel species in the genus Sphingomonas , for which the name Sphingomonas turrisvirgatae sp. nov. is proposed. The type strain is MCT13T (=DSM 105457T=BAC RE RSCIC 7T).
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Kushneria phyllosphaerae sp. nov. and Kushneria endophytica sp. nov., plant growth promoting endophytes isolated from the halophyte plant Arthrocnemum macrostachyum
Two endophytic bacteria (EAod3T and EAod7T) were isolated from the aerial part of plants of Arthrocnemum macrostachyum growing in the Odiel marshes (Huelva, Spain). Phylogenetic analysis based on 16S rRNA gene sequences indicated their affiliation to the genus Kushneria . 16S rRNA gene sequences of strains EAod3T and EAod7T showed the highest similarity to Kushneria marisflavi DSM 15357T (99.0 and 97.6 %, respectively). Digital DNA–DNA hybridization studies between the draft genomes of strain EAod3T and K. marisflavi DSM 15357T corresponded to 28.5 % confirming the novel lineage of strain EAod3T in the genus Kushneria . Cells of both strains were Gram-staining-negative, aerobic and motile rods able to grow at 4–37 °C, at pH 5.0-8.0 and tolerate 0.5–25 % NaCl (w/v). They presented ubiquinone Q9 and C16 : 0, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c as the major fatty acids. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on the phenotypic and phylogenetic results, strains EAod3T (=CECT 9073T=LMG 29856T) and EAod7T (=CECT 9075T=LMG 29858T) are proposed as new representatives of the genus Kushneria, and the proposed names are Kushneria phyllosphaerae sp. nov. and Kushneria endophytica sp. nov., respectively. The whole genome sequence of strain EAod3T has a total length of 3.8 Mbp and a G+C content of 59.3 mol%.
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Sphingobium aquiterrae sp. nov., a toluene, meta- and para-xylene-degrading bacterium isolated from petroleum hydrocarbon-contaminated groundwater
A Gram-negative, aerobic, slightly yellow-pigmented bacterium, designated as SKLS-A10T, was isolated from groundwater sample of the ‘Siklós’ petroleum hydrocarbon contaminated site (Hungary). Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain SKLS-A10T formed a distinct phyletic lineage within the genus Sphingobium . It shared the highest 16S rRNA gene homology with Sphingobium abikonense DSM 23268T (97.29 %), followed by Sphingobium lactosutens DSM 23389T (97.23 %), Sphingobium phenoxybenzoativorans KCTC 42448T (97.16 %) and Sphingobium subterraneum NBRC 109814T (96.74 %). The predominant fatty acids (>5 % of the total) are C18 : 1ω7c, C14 : 0 2-OH, C16 : 1 ω7c/iso C15 : 0 2-OH, C17 : 1ω6c and C16 : 0. The major ubiquinone is Q-10. The predominant polyamine is spermidine. The major polar lipids are sphingoglycolipid and diphosphatidylglycerol. The DNA G+C content of strain SKLS-A10T is 65.9 mol%. On the basis of evidence from this taxonomic study using a polyphasic approach, strain SKLS-A10T represents a novel species of the genus Sphingobium for which the name Sphingobium aquiterrae sp. nov. is proposed. The type strain is SKLS-A10T (=DSM 106441T=NCAIM B. 02634T).
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Saccharospirillum mangrovi sp. nov., a bacterium isolated from mangrove sediment
More LessA Gram-negative, spirilla, non-spore-forming, motile and strictly aerobic bacterium, designated HK-33T, was isolated from a mangrove sediment sample in Haikou city, Hainan Province, China. Strain HK-33T was able to grow at 10–45 °C (optimum 37 °C), 0.5–12.0 % (w/v) NaCl (2.0 %, w/v) and pH 5.5–8.5 (pH 7.0). The major cellular fatty acids were C16 : 0 and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). Ubiquinone-8 was the predominant respiratory quinone, and Q-9 was present in trace amounts. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids, two unidentified glycolipids, an unidentified aminophosphoglycolipid and two unidentified lipids. The DNA G+C content was 57.3 mol%. According to 16S rRNA gene sequences similarity, strain HK-33T shared 98.6 %, 96.4%, 95.7 and 94.9 % sequence similarities to the species Saccharospirillum correiae CPA1T, Saccharospirillum impatiens EL-105T, Saccharospirillum salsuginis YIM-Y25T and Saccharospirillum aestuarii IMCC 4453T, respectively. Phylogenetic analysis showed that strain HK-33T was clustered with S. correiae CPA1T, S. impatiens EL-105T, S. salsuginis YIM-Y25T and S. aestuarii IMCC 4453T. Results of DNA–DNA hybridization analysis revealed that strain HK-33T shared 36.3±1.7 % DNA relatedness with S. correiae CPA1T. On the basis of its phenotypic, chemotaxonomic and genotypic characteristics, strain HK-33T is considered to represent a novel species in the genus Saccharospirillum , for which the name Saccharospirillum mangrovi sp. nov. is proposed. The type strain is HK-33T (=KCTC 62178T=MCCC 1K03440T).
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Zhengella mangrovi gen. nov., sp. nov., a novel member of family Phyllobacteriaceae isolated from mangrove sediment
More LessA Gram-negative strain, designed X9-2-2T, was isolated from mangrove sediment in Yunxiao Mangrove National Nature Reserve, China. Strain X9-2-2T showed less than 96.2 % 16S rRNA gene sequence similarity to type strains of species with validly published names. Phylogenetic analysis based on 16S rRNA gene sequences and rpoB protein sequences revealed that strain X9-2-2T formed a distinct monophyletic clade within the family Phyllobacteriaceae and clustered distantly with the genera Aliihoeflea , Phyllobacterium and Hoeflea . Cells of X9-2-2T were rod-shaped, motile with subpolar or lateral flagella and facultative anaerobic. Optimal growth occurred at 30–37 °C, at pH 7 and in the presence of 2 % NaCl. The DNA G+C content of strain X9-2-2T was 64.9 mol%. The major fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c 56.0 %), iso -C17 : 0 (9.1 %) and C12 : 0 (6.6 %). The predominant respiratory quinone was ubiquinone-10 and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, an unidentified aminolipid and two unidentified polar lipids. According to its morphology, physiology, fatty acid composition and 16S rRNA gene signature nucleotide patterns, strain X9-2-2T represents a novel species of a novel genus in the family Phyllobacteriaceae , for which the name Zhengella mangrovi gen. nov., sp. nov. is proposed. The type strain is X9-2-2T (=MCCC 1K03307T=JCM 32107T).
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Mangrovicella endophytica gen. nov., sp. nov., a new member of the family Aurantimonadaceae isolated from Aegiceras corniculatum
A Gram-negative, aerobic, motile and short-rod-shaped bacterium, designated strain 5T4P-12-1T, was isolated from a piece of surface-sterilized bark of Aegiceras corniculatum collected from Cotai Ecological Zones in Macao, China and tested by a polyphasic approach to clarify its taxonomic position. Strain 5T4P-12-1T grew optimally with 0–1 % (w/v) NaCl at 30 °C and at pH 7.0–8.0. The 16S rRNA gene sequence of strain 5T4P-12-1T had the highest similarity (96.7 %) to Aureimonas altamirensis DSM 21988T. Phylogenic analysis based on 16S rRNA gene sequences and coding sequences of 98 protein clusters showed that the strain represented a novel genus of the family Aurantimonadaceae . The predominant quinone system of strain 5T4P-12-1T was ubiquinone 10. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmethylethanolamine, an unidentified aminophospholipid, three unidentified aminolipids, three unidentified phospholipids and three unidentified lipids. The major fatty acids (>10 % of total fatty acids) were C18 : 1ω7c (55.4 %) and C18 : 1 2-OH (15.6 %). The DNA G+C content of strain 5T4P-12-1T was 66.5 mol%. Based on the phylogenic, phenotypic and chemotaxonomic features, strain 5T4P-12-1T is considered to represent a novel species of a new genus in the family Aurantimonadaceae , for which the name Mangrovicella endophytica gen. nov., sp. nov. is proposed. The type strain is 5T4P-12-1T (=KCTC 62053T=CGMCC 1.16279 T).
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Emcibacter congregatus sp. nov., isolated from sediment cultured in situ
More LessA Gram-negative, aerobic, motile, rod-shaped, pale-yellow bacterial strain, designated as ZYLT, isolated from a cultured in situ sediment sample collected from the East China Sea coast, was studied using a polyphasic taxonomic approach. Strain ZYLT grew at 4–30 °C (optimum, 25 °C), at pH 6.0–8.5 (pH 7.0) and with 0–7.0 % (w/v) NaCl (2.0 %). Results of phylogenetic analysis based on 16S rRNA gene sequences clearly showed that strain ZYLT and Emcibacter nanhaiensis HTCJW17T, which was most closely related to strain ZYLT with 93.6 % sequence similarity, clustered together. The genomic DNA G+C content was 51.5 % (genome sequence). The quinone system was composed only of ubiquinone-10. Strain ZYLT possessed C18 : 1ω7c and/or C18 : 1 ω6c (summed feature 8), iso-C15 : 0 2-OH and/or C16 : 1 ω7c (summed feature 3), C14 : 0 2-OH and C14 : 0 as the major fatty acids. The content of summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c) in strain ZYLT was far greater than that in E. nanhaiensis . The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminophospholipids, three unidentified phospholipids, one unidentified aminolipid and four unidentified lipids. One unidentified aminophospholipid and two unidentified lipids present in strain ZYLT were not found in E. nanhaiensis in this research. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain ZYLT (=KCTC 62328T=JCM 32378T=MCCC 1K03526T) represents a novel species of the genus Emcibacter for which the name Emcibacter congregatus sp. nov. is proposed.
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Arcobacter haliotis Tanaka et al. 2017 is a later heterotypic synonym of Arcobacter lekithochrous Diéguez et al. 2017
More LessThe draft whole-genome sequence of Arcobacter haliotis strain LMG 28652T was obtained and compared against the type strain of Arcobacter lekithochrous LFT 1.7T. High similarity was found between the two strains, showing average nucleotide identity and in silico DNA–DNA hybridization values of 98.40 and 86.10 %, respectively. These values indicated that both genomes belonged to the same species, confirming the evidences derived from the phylogenetic analysis performed with the 16S rRNA gene and the concatenated sequences of five housekeeping genes. In addition, the metabolic, physiological and chemotaxonomic features of A. haliotis LMG 28652T were shown to be congruent with those of A. lekithochrous . We conclude that Arcobacter haliotis Tanaka et al. 2017 is a later heterotypic synonym of Arcobacter lekithochrous Diéguez et al. 2017.
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Phreatobacter cathodiphilus sp. nov., isolated from a cathode of a microbial fuel cell
A novel bacterial strain, S-12T, of a member of the genus Phreatobacter was isolated from a cathode of a microbial fuel cell from Suwon City, South Korea. Cells were Gram-staining-negative, aerobic, non-sporulating rods, motile by means of a polar flagellum, and formed white round colonies. The strain grew at the range of 10–40 °C (optimum, 28–30 °C), pH 6.0–10.0 (optimum 7.0–8.0) and 0–1 % NaCl. The 16S rRNA gene sequence analysis showed the relatedness of S-12T to Phreatobacter stygius YC6-17T (98.2 %) and Phreatobacter oligotrophus PI_21T (98.1 %). The major respiratory quinone was ubiquinone Q-10. Polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and an unidentified lipid. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content was 69.3 mol%. On the basis of its differences from species of the genus Phreatobacter with validly published names, strain S-12T is identified as representing a novel species, for which the proposed name is Phreatobacter cathodiphilus sp. nov., with S-12T as the type strain (=KACC 18497T=JCM 31612T).
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Sphingomonas aeria sp. nov., isolated from air
More LessA Gram-negative, aerobic, non-spore-forming, non-motile, yellow-pigmented and rod-shaped bacterial strain, designated B093034T, was isolated from air at the foot of Xiangshan mountain, located in Beijing, China. Cells of strain B093034T were oxidase-negative and catalase-positive. Growth was observed at 4–41 °C, at pH 4.5–10.0 and at 0–7 % (w/v) NaCl. The isolate contained Q-10 as the predominant isoprenoid quinone, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C14 : 02-OH as the major fatty acids, sym-homospermidine as the major polyamine, and sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol, aminolipid, two unidentified phospholipids and three unidentified polar lipids as the polar lipids. The DNA G+C content was 67.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain B093034T grouped with members of the genus Sphingomonas and was closely related to Sphingomonas sanguinis IFO 13937T (96.49 % similarity), Sphingomonas pseudosanguinis G1-2T (96.37 %), Sphingomonas ginsenosidimutans Gsoil 1429T (95.99 %) and Sphingomonas endophytica YIM 65583T (95.78 %). On the basis of the polyphasic evidence presented here, strain B093034T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas aeria sp. nov. is proposed. The type strain is B093034T (=CFCC 13949T=LMG 30133T).
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Amylibacter kogurei sp. nov., a novel marine alphaproteobacterium isolated from the coastal sea surface microlayer of a marine inlet
A novel Gram-negative bacterium, designated 4G11T, was isolated from the sea surface microlayer of a marine inlet. On the basis of 16S rRNA gene sequence analysis, the strain showed the closest similarity to Amylibacter ulvae KCTC 32465T (99.0 %). However, DNA–DNA hybridization values showed low DNA relatedness between strain 4G11T and its close phylogenetic neighbours, Amylibacter marinus NBRC 110140T (8.0±0.4 %) and Amylibacter ulvae KCTC 32465T (52.9±0.9 %). Strain 4G11T had C18 : 1, C16 : 0 and C18 : 2 as the major fatty acids. The only isoprenoid quinone detected for strain 4G11T was ubiquinone-10. The major polar lipids were phosphatidylglycerol, phosphatidylcholine, one unidentified polar lipid, one unidentified phospholipid and one unidentified aminolipid. The DNA G+C content of strain 4G11T was 50.0 mol%. Based on phenotypic and chemotaxonomic characteristics and analysis of the 16S rRNA gene sequence, the novel strain should be assigned to a novel species, for which the name Amylibacter kogurei sp. nov. is proposed. The type strain of Amylibacter kogurei is 4G11T (KY463497=KCTC 52506T=NBRC 112428T).
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Rhizobium wuzhouense sp. nov., isolated from roots of Oryza officinalis
More LessThree bacterial isolates, designated W44T, W15 and W11, were isolated from the root of Oryza officinalis grown in Wuzhou, China. These isolates were Gram-negative, aerobic, motile and rod-shaped; demonstrated cellulase and urea activities; and formed cream-coloured colonies. The 16S rRNA gene sequence analysis indicated that the similarities between strain W44T and strains W15 and W11 were 100 %; all of them belonged to the genus Rhizobium and had the highest sequence similarity to Rhizobium rosettiformans W3T (98.7 %), followed by Rhizobium ipomoeae shin9-1T (98.2 %). Sequencing of housekeeping genes (recA, atpD, rpoB and glnA) of the novel isolates revealed similarities to members of established Rhizobium species to be less than 94.3 %. The values of DNA–DNA hybridization between strain W44T and the reference strains ( R. rosettiformans W3T and R. ipomoeae shin9-1T) were 41.3 and 29.2 %, respectively. The major cellular fatty acid of strain W44T was summed feature 8 (C18 : 1ω9t and/or C18 : 1ω9c and/or C18 : 1ω7c). The polar lipid profile of strain W44T consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, two unidentified lipids and two unidentified aminophospholipids. The G+C content of strain W44T was 62.4 mol%. In nodulation tests, none of the three strains could induce nodule formation in Glycine max, Phaseolus vulgaris or Medicago sativa. The nodulation gene (nodA), nitrogenase reductase gene (nifH) and virulence gene (virC) were not detected by PCR in these strains. Based on the above results and phenotypic features, a novel species, Rhizobium wuzhouense sp. nov., is proposed, with strain W44T (=CCTCC AB 2017179T=GDMCC 1.1257T=KCTC 62194T) as the type strain.
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Mesorhizobium sanjuanii sp. nov., isolated from nodules of Lotus tenuis in the saline-alkaline lowlands of Flooding Pampa, Argentina
Two rhizobial strains, BSA136T and BSA150, related to the genus Mesorhizobium were isolated from root nodules of Lotus tenuis grown in saline-alkaline lowlands soil from Argentina. These strains showed different repetitive element palindromic PCR fingerprinting patterns but shared more than 99 % sequence similarity for both 16S rRNA and recA genes. Despite the symbiotic nodC gene sequences of our strains being related to the canonical Lotus biovar species comprising Mesorhizobium loti and Mesorhizobium japonicum , the 16S rRNA phylogenetic marker suggests that their taxonomical identities are closely related to Mesorhizobium helmanticense , Mesorhizobium metallidurans , Mesorhizobium thianshanense, Mesorhizobium gobiense and Mesorhizobium tarimense . Multilocus sequence analysis performed with seven housekeeping genes confirmed that BSA136T belongs to a separate clade within the genus Mesorhizobium . The results of comparisons for in silico DNA–DNA hybridization and average nucleotide identity indexes between the genomes of BSA136T and closest-related Mesorhizobium species were below the threshold for species delineation. Phenotypic features differentiated BSA136T from its closest-related species. On the basis of our results, BSA136T and BSA150 can be considered to represent a novel species of the genus Mesorhizobium , for which the name Mesorhizobium sanjuanii sp. nov. is hereby proposed. The type strain of this species is BSA136T (=CECT 9305T=LMG 30060T), for which the draft genome sequence is available.
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Thalassospira marina sp. nov., isolated from surface seawater
More LessTwo novel marine bacteria, designated strains CSC3H3T and CSC1P2, were isolated from surface seawater of the South China Sea. Both strains were Gram-negative, oxidase-positive, catalase-positive, curved rods and motile. They grew at 10–40 °C, pH 5–10 and in the presence of 0–15 % (w/v) NaCl. Their 16S rRNA gene sequences were identical to each other. Phylogenetic analysis based on 16S rRNA gene sequences indicated that they belong to the genus Thalassospira , and shared 97.5–98.3 % sequence similarity to all other validly type strains of the genus Thalassospira , and the highest similarity was to the type strain Thalassospira povalilytica Zumi 95T (98.3 %), followed by Thalassospira australica NP3b2T (98.2 %). The digital DNA–DNA hybridization value between the two strains was 80.4 %, while the values with T. povalilytica Zumi 95T and T. australica NP3b2T were only 20.5–20.7 % and 20.4–20.5 %, respectively. The two strains possess similar major cellular fatty acids including C18 : 1ω7c, C16 : 0, C19 : 0ω8c cyclo, C18 : 1 2-OH and C17 : 0 cyclo. The G+C contents of the chromosomal DNA of strains CSC3H3T and CSC1P2 were 54.6 and 54.5 mol%, respectively. The major respiratory quinone was ubiquinone 10. Phosphatidylethanolamine, phosphatidylglycerol and several unidentified phospholipids, aminolipid and lipids were present in both strains. Based on phenotypic and genotypic characteristics, the two strains represent a novel species within the genus Thalassospira, for which the name Thalassospira marina sp. nov. is proposed. The type strain is CSC3H3T (=MCCC 1A11786T=KCTC 62333T).
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Shewanella saliphila sp. nov., Shewanella ulleungensis sp. nov. and Shewanella litoralis sp. nov., isolated from coastal seawater
More LessThree Gram-negative, non-spore-forming, rod-shaped and motile bacterial strains, designated MMS16-UL250T, MMS16-UL253T and MMS16-UL482T, were isolated from coastal seawater and subjected to taxonomic characterization. All isolates grew at 4–30 °C (optimum, 25 °C), at pH 6–10 (pH 7) and in the presence of up to 8 % NaCl (2.5–4.5 %). The 16S rRNA gene sequence similarities between the three isolates and Shewanella algicola St-6T, the closest species, were 98.1–99.2 %, and those among the isolates were 98.5–99.0 %. In the phylogenetic tree, MMS16-UL250T formed a cluster with S. algicola St-6T, but the DNA–DNA relatedness between the two strains was 28.8±1.5 %, thus confirming their separation at species level. The other two strains formed separate phylogenetic lines respectively. The main quinones for all strains were Q-7, Q-8, MK-7 and MMK-7, which is typical for Shewanella . The major polar lipids of all strains were phosphatidylglycerol and phosphatidylethanolamine, and the common major fatty acid was a summed feature consisting of C16 : 1ω7c and/or C16 : 1ω6c while the proportions varied among the three strains. The DNA G+C contents of the strains also varied between 42.1 and 43.7 mol%. Phenotypic properties distinguished each strain from S. algicola as well as from one another. Based on the polyphasic analysis, each strain is considered to represent a novel species of Shewanella , for which the names Shewanella saliphila sp. nov. (type strain, MMS16-UL250T=KCTC 62131T=JCM 32304T), Shewanella ulleungensis sp. nov. (type strain, MMS16-UL253T=KCTC 62130T=JCM 32305T) and Shewanella litoralis sp. nov. (type strain, MMS16-UL482T=KCTC 62129T=JCM 32306T) are proposed.
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Chromobacterium pseudoviolaceum Kämpfer et al. 2009 is a later heterotypic synonym of Chromobacterium violaceum Bergonzini 1880
More LessPublished data on the genome sequences of Chromobacterium pseudoviolaceum LMG 3953T and Chromobacterium violaceum ATCC 12472T suggest that both isolates belong to the same species. Previous 16S rRNA gene sequence comparisons had demonstrated that these species share 99.9 % sequence similarity. Initial investigations of fatty acid patterns and substrate utilization had shown only a few differences between the type strains of both species. Despite the 47.5 % homology by DNA–DNA hybridization studies between these strains, in silico whole genome sequence comparisons have clearly demonstrated that OrthoANIu and Mash/MinHash values were >99.18 %. Molecular phylogeny based on the estimated phylogenetic positions of the published genome sequences of the two type strains, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analyses indicate that these strains are members of the same species. Due to priority of publication and validation of names, Chromobacterium pseudoviolaceum is reclassified as Chromobacterium violaceum .
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Oceanimonas marisflavi sp. nov., a polycyclic aromatic hydrocarbon-degrading marine bacterium
A Gram-stain-negative, strictly aerobic, motile and rod-shaped bacterial strain, designated 102-Na3T, was isolated from sediment of Sinduri beach in Taean, Republic of Korea. Strain 102-Na3T grew optimally at 28–37 °C, at pH 7.0–11.0 and in the presence of 1–3 % (w/v) NaCl, but NaCl was not an absolute requirement for growth. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain 102-Na3T joined the clade comprising the type strains of Oceanimonas species. Strain 102-Na3T exhibited 16S rRNA gene sequence similarity values of 98.8, 98.3 and 98.0 % to the type strains of Oceanimonas doudoroffii MBIC1298T, Oceanimonas baumannii GB6T and Oceanimonas smirnovii 31-13T, respectively. Strain 102-Na3T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C12 : 0 as major fatty acids. The major quinone was ubiquinone-8. The polar lipids were composed of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified amino lipids. The DNA G+C content was 56.8 mol%. Strain 102-Na3T exhibited DNA–DNA relatedness values of 25.7, 21.7 and 14.8 % to the type strains of O. doudoroffii , O. baumannii and O. smirnovii , respectively. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain 102-Na3T is separated from recognized species of the genus Oceanimonas . On the basis of the data presented, strain 102-Na3T (=KCTC 62271T=JCM 32358T=DSM 106032T) is considered the type strain of a novel species of the genus Oceanimonas , for which the name Oceanimonas marisflavi sp. nov. is proposed.
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Arenimonas caeni sp. nov., isolated from activated sludge
More LessA Gram-stain-negative, non-spore-forming, motile and rod-shaped strain, z29T, was isolated from the active sludge of a municipal wastewater treatment plant at Wuhu, Anhui, PR China. Phylogenetic analysis of the 16S rRNA gene revealed that strain z29T is most closely related to the genus Arenimonas , showing the highest similarity to Arenimonas donghaensis HO3-R19T (97.14 %), Arenimonas aestuarii S2-21T (96.46 %), Arenimonas daejeonensis T7-07T (96.24 %) and Arenimonas taoyuanensis YN2-31AT (96.23 %). The only respiratory quinone of strain z29T was ubiquinone 8 (Q-8). The major cellular fatty acids (>10 %) were iso-C15 : 0, iso-C16 : 0 and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 010-methyl). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The genomic DNA G+C content was 70.2 mol%. Genomic comparison between strain z29T and Arenimonas donghaensis HO3-R19T revealed 83.72 % average nucleotide identity. Based on the phenotypic and chemotaxonomic results together with phylogenetical analysis, strain z29T is classified as representing a novel species of the genus Arenimonas , for which the name Arenimonas caeni sp. nov. is proposed. The type strain is z29T (=JCM 32091T=CCTCC AB 2017067T).
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Kaistia algarum sp. nov., isolated from a freshwater green alga Paulinella chromatophora
Yunho Lee and Che Ok JeonA Gram-negative, strictly aerobic, non-motile and short rod- or coccus-shaped bacterium, designated strain LYH11T, was isolated from a freshwater green alga Paulinella chromatophora. The strain grew at 5–37 °C (optimum, 30 °C) and pH 6–9 (pH 7) and in the presence of 0–1 % (w/v) NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain LYH11T clearly belonged to the genus Kaistia of the family Rhizobiaceae . Strain LYH11T shared the highest 16S rRNA gene sequence similarity to Kaistia soli 5YN9-8T (98.3 %), Kaistia terrae 5YN3-3T (98.2 %), Kaistia geumhonensis B1-1T (97.8 %), Kaistia defluvii B6-12T (97.4 %) and Kaistia granuli Ko04T (97.2 %). The average nucleotide identity and in silico DNA–DNA hybridization values between strain LYH11T and K. soli 5YN9-8T, the closest Kaistia type strain, were 77.3 and 21.1 %, respectively. Major cellular fatty acids of strain LYH11T were cyclo-C19 : 0 ω8c, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), iso-C10 : 0, iso-C17 : 0 3-OH, iso-C17 : 1 ω5c and C18 : 0. Strain LYH11T contained phosphatidylglycerol, phosphatidylethanolamine, an unidentified phosphoaminolipid, an unidentified aminolipid, three unidentified phospholipids and five unidentified lipids as polar lipids. Ubiquinone-10 was the major respiratory quinone. The genomic DNA G+C content was 64.5 mol%. Based on the genotypic, chemotaxonomic and phenotypic analyses, strain LYH11T represents a novel species of the genus Kaistia , for which the name Kaistia algarum sp. nov. is proposed. The type strain is LYH11T (=KACC 19096T=JCM 31803T).
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- Eukaryotic Micro-Organisms
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Naganishia qatarensis sp. nov., a novel basidiomycetous yeast species from a hypersaline marine environment in Qatar
Two yeast strains (INY29 and INY13) representing a novel yeast species were isolated from the hypersaline marine environment of the Inland Sea, Qatar. Phylogenetic analysis based on the D1/D2 domains of the large subunit (LSU) regions and internal transcribed spacer (ITS1 and ITS2) regions showed that the two strains represent a single species in the genus Naganishia that is distinct from other species. These two strains were classified as members of the genus Naganishia and clustered in a strongly supported clade represented by Naganishia albidus in the Filobasidiales order in the phylogenetic tree drawn from ITS and D1/D2 sequences. The novel species was most closely related to the type strain of Naganishia cerealis but the two species differed by 1 % sequence divergence (four substitutions and one gap) in the D1/D2 domains and (five substitutions and one gap) in the ITS regions. In contrast to the closest relative, N. cerealis, the novel yeast species assimilated melibiose, glycerol, meso-erythritol, dl-lactate, methanol, propane 1-2-diol, butane 2-3-diol, and grew at 35 °C. The name Naganishia qatarensis sp. nov. is proposed to accommodate these strains, with INY29 as the holotype.
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- Evolution, Phylogeny and Biodiversity
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Morphologic and molecular characterization of Brachonella pulchra (Kahl, 1927) comb. nov. (Armophorea, Ciliophora) with comments on cyst structure and formation
More LessIn this article we provide morphologic and morphometric data based on in vivo observation, protargol impregnation, scanning electron microscopy and an 18S rRNA gene sequence for another member of the genus Brachonella, Brachonella pulchra comb. nov. (basionym: Metopus pulcher Kahl, 1927). We also provide preliminary data on resting cyst structure and formation in Brachonella pulchra and discuss the possible taxonomic usefulness of these structures.
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- Letter to the Editor
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Some facts about the respiratory enzymes of Pseudomonas pseudoalcaligenes KF707 recently renamed as Pseudomonas furukawaii sp. nov., type strain KF707
More LessKimura and co-workers (Kimura N et al. Int J Syst Evol Microbiol 2018;68:1429–1435) recently proposed renaming the obligate aerobe Pseudomonas pseudoalcaligenes KF707 as Pseudomonas furukawiisp. nov. type strain KF707. Since the first quasi-complete genome sequence of KF707 was reported in 2012 (accession number: PRJNA83639) numerous reports on chemotaxis and function/composition of the respiratory redox chain of KF707 have been published, demonstrating that KF707 contains three cheA genes for aerobic motility, four cytochrome oxidases of c(c)aa 3- and cbb 3-type and one bd-type quinol oxidase. With this background in mind, it has been quite a surprise to read within Table 1 of the paper by Kimura et al. that strain KF707 is phenotypically characterized as cytochrome oxidase-negative. Further, Table 1 also reports that KF707 is β-galactosidase-positive, an affirmation that is not consistent with results documented in the current literature. In this present ‘Letter to the Editor’ we show that Kimura et al. have contradicted themselves and provided inaccurate information in respect to the respiratory phenotypic features of P. furukawii. Based on this, an official corrigendum is requested since the publication, as it is, blurs the credibility of the International Journal of Systematic and Evolutionary Microbiology.
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- Request for Opinion
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Reclassification of Eubacterium combesii and discrepancies in the nomenclature of botulinum neurotoxin-producing clostridia: Challenging Opinion 69. Request for an Opinion
More LessTo clarify the taxonomic position of Eubacterium combesii , the whole genome of its type strain, DSM 20696T, was sequenced. Comparison of this sequence with known sequences of other bacteria confirmed that E. combesii represented a member of the Clostridium sporogenes / Clostridium botulinum Group I clade. However, the results of phylogenetic analysis also demonstrated that the latter two species did not form the same genetic entity and that E. combesii was in the C. botulinum Group I subclade. Meanwhile, we showed that E. combesii DSM 20696T did not produce botulinum neurotoxins (BoNTs) and thus should be identified as a strain of C. sporogenes in accordance with the current nomenclature of BoNT-producing clostridia, which is based, in particular, on Opinion 69 issued by the Judicial Commission of the ICSB. However, review of the corresponding Request for an Opinion revealed that it had been based on an erroneous statement. Therefore, we request reconsideration of Opinion 69 and propose to reclassify Eubacterium combesii as a later synonym of Clostridium botulinum . The results of phylogenetic analysis of the other five groups of BoNT-producing clostridia indicated that all the groups were far distant from each other. However, the members of Groups IV–VI are classified as strains of different species, while all members of Groups I–III are designated C. botulinum . Meanwhile, similarly to Group I, Groups II and III are also polyphyletic and appear to consist of two and four species, respectively. These results demonstrate, once again, discrepancies in the nomenclature of BoNT-producing bacteria and corroborate our request for reconsideration of Opinion 69.
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Volumes and issues
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Volume 74 (2024)
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