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1.
Artigo em Inglês | MEDLINE | ID: mdl-33906704

RESUMO

A novel Gram-stain-negative, facultatively anaerobic, rod-shaped bacterium, designated as D167-6-1T, was isolated from deep-sea sediment collected from the Pacific Ocean. The cells were catalase- and oxidase-positive, and motile by means of peritrichous flagella. Growth occurred at NaCl concentrations ranging from 0 to 19 % (optimum, 2-8 %, w/v), from pH 6 to 11 (optimum, 7-8) and at temperatures between 4 and 45 °C (optimum, 33 °C). Phylogenetic analysis based on 16S rRNA, gyrB and rpoD gene sequences and its genome sequence revealed that strain D167-6-1T formed a monophyletic branch within the genus Halomonas and was most closely related to Halomonas saliphila, Halomonas pellis, Halomonas kenyensis, Halomonas daqingensis, Halomonas desiderata and Halomonas lactosivorans (with 98.5, 98.5, 98.4, 98.1, 97.5 and 97.8 % 16S rRNA sequence similarity, respectively). The complete genome size of strain D167-6-1T was 4.49 Mb, with a DNA G+C content of 62.8 mol%. The estimated averagenucleotide identity and DNA-DNA hybridization values between strain D167-6-1T and other closely related species were 77.59-85.35 % and 22.0-30.6 %, respectively. The principal cellular fatty acids (>5 %) were C18 : 1 ω7c, C16 : 0, C19 : 0 cyclo ω8c, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c) and C17 : 0 cyclo. The polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, aminophospholipid and two unidentified phospholipids. The predominant respiratory quinones were Q-9 and Q-8. The combined genotypic and phenotypic data show that strain D167-6-1T represents a novel species of the genus Halomonas, for which the name Halomonas diversa sp. nov. is proposed, with the type strain D167-6-1T (=MCCC 1A13316T=KCTC 72441T).


Assuntos
Sedimentos Geológicos/microbiologia , Halomonas/classificação , Filogenia , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Halomonas/isolamento & purificação , Hibridização de Ácido Nucleico , Oceano Pacífico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
2.
Artigo em Inglês | MEDLINE | ID: mdl-33909549

RESUMO

A Gram-stain-negative, aerobic, flagellated, non-spore-forming, rod-shaped bacterium, named B2R-29T, was isolated from water collected from a crater lake on Da Hinggan mountain, PR China. Strain B2R-29T was oxidase- and catalase-positive. On the basis of the results of 16S rRNA gene sequence analyses, strain B2R-29T clearly belonged to the family Oxalobacteraceae, class Betaproteobacteria and showed the highest similarity to Undibacterium oligocarboniphilum EM1T (97.4 %) and to the other species of Undibacterium (less than 96.8 %). In the phylogenetic tree, strain B2R-29T formed a clade with U. oligocarboniphilum EM1T and Undibacterium squillarum CMJ-9T, indicating that is a member of the genus Undibacterium. Digital DNA-DNA hybridization and average nucleotide identity analyses were performed and the values between strain B2R-29T and its closely related Undibacterium species were less than 75.1 % and 16.9 %, respectively. The chemotaxonomic data of B2R-29T were as follows: major uniquinone, Q-8; predominant polar lipids, phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol; major fatty acids, C16 : 0 and summed feature 3 (C16 : 1 ω7c / C16 : 1 ω6c); predominant polyamines, putrescine, 2-hydroxyputrescine and spermidine. The DNA G+C content was 51.7 mol% from the genomic sequencing data. In accordance with the phenotypic, physiological and chemotaxonomic properties mentioned above, strain B2R-29T represents a novel species of the genus Undibacterium for which the name Undibacterium crateris sp. nov. is proposed. The type strain is B2R-29T (=CGMCC 1.13792T=KCTC 72018T).


Assuntos
Lagos/microbiologia , Oxalobacteraceae/classificação , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Oxalobacteraceae/isolamento & purificação , Fosfolipídeos/química , Poliaminas/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
3.
Artigo em Inglês | MEDLINE | ID: mdl-33886449

RESUMO

A Gram-stain-negative, ovoid-shaped, motile and strictly aerobic bacterium, designated ZQ172T, was isolated from marine sediment sampled on Zhoushan Island located in the East China Sea. Strain ZQ172T grew optimally at temperatures of 25-30 °C, at NaCl concentration of 2.0 % (w/v) and at pH 7.0-8.5. Catalase and oxidase activities, urease, and nitrate reduction were positive. Indole production, methyl red reaction, H2S production and hydrolysis of gelatin, starch, casein and Tweens 20, 40, 60 and 80 were negative. The major cellular fatty acid was summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The only respiratory quinone was ubiquinone-10. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. Comparative analysis of the 16S rRNA gene sequence showed highest similarities to Shimia aestuarii JC2049T (97.5 %), Shimia abyssi JAMH 043T (97.5 %) and Shimia thalassica CECT 7735T (97.3 %). Phylogenetic analyses indicated that strain ZQ172T clustered with the genus Shimia and was closely related to Shimia thalassica CECT 7735T. The average nucleotide identity and digital DNA-DNA hybridization values between strain ZQ172T and related species of the genus Shimia were well below the threshold limit for prokaryotic species delineation. The DNA G+C content was 59.6 mol%. Based on its phenotypic, chemotaxonomic and genotypic data, strain ZQ172T is considered to be a representative of a novel species in the genus Shimia, for which the name Shimia sediminis sp. nov. is proposed. The type strain is ZQ172T (=KCTC 62578T=MCCC 1K03531T).


Assuntos
Sedimentos Geológicos/microbiologia , Filogenia , Rhodobacteraceae/classificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Rhodobacteraceae/isolamento & purificação , Análise de Sequência de DNA , Ubiquinona/química
4.
Artigo em Inglês | MEDLINE | ID: mdl-33835910

RESUMO

A beige-pigmented, oxidase-positive bacterial isolate, Wesi-4T, isolated from charcoal in 2012, was examined in detail by applying a polyphasic taxonomic approach. Cells of the isolates were rod shaped and Gram-stain negative. Examination of the 16S rRNA gene sequence of the isolate revealed highest sequence similarities to the type strains of Pseudomonas matsuisoli and Pseudomonas nosocomialis (both 97.3 %). Phylogenetic analyses on the basis of the 16S rRNA gene sequences indicated a separate position of Wesi-4T, which was confirmed by multilocus sequence analyses (MLSA) based on the three loci gyrB, rpoB and rpoD and a core genome-based phylogenetic tree. Genome sequence based comparison of Wesi-4T and the type strains of P. matsuisoli and P. nosocomialis yielded average nucleotide identity values <95 % and in silico DNA-DNA hybridization values <70 %, respectively. The polyamine pattern contains the major amines putrescine, cadaverine and spermidine. The quinone system contains predominantly ubiquinone Q-9 and in the polar lipid profile diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine are the major lipids. The fatty acid contains predominantly C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1 ω6c). In addition, physiological and biochemical tests revealed a clear phenotypic difference from P. matsuisoli. These cumulative data indicate that the isolate represents a novel species of the genus Pseudomonas for which the name Pseudomonas carbonaria sp. nov. is proposed with Wesi-4T (=DSM 110367T=CIP 111764T=CCM 9017T) as the type strain.


Assuntos
Carvão Vegetal , Filogenia , Pseudomonas/classificação , Alabama , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Tipagem de Sequências Multilocus , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Pseudomonas/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
5.
Artigo em Inglês | MEDLINE | ID: mdl-33847555

RESUMO

A novel Gram-stain-negative, facultative aerobic and rod-shaped bacterium, designated as MKL-01T and isolated from the blood of immunocompromised patient, was genotypically and phenotypically characterized. The colonies were found to be creamy yellow and convex. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences revealed that strain MKL-01T was most closely related to Cupriavidus gilardii LMG 5886T, present within a large cluster in the genus Cupriavidus. The genome sequence of strain MKL-01T showed the highest average nucleotide identity value of 92.1 % and digital DNA-DNA hybridization value of 44.8 % with the closely related species C. gilardii LMG 5886T. The genome size of the isolate was 5 750 268 bp, with a G+C content of 67.87 mol%. The strain could grow at 10-45 °C (optimum, 37-40 °C), in the presence of 0-10 % (w/v) NaCl (optimum, 0.5%) and at pH 6.0-10.0 (optimum, pH 7.0). Strain MKL-01T was positive for catalase and negative for oxidase. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c and/or C16 : 1 ω6c/C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and one unidentified polar lipid. Moreover, strain MKL-01T contained ubiquinone Q-8 as the sole respiratory quinone. Based on its molecular, phenotypic and chemotaxonomic properties, strain MKL-01T represents a novel species of the genus Cupriavidus; the name Cupriavidus cauae sp. nov. is proposed for this strain. The type strain is MKL-01T.


Assuntos
Sangue/microbiologia , Cupriavidus/classificação , Hospedeiro Imunocomprometido , Filogenia , Adulto , Técnicas de Tipagem Bacteriana , Composição de Bases , Cupriavidus/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Feminino , Humanos , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Ubiquinona/química
6.
Artigo em Inglês | MEDLINE | ID: mdl-33847556

RESUMO

A novel bacterial strain, EJ-4T, isolated from stream water collected at Seo-ho in Suwon, Republic of Korea, was characterized based on a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain EJ-4T belonged to the genus Comamonas. The isolate is Gram-stain-negative, non-motile, aerobic, rod-shaped and forms pale yellow colonies on trypticase soy agar. The optimal growth of this strain was observed aerobically at 30 °C, pH 7 and 0.5 % NaCl. The major fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 39.7 %) and C16 : 0 (32.0 %). The G+C content of strain EJ-4T was 58.4mol %. The average nucleotide identity and digital DNA-DNA hybridization values between strain EJ-4T and Comamoas testosteroni were 91.8 and 31.2 %, respectively. The major polar lipids detected in the isolate were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant isoprenoid quinone was ubiquinone-8. Based on the results of polyphasic taxonomic analysis of strain EJ-4T, we describe a novel species of the genus Comamonas, for which the name Comamonas suwonensis sp. nov. has been proposed, with EJ-4T (=KCTC 82074T=JCM 34179T=KEMB 1602-279T) as the type strain.


Assuntos
Comamonas/classificação , Filogenia , Rios/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , Comamonas/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Ubiquinona/química
7.
Artigo em Inglês | MEDLINE | ID: mdl-33881985

RESUMO

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated as IMCC34836T, was isolated from a freshwater stream. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IMCC34836T was most closely related to Permianibacter aggregans HW001T (of the family Pseudomonadaceae) with 95.6 % sequence similarity and formed a robust clade with P. aggregans HW001T. The draft genome sequence of strain IMCC34836T was 4.4 Mbp in size with 59.1 mol% DNA G+C content. Average nucleotide identity and digital DNA-DNA hybridization values between strain IMCC34836T and P. aggregans HW001T were 71.2 and 22.0 %, respectively, indicating that the new strain represents a novel species. The strain contained iso-C15 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 1 10-methyl) as the major fatty acids and harboured phosphatidylethanolamine, two unidentified aminophospholipids and three unidentified lipids as major polar lipids. The isoprenoid quinone detected in the strain was ubiquinone-8. Based on the phylogenetic and phenotypic characteristics, strain IMCC34836T is considered to represent a novel species of the genus Permianibacter, for which the name Permianibacter fluminis sp. nov. is proposed. The type strain is IMCC34836T (=KACC 21755T=NBRC 114416T).


Assuntos
Filogenia , Pseudomonadaceae/classificação , Rios/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfatidiletanolaminas , Fosfolipídeos/química , Pseudomonadaceae/isolamento & purificação , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Ubiquinona/química
8.
Artigo em Inglês | MEDLINE | ID: mdl-33406032

RESUMO

A Gram-stain-negative, aerobic, mesophilic, non-motile bacterium, designated M0104T, was isolated from a gorgonian coral collected from Xieyang island, Guangxi Province, PR China. Colonies of the strain were non-motile cocci and pink. The strain grew at 15-34 °C (optimum, 28 °C), pH 4.5-8.0 (optimum, pH 7.0) and with 0-4% (w/v) NaCl (optimum, 0-2 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain M0104T was closely related to Roseomonas deserti JCM 31275T (96.2 %), Roseomonas vastitatis KCTC 62043T (96.0 %), Roseomonas aerofrigidensis JCM 31878T (95.9 %) and Roseomonas oryzae KCTC 42542T (95.7 %). The strain had an assembly size of 5.0 Mb and a G+C content of 71.0mol%. Genes involved in copper, cadmium, lead, arsenic and zinc resistance were identified in the genome of strain M0104T. The digital DNA-DNA hybridization and average nucleotide identity values between the genome sequence of strain M0104T and those of closely related type strains were 19.4-24.9 % and 74.3-81.8 %, respectively. Strain M0104T contained C18:1 ω7c, C18:3 ω3c, anteiso C11:0 and C16:0 as the major fatty acids (>7 %) and ubiquinone Q-10 as the sole isoprenoid quinone. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine were its major polar lipids. Based on its phenotypic, phylogenetic and chemotaxonomic properties, strain M0104T is proposed to represent a novel species within the genus Roseomonas, for which the name Roseomonas coralli sp. nov. is proposed. The type strain is M0104T (=KCTC 62359T=MCCC 1K03632T).


Assuntos
Antozoários/microbiologia , Metais Pesados , Methylobacteriaceae/classificação , Filogenia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Methylobacteriaceae/isolamento & purificação , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
9.
Artigo em Inglês | MEDLINE | ID: mdl-33411665

RESUMO

A Gram-stain-negative, aerobic, motile, short-rod-shaped bacterium with nicosulfuron-degrading ability, designated strain LAM1902T, was isolated from a microbial consortium enriched with nicosulfuron as a sole nitrogen and energy source. The optimal temperature and pH for growth of strain LAM1902T were 30 °C and pH 6.0, respectively. Strain LAM1902T could grow in the presence of NaCl with concentration up to 4.0 % (w/v). Comparative analysis of 16S rRNA gene sequences revealed that LAM1902T was closely related to the members of the family Pseudomonadaceae to the genus Pseudomonas, with the highest similarity to Pseudomonas nitroreducens DSM 14399T (99.6 %), Pseudomonas nitritireducens WZBFD3-5A2T (99.3 %) and Pseudomonas panipatensis Esp-1T (98.8 %). Multi-locus sequence analysis based on both concatenated sequences of the 16S rRNA gene and three housekeeping genes (gyrB, rpoB and rpoD) further confirmed the intrageneric phylogenetic position of strain LAM1902T. The genomic DNA G+C content of LAM1902T was 64.8 mol%. The low values of in silico DNA-DNA hybridization (less than 43.7 %) and average nucleotide identity (less than 90.9 %) also showed that the strain was distinctly different from known species of the genus Pseudomonas. The major fatty acids were C16 : 0, C17 : 0 cyclo and anteiso C15 : 0. Ubiquinone Q-9 was detected as the predorminant respiratory quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. Based on phylogenetic, phenotypic and chemotaxonomic analyses and genome comparisons, we conclude that strain LAM1902T represents a novel species, for which the name Pseudomonas nicosulfuronedens sp. nov. is proposed. The type strain is LAM1902T (=JCM 33860T=KCTC 72830T).


Assuntos
Consórcios Microbianos , Filogenia , Pseudomonas/classificação , Piridinas/metabolismo , Compostos de Sulfonilureia/metabolismo , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Fosfolipídeos/química , Pseudomonas/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
10.
Artigo em Inglês | MEDLINE | ID: mdl-33411666

RESUMO

Two yellow-pigmented, non-motile, Gram-stain-negative, and rod-shaped bacteria, designated TW-4T and TNP-2 were obtained from oil-contaminated soil. Both strains degrade diesel oil, hydrolyse aesculin, DNA, Tween 40 and Tween 60. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain TW-4T formed a lineage within the family Erythrobacteraceae and clustered as members of the genus Novosphingobium. The closest members of strain TW-4T were Novosphingobium subterraneum DSM 12447T (97.9 %, sequence similarity), Novosphingobium lubricantis KSS165-70T (97.8 %), Novosphingobium taihuense T3-B9T (97.8 %), Novosphingobium aromaticivorans DSM 12444T (97.7 %), Novosphingobium flavum UCT-28T (97.7 %), and Novosphingobium bradum STM-24T (97.6 %). The sequence similarity for other members was ≤97.6 %. The genome of strain TW-4T was 4 683 467 bp long with 44 scaffolds and 4280 protein-coding genes. The sole respiratory quinone was Q-10. The major cellular fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and C14 : 0 2-OH. The major polar lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylcholine (PC), phosphatidyl-n-methylethanolamine (PME) and sphingoglycolipid (SGL). The DNA G+C content of the type strain was 65.0 %. The average nucleotide identity (ANIu) and in silico DNA-DNA hybridization (dDDH) relatedness values between strain TW-4T and closest members were below the threshold value for species delineation. Based on polyphasic taxonomic analyses, strain TW-4T represents novel species in the genus Novosphingobium, for which the name Novosphingobium olei sp. nov. is proposed. The type strain is TW-4T (=KACC 21628T=NBRC 114364T) and strain TNP-2 (=KACC 21629=NBRC 114365) represents an additional strain. Based on new data obtained in this study, it is also proposed to reclassify Novosphingobium stygium as a later heterotypic synonym of Novosphingobium aromaticivorans.


Assuntos
Poluição por Petróleo , Filogenia , Microbiologia do Solo , Sphingomonadaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Poluentes do Solo , Sphingomonadaceae/isolamento & purificação , Ubiquinona/análogos & derivados , Ubiquinona/química
11.
Artigo em Inglês | MEDLINE | ID: mdl-33433309

RESUMO

A novel Gram-stain-negative, facultatively anaerobic, rod-shaped and non-motile bacterial strain, designated as 4C16AT, was isolated from a tidal flat sediment and characterized by using a polyphasic taxonomic approach. Strain 4C16AT was found to grow at 10-40 °C (optimum, 28 °C), at pH 5.0-10.0 (optimum, pH 6.0-7.0) and in 0-6 % (w/v) NaCl (optimum, 1 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 4C16AT fell into the genus Roseibium, and shared the highest identity of 98.9 % with the closest type strain Roseibium suaedae KACC 13772T and less than 98.0 % identity with other type strains of recognized species within this genus. The phylogenomic analysis indicated that strain 4C16AT formed an independent branch within this genus. The 28.6 % digital DNA-DNA hybridization estimate and 85.0 % average nucleotide identity between strains 4C16AT and R. suaedae KACC 13772T were the highest, but still far below their respective threshold for species definition, implying that strain 4C16AT should represent a novel genospecies. The predominant cellular fatty acid was summed feature 8; the polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylmonomethylethanolamine; the respiratory quinones were Q-9 and Q-10. The genomic DNA G+C content was 59.8mol %. Based on phylogenetic analyses and phenotypic and chemotaxonomic characteristics, strain 4C16AT is concluded to represent a novel species of the genus Roseibium, for which the name Roseibium litorale sp. nov. is proposed. The type strain of the species is 4C16AT (=GDMCC 1.1932T=KACC 22078T). We also propose the reclassification of Labrenzia polysiphoniae as Roseibium polysiphoniae comb. nov. and 'Labrenzia callyspongiae' as Roseibium callyspongiae sp. nov.


Assuntos
Sedimentos Geológicos/microbiologia , Filogenia , Rhodobacteraceae/classificação , Água do Mar , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Rhodobacteraceae/isolamento & purificação , Análise de Sequência de DNA , Ubiquinona/química
12.
Artigo em Inglês | MEDLINE | ID: mdl-33433313

RESUMO

Members of the metabolically diverse order Nitrosomonadales inhabit a wide range of environments. Two strains affiliated with this order were isolated from soils in Germany and characterized by a polyphasic approach. Cells of strains 0125_3T and Swamp67T are Gram-negative rods, non-motile, non-spore-forming, non-capsulated and divide by binary fission. They tested catalase-negative, but positive for cytochrome c-oxidase. Both strains form small white colonies on agar plates and grow aerobically and chemoorganotrophically on SSE/HD 1 : 10 medium, preferably utilizing organic acids and proteinaceous substrates. Strains 0125_3T and Swamp67T are mesophilic and grow optimally without NaCl addition at slightly alkaline conditions. Major fatty acids are C16 : 1 ω7c, C16 : 0 and C14 : 0. The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyglycerol. The predominant respiratory quinone is Q-8. The G+C content for 0125_3T and Swamp67T was 67 and 66.1 %, respectively. The 16S rRNA gene analysis indicated that the closest relatives (<91 % sequence similarity) of strain 0125_3T were Nitrosospira multiformis ATCC 25196T, Methyloversatilis universalis FAM5T and Denitratisoma oestradiolicum AcBE2-1T, while Nitrosospira multiformis ATCC 25196T, Nitrosospira tenuis Nv1T and Nitrosospira lacus APG3T were closest to strain Swamp67T. The two novel strains shared 97.4 % 16S rRNA gene sequence similarity with one another and show low average nucleotide identity of their genomes (83.8 %). Based on the phenotypic, chemotaxonomic, genomic and phylogenetic analysis, we propose the two novel species Usitatibacter rugosus sp. nov (type strain 0125_3T=DSM 104443T=LMG 29998T=CECT 9241T) and Usitatibacter palustris sp. nov. (type strain Swamp67T=DSM 104440T=LMG 29997T=CECT 9242T) of the novel genus Usitatibacter gen. nov., within the novel family Usitatibacteraceae fam. nov.


Assuntos
Betaproteobacteria/classificação , Filogenia , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , Betaproteobacteria/isolamento & purificação , DNA Bacteriano/genética , Ácidos Graxos/química , Alemanha , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
13.
Artigo em Inglês | MEDLINE | ID: mdl-33439113

RESUMO

As part of a study investigating the microbiome of bee hives and honey, two novel strains (TMW 2.1880T and TMW 2.1889T) of acetic acid bacteria were isolated and subsequently taxonomically characterized by a polyphasic approach, which revealed that they cannot be assigned to known species. The isolates are Gram-stain-negative, aerobic, pellicle-forming, catalase-positive and oxidase-negative. Cells of TMW 2.1880T are non-motile, thin/short rods, and cells of TMW 2.1889T are motile and occur as rods and long filaments. Morphological, physiological and phylogenetic analyses revealed a distinct lineage within the genus Bombella. Strain TMW 2.1880T is most closely related to the type strain of Bombella intestini with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 94.16 and 56.3 %, respectively. The genome of TMW 2.1880T has a size of 1.98 Mb and a G+C content of 55.3 mol%. Strain TMW 2.1889T is most closely related to the type strain of Bombella apis with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 85.12 and 29.5 %, respectively. The genome of TMW 2.1889T has a size of 2.07 Mb and a G+C content of 60.4 mol%. Ubiquinone analysis revealed that both strains contained Q-10 as the main respiratory quinone. Major fatty acids for both strains were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8, respectively, and additionally C14 : 0 2-OH only for TMW 2.1880T and C14 : 0 only for TMW 2.1889T. Based on polyphasic evidence, the two isolates from honeycombs of Apis mellifera represent two novel species of the genus Bombella, for which the names Bombella favorum sp. nov and Bombella mellum sp. nov. are proposed. The designated respective type strains are TMW 2.1880T (=LMG 31882T=CECT 30114T) and TMW 2.1889T (=LMG 31883T=CECT 30113T).


Assuntos
Acetobacteraceae/classificação , Abelhas/microbiologia , Mel/microbiologia , Filogenia , Acetobacteraceae/isolamento & purificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Alemanha , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
14.
Artigo em Inglês | MEDLINE | ID: mdl-33470926

RESUMO

Over a period of 1 year, 270 isolates identified as Taxon 39 of Bisgaard were obtained from the nasopharynx of veal calves at 11 epidemiologically independent Swiss fattening farms. Two isolates from each farm and the Australian Taxon 39 reference strain BNO311 were further characterized by genetic and phenotypic methods. Phylogenetic analysis of 16S rRNA and recN gene sequences placed the isolates in a single, distinct cluster within the genus Mannheimia. As to the rpoB gene, most isolates clustered together, but four strains formed a separate cluster close to Mannheimia varigena. Genome sequence analysis of isolates from both rpoB clusters confirmed their species status, with an average nucleotide identity (ANI) >98.9 % between isolates and <84 % to the closest species, M. varigena. Based upon whole genome sequences, the G+C content was determined as 39.1 mol%. Similarly, analysis of MALDI-TOF MS reference spectra clustered the isolates clearly separated from the other Mannheimia species, making this the method of choice for identification. In addition, numerous biochemical markers based on classical as well as commercial identification schemes were determined, allowing separation from other Mannheimia species and identification of the new taxon. Major fatty acids for strain 17CN0883T are C14 : 0, C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. Major respiratory quinones are ubiquinone-7 and ubiquinone-8. We propose the name Mannheimia pernigra sp. nov. for former Taxon 39 of Bisgaard. The type strain is 17CN0883T (=CCUG 74657T=DSM 111153T) isolated from a veal calf in Switzerland.


Assuntos
Bovinos/microbiologia , Mannheimia/classificação , Filogenia , Sistema Respiratório/microbiologia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Genes Bacterianos , Mannheimia/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Suíça , Ubiquinona/química
15.
Artigo em Inglês | MEDLINE | ID: mdl-33480837

RESUMO

Four novel strains isolated from the cloacal contents of snow finches (Montifringilla taczanowskii) were characterized as aerobic, Gram-stain-negative, slightly motile, and rod-shaped. Analysis of the 16S rRNA gene sequence revealed that strain CF-458T had the highest similarities of 96.9 and 96.4 % with Limnobaculum parvum HYN0051T and Pragia fontium DSM 5563T, while strain CF-1111T shared the highest similarities of 96.4 and 96.1 % with Pantoea rodasii LMG 26273T and Pectobacterium punjabense SS95T. Phylogenomic analysis showed the four isolates were separated into group Ⅰ (CF-458T and CF-917) and group Ⅱ (CF-1111T and CF-509), and clustered independently in the vicinity of the genera Limnobaculum and Pragia. Summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c, 23.9 and 17.2 %, respectively), C16 : 0 (21.8 and 22.1 %, respectively) and C14 : 0 (10.6 and 17.7 %, respectively) were the common major fatty acids, and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c, 12.3 %) was also a major fatty acid for strain CF-458T while cyclo-C17 : 0 (13.1%) was for strain CF-1111T. Both had Q-8 as the sole quinone and contained phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as the major polar lipids. The DNA G+C content of strains CF-458T and CF-1111T was 45.7 and 45.4 mol%, respectively. Based on taxonomic position in the phylogenomic tree and phenotypic properties, two novel species of a new genus within the family Budviciaceae are thus proposed, with the name Jinshanibacter gen. nov., zhutongyuii sp. nov. (type strain CF-458T=CGMCC 1.16483T=GDMCC 1.1586T=JCM 33489T) and Jinshanibacter xujianqingii sp. nov. (type strain CF-1111T=CGMCC 1.16786T=GDMCC 1.1587T=JCM 33490T), respectively.


Assuntos
Cloaca/microbiologia , Tentilhões/microbiologia , Gammaproteobacteria/classificação , Filogenia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Gammaproteobacteria/isolamento & purificação , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química
16.
Artigo em Inglês | MEDLINE | ID: mdl-33492207

RESUMO

A bisphenol A-degrading bacterium, designated as strain H4T, was isolated from surface seawater, which was sampled from the Jiulong River estuary in southeast PR China. Strain H4T is Gram-stain-negative, aerobic, short rod-shaped, lacking bacteriochlorophyll a, motile with multifibrillar stalklike fascicle structures and capable of degrading bisphenol A. Growth of strain H4T was observed at 24-45 °C (optimum, 32 °C), at pH 5.5-9 (optimum, pH 7.0) and in 0-7 % NaCl (optimum, 2 %; w/v) . The 16S rRNA gene sequence of strain H4T showed highest similarity to Croceicoccus pelagius Ery9T (98.7 %), Croceicoccus sediminis (98.3 %), Croceicoccus naphthovorans PQ-2T (98.1 %) and Croceicoccus ponticola GM-16T (97.6 %), followed by Croceicoccus marinus E4A9T (96.7 %) and Croceicoccus mobilis Ery22T (96.0 %). Phylogenetic analysis revealed that strain H4T fell within a clade comprising the type strains of Croceicoccus species and formed a phyletic line with them that was distinct from other members of the family Erythrobacteraceae. The sole respiratory quinone was quinone 10 (Q-10). The predominant fatty acids (>5 % of the total fatty acids) of strain H4T were summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), C17 : 1 ω6c and C14 : 02-OH. The genomic DNA G+C content was 62.8 mol%. In the polar lipid profile, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids, two sphingoglycolipids and three unknown lipids were the major compounds. Based on the genotypic and phenotypic data, strain H4T represents a novel species of the genus Croceicoccus, for which the name Croceicoccus bisphenolivorans sp. nov. is proposed. The type strain is H4T (=DSM 102182T=MCCC1 K02301T).


Assuntos
Alphaproteobacteria/classificação , Compostos Benzidrílicos/metabolismo , Fenóis/metabolismo , Filogenia , Água do Mar/microbiologia , Alphaproteobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Estuários , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
17.
Artigo em Inglês | MEDLINE | ID: mdl-33502295

RESUMO

A facultatively anaerobic bacterium, strain S0837T, was isolated from the marine sediment of Jingzi Wharf, Weihai, China. Cells of the novel strain were Gram-stain-negative, non-flagellated, non-gliding, non-pigmented and rod-shaped. Cells were around 0.3-0.5×1.0-1.4 µm in size and often appeared singly. Optimum growth occurred at 33 °C, with 2 % (w/v) NaCl and at pH 7.0-7.5. On the basis of the results of 16S rRNA gene sequences, stain S0837T had the closest relative with Sulfitobacter delicatus KCTC 32183T (98.0 %). Genome sequencing revealed a genome size of 3 785 026 bp, a G+C content of 59.8 mol% and several genes related with sulphur oxidation. The strain shared 98.0 % 16S rRNA sequence similarities with closely related type species and shared ANI value below 95-96 %, dDDH value of showed relatedness of 27.4, 25.2 and 25.2 % respectively with the closely related type species. Strain S0837T had ubiquinone-10 as the sole respiratory quinone, and possessed summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) as the major fatty acid. The major polar lipids were phosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic properties and genome analysis, strain S0837T should represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter maritimus sp. nov. is proposed. The type strain is S0837T (=MCCC 1K04635T=KCTC 72860T).


Assuntos
Sedimentos Geológicos/microbiologia , Filogenia , Rhodobacteraceae/classificação , Água do Mar/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Rhodobacteraceae/isolamento & purificação , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
18.
J Mater Chem B ; 9(3): 824-831, 2021 01 28.
Artigo em Inglês | MEDLINE | ID: mdl-33338098

RESUMO

Successful applications of photodynamic therapy (PDT) in cancer treatment require the development of effective photosensitizers with controllable singlet oxygen generation. Here we report a ubiquinone-BODIPY photosensitizer that self-assembles into nanoparticles (PS-Q-NPs) and undergoes selective activation and deaggregation within the highly reductive intracellular environment of tumor cells. PS-Q-NPs are highly stable in aqueous buffer solution, and exhibit minimal fluorescence and photosensitization due to a rapid non-radiative relaxation process. Upon endocytosis by cancer cells, reduction of the ubiquinone moiety by intracellular glutathione (GSH) triggers the conversion of the aggregated hydrophobic precursor into the active hydrophilic carboxylate derivative PS-A. The conversion results in enhanced fluorescence and therapeutic singlet oxygen generation, portending to its application as an activatable photosensitizer for fluorescence imaging-guided photodynamic cancer therapy.


Assuntos
Antineoplásicos/farmacologia , Compostos de Boro/farmacologia , Glioblastoma/tratamento farmacológico , Nanopartículas/química , Fotoquimioterapia , Fármacos Fotossensibilizantes/farmacologia , Ubiquinona/farmacologia , Animais , Antineoplásicos/síntese química , Antineoplásicos/química , Compostos de Boro/química , Linhagem Celular Tumoral , Sobrevivência Celular/efeitos dos fármacos , Glioblastoma/diagnóstico por imagem , Humanos , Raios Infravermelhos , Camundongos , Estrutura Molecular , Neoplasias Experimentais/diagnóstico por imagem , Neoplasias Experimentais/tratamento farmacológico , Imagem Óptica , Oxirredução , Oxigênio/análise , Tamanho da Partícula , Fármacos Fotossensibilizantes/síntese química , Fármacos Fotossensibilizantes/química , Propriedades de Superfície , Microambiente Tumoral/efeitos dos fármacos , Ubiquinona/química
19.
Biochim Biophys Acta Bioenerg ; 1862(1): 148307, 2021 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-32926863

RESUMO

Redox-active quinones play essential roles in efficient light energy conversion in type-II reaction centers of purple phototrophic bacteria. In the light-harvesting 1 reaction center (LH1-RC) complex of purple bacteria, QB is converted to QBH2 upon light-induced reduction and QBH2 is transported to the quinone pool in the membrane through the LH1 ring. In the purple bacterium Rhodobacter sphaeroides, the C-shaped LH1 ring contains a gap for quinone transport. In contrast, the thermophilic purple bacterium Thermochromatium (Tch.) tepidum has a closed O-shaped LH1 ring that lacks a gap, and hence the mechanism of photosynthetic quinone transport is unclear. Here we detected light-induced Fourier transform infrared (FTIR) signals responsible for changes of QB and its binding site that accompany photosynthetic quinone reduction in Tch. tepidum and characterized QB and QBH2 marker bands based on their 15N- and 13C-isotopic shifts. Quinone exchanges were monitored using reconstituted photosynthetic membranes comprised of solubilized photosynthetic proteins, membrane lipids, and exogenous ubiquinone (UQ) molecules. In combination with 13C-labeling of the LH1-RC and replacement of native UQ8 by ubiquinones of different tail lengths, we demonstrated that quinone exchanges occur efficiently within the hydrophobic environment of the lipid membrane and depend on the side chain length of UQ. These results strongly indicate that unlike the process in Rba. sphaeroides, quinone transport in Tch. tepidum occurs through the size-restricted hydrophobic channels in the closed LH1 ring and are consistent with structural studies that have revealed narrow hydrophobic channels in the Tch. tepidum LH1 transmembrane region.


Assuntos
Proteínas de Bactérias/química , Chromatiaceae/enzimologia , Complexos de Proteínas Captadores de Luz/química , Ubiquinona/química , Proteínas de Bactérias/metabolismo , Sítios de Ligação , Transporte Biológico Ativo , Complexos de Proteínas Captadores de Luz/metabolismo , Oxirredução , Ubiquinona/metabolismo
20.
Artigo em Inglês | MEDLINE | ID: mdl-33332260

RESUMO

A Gram-negative, aerobic, rod-shaped, non-motile bacterium, designated strain HQ09T, was isolated from a marine sponge off the coast of Fields Peninsula, West Antarctica. Strain HQ09T grew at 4-35 °C (optimum, 25 °C), pH 5-9 (optimum, pH 7.0), and with 1-10% NaCl (optimum, 2 %). Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain HQ09T was affiliated with the genus Pseudopuniceibacterium in the family Rhodobacteraceae, sharing 99.64 % identity with the type strain of Pseudopuniceibacterium sediminis, the only known species in the genus. However, the low digital DNA-DNA hybridization (dDDH) (27.2 %) and average nucleotide identity (ANI) (83.63 %) values between strain HQ09T and the type strain of Pseudopuniceibacterium sediminis indicated that they did not belong to the same species. Strain HQ09T could also be differentiated from Pseudopuniceibacterium sediminis by many phenotypic characteristics. The major fatty acids (>5 %) of strain HQ09T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), 11-methyl C18 : 1 ω7c, C16 : 0 and C19 : 0 cyclo ω8c. The polar lipids included phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids and one unidentified phospholipid. The predominant respiratory quinone was ubiquinone 10 (Q-10). The genomic DNA G+C content was 62.63 mol%. Four secondary metabolite biosynthetic gene clusters were detected in the genome, potentially producing ectoine and three types of unknown compounds. On the basis of the polyphasic evidences obtained in this study, strain HQ09T represents a novel species of the genus Pseudopuniceibacterium, for which the name Pseudopuniceibacterium antarcticum sp. nov. is proposed, with the type strain being HQ09T (=KCTC 52229T=CGMCC 1.15538T).


Assuntos
Filogenia , Poríferos/microbiologia , Rhodobacteraceae/classificação , Animais , Regiões Antárticas , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Rhodobacteraceae/isolamento & purificação , Análise de Sequência de DNA , Ubiquinona/análogos & derivados , Ubiquinona/química
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