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1.
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
2.
Int J Syst Evol Microbiol ; 70(10): 5243-5254, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32886598

RESUMO

A bacterial strain, designated FSY-8T, was isolated from a freshwater mesocosm in Taiwan and characterized using the polyphasic taxonomy approach. Cells of strain FSY-8T were aerobic, Gram-stain-negative, rod-shaped, non-motile and formed yellow coloured colonies on Reasoner's 2A agar. Growth occurred at 20-40 °C (optimum, 30-37 °C) and pH 5-7 (optimum, pH 6) and in the presence of 0-0.5 % NaCl (optimum, 0 %, w/v). The major fatty acids (>10 %) of strain FSY-8T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, diphosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized glycolipid and an uncharacterized lipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 64.8 mol %. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-8T formed a phylogenetic lineage in the genus Novosphingobium. Strain FSY-8T showed 71.6-77.2 % average nucleotide identity and 19.9-22.8 % digital DNA-DNA hybridization identity with the strains of other Novosphingobium species. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain FSY-8T should be classified in a novel species of the genus Novosphingobium, for which the name Novosphingobium ovatum sp. nov. is proposed. The type strain is FSY-8T (=BCRC 81051T=LMG 30053T=KCTC 52812T).


Assuntos
Água Doce/microbiologia , Filogenia , 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 , Espermidina/química , Sphingomonadaceae/isolamento & purificação , Taiwan , Ubiquinona/análogos & derivados , Ubiquinona/química
3.
Int J Syst Evol Microbiol ; 70(10): 5561-5566, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32924915

RESUMO

A Gram-stain-negative, facultatively anaerobic, yellow-pigmented, non-motile, rod-shaped bacterium, designated zrk23T, was isolated from a deep-sea cold seep. The strain was characterized by a polyphasic approach to clarify its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences placed zrk23T within the genus Sphingosinithalassobacter and showed the highest similarity to Sphingosinithalassobacter portus FM6T (97.93 %). Growth occurs at temperatures from 16 to 45 °C (optimum, 30 °C), at pH values between pH 6.0 and 8.5 (optimum, pH 7.0) and in 0-5.0 % (w/v) NaCl (optimum, 1.5 %). The major fatty acids were C16 : 0, C14 : 0 2-OH and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major isoprenoid quinone was ubiquinone-10. Predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unidentified phosphoglycolipid, three unidentified glycolipids and three unidentified phospholipids. The G+C content of the genomic DNA was 64.69 %. The average nucleotide identity values between zrk23T and the most closely related available genome, of Sphingosinithalassobacter portus FM6T, was 82.21 %, indicating that zrk23T was clearly distinguished from S. portus. The analysis of genome sequence of zrk23T revealed that there were many genes associated with degradation of aromatic compounds existing in the genome of zrk23T. As a result of the combination of the results of phylogenetic analysis and phenotypic and chemotaxonomic data, zrk23T was considered to represent a novel species of the genus Sphingosinithalassobacter, for which the name Sphingosinithalassobacter tenebrarum sp. nov. is proposed. The type strain is zrk23T (=KCTC 72896T=MCCC 1K04416T).


Assuntos
Filogenia , Água do Mar/microbiologia , Sphingomonadaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , Temperatura Baixa , DNA Bacteriano/genética , Ácidos Graxos/química , Sedimentos Geológicos/microbiologia , Glicolipídeos/química , Oceano Pacífico , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sphingomonadaceae/isolamento & purificação , Ubiquinona/análogos & derivados , Ubiquinona/química
4.
Int J Syst Evol Microbiol ; 70(8): 4698-4703, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32701426

RESUMO

A Gram-stain-negative, non-motile, facultatively anaerobic and rod-shaped bacterial strain, designated PAMC 28131T, was isolated from a sea surface microlayer sample in the open water of the Pacific Ocean. Phylogenetic analysis of the 16S rRNA gene sequence of strain PAMC 28131T revealed an affiliation to the genus Sandaracinobacter with the closest species Sandaracinobacter sibiricus RB16-17T (sequence similarity of 98.2 %). Strain PAMC 28131T was able to grow optimally with 0.5-1.0 % NaCl and at pH 6.5-7.0 and 30 °C. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, an unidentified aminolipid, an unidentified glycolipid and an unidentified lipid. The major cellular fatty acids (>10 %) were C18 : 1 ω6c and/or C18 : 1 ω7c, (42.6 %), C17 : 1 ω6c (19.3 %) and C16 : 1 ω6c and/or C16 : 1 ω7c (15.8 %), and the respiratory quinone was Q-10. The genomic DNA G+C content was 65.3 mol%. The phylogenetic, phenotypic and chemotaxonomic data showed that strain PAMC 28131T could be clearly distinguished from S. sibiricus RB16-17T. Thus, strain PAMC 28131T should be classified as representing a novel species in the genus Sandaracinobacter, for which the name Sandaracinobacter neustonicus sp. nov. is proposed. The type strain is PAMC 28131T (=KCCM 43127T=JCM 30734T).


Assuntos
Filogenia , Água do Mar/microbiologia , Sphingomonadaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Oceano Pacífico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sphingomonadaceae/isolamento & purificação
5.
Int J Syst Evol Microbiol ; 70(5): 3202-3209, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32320377

RESUMO

Two Gram-stain-negative, aerobic, non-motile bacteria, designated IMCC1753T and IMCC26285T, were isolated from a shallow eutrophic pond and a deep oligotrophic lake, respectively. Results of 16S rRNA gene sequence analysis indicated that the two strains shared 99.8 % sequence similarity and were most closely related to Sphingorhabdus contaminans JC216T(98.7-98.8 %). The whole genome sequences of strains IMCC1753T and IMCC26285T were 3.5 and 2.9 Mbp in size with 56.6 and 55.5 mol% DNA G+C content, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 82.2 and 25.8 %, respectively, indicating that they are separate species. The two strains showed ≤98.8 % 16S rRNA gene sequence similarities and ≤82.2 % ANI and ≤28.7 % dDDH values to closely related species of the genus Sphingorhabdus, indicating that the two strains each represent novel species. Major fatty acid constituents of strain IMCC1753T were C17 : 1 ω6c, C17 : 1 ω8c and summed features 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and 8 (C18 : 1 ω6c and/or C18 : 1 ω7c); those of strain IMCC26285T were summed features 3 and 8. The predominant isoprenoid quinone detected in both strains was ubiquinone-10 and the most abundant polyamine was spermidine. Both strains contained phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol and sphingoglycolipid as major polar lipids. On the basis of the phylogenetic and phenotypic characteristics, strains IMCC1753T and IMCC26285T were considered to represent two distinct novel species in the genus Sphingorhabdus, for which the names Sphingorhabdus lacus (IMCC1753T=KCTC 52480T=KACC 18985T=NBRC 112442T) and Sphingorhabdus profundilacus (IMCC26285T=KCTC 52479T=KACC 18986T=NBRC 112454T) are proposed, respectively.


Assuntos
Lagos/microbiologia , Filogenia , Sphingomonadaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Sphingomonadaceae/isolamento & purificação , Ubiquinona/análogos & derivados , Ubiquinona/química
6.
Sci Rep ; 10(1): 6662, 2020 04 20.
Artigo em Inglês | MEDLINE | ID: mdl-32313127

RESUMO

The environment affects the composition and function of soil microbiome, which indirectly influences the quality of plants. In this study, 16S amplicon sequencing was used to reveal the differences in soil microbial community composition of Cistanche deserticola in three ecotypes (saline-alkali land, grassland and sandy land). Through the correlation analysis of microbial community abundance, phenylethanoid glycoside contents and ecological factors, the regulatory relationship between microbial community and the quality variation of C. deserticola was expounded. The metabolic function profile of soil microbiome was predicted using Tax4Fun. Data showed that the soil microbial communities of the three ecotypes were significantly different (AMOVA, P < 0.001), and the alpha diversity of grassland soil microbial community was the highest. Core microbiome analysis demonstrated that the soil microbial communities of C. deserticola were mostly have drought, salt tolerance, alkali resistance and stress resistance, such as Micrococcales and Bacillales. The biomarkers, namely, Oceanospirillales (saline-alkali land), Sphingomonadales (grassland) and Propionibacteriales (sandy land), which can distinguish three ecotype microbial communities, were excavated through LEfSe and random forest. Correlation analysis results demonstrated that 2'-acetylacteoside is positively correlated with Oceanospirillales in saline-alkali land soil. The metabolic function profiles displayed highly enriched metabolism (carbohydrate and amino acid metabolisms) and environmental information processing (membrane transport and signal transduction) pathways. Overall, the composition and function of soil microbiomes were found to be important factors to the quality variation of C. deserticola in different ecotypes. This work provided new insight into the regulatory relationship amongst the environment, soil microbial community and plant quality variation.


Assuntos
Bacillales/classificação , Cistanche/microbiologia , Micrococcaceae/classificação , Oceanospirillaceae/classificação , Propionibacteriaceae/classificação , Microbiologia do Solo , Sphingomonadaceae/classificação , Bacillales/genética , Bacillales/isolamento & purificação , Técnicas de Tipagem Bacteriana , China , Cistanche/fisiologia , Secas , Ecótipo , Variação Genética , Glicosídeos/biossíntese , Pradaria , Concentração de Íons de Hidrogênio , Micrococcaceae/genética , Micrococcaceae/isolamento & purificação , Oceanospirillaceae/genética , Oceanospirillaceae/isolamento & purificação , Filogenia , Propionibacteriaceae/genética , Propionibacteriaceae/isolamento & purificação , RNA Ribossômico 16S/genética , Salinidade , Tolerância ao Sal/genética , Areia/microbiologia , Solo/química , Sphingomonadaceae/genética , Sphingomonadaceae/isolamento & purificação
7.
Int J Syst Evol Microbiol ; 70(4): 2901-2906, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32223836

RESUMO

A novel bacterial strain, designated FGD1T, was isolated from subtropical forest soil of the Nanling National Forest Park located in Guangdong Province, P.R. China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain FGD1T was most closely related to Novosphingobium lindaniclasticum DSM 25049T (98.8 %), followed by N. barchaimii DSM 25411T (98.7 %), N. guangzhouense DSM 32207T (98.2 %), N. panipatense DSM 22890T (98.1 %) and other species of Novosphingobium (<98 %). The draft genome sequence was 4.58 Mb in length with a G+C content of 65.1 mol%. The calculated average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain FGD1T and closely related type strains were 77.7‒79.6 % and 21.7-22.9 %, respectively. Major 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), C14 : 0 2-OH and C16 : 0. The predominant respiratory quinone was ubiquinone 10 and the major polyamine was spermidine. Polar lipids were composed of sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, an unidentified phospholipid and lipid. The polyphasic taxonomic results indicated that strain FGD1T represents a novel species of the genus Novosphingobium, for which the name Novosphingobium silvae sp. nov. is proposed. The type strain is FGD1T (=GDMCC 1.1761T=KACC 21283T).


Assuntos
Florestas , Filogenia , Microbiologia do Solo , Sphingomonadaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sphingomonadaceae/isolamento & purificação , Ubiquinona/análogos & derivados , Ubiquinona/química
8.
Artif Cells Nanomed Biotechnol ; 48(1): 672-682, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32075448

RESUMO

The present study highlights the biological synthesis of silver nanoparticles (AgNPs) using Sphingobium sp. MAH-11 and also their antibacterial mechanisms against drug-resistant pathogenic microorganisms. The nanoparticle synthesis method used in this study was reliable, facile, rapid, cost-effective and ecofriendly. The AgNPs exhibited the highest absorbance at 423 nm. The TEM image expressed spherical shape of AgNPs and the size of synthesized AgNPs was 7-22 nm. The selected area diffraction (SAED) pattern and XRD spectrum revealed the crystalline structure of AgNPs. The results of FTIR analysis disclosed the functional groups responsible for the reduction of silver ion to metal nanoparticles. The biosynthesized AgNPs showed strong anti-microbial activity against drug-resistant pathogenic microorganisms. Moreover, Escherichia coli and Staphylococcus aureus were used to explore the antibacterial mechanisms of biosynthesized AgNPs. Minimal inhibitory concentrations (MICs) of E. coli and S. aureus were 6.25 µg/mL and 50 µg/mL, respectively and minimum bactericidal concentrations (MBCs) of E. coli and S. aureus were 25 µg/mL and 100 µg/mL, respectively. Results exhibited that biosynthesized AgNPs caused morphological changes and injured the membrane integrity of strains E. coli and S. aureus. The AgNPs synthesized by Sphingobium sp. MAH-11 may serve as a potent antimicrobial agent for many therapeutic applications.


Assuntos
Antibacterianos/biossíntese , Antibacterianos/farmacologia , Farmacorresistência Bacteriana/efeitos dos fármacos , Nanopartículas Metálicas/química , Prata/metabolismo , Sphingomonadaceae/metabolismo , Antibacterianos/química , Membrana Celular/efeitos dos fármacos , Escherichia coli/efeitos dos fármacos , Nanopartículas Metálicas/ultraestrutura , Testes de Sensibilidade Microbiana , Tamanho da Partícula , Filogenia , RNA Ribossômico 16S/genética , Prata/química , Prata/farmacologia , Sphingomonadaceae/classificação , Sphingomonadaceae/genética , Staphylococcus aureus/efeitos dos fármacos
9.
Int J Syst Evol Microbiol ; 70(3): 1822-1829, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32048985

RESUMO

Two Gram-stain-negative, aerobic, motile and rod-shaped bacteria, one designated as strain AXBT, capable of degrading estrogens, and another, YL23T, capable of degrading estrogen and bisphenol A, were isolated from activated sludge in Xiamen City, PR China. The optimum temperature and pH of both strains were 25-35 °C and pH 7.0-8.0. While strain AXBT could tolerate 3 % (w/v) NaCl, YL23T could only grow between 0-1 % (w/v) NaCl. They contained ubiquinone-10 as the major quinone, spermidine as the major polyamine, summed feature 8 (comprising C18:1ω6c and/or C18:1ω7c) as the major fatty acids and diphosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid as the major polar lipids. The DNA G+C contents of strains AXBT and YL23T were 63.6 and 63.7 mol%, respectively. Based on the results of 16S rRNA gene sequence analysis, strains AXBT and YL23T belonged to the genus Sphingobium. Strain AXBT was most closely related to Sphingobium chlorophenolicum NBRC 16172T (97.5 %) and Sphingobium chungbukense DJ77T (97.2 %), and strain YL23T was most closely related to S. chlorophenolicum NBRC 16172T (97.4 %) and S. quisquiliarum P25T (97.1 %). Average nucleotide identity values between these two strains and S. chlorophenolicum NBRC 16172T, S. chungbukense DJ77T, Sphingobium chinhatense IP26T, Sphingobium quisquiliarum P25T and Sphingobium japonicum UT26ST were from 80.7 to 85.8 %. In conclusion, strains AXBT and YL23T represent novel species of the genus Sphingobium, for which the names Sphingobium estronivorans sp. nov. and Sphingobium bisphenolivorans sp. nov. are proposed, respectively. The type strains of S. estronivorans and S. bisphenolivorans are AXBT (=MCCC 1K01232T=DSM 102173T) and YL23T (=MCCC 1K02300T=DSM 102172T), respectively.


Assuntos
Filogenia , Esgotos/microbiologia , Sphingomonadaceae/classificação , Águas Residuárias/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espermidina/química , Sphingomonadaceae/isolamento & purificação , Ubiquinona/análogos & derivados , Ubiquinona/química
10.
Int J Syst Evol Microbiol ; 70(3): 1470-1477, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32100685

RESUMO

A Gram-staining-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated as JBTF-M21T, was isolated from a tidal flat sediment on the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences indicated that JBTF-M21T fell within the clade comprising the type strains of species of the genus Erythrobacter. JBTF-M21T exhibited 16S rRNA gene sequence similarities of 97.0-98.4 % to the type strains of Erythrobacter longus, Erythrobacter aquimaris, Erythrobacter nanhaisediminis, Erythrobacter vulgaris, Erythrobacter seohaensis, Erythrobacter litoralis and Erythrobacter citreus and 93.7-96.6 % to the type strains of the other species of the genus Erythrobacter. The ANI and dDDH values between JBTF-M21T and the type strains of E. longus, E. nanhaisediminis, E. seohaensis and E. litoralis were 70.83-72.93 % and 18.0-18.8 %, respectively. Mean DNA-DNA relatedness values between JBTF-M21T and the type strains of E. aquimaris, E. vulgaris and E. citreus were 12-24 %. The DNA G+C content of JBTF-M21T was 57.0 mol%. JBTF-M21T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C17 : 1ω6c as the major fatty acids. The major polar lipids ofJBTF-M21T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. Distinguishing phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that JBTF-M21T is separated from species of the genus Erythrobacter with validly published names. On the basis of the data presented, strain JBTF-M21T is considered to represent a novel species of the genus Erythrobacter, for which the name Erythrobacter insulae sp. nov. is proposed. The type strain is JBTF-M21T (=KACC 19864T=NBRC 113584T).


Assuntos
Sedimentos Geológicos/microbiologia , Filogenia , Água do Mar/microbiologia , Sphingomonadaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Sphingomonadaceae/isolamento & purificação , Ubiquinona/análogos & derivados , Ubiquinona/química
11.
Int J Syst Evol Microbiol ; 70(3): 2147-2154, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32011975

RESUMO

During a phylogenetic analysis of Sphingorhabdus and its closely related genera in the family Sphingomonadaceae, we found that the genus Sphingorhabdus and the species Sphingopyxis baekryungensis might not be properly assigned in the taxonomy. Phylogenetic, phenotypic and chemotaxonomic characterizations clearly showed that the genus Sphingorhabdus should be reclassified into two genera (Clade I and Clade II), for which the original genus name, Sphingorhabdus, is proposed to be retained only for Clade I, and a new genus named as Parasphingorhabdus gen. nov. is proposed for Clade II with four new combinations: Parasphingorhabdus marina comb. nov., Parasphingorhabdus litoris comb. nov., Parasphingorhabdus flavimaris comb. nov. and Parasphingorhabdus pacifica comb. nov. Moreover, Sphingopyxis baekryungensis should represent a novel genus in the family Sphingomonadaceae, for which the name Novosphingopyxis gen. nov. is proposed, with a combination of Novosphingopyxis baekryungensis comb. nov. The study provides a new insight into the taxonomy of closely related genera in the family Sphingomonadaceae.


Assuntos
Filogenia , Sphingomonadaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
12.
Int J Syst Evol Microbiol ; 70(3): 1610-1616, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31904318

RESUMO

A Gram-stain-negative, strictly aerobic, rod-shaped and non-motile bacterial strain, designated D-2Q-5-6T, was isolated from a soil sample collected from the Arctic region. Strain D-2Q-5-6T was found to grow at 10-43 °C (optimum, 28 °C), at pH 6.0-9.0 (pH 7.0) and in 0-5 % (w/v) NaCl (0-1 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain D-2Q-5-6T fell into the genus Sphingorhabdus and shared less than 95.8 % identity with all type strains of recognized species of this genus. The major cellular fatty acids of strain D-2Q-5-6T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c; 31.4 %), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c; 26.8 %) and C14 : 0 2OH (11.7 %). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. The predominant quinone was identified as Q10. The DNA G+C content of strain D-2Q-5-6T was 64.5 mol%. Based on the results of phylogenetic analysis and distinctive phenotypic characteristics, strain D-2Q-5-6T is concluded to represent a novel species of the genus Sphingorhabdus, for which the name Sphingorhabdus soli sp. nov. is proposed. The type strain of the species is D-2Q-5-6T (=MCCC 1A06070T=KCTC 52311T).


Assuntos
Filogenia , Microbiologia do Solo , Sphingomonadaceae/classificação , Regiões Árticas , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sphingomonadaceae/isolamento & purificação , Svalbard , Ubiquinona/análogos & derivados , Ubiquinona/química
13.
Int J Syst Evol Microbiol ; 70(3): 1644-1647, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31909705

RESUMO

Phylogenetic analysis of the genus Sphingobium had shown that the type strains of Sphingobium paulinellae, Sphingobium algicola and Sphingobium limneticum shared a very close relationship between each other. The 16S rRNA gene sequences similarity values between each other ranged from 99.65 to 99.93 %. Whole genome sequencing was performed and genomic relatedness values between each pair of the species were 97.49-100 % (ANI) and 79.3-100 % (dDDH), respectively, all higher than the threshold values of 95-96 % ANI and 70 % dDDH suggested for species discrimination, and implicated that the type strains should belong to the same species of the genus Sphingobium. The phenotypic and chemotaxonomic characterizations performed in the original descriptions of S. paulinellae and S. algicola also supported the same conclusion. Due to priority of publication Sphingobium paulinellae and Sphingobium algicola Lee and Jeon 2017, should be taken as two later heterotypic synonyms of Sphingobium limneticum Chen et al. 2013. Correspondingly, the species description of Sphingobium limneticum was emended based on this study.


Assuntos
Filogenia , Sphingomonadaceae/classificação , Técnicas de Tipagem Bacteriana , DNA Bacteriano/genética , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sequenciamento Completo do Genoma
14.
Antonie Van Leeuwenhoek ; 113(5): 719-727, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-31980980

RESUMO

In this study, a novel ginsenoside transforming bacterium, strain W1-2-3T, was isolated from mineral water. The 16S rRNA gene sequence analysis showed that strain W1-2-3T shares 93.7-92.2% sequence similarity with the members of the family Sphingomonadaceae and makes a group with Sphingoaurantiacus capsulatus YLT33T (93.7%) and S. polygranulatus MC 3718T (93.4%). The novel isolate efficiently hydrolyses the ginsenoside Rc to Rd. The genome comprises a single circular 2,880,809, bp chromosome with 3211 genes in total, and 1993 protein coding genes. The isolate was observed to grow at 10-37 °C and at pH 6-10 on R2A agar medium; maximum growth was found to occur at 25 °C and pH 7.0. Strain W1-2-3T was found to contain ubiquinone-10 as the predominant quinone and the fatty acids C16:1, C17:1ω6c, C14:0 2-OH, summed feature 3 (C16:1ω6c/C16:1ω7c) and summed feature 8 (C18:1ω6c/C18:1ω7c). The DNA G+C content was determined to be 65.9 mol%. Strain W1-2-3T can be distinguished from the other members of the family Sphingomonadaceae by a number of chemotaxonomic and phenotypic characteristics. The major polar lipids of strain W1-2-3T were identified as phosphatidylethanolamine, an unidentified glycolipid and an unidentified polar lipid. The major poly amine was found to be homospermidine. Based on polyphasic taxonomic analysis, strain W1-2-3T is concluded to represent a novel species within a new genus, for which the name Hankyongella ginsenosidimutans gen. nov., sp. nov. is proposed. The type strain of Hankyongella ginsenosidimutans is W1-2-3T (= KACC 18307T = LMG 28594T).


Assuntos
Ginsenosídeos/metabolismo , Águas Minerais/microbiologia , Sphingomonadaceae , Técnicas de Tipagem Bacteriana , DNA Bacteriano/genética , Ácidos Graxos/análise , Fosfolipídeos/análise , Filogenia , RNA Ribossômico 16S/genética , Sphingomonadaceae/classificação , Sphingomonadaceae/genética , Sphingomonadaceae/isolamento & purificação , Sphingomonadaceae/metabolismo , Ubiquinona/análogos & derivados , Ubiquinona/análise
15.
Int J Syst Evol Microbiol ; 70(2): 1093-1098, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31851602

RESUMO

An aerobic, Gram-stain-negative, yellowish, rod-shaped bacterium, designated DJ1R-1T, was isolated from water sample from a volcanic lake, located on Da Hinggan Ling Mountain, PR China. Growth of DJ1R-1T optimally occurred at pH 7.0, at 22-25 °C and with 0-0.5 % (w/v) NaCl concentration. Phylogenetic analysis of 16S rRNA gene sequences indicated that DJ1R-1T was clustered into the genus Polymorphobacter, and showed 96.5 %, 95.9 % and 95.6 % similarities to Polymorphobacter fuscus D40PT, Polymorphobacter multimanifer 262-7T and Polymorphobacter glacialis B555-2T, respectively. The predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid, three unidentified aminolipids and one unidentified phospholipid. The major fatty acids were summed feature 8 (C18 : 1ω7c / C18 : 1ω6c, 40.0 %), summed feature 3 (C16 : 1ω7c / C16 : 1ω6c, 25.6 %) and C16 : 0 (13.7 %). The respiratory quinone was ubiquinone-10. The DNA G+C content was 65.0 % according to the genomic sequencing results. On the basis of the results of the phylogenetic analysis, physiological and biochemical properties comparisons, DJ1R-1T was proposed to represent a novel species of the genus Polymorphobacter, with the name Polymorphobacter arshaanensis. The type strain is DJ1R-1T (=CGMCC 1.13788T=KCTC 72014T).


Assuntos
Lagos/microbiologia , Filogenia , Sphingomonadaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sphingomonadaceae/isolamento & purificação , Ubiquinona/análogos & derivados , Ubiquinona/química
16.
Int J Syst Evol Microbiol ; 70(2): 1122-1132, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31804916

RESUMO

A bacterial strain designated FSY-9T was isolated from a freshwater mesocosm in Taiwan and characterized to determine its taxonomic affiliation. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-9T formed a phylogenetic lineage in the genus Novosphingobium. Strain FSY-9T was most closely related to Novosphingobium humi R1-4T with a 97.2 % 16S rRNA gene sequence similarity. Strain FSY-9T showed 71.3-72.6 % average nucleotide identity and 17.7-23.0 % digital DNA-DNA hybridization identity with the strains of other Novosphingobium species. Cells of strain FSY-9T were facultatively anaerobic, Gram-negative, rod-shaped, non-motile and formed light yellow coloured colonies. Growth occurred at 15-37 °C and pH 5.5-7, and in the presence of 0-0.5 % NaCl. The major fatty acids (>10 %) of strain FSY-9T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c and C16 : 0. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, sphingoglycolipid, an uncharacterized aminophospholipid, an uncharacterized glycolipid and an uncharacterized lipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 61.5 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain FSY-9T should be classified as a novel species of the genus Novosphingobium, for which the name Novosphingobium umbonatum sp. nov. is proposed. The type strain is FSY-9T (=BCRC 81052T=LMG 30054T=KCTC 52813T).


Assuntos
Água Doce/microbiologia , Filogenia , Sphingomonadaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espermidina/química , Sphingomonadaceae/isolamento & purificação , Taiwan , Ubiquinona/análogos & derivados , Ubiquinona/química
17.
Int J Syst Evol Microbiol ; 70(1): 309-316, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31596696

RESUMO

Strain TLA-22T, isolated from a cold spring in Taiwan, was characterized using a polyphasic taxonomy approach. Cells were Gram-stain-negative, aerobic, poly-ß-hydroxybutyrate-accumulating, motile by means of a single polar flagellum, rod-shaped and formed bright yellow colonies. Optimal growth occurred at 20-25 °C, pH 6-6.5, and in the presence of 0.5 % NaCl. The major fatty acids of TLA-22T were C18 : 1 ω7 c and C17 : 1ω6c. The predominant hydroxy fatty acids were C15 : 0 2-OH and C14 : 0 2-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine, sphingoglycolipid, an unidentified aminophospholipid, an unidentified phospholipid and three unidentified lipids. TLA-22T contained spermidine as the major polyamine and putrescine as the minor component. The only isoprenoid quinone was Q-10. The genomic DNA G+C content of TLA-22T was 63.2 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that TLA-22T was a mem,ber of a phylogenetic lineage including members of the genus Sphingobium. TLA-22T was most closely related to Sphingobium aromaticiconvertens RW16T, with a 97.4 % 16S rRNA gene sequence similarity. TLA-22T showed 74.8-75.7 % average nucleotide identity and 20.1-22.0 % digital DNA-DNA hybridization identity with the strains of other species of the genus Sphingobium. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TLA-22T should be classified as representing a novel species of the genus Sphingobium, for which the name Sphingobium algorifonticola sp. nov. is proposed. The type strain is TLA-22T (=BCRC 81097T =LMG 30309T=KCTC 62189T).


Assuntos
Nascentes Naturais/microbiologia , Filogenia , Sphingomonadaceae/classificação , Microbiologia da Água , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hidroxibutiratos , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Pigmentação , Poliésteres , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espermidina/química , Sphingomonadaceae/isolamento & purificação , Taiwan , Ubiquinona/análogos & derivados , Ubiquinona/análise
18.
Int J Syst Evol Microbiol ; 70(2): 827-834, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31675289

RESUMO

A Gram-stain-negative, rod-shaped, non-motile, poly-ß-hydroxybutyrate-accumulating and aerobic bacterial strain, designated CHR27T, was isolated and characterized by using the polyphasic taxonomy approach. The results of phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of an up-to-date bacterial core gene set (92 protein clusters) indicated that strain CHR27T is affiliated with species in the genus Sphingobium. 16S rRNA gene sequence similarity results indicated that strain CHR27T was closely related to species of the genus Sphingobium (94.3-97.0 %), and had the highest sequence similarity to Sphingobium qiguonii X23T (97.0 %). Strain CHR27T showed 19.4-22.1 % digital DNA-DNA hybridization values and 73.2-74.8 % average nucleotide identity values with the strains of other Sphingobium species. Optimal growth occurred at 25 °C, pH 7.5 and in the absence of NaCl. The major fatty acids of strain CHR27T were C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The predominant hydroxy fatty acid was C14 : 0 2-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, two unidentified sphingoglycolipids and an unidentified aminophospholipid. Strain CHR27T contained spermidine as the major polyamine and putrescine as a minor component. The only isoprenoid quinone was ubiquinone-10. The genomic DNA G+C content of strain CHR27Twas 61.8 mol%. On the basis of the phylogenetic inference and phenotypic data, strain CHR27T was considered a representative of a novel species within the genus Sphingobium. The name Sphingobium fluviale sp. nov. is proposed, with strain CHR27T (=BCRC 81121T=LMG 30596T=KCTC 62510T) as the type strain.


Assuntos
Filogenia , Rios/microbiologia , Sphingomonadaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hidroxibutiratos/metabolismo , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Poliésteres/metabolismo , Putrescina/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espermidina/química , Sphingomonadaceae/isolamento & purificação , Taiwan , Ubiquinona/química
19.
Int J Syst Evol Microbiol ; 69(11): 3593-3598, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31460859

RESUMO

A Gram-stain-negative, yellow-pigmented, aerobic bacterial strain, designated LPB0140T, was isolated from sea water. The 16S rRNA gene sequence similarity analysis demonstrated that the closest relative of the isolate is Sphingorhabdus contaminans (96.4 %), but the new isolate formed an independent phyletic line within the genus Sphingorhabdus. Its genome is composed of a circular chromosome of 2.53 Mb with DNA G+C content of 46.1 mol%. The genome includes 2359 protein-coding genes, and two copies of rRNA operons. Strain LPB0140T possessed C14 : 0 2-OH, C16 : 1ω7c and/or C16 : 1ω6c, and C18 : 1ω7c and/or C18 : 1ω6c as the major cellular fatty acids and Q-10 as the isoprenoid quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, and sphingoglycolipid, but phosphatidylmonomethylethanolamine and phosphatidyldimethylethanolamine were also detected as minor polar lipids. The chemotaxonomic properties and enzymatic activities of the novel isolate clearly differed from those of its closest relatives. Thus, based on the phylogenetic and phenotypic data presented in this study, strain LPB0140T should be classified as a novel species in the genus Sphingorhabdus. The type strain is LPB0140T (=KACC18891T=JCM31568T).


Assuntos
Filogenia , Água do Mar/microbiologia , Sphingomonadaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Sphingomonadaceae/isolamento & purificação , Ubiquinona/análogos & derivados , Ubiquinona/química
20.
Int J Syst Evol Microbiol ; 69(10): 3287-3292, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31355742

RESUMO

The taxonomic status of a Gram-reaction-negative, aerobic, motile, rod-shaped bacterium, designated strain GH3-15T, was examined by a polyphasic approach. The strain, which was isolated from the rhizosphere mudflat of a halophyte at the seashore of Gangwha Island, Republic of Korea, was found to belong to the family Erythrobacteraceae based on 16S rRNA gene sequences. The closest phylogenetic neighbour was Erythrobacter xanthus SM1501T (98.3 % sequence similarity). Levels of 16S rRNA gene sequence similarity of strain GH3-15T to other members of the family Erythrobacteracae were <97.1 %. The respiratory quinone was Q-10. The major fatty acids were C17 : 1ω6c, C18 : 1ω7c, C15 : 0 2-OH, 11-methyl C18 : 1ω7c and C17 : 0. The polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. The novel isolate exhibited growth at 20-40 °C, at pH 5-9, and in the presence of 1-7 % (w/v) NaCl. DNA relatedness between strain GH3-15T and its closet relative was 32.9±8.8 %. On the basis of phenotypic, chemotaxonomic and DNA-DNA hybridization data, in addition to a distinct phylogenetic position, strain GH3-15T (=KCTC 62380T=JCM 32445T) represents a novel species of the genus Erythrobacter, for which the name Erythrobactersuaedae sp. nov. is proposed.


Assuntos
Chenopodiaceae/microbiologia , Filogenia , Rizosfera , Plantas Tolerantes a Sal/microbiologia , Água do Mar/microbiologia , Sphingomonadaceae/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Ilhas , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Sphingomonadaceae/isolamento & purificação , Ubiquinona/análogos & derivados , Ubiquinona/química
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