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Jindong Zhao - One of the best experts on this subject based on the ideXlab platform.
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microcystin lr degradation and gene regulation of microcystin degrading Novosphingobium sp thn1 at different carbon concentrations
Frontiers in Microbiology, 2019Co-Authors: Juanping Wang, Chang Wang, Mengyuan Shen, Jindong Zhao, Qi Li, Jionghui Li, Tao LiAbstract:The bacterium Novosphingobium sp. THN1 (THN1) is capable of degrading microcystin-LR (MC-LR). To study the ability of THN1 to degrade MC-LR and its possible mechanism(s) of regulation, we analyzed the effect of carbon concentrations on the degradation process. The MC-LR degradation rate peaked early and then declined during MC-LR biodegradation. Decreased levels of carbon in the medium caused the degradation peak to occur earlier. The expression of the functional gene mlrA, encoding a microcystinase, showed a similar trend to the MC-LR degradation rate at various carbon concentrations (r2 = 0.717, p < 0.05), suggesting that regulation of mlrA expression may play an important role in MC-LR degradation by THN1. The total bacterial biomass decreased when the carbon source was limited and did not correlate with the MC-LR degradation rate. Transcriptomic analysis showed that MC-LR degradation differentially regulated 62.16% (2597/4178) of THN1 genes. A considerable number of differentially expressed genes (DEGs) during MC-LR degradation encoded proteins related to carbon-, nitrogen- and amino acid-related pathways. At 2 h of MC-LR degradation, most DEGs (29/33) involved in carbon and nitrogen metabolism were downregulated. This indicated that MC-LR may regulate carbon and nitrogen pathways of Novosphingobium sp. THN1. KEGG pathway analysis indicated that the upregulated DEGs during MC-LR degradation were mainly related to amino acid degradation and substrate metabolism pathways. Particularly, we detected increased expression of glutathione metabolism-related genes from transcriptomic data at 2 h of MC-LR degradation compared with the gene expression of 0 h, such as GST family protein, glutathione peroxidase, S-(hydroxymethyl) glutathione dehydrogenase, and glutathione-dependent disulfide-bond oxidoreductase that have been reported to be involved in microcystin degradation.
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comparative genomics of degradative Novosphingobium strains with special reference to microcystin degrading Novosphingobium sp thn1
Frontiers in Microbiology, 2018Co-Authors: Juanping Wang, Chang Wang, Peng Bai, Mengyuan Shen, Jindong ZhaoAbstract:Bacteria in genus Novosphingobium associated with biodegradation of substrates are prevalent in environments such as lakes, soil, sea, wood and sediments. To better understand the characteristics linked to their wide distribution and metabolic versatility, we report the whole genome sequence of Novosphingobium sp. THN1, a microcystin-degrading strain previously isolated by Jiang et al. (2011) from cyanobacteria-blooming water samples from Lake Taihu, China. We performed a genomic comparison analysis of Novosphingobium sp. THN1 with 21 other degradative Novosphingobium strains downloaded from GenBank. Phylogenetic trees were constructed using 16S rRNA genes, core genes, protein-coding sequences, and average nucleotide identity of whole genomes. Orthologous protein analysis showed that the 22 genomes contained 674 core genes and each strain contained a high proportion of distributed genes that are shared by a subset of strains. Inspection of their genomic plasticity revealed a high number of insertion sequence elements and genomic islands that were distributed on both chromosomes and plasmids. We also compared the predicted functional profiles of the Novosphingobium protein-coding genes. The flexible genes and all protein-coding genes produced the same heatmap clusters. The COG annotations were used to generate a dendrogram correlated with the compounds degraded. Furthermore, the metabolic profiles predicted from KEGG pathways showed that the majority of genes involved in central carbon metabolism, nitrogen, phosphate, sulfate metabolism, energy metabolism and cell mobility (above 62.5%) are located on chromosomes. Whereas, a great many of genes involved in degradation pathways (21-50%) are located on plasmids. The abundance and distribution of aromatics-degradative mono- and dioxygenases varied among 22 Novosphingoibum strains. Comparative analysis of the microcystin-degrading mlr gene cluster provided evidence for horizontal acquisition of this cluster. The Novosphingobium sp. THN1 genome sequence contained all the functional genes crucial for microcystin degradation and the mlr gene cluster shared high sequence similarity (≥85%) with the sequences of other microcystin-degrading genera isolated from cyanobacteria-blooming water. Our results indicate that Novosphingobium species have high genomic and functional plasticity, rearranging their genomes according to environment variations and shaping their metabolic profiles by the substrates they are exposed to, to better adapt to their environments.
Kae Kyoung Kwon - One of the best experts on this subject based on the ideXlab platform.
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proteomic characterization of the outer membrane vesicle of the halophilic marine bacterium Novosphingobium pentaromativorans us6 1
Journal of Microbiology, 2017Co-Authors: Sung Ho Yun, Kae Kyoung Kwon, Yong Min Kwon, Sang-jin Kim, Sangyeop Lee, Chiwon Choi, Ha Young Lee, Sangmi Jun, Gunhwa Kim, Seung Il KimAbstract:Novosphingobium pentaromativorans US6-1 is a Gram-negative halophilic marine bacterium able to utilize several polycyclic aromatic hydrocarbons such as phenanthrene, pyrene, and benzo[a]pyrene. In this study, using transmission electron microscopy, we confirmed that N. pentaromativorans US6-1 produces outer membrane vesicles (OMVs). N. pentaromativorans OMVs (hereafter OMVNovo) are spherical in shape, and the average diameter of OMVNovo is 25-70 nm. Proteomic analysis revealed that outer membrane proteins and periplasmic proteins of N. pentaromativorans are the major protein components of OMVNovo. Comparative proteomic analysis with the membrane-associated protein fraction and correlation analysis demonstrated that the outer membrane proteins of OMVNovo originated from the membrane- associated protein fraction. To the best of our knowledge, this study is the first to characterize OMV purified from halophilic marine bacteria.
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SHORT GENOME REPORT Open Access Complete genome sequence of
2016Co-Authors: Novosphingobium Pentaromativorans, Kae Kyoung Kwon, Dong Hee Choi, Yong Min Kwon, Sang-jin KimAbstract:Novosphingobium pentaromativorans US6-1T is a species in the family Sphingomonadaceae. According to the phylogenetic analysis based on 16S rRNA gene sequence of the N. pentaromativorans US6-1T and nine genome-sequenced strains in the genus Novosphingobium, the similarity ranged from 93.9 to 99.9 % and the highest similarity was found with Novosphingobium sp. PP1Y (99.9 %), whereas the ANI value based on genomes ranged from 70.9 to 93 % and the highest value was 93 %. This microorganism was isolated from muddy coastal bay sediments where the environment is heavily polluted by polycyclic aromatic hydrocarbons (PAHs). It was previously shown to be capable of degrading multiple PAHs, including benzo[a]pyrene. To further understand the PAH biodegradation pathways the previous draft genome of this microorganism was revised to obtain a complete genome using Illumina MiSeq and PacBio platform. The genome of strain US6-1T consists of 5,457,578 bp, which includes the 3,979,506 bp chromosome and five megaplasmids. It comprises 5110 protein-coding genes and 82 RNA genes. Here, we provide an analysis of the complete genome sequence which enables the identification of new characteristics of this strain
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Complete genome sequence of Novosphingobium pentaromativorans US6-1 T
Standards in genomic sciences, 2015Co-Authors: Dong Hee Choi, Kae Kyoung Kwon, Yong Min Kwon, Sang-jin KimAbstract:Novosphingobium pentaromativorans US6-1T is a species in the family Sphingomonadaceae. According to the phylogenetic analysis based on 16S rRNA gene sequence of the N. pentaromativorans US6-1T and nine genome-sequenced strains in the genus Novosphingobium, the similarity ranged from 93.9 to 99.9 % and the highest similarity was found with Novosphingobium sp. PP1Y (99.9 %), whereas the ANI value based on genomes ranged from 70.9 to 93 % and the highest value was 93 %. This microorganism was isolated from muddy coastal bay sediments where the environment is heavily polluted by polycyclic aromatic hydrocarbons (PAHs). It was previously shown to be capable of degrading multiple PAHs, including benzo[a]pyrene. To further understand the PAH biodegradation pathways the previous draft genome of this microorganism was revised to obtain a complete genome using Illumina MiSeq and PacBio platform. The genome of strain US6-1T consists of 5,457,578 bp, which includes the 3,979,506 bp chromosome and five megaplasmids. It comprises 5110 protein-coding genes and 82 RNA genes. Here, we provide an analysis of the complete genome sequence which enables the identification of new characteristics of this strain.
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genome sequence of benzo a pyrene degrading bacterium Novosphingobium pentaromativorans us6 1
Journal of Bacteriology, 2012Co-Authors: Yuanrong Luo, Sang-jin Kim, Sung Gyun Kang, Miree Kim, Junghyun Lee, Kae Kyoung KwonAbstract:Novosphingobium pentaromativorans US6-1 showed a good ability to degrade high-molecular-weight polycyclic aromatic hydrocarbons. We report the draft genome sequence of strain US6-1, which contains a main chromosome (5,096,413 bp, G+C content of 63.1%) and two plasmids (188,476 and 60,085 bp). The majority of the aromatic-hydrocarbon-degrading genes are encoded in the larger plasmid.
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Novosphingobium pentaromativorans sp nov a high molecular mass polycyclic aromatic hydrocarbon degrading bacterium isolated from estuarine sediment
International Journal of Systematic and Evolutionary Microbiology, 2004Co-Authors: Jae Hak Sohn, Kae Kyoung Kwon, Jihyun Kang, Hongbae JungAbstract:A Gram-negative, yellow-pigmented, halophilic bacterial strain US6-1T, which degrades high-molecular-mass polycyclic aromatic hydrocarbons of two to five rings, was isolated from muddy sediment of Ulsan Bay, Republic of Korea. The 16S rRNA gene of the isolate showed high sequence similarity to Novosphingobium subarcticum (96·23 %) and Sphingopyxis alaskensis (96·18 %); however, the isolate formed a distinct phyletic line within the genus Novosphingobium. DNA–DNA relatedness between US6-1T and the closest strain N. subarcticum revealed that strain US6-1T was independent from this species. Isolate US6-1T had ubiquinone 10 and a DNA G+C ratio of 61·1 mol%. Major fatty acids were octadecanoic acid (18 : 1ω7), hexadecanoic acid (16 : 1ω7) and 2-hydroxy-myristic acid (14 : 0 2-OH). On the basis of polyphasic taxonomic evidence, strain US6-1T is proposed to represent a novel species in the genus Novosphingobium for which the name Novosphingobium pentaromativorans sp. nov. is proposed. The type strain is US6-1T (=KCTC 10454T=JCM 12182T).
Sang-jin Kim - One of the best experts on this subject based on the ideXlab platform.
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proteomic characterization of the outer membrane vesicle of the halophilic marine bacterium Novosphingobium pentaromativorans us6 1
Journal of Microbiology, 2017Co-Authors: Sung Ho Yun, Kae Kyoung Kwon, Yong Min Kwon, Sang-jin Kim, Sangyeop Lee, Chiwon Choi, Ha Young Lee, Sangmi Jun, Gunhwa Kim, Seung Il KimAbstract:Novosphingobium pentaromativorans US6-1 is a Gram-negative halophilic marine bacterium able to utilize several polycyclic aromatic hydrocarbons such as phenanthrene, pyrene, and benzo[a]pyrene. In this study, using transmission electron microscopy, we confirmed that N. pentaromativorans US6-1 produces outer membrane vesicles (OMVs). N. pentaromativorans OMVs (hereafter OMVNovo) are spherical in shape, and the average diameter of OMVNovo is 25-70 nm. Proteomic analysis revealed that outer membrane proteins and periplasmic proteins of N. pentaromativorans are the major protein components of OMVNovo. Comparative proteomic analysis with the membrane-associated protein fraction and correlation analysis demonstrated that the outer membrane proteins of OMVNovo originated from the membrane- associated protein fraction. To the best of our knowledge, this study is the first to characterize OMV purified from halophilic marine bacteria.
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SHORT GENOME REPORT Open Access Complete genome sequence of
2016Co-Authors: Novosphingobium Pentaromativorans, Kae Kyoung Kwon, Dong Hee Choi, Yong Min Kwon, Sang-jin KimAbstract:Novosphingobium pentaromativorans US6-1T is a species in the family Sphingomonadaceae. According to the phylogenetic analysis based on 16S rRNA gene sequence of the N. pentaromativorans US6-1T and nine genome-sequenced strains in the genus Novosphingobium, the similarity ranged from 93.9 to 99.9 % and the highest similarity was found with Novosphingobium sp. PP1Y (99.9 %), whereas the ANI value based on genomes ranged from 70.9 to 93 % and the highest value was 93 %. This microorganism was isolated from muddy coastal bay sediments where the environment is heavily polluted by polycyclic aromatic hydrocarbons (PAHs). It was previously shown to be capable of degrading multiple PAHs, including benzo[a]pyrene. To further understand the PAH biodegradation pathways the previous draft genome of this microorganism was revised to obtain a complete genome using Illumina MiSeq and PacBio platform. The genome of strain US6-1T consists of 5,457,578 bp, which includes the 3,979,506 bp chromosome and five megaplasmids. It comprises 5110 protein-coding genes and 82 RNA genes. Here, we provide an analysis of the complete genome sequence which enables the identification of new characteristics of this strain
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Complete genome sequence of Novosphingobium pentaromativorans US6-1 T
Standards in genomic sciences, 2015Co-Authors: Dong Hee Choi, Kae Kyoung Kwon, Yong Min Kwon, Sang-jin KimAbstract:Novosphingobium pentaromativorans US6-1T is a species in the family Sphingomonadaceae. According to the phylogenetic analysis based on 16S rRNA gene sequence of the N. pentaromativorans US6-1T and nine genome-sequenced strains in the genus Novosphingobium, the similarity ranged from 93.9 to 99.9 % and the highest similarity was found with Novosphingobium sp. PP1Y (99.9 %), whereas the ANI value based on genomes ranged from 70.9 to 93 % and the highest value was 93 %. This microorganism was isolated from muddy coastal bay sediments where the environment is heavily polluted by polycyclic aromatic hydrocarbons (PAHs). It was previously shown to be capable of degrading multiple PAHs, including benzo[a]pyrene. To further understand the PAH biodegradation pathways the previous draft genome of this microorganism was revised to obtain a complete genome using Illumina MiSeq and PacBio platform. The genome of strain US6-1T consists of 5,457,578 bp, which includes the 3,979,506 bp chromosome and five megaplasmids. It comprises 5110 protein-coding genes and 82 RNA genes. Here, we provide an analysis of the complete genome sequence which enables the identification of new characteristics of this strain.
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genome sequence of benzo a pyrene degrading bacterium Novosphingobium pentaromativorans us6 1
Journal of Bacteriology, 2012Co-Authors: Yuanrong Luo, Sang-jin Kim, Sung Gyun Kang, Miree Kim, Junghyun Lee, Kae Kyoung KwonAbstract:Novosphingobium pentaromativorans US6-1 showed a good ability to degrade high-molecular-weight polycyclic aromatic hydrocarbons. We report the draft genome sequence of strain US6-1, which contains a main chromosome (5,096,413 bp, G+C content of 63.1%) and two plasmids (188,476 and 60,085 bp). The majority of the aromatic-hydrocarbon-degrading genes are encoded in the larger plasmid.
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enantioselective hydrolysis of racemic epichlorohydrin using an epoxide hydrolase from Novosphingobium aromaticivorans
Journal of Bioscience and Bioengineering, 2010Co-Authors: Junghee Woo, Jihyun Kang, Sang-jin Kim, Youngok Hwang, Hyun Sook Lee, Sung Gyun KangAbstract:Previously we reported that an epoxide hydrolase (EHase) from Novosphingobium aromaticivorans could preferentially hydrolyze (R)-styrene oxide. In this study, we demonstrate that the purified NEH could be also effective in chiral resolution of racemic epichlorohydrin (ECH). Particularly, the purified NEH showed excellent hydrolyzing activity toward ECH to complete the reaction at a short period of incubation time. Enantiopure (S)-ECH could be obtained with a high enantiopurity of more than 99.99% enantiomeric excess (ee) and yield of 20.7% (theoretical, 50%). The chiral resolution of the purified NEH toward ECH was not susceptible to substrate inhibition by 500 mM racemic ECH.
Juanping Wang - One of the best experts on this subject based on the ideXlab platform.
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microcystin lr degradation and gene regulation of microcystin degrading Novosphingobium sp thn1 at different carbon concentrations
Frontiers in Microbiology, 2019Co-Authors: Juanping Wang, Chang Wang, Mengyuan Shen, Jindong Zhao, Qi Li, Jionghui Li, Tao LiAbstract:The bacterium Novosphingobium sp. THN1 (THN1) is capable of degrading microcystin-LR (MC-LR). To study the ability of THN1 to degrade MC-LR and its possible mechanism(s) of regulation, we analyzed the effect of carbon concentrations on the degradation process. The MC-LR degradation rate peaked early and then declined during MC-LR biodegradation. Decreased levels of carbon in the medium caused the degradation peak to occur earlier. The expression of the functional gene mlrA, encoding a microcystinase, showed a similar trend to the MC-LR degradation rate at various carbon concentrations (r2 = 0.717, p < 0.05), suggesting that regulation of mlrA expression may play an important role in MC-LR degradation by THN1. The total bacterial biomass decreased when the carbon source was limited and did not correlate with the MC-LR degradation rate. Transcriptomic analysis showed that MC-LR degradation differentially regulated 62.16% (2597/4178) of THN1 genes. A considerable number of differentially expressed genes (DEGs) during MC-LR degradation encoded proteins related to carbon-, nitrogen- and amino acid-related pathways. At 2 h of MC-LR degradation, most DEGs (29/33) involved in carbon and nitrogen metabolism were downregulated. This indicated that MC-LR may regulate carbon and nitrogen pathways of Novosphingobium sp. THN1. KEGG pathway analysis indicated that the upregulated DEGs during MC-LR degradation were mainly related to amino acid degradation and substrate metabolism pathways. Particularly, we detected increased expression of glutathione metabolism-related genes from transcriptomic data at 2 h of MC-LR degradation compared with the gene expression of 0 h, such as GST family protein, glutathione peroxidase, S-(hydroxymethyl) glutathione dehydrogenase, and glutathione-dependent disulfide-bond oxidoreductase that have been reported to be involved in microcystin degradation.
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comparative genomics of degradative Novosphingobium strains with special reference to microcystin degrading Novosphingobium sp thn1
Frontiers in Microbiology, 2018Co-Authors: Juanping Wang, Chang Wang, Peng Bai, Mengyuan Shen, Jindong ZhaoAbstract:Bacteria in genus Novosphingobium associated with biodegradation of substrates are prevalent in environments such as lakes, soil, sea, wood and sediments. To better understand the characteristics linked to their wide distribution and metabolic versatility, we report the whole genome sequence of Novosphingobium sp. THN1, a microcystin-degrading strain previously isolated by Jiang et al. (2011) from cyanobacteria-blooming water samples from Lake Taihu, China. We performed a genomic comparison analysis of Novosphingobium sp. THN1 with 21 other degradative Novosphingobium strains downloaded from GenBank. Phylogenetic trees were constructed using 16S rRNA genes, core genes, protein-coding sequences, and average nucleotide identity of whole genomes. Orthologous protein analysis showed that the 22 genomes contained 674 core genes and each strain contained a high proportion of distributed genes that are shared by a subset of strains. Inspection of their genomic plasticity revealed a high number of insertion sequence elements and genomic islands that were distributed on both chromosomes and plasmids. We also compared the predicted functional profiles of the Novosphingobium protein-coding genes. The flexible genes and all protein-coding genes produced the same heatmap clusters. The COG annotations were used to generate a dendrogram correlated with the compounds degraded. Furthermore, the metabolic profiles predicted from KEGG pathways showed that the majority of genes involved in central carbon metabolism, nitrogen, phosphate, sulfate metabolism, energy metabolism and cell mobility (above 62.5%) are located on chromosomes. Whereas, a great many of genes involved in degradation pathways (21-50%) are located on plasmids. The abundance and distribution of aromatics-degradative mono- and dioxygenases varied among 22 Novosphingoibum strains. Comparative analysis of the microcystin-degrading mlr gene cluster provided evidence for horizontal acquisition of this cluster. The Novosphingobium sp. THN1 genome sequence contained all the functional genes crucial for microcystin degradation and the mlr gene cluster shared high sequence similarity (≥85%) with the sequences of other microcystin-degrading genera isolated from cyanobacteria-blooming water. Our results indicate that Novosphingobium species have high genomic and functional plasticity, rearranging their genomes according to environment variations and shaping their metabolic profiles by the substrates they are exposed to, to better adapt to their environments.
Peter Kampfer - One of the best experts on this subject based on the ideXlab platform.
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Novosphingobium lubricantis sp nov isolated from a coolant lubricant emulsion
International Journal of Systematic and Evolutionary Microbiology, 2018Co-Authors: Peter Kampfer, Hansjurgen Busse, Stefanie P GlaeserAbstract:A yellow-pigmented, Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain KSS165-70T) was isolated from a coolant lubricant emulsion. The 16S rRNA gene sequence analysis of strain KSS165-70T showed high sequence similarity to the type strains of Novosphingobium subterraneum (98.1 %), Novosphingobium lentum (97.9 %) and Novosphingobium taihuense (97.8 %). Sequence similarities to type strains of all other Novosphingobium species were below 97.5 %. Ubiquinone Q-10 was detected as the major respiratory quinone. The predominant fatty acid C18 : 1ω7c and the typical 2-hydroxy fatty acid C14 : 0 2-OH were detected. The polar lipid profile contained the major lipids diphosphatidylglycerol, phosphatedylethanolamine, sphingoglycolipid, phosphatidylcholine and two unidentified phospholipids. The polyamine pattern contained the major compound spermidine. Characterization by 16S rRNA gene sequence analysis, physiological parameters, pigment analysis, and ubiquinone, polar lipid and fatty acid composition revealed that strain KSS165-70T represents a new species of the genus Novosphingobium . For this reason, we propose the name Novosphingobium lubricantis sp. nov. with the type strain KSS165-70T (=CIP 111490T=CCM 8814T).
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Novosphingobium gossypii sp nov isolated from gossypium hirsutum
International Journal of Systematic and Evolutionary Microbiology, 2015Co-Authors: Peter Kampfer, Karin Martin, John A Mcinroy, Stefanie P GlaeserAbstract:A Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain JM-1396T) producing a yellow pigment, was isolated from the healthy internal stem tissue of post-harvest cotton (Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit at the E. V. Smith Research Center in Tallassee (Macon county), AL, USA. 16S rRNA gene sequence analysis of strain JM-1396T showed high sequence similarity values to the type strains of Novosphingobium mathurense, Novosphingobium panipatense (both 98.6 %) and Novosphingobium barchaimii (98.5 %); sequence similarities to all other type strains of species of the genus Novosphingobium were below 98.3 %. DNA–DNA pairing experiments of the DNA of strain JM-1396T and N. mathurense SM117T, N. panipatense SM16T and N. barchaimii DSM 25411T showed low relatedness values of 8 % (reciprocal 7 %), 24 % (reciprocal 26 %) and 19 % (reciprocal 25 %), respectively. Ubiquinone Q-10 was detected as the dominant quinone; the fatty acids C18 : 1ω7c (71.0 %) and the typical 2-hydroxy fatty acid, C14 : 0 2-OH (11.7 %), were detected as typical components. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. The polyamine pattern contained the major compound spermidine and only minor amounts of other polyamines. All these data revealed that strain JM-1396T represents a novel species of the genus Novosphingobium. For this reason we propose the name Novosphingobium gossypii sp. nov. with the type strain JM-1396T ( = LMG 28605T = CCM 8569T = CIP 110884T).
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proposal of Novosphingobium rhizosphaerae sp nov isolated from the rhizosphere
International Journal of Systematic and Evolutionary Microbiology, 2015Co-Authors: Peter Kampfer, Karin Martin, John A Mcinroy, Stefanie P GlaeserAbstract:A yellow, Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain JM-1T) was isolated from the rhizosphere of a field-grown Zea mays plant in Auburn, AL, USA. 16S rRNA gene sequence analysis of strain JM-1T showed high sequence similarity to the type strains of Novosphingobium capsulatum (98.9 %), Novosphingobium aromaticivorans (97.4 %), Novosphingobium subterraneum (97.3 %) and Novosphingobium taihuense (97.1 %); sequence similarities to all other type strains of species of the genus Novosphingobium were below 97.0 %. DNA–DNA hybridizations of strain JM-1T and N. capsulatum DSM 30196T, N. aromaticivorans SMCC F199T and N. subterraneum SMCC B0478T showed low similarity values of 33 % (reciprocal: 21 %), 14 % (reciprocal 16 %) and 36 % (reciprocal 38 %), respectively. Ubiquinone Q-10 was detected as the major respiratory quinone. The predominant fatty acid was C18 : 1ω7c (71.0 %) and the typical 2-hydroxy fatty acid C14 : 0 2-OH (11.7 %) was detected. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. Characterization by 16S rRNA gene sequence analysis, physiological parameters, pigment analysis, and ubiquinone, polar lipid and fatty acid composition revealed that strain JM-1T represents a novel species of the genus Novosphingobium . For this species we propose the name Novosphingobium rhizosphaerae sp. nov. with the type strain JM-1T ( = LMG 28479T = CCM 8547T).
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Novosphingobium aquaticum sp nov isolated from the humic matter rich bog lake grosse fuchskuhle
International Journal of Systematic and Evolutionary Microbiology, 2013Co-Authors: Stefanie P Glaeser, Hansjurgen Busse, Peter Kampfer, Kathrin Bolte, Hanspeter Grossart, Jens GlaeserAbstract:A yellow‐pigmented, Gram-negative rod, designated FNE08-86T, was isolated from subsurface water of the humic-matter-rich and almost-neutral north-east basin of the experimentally divided bog lake Grosse Fuchskuhle (Brandenburg, Germany). Analysis of the nearly full-length 16S rRNA gene sequence showed the highest 16S rRNA gene sequence similarity with Novosphingobium rosa IAM 14222T (96.3 %). Sequence similarities with all other members of the genus Novosphingobium species were <96 %, but phylogenetic tree construction clearly showed the placement of strain FNE08-86T within the genus Novosphingobium . The predominant fatty acids were C18 : 1ω7c and C16 : 0, and only a single 2-hydroxy fatty acid, C14 : 0 2-OH, was detected. The polar lipid profile revealed phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine as major compounds, with smaller amounts of sphingoglycolipid, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and several unidentified lipids. In the quinone system ubiquinone Q-10 was predominant and in the polyamine pattern spermidine was predominant. Characterization by genotypic, chemotaxonomic and phenotypic analysis indicated that strain FNE08-86T represents a novel species of the genus Novosphingobium , for which we propose the name Novosphingobium aquaticum sp. nov. (type strain FNE08-86T = DSM 25088T = CCM 7983T).
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Novosphingobium fuchskuhlense sp nov isolated from the north east basin of lake grosse fuchskuhle
International Journal of Systematic and Evolutionary Microbiology, 2013Co-Authors: Stefanie P Glaeser, Hansjurgen Busse, Peter Kampfer, Karin Martin, Kathrin Bolte, Hanspeter Grossart, Jens GlaeserAbstract:A yellow pigmented, Gram-negative, rod-shaped bacterium designated FNE08-7T was isolated from subsurface water of the north-east basin of the bog lake Grosse Fuchskuhle (Brandenburg, Germany). A first analysis of the nearly full-length 16S rRNA gene sequence analysis including environmental 16S rRNA gene sequences derived from freshwater ecosystems showed that strain FNE08-7T is the first cultured representative, to our knowledge, of the freshwater tribe Novo-A2. Further analysis indicates highest 16S rRNA gene sequence similarities to the type strains of Novosphingobium stygium (98.0 %) and Novosphingobium taihuense (97.4 %) and between 94.0 % and 96.9 % sequence similarity to other members of the genus Novosphingobium . Reconstruction of phylogenetic trees showed that strain FNE08-7T formed a distinct cluster with the type strains of N. stygium and N. taihuense supported by high bootstrap values. DNA–DNA hybridization of strain FNE08-7T with N. stygium SMCC B0712T and N. taihuense DSM 17507T revealed low similarity values of 18.4 % (reciprocal: 11.4 %) and 23.1 % (reciprocal: 54.2 %), respectively. The predominant fatty acid of the isolate is C18 : 1ω7c (56.4 %) and two characteristic 2-hydroxy fatty acids, C14 : 0 2-OH (16.5 %) and C15 : 0 2-OH (3.3 %) occur. Ubiquinone Q-10 is the major respiratory quinone. The predominant polar lipids are phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine and minor amounts of diphosphatidylglycerol. Spermidine is the predominant polyamine. Characterization by genotypic, chemotaxonomic and phenotypic analysis indicate that strain FNE08-7T represents a novel species of the genus Novosphingobium within the Alphaproteobacteria . Therefore, we propose the species Novosphingobium fuchskuhlense sp. nov., with FNE08-7T ( = DSM 25065T = CCM 7978T = CCUG 61508T) as the type strain.
