| proposal of the genus sphingomonas sensu stricto and three new genera, sphingobium, novosphingobium and sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. | phylogenetic analyses of 16s rrna gene sequences by distance matrix and parsimony methods indicated that the currently known species of the genus sphingomonas can be divided into four clusters. some chemotaxonomic and phenotypic differences were noted among these clusters. three new genera, sphingobium, novosphingobium and sphingopyxis, are proposed in addition to the genus sphingomonas sensu stricto. the genus sphingobium is proposed to accommodate sphingomonas chlorophenolica, sphingomonas her ... | 2001 | 11491340 |
| the unique aromatic catabolic genes in sphingomonads degrading polycyclic aromatic hydrocarbons (pahs). | many members of the sphingomonad genus isolated from different geological areas can degrade a wide variety of polycyclic aromatic hydrocarbons (pahs) and related compounds. these sphingomonads such as sphingobium yanoikuyae strain b1, novosphingobium aromaticivorans strain f199, and sphingobium sp. strain p2 have been found to possess a unique group of genes for aromatic degradation, which are distantly related with those in pseudomonads and other genera reported so far both in sequence homology ... | 2003 | 12682862 |
| sphingobium amiense sp. nov., a novel nonylphenol-degrading bacterium isolated from a river sediment. | a nonylphenol-degrading bacterial strain (yt(t)) was isolated previously from a river sediment sample obtained in ami-machi, ibaraki, japan, and identified as a sphingomonas species. in this study, the taxonomic relationship between strain yt(t), a recently described nonylphenol-degrading strain, sphingomonas cloacae, and sphingobium yanoikuyae, which is phylogenetically related, was examined. their phenotypic characteristics were compared and levels of dna-dna relatedness between these strains ... | 2003 | 14657143 |
| effect of sphingobium yanoikuyae b1 inoculation on bacterial community dynamics and polycyclic aromatic hydrocarbon degradation in aged and freshly pah-contaminated soils. | sphingobium yanoikuyae b1 is able to degrade a range of polycyclic aromatic hydrocarbons (pahs) and as a sphingomonad belongs to one of the dominant genera found in pah-contaminated soils. we examined the ecological effect that soil inoculation with s. yanoikuyae b1 has on the native bacterial community in three different soils: aged pah-contaminated soil from an industrial site, compost freshly contaminated with pahs and un-contaminated compost. survival of s. yanoikuyae b1 was dependent on the ... | 2006 | 16524654 |
| autecological properties of soil sphingomonads involved in the degradation of polycyclic aromatic hydrocarbons. | autecological properties that are thought to be important for polycyclic aromatic hydrocarbon (pah)-degradation by bacteria in contaminated soils include the ability to utilize a broad range of carbon sources, efficient biofilm formation, cell-surface hydrophobicity, surfactant production, motility, and chemotaxis. sphingomonas species are common pah-degraders, and a selection of pah-degrading sphingomonad strains isolated from contaminated soils was therefore characterized in terms of these pro ... | 2006 | 16568318 |
| effect of inoculum pretreatment on survival, activity and catabolic gene expression of sphingobium yanoikuyae b1 in an aged polycyclic aromatic hydrocarbon-contaminated soil. | the survival and effectiveness of a bioaugmentation strain in its target environment depend not only on physicochemical parameters in the soil but also on the physiological state of the inoculated organism. this study examined the effect of variations in inoculum pretreatment on the survival, metabolic activity (measured as rrna content) and polycyclic aromatic hydrocarbon (pah)-catabolic gene expression of sphingobium yanoikuyae b1 in an aged pah-contaminated soil. rna denaturing gradient gel e ... | 2006 | 17117981 |
| purification, characterization, and crystallization of the components of a biphenyl dioxygenase system from sphingobium yanoikuyae b1. | sphingobium yanoikuyae b1 initiates the catabolism of biphenyl by adding dioxygen to the aromatic nucleus to form (+)-cis-(2r, 3s)-dihydroxy-1-phenylcyclohexa-4,6-diene. the present study focuses on the biphenyl 2,3-dioxygenase system, which catalyzes the dioxygenation reaction. this enzyme has been shown to have a broad substrate range, catalyzing the dioxygenation of not only biphenyl, but also three- and four-ring polycyclic aromatic hydrocarbons. extracts prepared from biphenyl-grown b1 cell ... | 2007 | 17211635 |
| structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from sphingobium yanoikuyae b1. | the initial step involved in oxidative hydroxylation of monoaromatic and polyaromatic compounds by the microorganism sphingobium yanoikuyae strain b1 (b1), previously known as sphingomonas yanoikuyae strain b1 and beijerinckia sp. strain b1, is performed by a set of multiple terminal rieske non-heme iron oxygenases. these enzymes share a single electron donor system consisting of a reductase and a ferredoxin (bpdo-fb1). one of the terminal rieske oxygenases, biphenyl 2,3-dioxygenase (bpdo-ob1), ... | 2007 | 17349044 |
| identification, cloning, and characterization of a multicomponent biphenyl dioxygenase from sphingobium yanoikuyae b1. | sphingobium yanoikuyae b1 utilizes both polycyclic aromatic hydrocarbons (biphenyl, naphthalene, and phenanthrene) and monocyclic aromatic hydrocarbons (toluene, m- and p-xylene) as its sole source of carbon and energy for growth. the majority of the genes for these intertwined monocyclic and polycyclic aromatic pathways are grouped together on a 39 kb fragment of chromosomal dna. however, this gene cluster is missing several genes encoding essential enzymatic steps in the aromatic degradation p ... | 2007 | 17647036 |
| degradation of bis(4-hydroxyphenyl)methane (bisphenol f) by sphingobium yanoikuyae strain fm-2 isolated from river water. | three bacteria capable of utilizing bis(4-hydroxyphenyl)methane (bisphenol f [bpf]) as the sole carbon source were isolated from river water, and they all belonged to the family sphingomonadaceae. one of the isolates, designated sphingobium yanoikuyae strain fm-2, at an initial cell density of 0.01 (optical density at 600 nm) completely degraded 0.5 mm bpf within 9 h without any lag period under inductive conditions. degradation assays of various bisphenols revealed that the bpf-metabolizing sys ... | 2008 | 18024680 |
| effectiveness of bacterial inoculum and mangrove plants on remediation of sediment contaminated with polycyclic aromatic hydrocarbons. | the remediation of mangrove sediment contaminated with mixed polycyclic aromatic hydrocarbons (pahs) having 3-, 4- and 5-rings by natural attenuation, bioaugmentation, phytoremediation and its combination was compared by greenhouse microcosm studies. at days 90 and 154, the decreases of pahs in contaminated mangrove sediment by phytoremediation, planted with one-year old aegiceras corniculatum, and bioaugmentation, the inoculation of pah-degrading bacterial strains isolated from mangrove sedimen ... | 2008 | 18374368 |
| characterization of two compatible small plasmids from sphingobium yanoikuyae. | we isolated and characterized two small cryptic indigenous plasmids, pyan-1 (4,896 bp) and pyan-2 (4,687 bp), from sphingobium yanoikuyae, and developed a versatile system that permitted genetic manipulation of the genus sphingomonas. nucleotide sequencing of both plasmids revealed that they contained moba, mobs, and repa genes, which are predicted to encode proteins associated with mobilization and replication, in common. transformation with each plasmid harboring the antibiotic resistance gene ... | 2008 | 18391447 |
| one-way biohydrogen transfer for oxidation of sec-alcohols. | quasi-irreversible oxidation of sec-alcohols was achieved via biocatalytic hydrogen transfer reactions using alcohol dehydrogenases employing selected ketones as hydrogen acceptors, which can only be reduced but not oxidized. thus, only 1 equiv of oxidant was required instead of a large excess. for the oxidation of both isomers of methylcarbinols a single nonstereoselective short-chain dehydrogenase/reductase from sphingobium yanoikuyae was identified and overexpressed in e. coli. | 2008 | 18459797 |
| bacterial diversity of a consortium degrading high-molecular-weight polycyclic aromatic hydrocarbons in a two-liquid phase biosystem. | high-molecular-weight (hmw) polycyclic aromatic hydrocarbons (pahs) are pollutants that persist in the environment due to their low solubility in water and their sequestration by soil and sediments. although several pah-degrading bacterial species have been isolated, it is not expected that a single isolate would exhibit the ability to degrade completely all pahs. a consortium composed of different microorganisms can better achieve this. two-liquid phase (tlp) culture systems have been developed ... | 2009 | 18615233 |
| phenanthrene metabolites bound to soil organic matter by birnessite following partial biodegradation. | the hypothesis that phenanthrene, an aromatic compound without a hydroxyl group, can form nonextractable residues in soil with the aid of phenanthrene-biodegrading bacteria and birnessite was tested. the mutant strain sphingobium yanoikuyae b8/36 successfully accumulated cis-phenanthrene dihydrodiol, and the intermediate was readily radicalized and coupled into soil organic matter in the presence of birnessite. phenanthrene and the intermediate disappeared from the soil in 96 h in the presence o ... | 2009 | 19125546 |
| characterization of a ring-hydroxylating dioxygenase from phenanthrene-degrading sphingomonas sp. strain lh128 able to oxidize benz[a]anthracene. | sphingomonas sp. strain lh128 was isolated from a polycyclic aromatic hydrocarbon (pah)-contaminated soil using phenanthrene as the sole source of carbon and energy. a dioxygenase complex, phna1fa2f, encoding the alpha and beta subunit of a terminal dioxygenase responsible for the initial attack on pahs, was identified and isolated from this strain. phna1f showed 98%, 78%, and 78% identity to the alpha subunit of pah dioxygenase from novosphingobium aromaticivorans strain f199, sphingomonas sp. ... | 2009 | 19172265 |
| biodegradation of bisphenol a and bisphenol f in the rhizosphere sediment of phragmites australis. | the accelerated removal of bisphenols a and f (bpa, bpf) was observed in the rhizosphere sediment of phragmites australis, while they persisted in the absence of p. australis. a bpa-degrading bacterium, novosphingobium sp. strain tya-1, and a bpf-degrading bacterium, sphingobium yanoikuyae strain tyf-1, were isolated from the rhizosphere of p. australis. the results suggested that interactions between p. australis and these bacteria can accelerate the removal of bisphenols from sediment. | 2009 | 19619863 |
| detection of iron-depositing pedomicrobium species in native biofilms from the odertal national park by a new, specific fish probe. | iron-depositing bacteria play an important role in technical water systems (water wells, distribution systems) due to their intense deposition of iron oxides and resulting clogging effects. pedomicrobium is known as iron- and manganese-oxidizing and accumulating bacterium. the ability to detect and quantify members of this species in biofilm communities is therefore desirable. in this study the fluorescence in situ hybridization (fish) method was used to detect pedomicrobium in iron and manganes ... | 2009 | 19638289 |
| sphingobium scionense sp. nov., an aromatic hydrocarbon-degrading bacterium isolated from contaminated sawmill soil. | this study characterized strain wp01(t), a gram-staining-negative, rod-shaped, aerobic bacterium isolated from a polycyclic aromatic hydrocarbon-contaminated soil in new zealand. strain wp01(t) shared many characteristics of the genus sphingobium: the predominant respiratory quinone (89 %) was ubiquinone with ten isoprene units (q-10); the major fatty acids were c(18 : 1)omega7c, c(16 : 1)omega7c, c(16 : 0) and c(14 : 0) 2-oh; spermidine was the major polyamine; the dna g+c content was 63.8 mol% ... | 2010 | 19651723 |
| genome sequence of sphingobium yanoikuyae xldn2-5, an efficient carbazole-degrading strain. | sphingobium yanoikuyae xldn2-5 is an efficient carbazole-degrading strain. carbazole-degrading genes are accompanied on both sides by two copies of is6100 elements. here, we describe the draft genome sequence of strain xldn2-5, which may provide important clues as to how it recruited exogenous genes to establish pathways to degrade the xenobiotics. | 2011 | 22038966 |
| whole genome sequencing and analysis reveal insights into the genetic structure, diversity and evolutionary relatedness of luxi and luxr homologs in bacteria belonging to the sphingomonadaceae family. | here we report the draft genomes and annotation of four n-acyl homoserine lactone (ahl)-producing members from the family sphingomonadaceae. comparative genomic analyses of 62 sphingomonadaceae genomes were performed to gain insights into the distribution of the canonical luxi/r-type quorum sensing (qs) network within this family. forty genomes contained at least one luxr homolog while the genome of sphingobium yanoikuyae b1 contained seven open reading frames (orfs) that have significant homolo ... | 2014 | 25621282 |
| carotenoids play a positive role in the degradation of heterocycles by sphingobium yanoikuyae. | microbial oxidative degradation is a potential way of removing pollutants such as heterocycles from the environment. during this process, reactive oxygen species or other oxidants are inevitably produced, and may cause damage to dna, proteins, and membranes, thereby decreasing the degradation rate. carotenoids can serve as membrane-integrated antioxidants, protecting cells from oxidative stress. | 2012 | 22745775 |
| cyp101j2, cyp101j3, and cyp101j4, 1,8-cineole-hydroxylating cytochrome p450 monooxygenases from sphingobium yanoikuyae strain b2. | we report the isolation and characterization of three new cytochrome p450 monooxygenases: cyp101j2, cyp101j3, and cyp101j4. these p450s were derived from sphingobium yanoikuyae b2, a strain that was isolated from activated sludge based on its ability to fully mineralize 1,8-cineole. genome sequencing of this strain in combination with purification of native 1,8-cineole-binding proteins enabled identification of 1,8-cineole-binding p450s. the p450 enzymes were cloned, heterologously expressed (n- ... | 2016 | 27590809 |
| analysis of a dna region from low-copy-number plasmid pyan-1 of sphingobium yanoikuyae responsible for plasmid stability. | we identified and analyzed a dna region that is required for the stable maintenance of plasmids in the genus sphingomonas. this dna fragment, a 244 bp, is localized in the upstream region of the repa gene of low-copy-number small plasmid pyan-1 (4896 bp) of sphingobium yanoikuyae. it has four inverted repeats and one direct repeat for possible secondary structures. we were able to stabilize not only another unstable plasmid, pyan-2, in the genus sphingomonas, but also the unstable plasmid psc101 ... | 2014 | 25036843 |
| dna regions responsible for maintenance of shingobium plasmid pyan-2. | we have identified and analyzed two dna regions responsible for stable maintenance of a plasmid in the genus sphingomonas and escherichia coli. a 37 bp fragment, upstream of the repa gene, is required for stable maintenance of the low-copy-number small plasmid pyan-2 (4,687 bp) from sphingobium yanoikuyae. it does not encode any significant protein sequence and has one direct repeat for possible secondary structures. moreover, a 70 bp fragment, upstream of the above sequence, completely stabiliz ... | 2014 | 24441514 |
| effect of high pressure on hydrocarbon-degrading bacteria. | the blowout of the deepwater horizon in the gulf of mexico in 2010 occurred at a depth of 1500 m, corresponding to a hydrostatic pressure of 15 mpa. up to now, knowledge about the impact of high pressure on oil-degrading bacteria has been scarce. to investigate how the biodegradation of crude oil and its components is influenced by high pressures, like those in deep-sea environments, hydrocarbon degradation and growth of two model strains were studied in high-pressure reactors. the alkane-degrad ... | 2014 | 25401077 |
| x-ray crystal structure of cytochrome p450 monooxygenase cyp101j2 from sphingobium yanoikuyae strain b2. | the cytochrome p450 monooxygenases (p450s) catalyze a vast array of oxygenation reactions that can be useful in biocatalytic applications. cyp101j2 from sphingobium yanoikuyae is a p450 that catalyzes the hydroxylation of 1,8-cineole. here we report the crystallization and x-ray structure elucidation of recombinant cyp101j2 to 1.8 å resolution. the cyp101j2 structure shows the canonical p450-fold and has an open conformation in the absence of substrate. analysis of the structure revealed that cy ... | 2016 | 27936485 |
| draft genome sequence of sphingobium yanoikuyae tj, a halotolerant di-n-butyl-phthalate-degrading bacterium. | sphingobium yanoikuyae tj is a halotolerant di-n-butyl-phthalate-degrading bacterium, isolated from the haihe estuary in bohai bay, tianjin, china. here, we report the 5.1-mb draft genome sequence of this strain, which will provide insights into the diversity of sphingobium spp. and the mechanism of phthalate ester degradation in the estuary. | 2016 | 27313307 |
| genome sequence of sphingobium yanoikuyae b1, a polycyclic aromatic hydrocarbon-degrading strain. | sphingobium yanoikuyae b1 can utilize biphenyl, naphthalene, phenanthrene, toluene, and m-/p-xylene as sole sources of carbon and energy. here, we present a 5.2-mb assembly of its genome. an analysis of the genome can provide insights into the mechanisms of polycyclic aromatic hydrocarbon (pah) degradation and potentially aid in bioremediation applications. | 2015 | 25657282 |
| experimental results and integrated modeling of bacterial growth on an insoluble hydrophobic substrate (phenanthrene). | metabolism of a low-solubility substrate is limited by dissolution and availability and can hardly be determined. we developed a numerical model for simultaneously calculating dissolution kinetics of such substrates and their metabolism and microbial growth (monod kinetics with decay) and tested it with three aerobic phenanthrene (phe) degraders: novosphingobium pentaromativorans us6-1, sphingomonas sp. epa505, and sphingobium yanoikuyae b1. phe was present as microcrystals, providing non-limiti ... | 2014 | 24967613 |
| sphingobium fontiphilum sp. nov., isolated from a freshwater spring. | to investigate the biodiversity of bacteria in the spring water of the chengcing lake park in taiwan, a gram-stain-negative, rod-shaped, non-motile, non-spore-forming and aerobic bacterial strain, designated strain chen16-4(t), was isolated and characterized in a taxonomic study using a polyphasic approach. phylogenetic analyses based on 16s rrna gene sequences showed that the closest relatives of strain chen16-4(t) were sphingobium amiense yt(t), sphingobium yanoikuyae gifu 9882(t) and sphingob ... | 2013 | 23024141 |
| sphingobium limneticum sp. nov. and sphingobium boeckii sp. nov., two freshwater planktonic members of the family sphingomonadaceae, and reclassification of sphingomonas suberifaciens as sphingobium suberifaciens comb. nov. | two novel chemo-organoheterotrophic members of the sphingomonadaceae were isolated from alpine and pre-alpine lakes. cells stained gram-negative, were motile and rod-shaped, and formed yellow, circular, convex colonies on different agar media. strains 301(t) and 469(t) were strictly aerobic, catalase- and oxidase-positive, and grew at temperatures between 10 and 40 °c (optimum, 28 °c), and at ph values between 5 and 10 (optimum, ph 7). both strains contained q-10 as the dominant quinone, sphingo ... | 2013 | 22561591 |
| sphingobium cupriresistens sp. nov., a copper-resistant bacterium isolated from copper mine soil, and emended description of the genus sphingobium. | a gram-negative, aerobic, copper-resistant bacterium, designated strain cu4(t), was isolated from copper mine soil in daye, china. phylogenetic analysis based on 16s rrna gene sequences showed highest similarity to sphingobium rhizovicinum cc-fh12-1(t) (98.4 %), followed by sphingobium francense sp+(t) (97.2 %), sphingobium japonicum ut26(t) (97.1 %), sphingobium abikonense nbrc 16140(t) (97.0 %), sphingobium xenophagum dsm 6383(t) (96.9 %) and sphingobium yanoikuyae dsm 7462(t) (95.5 %). the ma ... | 2013 | 22544784 |