Publications
| Title | Abstract | Year(sorted ascending) Filter | PMID Filter |
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| proteins encoded by sphingomonas elodea atcc 31461 rmla and ugpg genes, involved in gellan gum biosynthesis, exhibit both dtdp- and udp-glucose pyrophosphorylase activities. | the commercial gelling agent gellan is a heteropolysaccharide produced by sphingomonas elodea atcc 31461. in this work, we carried out the biochemical characterization of the enzyme encoded by the first gene (rmla) of the rml 4-gene cluster present in the 18-gene cluster required for gellan biosynthesis (gel cluster). based on sequence homology, the putative rml operon is presumably involved in the biosynthesis of dtdp-rhamnose, the sugar necessary for the incorporation of rhamnose in the gellan ... | 2005 | 16085866 |
| degradation of chlorophenols using pentachlorophenol-degrading bacteria sphingomonas chlorophenolica in a batch reactor. | chlorophenols are common environmental contaminants that have been used as the major component in wide-spectrum biocides in industry and agriculture. many chlorophenols tend to persist in the environment and may become public health hazards. this research studied the ability of the pentachlorophenol (pcp)-degrading bacterium sphingomonas chlorophenolica to degrade and dechlorinate other chlorophenols. in addition, the characteristics of s. chlorophenolica were also investigated. when s. chloroph ... | 2005 | 16086107 |
| degradation of beta-hexachlorocyclohexane by haloalkane dehalogenase linb from sphingomonas paucimobilis ut26. | beta-hexachlorocyclohexane (beta-hch) is the most recalcitrant among the alpha-, beta-, gamma-, and delta-isomers of hch and causes serious environmental pollution problems. we demonstrate here that the haloalkane dehalogenase linb, reported earlier to mediate the second step in the degradation of gamma-hch in sphingomonas paucimobilis ut26, metabolizes beta-hch to produce 2,3,4,5,6-pentachlorocyclohexanol. | 2005 | 15812056 |
| characterization of sphingomonas aldehyde dehydrogenase catalyzing the conversion of various aromatic aldehydes to their carboxylic acids. | an aldehyde dehydrogenase gene, designated phnn, was isolated from a genome library of the 1,4-dimethylnaphthalene-utilizing soil bacterium, sphingomonas sp. 14dn61. escherichia coli expressing the phnn gene converted 1,4-dihydroxymethylnaphthalene to 1-hydroxymethyl-4-naphthoic acid. the putative amino acid sequence of the phnn gene product had 31-42% identity with those of nad(+)-dependent short-chain aliphatic aldehyde dehydrogenases and a secondary alcohol dehydrogenase. the nad(p)(+)-bindin ... | 2005 | 15812642 |
| biochemical and molecular characterization of a periplasmic hydrolase for oxidized polyvinyl alcohol from sphingomonas sp. strain 113p3. | oxidized polyvinyl alcohol hydrolase (oph) and polyvinyl alcohol dehydrogenase were found to be constitutively present in the periplasm of sphingomonas sp. strain 113p3 (formerly pseudomonas sp. 113p3). the oph was purified to homogeneity with a yield of 40 % and a 5.9-fold increase in specific activity. the enzyme was a homodimer consisting of 35 kda subunits. its activity was inhibited by pmsf, hg(2+) and zn(2+). the enzyme hydrolysed oxidized polyvinyl alcohol (oxidized pva) and p-nitrophenyl ... | 2005 | 15817792 |
| osteomyelitis and secondary septic arthritis caused by sphingomonas paucimobilis. | we describe a case of osteomyelitis and secondary septic arthritis caused by sphingomonas paucimobilis in an immunosupressed adolescent which did not present typically, leading to a delay in diagnosis. this case highlights the need to thoroughly investigate musculoskeletal pain in the immunocompromised patient in order to exclude an infection as a cause. | 2005 | 15827879 |
| [auxin production by bacteria associated with orchid roots]. | bacteria associated with the roots of greenhouse tropical orchids were shown to produce indole-3-acetic acid (iaa) and to excrete it into the culture liquid. the presence and activity of iaa were demonstrated colorimetrically, by thin-layer chromatography, and by biotests. the associated bacteria varied in their ability to excrete indole compounds (1-28 microg/ml nutrient broth). addition of tryptophan to the growth medium enhanced phytohormone production. upon addition of 200 microg/ml tryptoph ... | 2005 | 15835779 |
| [cloning, expression of the gene of dehydrochlorination of bhc from enrichment and its degradation experiment]. | a high effective enrichment that could degrade four isomers of bhc completely was got from the soil polluted by gamma-bhc, but the pure culture was not obtained yet. the 471 bp sequence of linn was amplified from the total dna of enrichment by polymerase chain reaction (pcr). the nucleotide sequence analysis showed that the linn gene had high homology with reported lina up to 99%. then the amplified fragment linn was cloned in the proper orientation into the site between nde i and hind iii of pe ... | 2005 | 15847161 |
| structure and function of bacterial super-biosystem responsible for import and depolymerization of macromolecules. | generally, when microbes assimilate macromolecules, they incorporate low-molecular-weight products derived from macromolecules through the actions of extracellular degrading enzymes. however, a gram-negative bacterium, sphingomonas sp. a1, has a smart biosystem for the import and depolymerization of macromolecules. the bacterial cells directly incorporate a macromolecule, alginate, into the cytoplasm through a "superchannel", as we named it. the superchannel consists of a pit on the cell surface ... | 2005 | 15849405 |
| [ion beam implantation in breeding efficient degradation bacteria]. | sphingomonas sp. an1 was mutagenized and breeded by n+ implantation, mutants capable of degrading anthrancene was obtained. the research review that the degrading rate increased by 29.3% and 36.2% while the mutagenized rate was 80% - 100% and 60% - 80%. in addition, the maximum concentration of enduring anthracene reached 300mg/l and 400mg/l. their heritance stability were examined for fifteen transfers. among these strains, two strains,an815-3 and an315-5s,showed predominant character of surviv ... | 2005 | 15859427 |
| benzo[a]pyrene co-metabolism in the presence of plant root extracts and exudates: implications for phytoremediation. | benzo[a]pyrene, a high molecular weight (hmw) polycyclic aromatic hydrocarbon (pah) was removed from solution by sphingomonas yanoikuyae jar02 while growing on root products as a primary carbon and energy source. plant root extracts of osage orange (maclura pomifera), hybrid willow (salix albaxmatsudana), or kou (cordia subcordata), or plant root exudates of white mulberry (morus alba) supported 15-20% benzo[a]pyrene removal over 24 h that was similar to a succinate grown culture and an unfed ac ... | 2005 | 15862401 |
| isolation and characterization of phenanthrene-degrading sphingomonas paucimobilis strain zx4. | phenanthrene-degrading bacterium strain zx4 was isolated from an oil-contaminated soil, and identified as sphingomonas paucimobilis based on 16s rdna sequence, cellular fatty acid composition, mol% g + c and biolog-gn tests. besides phenanthrene, strain zx4 could also utilize naphthalene, fluorene and other aromatic compounds. the growth on salicylic acid and catechol showed that the strain degraded phenanthrene via salicylate pathway, while the assay of catechol 2,3-dioxygenase revealed catecho ... | 2005 | 15865153 |
| biodegradation of bisphenol a by cells and cell lysate from sphingomonas sp. strain ao1. | the capacity and pathway of bisphenol a [bpa; 2,2-bis(4-hydroxyphenyl)propane] degradation in sphingomonas sp. strain ao1, which was isolated from the soil of a vegetable-growing field in japan, were investigated. the bacterial strain was able to grow in a basal mineral salt medium containing bpa as the sole carbon source (bsmb medium), and was able to degrade 115 microg ml(-1) bpa in 6 h in l medium. several bpa metabolites were detected in the culture supernatant by hplc and then identified by ... | 2005 | 15865158 |
| microbial community dynamics in bioaugmented sequencing batch reactors for bromoamine acid removal. | sphingomonas xenophaga qyy with the ability to degrade bromoamine acid (baa) was previously isolated from sludge samples. the enhancement of baa removal by strain qyy in sequencing batch reactors (sbrs) was investigated in this study. the results showed that augmented sbrs exhibited stronger abilities to degrade baa than the non-augmented control one. in order to estimate the relationship between community dynamics and function of augmented sbrs, a combined method based on fingerprints (ribosoma ... | 2005 | 15869973 |
| identification and phenotypic characterization of sphingomonas wittichii strain rw1 by peptide mass fingerprinting using matrix-assisted laser desorption ionization-time of flight mass spectrometry. | mass spectrometry is a potentially attractive means of monitoring the survival and efficacy of bioaugmentation agents, such as the dioxin-mineralizing bacterium sphingomonas wittichii strain rw1. the biotransformation activity of rw1 phenotypes is determined primarily by the presence and concentration of the dioxin dioxygenase, an enzyme initiating the degradation of both dibenzo-p-dioxin and dibenzofuran (df). we explored the possibility of identifying and characterizing putative cultures of rw ... | 2005 | 15870332 |
| architecture of a nascent sphingomonas sp. biofilm under varied hydrodynamic conditions. | the architecture of a sphingomonas biofilm was studied during early phases of its formation, using strain l138, a gfp-tagged derivative of sphingomonas sp. strain lb126, as a model organism and flow cells and confocal laser scanning microscopy as experimental tools. spatial and temporal distribution of cells and exopolymer secretions (eps) within the biofilm, development of microcolonies under flow conditions representing varied reynolds numbers, and changes in diffusion length with reference to ... | 2005 | 15870359 |
| optimizing contaminant desorption and bioavailability in dense slurry systems. 2. pah bioavailability and rates of degradation. | the effects of mechanical mixing on rates of polycyclic aromatic hydrocarbon (pah) biodegradation in dense geosorbent slurry (67% solids content, w/w) systems were evaluated using laboratory-scale intermittently mixed batch bioreactors. a pah-contaminated soil and a phenanthrene-sorbed mineral sorbent (alpha-al2o3) were respectively employed as slurry solids in aerobic and anaerobic biodegradation studies. both slurries exhibited a characteristic behavior of pseudoplastic non-newtonian fluids, a ... | 2005 | 15871264 |
| fluorescent methods to study dna, rna, proteins and cytoplasmic membrane polarization in the pentachlorophenol-mineralizing bacterium sphingomonas sp. ug30 during nutrient starvation in water. | the effect of sodium pentachlorophenolate (napcp) exposure on the nutrient-starved pentachlorophenol (pcp)-mineralizing bacterium sphingomonas sp. ug30 was assessed using fluorescent methods to measure dna, rna, total cellular protein, and cytoplasmic membrane proteins. ug30 cells were inoculated into sterilized speed river (guelph, on, canada) water samples in the presence of 50, 100, and 250 ppm napcp. no marked changes were observed in the total cellular dna, rna or protein levels over 90 d, ... | 2005 | 15883769 |
| cell wall glycosphingolipids of sphingomonas paucimobilis are cd1d-specific ligands for nkt cells. | the current consensus on characterization of nkt cells is based on their reactivity to the synthetic glycolipid, alpha-galactosylceramide (alpha-galcer) in a cd1d-dependent manner. because of the limited availability of alpha-galcer, there is a constant search for cd1d-presented ligands that activate nkt cells. the alpha-anomericity of the carbohydrate is considered to be an important requisite for the cd1d-specific activation of nkt cells. the gram-negative, lipopolysaccharide-free bacterium sp ... | 2005 | 15915536 |
| two kinds of chlorocatechol 1,2-dioxygenase from 2,4-dichlorophenoxyacetate-degrading sphingomonas sp. strain tfd44. | two kinds of chlorocatechol 1,2-dioxygenase (ccd), tfdc and tfdc2 were detected in sphingomonas sp. strain tfd44. these two ccds could be simultaneously synthesized in tfd44 during its growth with 2,4-d as the sole carbon and energy sources. the apparent subunit molecular masses of tfdc and tfdc2 estimated by sds-page analysis were 33.8 and 33.1 kda, respectively. the genes encoding the two ccds were cloned and expressed in escherichia coli. the two purified ccds showed broad substrate specifici ... | 2005 | 15916749 |
| structural and replicative diversity of large plasmids from sphingomonads that degrade polycyclic aromatic compounds and xenobiotics. | the plasmids from 16 sphingomonads which degrade various xenobiotics and polycyclic aromatic compounds were compared with the previously sequenced plasmid pnl1 from sphingomonas aromaticivorans f199. the replicase genes repaaab from plasmid pnl1 were amplified by pcr and used as a gene probe for the identification of plasmids belonging to the same incompatibility group as plasmid pnl1. plasmids were prepared from various sphingomonads and hybridized with the repa gene probe. positive hybridizati ... | 2005 | 15942009 |
| cloning, sequence analysis, and expression of the gene encoding sphingomonas paucimobilis fp2001 alpha-l -rhamnosidase. | the gene (rham) encoding the alpha-l-rhamnosidase of sphingomonas paucimobilis fp2001 was cloned, sequenced, and expressed in escherichia coli. the rham consisted of 3,354 nucleotides and had a promoter and shine-dalgarno sequences typical in bacteria. the rham encoding a protein (rham) deducted from the sequence consisted of 1,117 amino acids and had a putative signal peptide of 25 amino acids. rham has no similarity to other known rhamnosidases. rham has a sugar-binding domain of glycoside hyd ... | 2005 | 15991055 |
| ['in vitro' activity of different antimicrobial agents on gram-negative nonfermentative bacilli, excluding pseudomonas aeruginosa and acinetobacter spp]. | gram-negative nonfermentative bacilli (nfb) are widely spread in the environment. besides of difficulties for identification, they often have a marked multiresistance to antimicrobial agents, including those active against pseudomonas aeruginosa. the objective of this study was to evaluate the 'in vitro' activity of different antimicrobial agents on 177 gram-negative nonfermentative bacilli isolates (excluding pseudomonas aeruginosa and acinetobacter spp.) isolated from clinical specimens. minim ... | 2005 | 15991478 |
| isolation of soil bacteria adapted to degrade humic acid-sorbed phenanthrene. | the goal of these studies was to determine how sorption by humic acids affected the bioavailability of polynuclear aromatic hydrocarbons (pahs) to pah-degrading microbes. micellar solutions of humic acid were used as sorbents, and phenanthrene was used as a model pah. enrichments from pah-contaminated soils established with nonsorbed phenanthrene yielded a total of 25 different isolates representing a diversity of bacterial phylotypes. in contrast, only three strains of burkholderia spp. and one ... | 2005 | 16000791 |
| culture independent detection of sphingomonas sp. epa 505 related strains in soils contaminated with polycyclic aromatic hydrocarbons (pahs). | the sphingomonas genus hosts many interesting pollutant-degrading strains. sphingomonas sp. epa505 is the best studied polycyclic aromatic hydrocarbon (pah)-degrading sphingomonas strain. based on 16s rrna gene sequence analysis, sphingomonas sp. strain epa505 forms a separate branch in the sphingomonas phylogenetic tree grouping exclusively pah-degrading isolates. for specific pcr detection and monitoring of sphingomonas sp. epa505 and related strains in pah-contaminated soils, a new 16s rrna g ... | 2005 | 16003481 |
| cooperative catabolic pathways within an atrazine-degrading enrichment culture isolated from soil. | atrazine degradation previously has been shown to be carried out by individual bacterial species or by relatively simple consortia that have been isolated using enrichment cultures. here, the degradative pathway for atrazine was examined for a complex 8-membered enrichment culture. the species composition of the culture was determined by pcr-dgge. the bacterial species included agrobacterium tumefaciens, caulobacter crescentus, pseudomonas putida, sphingomonas yaniokuyae, nocardia sp., rhizobium ... | 2005 | 16329946 |
| non-specific biodegradation of the organophosphorus pesticides, cadusafos and ethoprophos, by two bacterial isolates. | an enrichment culture technique was used for the isolation of microorganisms responsible for the enhanced biodegradation of the nematicide cadusafos in soils from a potato monoculture area in northern greece. mineral salts medium supplemented with nitrogen (msmn), where cadusafos (10 mg l(-1)) was the sole carbon source, and soil extract medium (sem) were used for the isolation of cadusafos-degrading bacteria. two pure bacterial cultures, named cadi and cadii, were isolated and subsequently char ... | 2005 | 16329956 |
| purification of cytochrome p450 and ferredoxin, involved in bisphenol a degradation, from sphingomonas sp. strain ao1. | in a previous study (m. sasaki, j. maki, k. oshiman, y. matsumura, and t. tsuchido, biodegradation 16:449-459, 2005), the cytochrome p450 monooxygenase system was shown to be involved in bisphenol a (bpa) degradation by sphingomonas sp. strain ao1. in the present investigation, we purified the components of this monooxygenase, cytochrome p450 (p450bisd), ferredoxin (fd(bisd)), and ferredoxin reductase (red(bisd)). we demonstrated that p450bisd and fd(bisd) are homodimeric proteins with molecular ... | 2005 | 16332782 |
| enantioselective transformation of alpha-hexachlorocyclohexane by the dehydrochlorinases lina1 and lina2 from the soil bacterium sphingomonas paucimobilis b90a. | sphingomonas paucimobilis b90a contains two variants, lina1 and lina2, of a dehydrochlorinase that catalyzes the first and second steps in the metabolism of hexachlorocyclohexanes (r. kumari, s. subudhi, m. suar, g. dhingra, v. raina, c. dogra, s. lal, j. r. van der meer, c. holliger, and r. lal, appl. environ. microbiol. 68:6021-6028, 2002). on the amino acid level, lina1 and lina2 were 88% identical to each other, and lina2 was 100% identical to lina of s. paucimobilis ut26. incubation of chir ... | 2005 | 16332842 |
| application of stereolithographic custom models for studying the impact of biofilms and mineral precipitation on fluid flow. | here we introduce the use of transparent experimental models fabricated by stereolithography for studying the impacts of biomass accumulation, minerals precipitation, and physical configuration of flow paths on liquid flow in fracture apertures. the internal configuration of the models ranged in complexity from simple geometric shapes to those that incorporate replicated surfaces of natural fractures and computationally derived fracture surfaces. high-resolution digital time-lapse imaging was em ... | 2005 | 16332867 |
| culture-dependent and -independent approaches establish the complexity of a pah-degrading microbial consortium. | a microbial consortium (am) obtained by sequential enrichment in liquid culture with a polycyclic aromatic hydrocarbon (pah) mixture of three- and four-ringed pahs as a sole source of carbon and energy was examined using a triple-approach method based on various cultivation strategies, denaturing gradient gel electrophoresis (dgge), and the screening of 16s and 18s rrna gene clone libraries. eleven different sequences by culture-dependent techniques and seven by both dgge and clone libraries wer ... | 2005 | 16333329 |
| [isolation and characterization of a hch degradation sphingomanas sp. stain bhc-a]. | an aerobic bacterium was isolated successfully from a long-term contaminated upland field, which was named bhc-a. the bacterium can utilize hexachlorocycloexane as a sole carbon source and decompose this substance rapidly and completely. according to its physiological & biochemical characters and the homology analysis of its 16s rdna sequence, this strain was identified as sphingomonas sp. stain bhc-a canmineralize not only alpha, gamma and delta-hch rapidly, but also 5 mg/l beta-hch in 12h comp ... | 2005 | 16342765 |
| dual substrate biodegradation of a nonionic surfactant and pentachlorophenol by sphingomonas chlorophenolica ra2. | the simultaneous biodegradation of the nonionic surfactant tween 20 (tw20) and pentachlorophenol (pcp) by sphingomonas chlorophenolica sp. strain ra2 (ra2) was measured. as a sole substrate, tw20 biodegradation was best described by the contois kinetic model. during concurrent biodegradation of tw20 and pcp, the biodegradation rates of tw20 were not significantly affected by 50 or 100 mg/l pcp, but were significantly inhibited by 500 mg/l pcp. decreases in cell yield in the presence of pcp sugge ... | 2005 | 15685600 |
| [metabolic pathway, genes, and enzymes for the degradation of chlorinated pesticide, gamma-hexachlorocyclohexane]. | 2005 | 16218450 | |
| proteomics-based identification of outer-membrane proteins responsible for import of macromolecules in sphingomonas sp. a1: alginate-binding flagellin on the cell surface. | a nonmotile gram-negative bacterium, sphingomonas sp. a1, directly incorporates macromolecules such as alginate through a "super-channel" consisting of a pit formed on the cell surface, alginate-binding proteins in the periplasm, and an atp-binding cassette transporter in the inner membrane. here, we demonstrate the proteomics-based identification of cell-surface proteins involved in the formation of the pit and/or import of alginate. cell-surface proteins were prepared from the outer membrane r ... | 2005 | 16229468 |
| diversity of n-acyl homoserine lactone-producing and -degrading bacteria in soil and tobacco rhizosphere. | in gram-negative bacteria, quorum-sensing (qs) communication is mostly mediated by n-acyl homoserine lactones (n-ahsl). the diversity of bacterial populations that produce or inactivate the n-ahsl signal in soil and tobacco rhizosphere was investigated by restriction fragment length polymorphism (rflp) analysis of amplified 16s dna and dna sequencing. such analysis indicated the occurrence of n-ahsl-producing strains among the alpha-, beta- and gamma-proteobacteria, including genera known to pro ... | 2005 | 16232294 |
| molecular identification of sphingomonas sp. a1 alginate lyase (a1-iv') as a member of novel polysaccharide lyase family 15 and implications in alginate lyase evolution. | sphingomonas sp. a1 (strain a1) produces three endotypes (a1-i [65 kda], a1-ii [25 kda], and a1-iii [40 kda]) and an exotype (a1-iv [86 kda]) alginate lyases in cytoplasm. these four enzymes cooperatively depolymerize alginate into constituent monosaccharides. in addition to the genes for these lyases, novel genes encoding hypothetical proteins homologous with a1-iv were found in the genomes of many bacteria including strain a1. one such protein, a1-iv' (90 kda) of strain a1, was overexpressed i ... | 2005 | 16233753 |
| characterization of floating activity of indigenous diesel-assimilating bacterial isolates. | six diesel-degrading bacterial strains were isolated from oil-polluted sites located in central taiwan. the floating activity of the isolates in an oil-supplemented liquid medium was monitored. cell-surface hydrophobicity as well as cell-free and cell-residue emulsification activities were also investigated. three isolates, identified as gordonia alkanivorans cc-jg 39, rhodococcus erythropolis cc-bc 04, and r. erythropolis cc-bc 11, were found to float and grow near the diesel layer on the surfa ... | 2005 | 16233818 |
| biofilm formation characteristics of bacterial isolates retrieved from a reverse osmosis membrane. | high-quality water purification systems using reverse osmosis (ro) membrane separation have faced a major challenge related to biofilm formation on the membrane surface, or biofouling. to understand this issue, the biofilm formation characteristics of four bacterial isolates previously retrieved from an ro membrane treating potable water were investigated. biofilm formation of all four isolates occurred to different extents in microtiter plates and could be related to one or more cell properties ... | 2005 | 16245826 |
| biological removal of polychlorinated dibenzo-p-dioxins from incinerator fly ash by sphingomonas wittichii rw1. | the ability of sphingomonas wittichii strain rw1 to remove polychlorinated dibenzo-p-dioxins (pcdds) from fly ash was investigated. all experiments were carried out in a slurry-phase system. preliminary studies with resting cells of strain rw1 in a model fly ash system showed the complete removal of dibenzofuran (df) and 81% of dibenzo-p-dioxin (dd). incubation of real fly ash collected from municipal waste incinerators with strain rw1 for 15 days resulted in a 75.5% reduction in toxic pcdds. wh ... | 2005 | 16256169 |
| bacterial community dynamics and polycyclic aromatic hydrocarbon degradation during bioremediation of heavily creosote-contaminated soil. | bacterial community dynamics and biodegradation processes were examined in a highly creosote-contaminated soil undergoing a range of laboratory-based bioremediation treatments. the dynamics of the eubacterial community, the number of heterotrophs and polycyclic aromatic hydrocarbon (pah) degraders, and the total petroleum hydrocarbon (tph) and pah concentrations were monitored during the bioremediation process. tph and pahs were significantly degraded in all treatments (72 to 79% and 83 to 87%, ... | 2005 | 16269736 |
| microbial conversion of major ginsenoside rb(1) to pharmaceutically active minor ginsenoside rd. | more than seventy strains of aerobic bacteria showing beta-glucosidase activity were isolated from a ginseng field, using a newly designed esculin-r2a agar, and identified by their 16s rrna gene sequences. of these microorganisms, twelve strains could convert the major ginsenoside, rb(1), to the pharmaceutically active minor ginsenoside rd. three strains, burkholderia pyrrocinia gp16, bacillus megaterium gp27 and sphingomonas echinoides gp50, were phylogenetically studied, and observed to be mos ... | 2005 | 16273039 |
| sphingomonas yunnanensis sp. nov., a novel gram-negative bacterium from a contaminated plate. | a gram-negative bacterium, yim 003t, which was isolated from a contaminated plate in the laboratory, was subjected to a polyphasic taxonomic study. the organism had short-rod-shaped, motile cells, formed yellow-pigmented colonies on isp2 medium and its optimum growth ph was 7.0-7.5. the major respiratory lipoquinone was ubiquinone q-10. the phosphate-containing lipids detected in strain yim 003t were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sph ... | 2005 | 16280497 |
| description of two novel species, sphingomonas abaci sp. nov. and sphingomonas panni sp. nov. | two gram-negative, rod-shaped, non-spore-forming bacterial strains designated c42t and c52t were isolated in the medical clinic for small animals and ungulates at the university for veterinary medicine vienna, austria. on the basis of 16s rrna gene sequence similarity, both strains were shown to belong to the genus sphingomonas. strain c42t showed the greatest levels of sequence similarity with sphingomonas melonis dsm 14444t and sphingomonas aquatilis kctc 2881t (both 97.7 %). strain c52t showe ... | 2005 | 16280528 |
| nonionic surfactant sorption onto the bacterial cell surface: a multi-interaction isotherm. | the adsorption of linear polyoxyethylene (poe) alcohol surfactants of the form cxey onto the surface of a sphingomonas sp. has been examined. for this study, the alkyl chain length (x) was fixed at 12 and the poe chain length (y) was varied, with y = 4, 7, 9, 10, and 23 ethylene oxide units. langmuirian isotherms were observed for c12e4 and c12e23, and more complex isotherms were observed for the three intermediate poe chain length surfactants, with c12e7 and c12e9 exhibiting strong s-shaped iso ... | 2005 | 16285812 |
| isolation of pah-degrading bacteria from mangrove sediments and their biodegradation potential. | surface sediment samples were collected from seven mangrove swamps in hong kong sar with different degrees of contamination. the total concentrations of 16 pahs in these sediments ranged from 169.41 to 1058.37 ng g(-1) with the highest concentration found in ma wan and the lowest in kei ling ha lo wai mangrove swamp. in each swamp, three bacterial consortia were enriched from sediments using phenanthrene (phe) as the sole carbon and energy source, and individual bacterial colony showing phe degr ... | 2005 | 16291206 |
| [screening methods for detection of metallo-beta-lactamase producing gram negative rods]. | modified hodge test and a method using a disk with imipenem plus 1000 mg of edta were used to determine the presence of metallo-beta-lactamase producing gram-negative rods among 166 clinical isolates from hospitals in iaşi and galaţi. of 9 imipenem resistant strains found, only one pseudomonas aeruginosa gave positive results with both tests and other two p. aeruginosa clinical isolates gave negative results with both tests. the rest of the strains (2 p. aeruginosa, 2 acinetobacter baumanii, 1 s ... | 2005 | 16607806 |
| effect of slow desorption on the kinetics of biodegradation of polycyclic aromatic hydrocarbons. | the bioavailability to bacteria of 14c-labeled polycyclic aromatic hydrocarbons (pahs) sorbed onto lake sediments was assessed using a mathematical model and three experimental series. the experiments were performed under similar conditions and included: (1) abiotic desorption of pahs from sediments by tenax extraction, (2) mineralization of dissolved pahs with no sediment present, and (3) mineralization of pahs sorbed onto sediments. results obtained from the first two series were used to obtai ... | 2005 | 16323776 |
| symbiotic association in chlorella culture. | chlorella sorokiniana iam c-212 has long been maintained in slant culture as a mixed strain, representing an associated natural microbial consortium. in this study, the consortium was separated and five nonalgal constituents, a fungal strain (cssf-1), and four bacterial strains (cssb-1, cssb-2, cssb-3, and cssb-4) were isolated and identified. 16s rdna sequence analysis revealed that strains cssb-1, cssb-2, cssb-3, and cssb-4 were close to ralstonia pickettii (99.8% identity), sphingomonas sp. d ... | 2005 | 16329867 |
| toxic effect of biosurfactant addition on the biodegradation of phenanthrene. | the effect of the biosurfactant rhamnolipid on phenanthrene biodegradation and cell growth of phenanthrene degraders was investigated. to compare the effect of rhamnolipid addition, two bacterial strains, 3y and 4-3, which were isolated from a diesel-contaminated site in korea, were selected. without the biosurfactant, large amounts of phenanthrene were degraded with both strains at neutral ph, with higher rates of phenanthrene degradation when the cell growth was higher. upon the addition of 24 ... | 2005 | 16398112 |
| crystallization and preliminary x-ray analysis of alginate lyases a1-ii and a1-ii' from sphingomonas sp. a1. | alginate lyases depolymerize alginate, a heteropolysaccharide consisting of alpha-l-guluronate and beta-d-mannuronate, through a beta-elimination reaction. the alginate lyases a1-ii (25 kda) and a1-ii' (25 kda) from sphingomonas sp. a1, which belong to polysaccharide lyase family pl-7, exhibit 68% homology in primary structure but have different substrate specificities. to determine clearly the structural basis for substrate recognition in the depolymerization mechanism by alginate lyases, both ... | 2005 | 16511020 |
| [rare bacteria species found in wounds of tsunami patients. predominance of gram-negative rods, increased antibiotic resistance]. | microbiological cultures from 229 patients seeking medical advise in stockholm after the tsunami catastrophe december 2004 were analysed at the clinical microbiology laboratory, karolinska university hospital, stockholm, sweden. gram-negative rods were the most common findings from wound cultures. common human pathogens as escherichia coli, proteus species, klebsiella spp, and pseudomonas aeruginosa were isolated. however, more rare species of gram-negative rods were also isolated, e.g. myroides ... | 2005 | 16416946 |
| [construction of multifunctional genetically engineered pesticides-degrading bacteria by homologous recombination]. | construction of multifunctional pesticides-degrading genetically engineered microorganisms (gems) is increasing important in the bioremediation of various pesticides contaminants in environment. however, construction of genetically stable gems without any exogenous antibiotic resistance is thought to be one of the bottlenecks in gems construction. in this article, homologous recombination vectors with the recipient's 16s rdna as homologous recombination directing sequence (hrds) and sacb gene as ... | 2005 | 16468341 |
| surveying biotransformations with à la carte genetic traps: translating dehydrochlorination of lindane (gamma-hexachlorocyclohexane) into lacz-based phenotypes. | the ability of the product of a desired reaction to activate a bacterial transcriptional regulator was exploited to develop genetic traps that render the catalytic activity born by a dna clone into a selectable/scorable phenotype. we established this strategy with a system to expose the activity of dehydrochlorinases acting upon gamma-hexachlorocyclohexane (gamma-hch or lindane). to this end, the effector-binding protein, xylr, was evolved by gene shuffling plus mutagenic polymerase chain reacti ... | 2006 | 16478460 |
| glycolipid activation of invariant t cell receptor+ nk t cells is sufficient to induce airway hyperreactivity independent of conventional cd4+ t cells. | asthma is an inflammatory lung disease, in which conventional cd4+ t cells producing il-4/il-13 appear to play an obligatory pathogenic role. here we show, in a mouse model of asthma, that activation of pulmonary il-4/il-13 producing invariant tcr+ cd1d-restricted natural killer t (nkt) cells is sufficient for the development of airway hyperreactivity (ahr), a cardinal feature of asthma, in the absence of conventional cd4+ t cells and adaptive immunity. respiratory administration of glycolipid a ... | 2006 | 16478801 |
| degradation of microcystin-rr by sphingomonas sp. cba4 isolated from san roque reservoir (córdoba - argentina). | we report the aerobic biodegradation of microcystin-rr (mc-rr) by a bacterial strain isolated from san roque reservoir (córdoba - argentina). this bacterium was identified as sphingomonas sp. (cba4) on the basis of 16s rdna sequencing. the isolated strain was capable of degrading completely mc-rr (200 mug l(-1)) within 36 h. we have found evidence that mc-rr biodegradation pathway by this sphingomonas sp. strain would start by demethylating mc-rr, affording an intermediate product, which is fina ... | 2006 | 16485086 |
| distribution of gamma-hexachlorocyclohexane-degrading genes on three replicons in sphingobium japonicum ut26. | sphingobium japonicum (formerly sphingomonas paucimobilis) ut26 utilizes the important insecticide gamma-hexachlorocyclohexane as a sole source of carbon and energy. in previous studies, we isolated and characterized six structural genes (lina to linf) and one regulatory gene (linr) of ut26 for the degradation of gamma-hexachlorocyclohexane to beta-ketoadipate. our analysis in this study indicated that the ut26 genome consists of three large circular replicons of 3.6 mb, 670 kb, and 185 kb. the ... | 2006 | 16487327 |
| identifying the bacterial community on the surface of intralox belting in a meat boning room by culture-dependent and culture-independent 16s rdna sequence analysis. | we examined the bacterial community present on an intralox conveyor belt system in an operating lamb boning room by sequencing the 16s ribosomal dna (rdna) of bacteria extracted in the presence or absence of cultivation. rflp patterns for 16s rdna clone library and cultures were generated using haeiii and mspi restriction endonucleases. 16s rdna amplicons produced 8 distinct rflp pattern groups. rflp groups i-iv were represented in the clone library and rflp groups i and v-viii were represented ... | 2006 | 16488497 |
| comparison of mineralization of solid-sorbed phenanthrene by polycyclic aromatic hydrocarbon (pah)-degrading mycobacterium spp. and sphingomonas spp. | the mineralization of 14c-phenanthrene, sorbed to porous synthetic amberlite sorbents, i.e., irc50, xad7-hp, and xad2, by three phenanthrene-degrading mycobacterium soil isolates, i.e., strains vm552, vm531, and vm451 and three phenanthrene-degrading sphingomonas soil isolates, i.e., strains lh162, epa505 and lh227, was compared. in p-buffer and in the presence of irc50, for all strains the maximum rate of mineralization of 14c-phenanthrene was significantly higher (1.1-1.9 ng ml(-1) h(-1)) than ... | 2006 | 16496139 |
| microbial contamination of nebulization solution and its measures. | we evaluated the microbial contamination of nebulization solutions in medication cups from a total of 76 ultrasonic nebulizers in use in 10 hospitals. in addition, an interview survey was given to nurses to evaluate the disinfection methods of these ultrasonic nebulizers. of a total of 76 nebulization solution samples, 11 (14.5%) were contaminated with 10-10(2) colony-forming units (cfu)/ml and 9 (11.8%) with 10(3)-10(5) cfu/ml. the major contaminants were glucose non-fermentative bacilli such a ... | 2006 | 16508154 |
| effect of bioaugmentation and supplementary carbon sources on degradation of polycyclic aromatic hydrocarbons by a soil-derived culture. | the degradation of polycyclic aromatic hydrocarbons (pahs) by an undefined culture obtained from a pah-polluted soil and the same culture bioaugmented with three pah-degrading strains was studied in carbon-limited chemostat cultures. the pahs were degraded efficiently by the soil culture and bioaugmentation did not significantly improve the pah degrading performance. the presence of pahs did, however, influence the bacterial composition of the bioaugmented and non-bioaugmented soil cultures, res ... | 2006 | 16420621 |
| confirmation of the anomeric structure of galacturonic acid in the galacturonosyl-ceramide of sphingomonas yanoikuyae. | the anomeric structure of glycosphingolipids significantly influences their activity to stimulate natural killer t cells. in this study the chemical structure of the galacturonosyl-ceramide in sphingomonas yanoikuyae, designated gsl-1'sy, was re-examined to prove the anomeric structure of the dgalacturonic acid (gala) in the lipid, which was reported as beta-configuration by naka et al., but was suggested as alpha-configuration in our preliminary study. gsl-1'sy was purified from the bacterial c ... | 2006 | 16428876 |
| effects of nonionic surfactants on the cell surface hydrophobicity and apparent hamaker constant of a sphingomonas sp. | nonionic surfactants of the form cxey were studied for their ability to alter the cell surface hydrophobicity and apparent hamaker constants of a sphingomonas sp. through contact angle measurements on hydrated and dried bacterial lawns, it was found that the cell surface hydrophobicity changed systematically with both the alkyl (x) and polyoxyethylene (y) chain lengths. while differences in contact angles were observed between hydrated and dried lawns, they could not be attributed to the mere pr ... | 2006 | 16433351 |
| suspected ventilator-associated pneumonia in cardiac patients admitted to the coronary care unit. | to determine the incidence, risk factors, associated pathogens, and outcome of ventilator-associated pneumonia (vap) in patients admitted to a coronary care unit (ccu). | 2006 | 16438476 |
| a novel automated waterline cleaning system that facilitates effective and consistent control of microbial biofilm contamination of dental chair unit waterlines: a one-year study. | microbial contamination of dental chair unit (dcu) output water caused by biofilm growth in dental unit waterlines (duws) is a universal problem and a potentially significant source of cross-infection. the microbial quality of output water from a planmeca compact i dcu equipped with the novel water management system (wms), an integrated and automated duw cleaning system, was investigated over a 12-month period with the hydrogen peroxide- and silver ion-containing disinfectants planosil and plano ... | 2006 | 16442201 |
| sequence and analysis of the 46.6-kb plasmid pa1 from sphingomonas sp. a1 that corresponds to the typical incp-1beta plasmid backbone without any accessory gene. | sphingomonas sp. a1 (strain a1) is capable of directly incorporating macromolecules (e.g., alginate) through the specialized import system--"super-channel." here, we report the complete dna sequence and genetic organization of plasmid pa1 from strain a1. nucleotide sequence analysis revealed that pa1 comprises 46,557 bp encoding 49 open reading frames (orfs) with 65% g+c content and abundant gccg/cggc motifs. many predicted pa1 orfs showed high similarity to pa81 orfs; pa81 is supposedly a self- ... | 2006 | 16445980 |
| bioaugmentation of bromoamine acid degradation with sphingomonas xenophaga qyy and dna fingerprint analysis of augmented systems. | one high-effective bromoamine acid (1-amino-4-bromoanthraquinone-2-sulfonic acid, baa) degrading strain was isolated previously with the ability to use baa as sole source of carbon and nitrogen. it was identified as sphingomonas xenophaga qyy by 16s rdna sequence analysis and physio-biochemical tests. in this study, bioaugmentation of baa degradation with suspended and immobilized cells of strain qyy was investigated. the optimal degradation conditions were as follows: temperature 30 degrees c, ... | 2006 | 16453174 |
| proposal to reclassify [sphingomonas] xenophaga stolz et al. 2000 and [sphingomonas] taejonensis lee et al. 2001 as sphingobium xenophagum comb. nov. and sphingopyxis taejonensis comb. nov., respectively. | the sphingomonad group contains bacterial isolates that are quite diverse in terms of their phylogenetic, ecological and physiological properties. thus, the genus sphingomonas was divided into four distinct genera, sphingomonas sensu stricto, sphingobium, novosphingobium and sphingopyxis on the basis of 16s rrna gene sequence phylogenetic analysis, signature nucleotides, fatty acid profiles and polyamine patterns and this classification is currently widely accepted. in this study, a complete ana ... | 2006 | 16514047 |
| bioremediation of hydrocarbon-contaminated polar soils. | bioremediation is increasingly viewed as an appropriate remediation technology for hydrocarbon-contaminated polar soils. as for all soils, the successful application of bioremediation depends on appropriate biodegradative microbes and environmental conditions in situ. laboratory studies have confirmed that hydrocarbon-degrading bacteria typically assigned to the genera rhodococcus, sphingomonas or pseudomonas are present in contaminated polar soils. however, as indicated by the persistence of sp ... | 2006 | 16514512 |
| sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium. | three strains of bacteria that degrade the cyanobacterial hepatotoxin microcystin, y2t, mdb2 and mdb3, were isolated from a eutrophic lake, lake suwa, and the tenryu river, japan, and characterized. these strains were aerobic and chemo-organotrophic and their cells were gram-negative, non-spore-forming rods, motile by means of single polar flagella. yellow-pigmented colonies were formed on nutrient agar media. the strains assimilated only citrate among the organic compounds tested as carbon sour ... | 2006 | 16403871 |
| engineered membrane superchannel improves bioremediation potential of dioxin-degrading bacteria. | sphingomonas sp. a1 possesses specialized membrane structures termed 'superchannels' that enable the direct incorporation of macromolecules into the cell. we have engineered two related sphingomonads, the dioxin-degrading s. wittichii rw1 and the polypropylene glycol-degrading s. subarctica ifo 16058(t), to incorporate this superchannel into their cell membranes. in both cases the bioremediation capability of the organisms was substantially increased pointing at the potential of this approach as ... | 2006 | 16415854 |
| design of natural killer t cell activators: structure and function of a microbial glycosphingolipid bound to mouse cd1d. | natural killer t (nkt) cells provide an innate-type immune response upon t cell receptor interaction with cd1d-presented antigens. we demonstrate through equilibrium tetramer binding and antigen presentation assays with valpha14i-positive nkt cell hybridomas that the sphingomonas glycolipid alpha-galacturonosyl ceramide (gala-gsl) is a nkt cell agonist that is significantly weaker than alpha-galactosylceramide (alpha-galcer), the most potent known nkt agonist. for gala-gsl, a shorter fatty acyl ... | 2006 | 16537470 |
| a biosystem for alginate metabolism in agrobacterium tumefaciens strain c58: molecular identification of atu3025 as an exotype family pl-15 alginate lyase. | the gram-negative bacterium sphingomonas sp. strain a1 (strain a1) has a peculiar biosystem to directly import and depolymerize a macromolecule, alginate, which is encoded by a cluster of genes on the genome. we identified five clustered orfs homologous to some genes of the strain a1 cluster in the genome of agrobacterium tumefaciens strain c58 (strain c58). these orfs are atu3021, atu3022, atu3023, and atu3024, encoding a putative sugar abc transporter system and atu3025, which encodes a putati ... | 2006 | 16545947 |
| plasmid-encoded gamma-hexachlorocyclohexane degradation genes and insertion sequences in sphingobium francense (ex-sphingomonas paucimobilis sp+). | the lin genes encode the gamma-hexachlorocyclohexane (gamma-hch or lindane) catabolic pathway in lindane-degrading strains. the location and stability of these genes have been explored in the lindane-degrading sphingobium francense strain sp+, and in two non-lindane-degrading mutants (sp1- and sp2-). the lin genes, lina, linb, line and linx were localized by hybridization on three of the six plasmids of the s. francense strain sp+ showing dispersal within the genome. the linc gene was detected b ... | 2006 | 16553860 |
| degradation of microcystins using immobilized microorganism isolated in an eutrophic lake. | the final purpose of our series of studies is to establish a biological removal method of cyanobacteria and their toxic products using immobilized microorganisms that can lyse cyanobacteria and decompose microcystins. to establish the biological removal method in non-point areas and water purification plants, as the first step, we explored bacteria active against the cyanobacterial hepatotoxin microcystin in the present study. eleven active bacteria were isolated from samples taken from lakes ts ... | 2006 | 16563465 |
| comment on "biological removal of polychlorinated dibenzo-p-dioxins from incinerator fly ash by sphingomonas wittichii rw1" by i.-h. nam, y.-m. kim, b.-h. kim, k. murugesan, and y.-s. chang. | 2006 | 16620903 | |
| 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 |
| characterization of psychrotolerant heterotrophic bacteria from finnish lapland. | a total of 331 aerobic heterotrophic bacterial strains were isolated from various ecosystems of finnish lapland (68-69 degrees n) including forest soil, arctic alpine-tundra soil, stream water, lake and mire sediments, lichen and snow algae. whole cell fatty acid and 16s rrna gene sequence analysis and microscopy indicated that the isolates were dominated by gram-negative bacteria, while only 20 gram-positive strains were isolated. based on 16s rrna gene sequences the isolates were members of al ... | 2006 | 16564959 |
| 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 |
| replicability of dominant bacterial populations after long-term surfactant-enrichment in lab-scale activated sludge. | bacterial communities were examined in replicate lab-scale activated sludge reactors after a period of several months of enrichment with non-ionic nonylphenol ethoxylate (npe) surfactants. four sequential batch reactors were fed with synthetic sewage, two of which received additionally npe. small subunit rdna-derived denaturing gel gradient electrophoresis (dgge) profiles and 16s rdna clone libraries were dominated by clones of gammaproteobacteria class. sequences of the other codominant rdna ph ... | 2006 | 16584474 |
| sphingomonas soli sp. nov., a beta-glucosidase-producing bacterium in the family sphingomonadaceae in the alpha-4 subgroup of the proteobacteria. | strain t5-04t, a gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from soil of a ginseng field in south korea and characterized in order to determine its taxonomic position. 16s rrna gene sequence analysis revealed that strain t5-04t belongs to the alpha-4 subgroup of the proteobacteria, and the highest degrees of sequence similarity determined were to sphingomonas asaccharolytica ifo 10564t (97.5 %), sphingomonas koreensis jss26t (97.1 %), sphingomonas mali ifo 15500t (96.7 ... | 2006 | 16585680 |
| sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of oryza sativa. | three yellow-pigmented strains associated with rice plants were characterized by using a polyphasic approach. the nitrogen-fixing abilities of these strains were confirmed by acetylene reduction assay and nifh gene detection. the three strains were found to be very closely related, with 99.9 % 16s rrna gene sequence similarity and greater than 70 % dna-dna hybridization values, suggesting that the three strains represent a single species. 16s rrna gene sequence analysis indicated that the strain ... | 2006 | 16585711 |
| diverse bacteria associated with root nodules of spontaneous legumes in tunisia and first report for nifh-like gene within the genera microbacterium and starkeya. | we characterized 34 endophytic bacterial isolates associated to root nodules collected from spontaneous legumes in the arid zone of tunisia by 16s rdna polymerase chain reaction (pcr)-restriction fragment length polymorphism, whole cell protein sodium dodecyl sulfate-polyacrylamide gel electrophoresis (sds-page), 16s rdna and 16s-23s rdna internal transcribed spacer sequencing. phylogenetically, these isolates belong to the branches containing the genera inquilinus, bosea, rhodopseudomonas, para ... | 2006 | 16598639 |
| cloning, expression, and characterization of a self-sufficient cytochrome p450 monooxygenase from rhodococcus ruber dsm 44319. | a new member of class iv of cytochrome p450 monooxygenases was identified in rhodococcus ruber strain dsm 44319. as the genome of r. ruber has not been sequenced, a p450-like gene fragment was amplified using degenerated primers. the flanking regions of the p450-like dna fragment were identified by directional genome walking using polymerase chain reaction. the primary protein structure suggests a natural self-sufficient fusion protein consisting of ferredoxin, flavin-containing reductase, and p ... | 2006 | 16607529 |
| growth inhibition by metabolites of gamma-hexachlorocyclohexane in sphingobium japonicum ut26. | the growth of a gamma-hexachlorocyclohexane (gamma-hch)-degrading bacterium sphingobium japonicum (formerly sphingomonas paucimobilis) ut26 in rich medium was inhibited by gamma-hch. this growth inhibition was not observed in a mutant that lacked the initial or second step enzymatic activity for gamma-hch degradation, suggesting that metabolites of gamma-hch are toxic to ut26. two metabolites of gamma-hch, 2,5-dichlorophenol (2,5-dcp) and 2,5-dichlorohydroquinone (2,5-dchq), showed a direct toxi ... | 2006 | 16636477 |
| plasmid pcar3 contains multiple gene sets involved in the conversion of carbazole to anthranilate. | the carbazole degradative car-i gene cluster (caraaibaibbiciaci) of sphingomonas sp. strain ka1 is located on the 254-kb circular plasmid pcar3. carbazole conversion to anthranilate is catalyzed by carbazole 1,9a-dioxygenase (cardo; caraaiaci), meta-cleavage enzyme (carbaibbi), and hydrolase (carci). cardo is a three-component dioxygenase, and caraai and caraci are its terminal oxygenase and ferredoxin components. the car-i gene cluster lacks the gene encoding the ferredoxin reductase component ... | 2006 | 16672458 |
| characterization of novel carbazole catabolism genes from gram-positive carbazole degrader nocardioides aromaticivorans ic177. | nocardioides aromaticivorans ic177 is a gram-positive carbazole degrader. the genes encoding carbazole degradation (car genes) were cloned into a cosmid clone and sequenced partially to reveal 19 open reading frames. the car genes were clustered into the caraacbabbacad and cardfe gene clusters, encoding the enzymes responsible for the degradation of carbazole to anthranilate and 2-hydroxypenta-2,4-dienoate and of 2-hydroxypenta-2,4-dienoate to pyruvic acid and acetyl coenzyme a, respectively. th ... | 2006 | 16672473 |
| modeling for gellan gum production by sphingomonas paucimobilis atcc 31461 in a simplified medium. | gellan gum production was carried out by sphingomonas paucimobilis atcc 31461 in a simplified medium with a short incubation time, and a kinetic model for understanding, controlling, and optimizing the fermentation process was proposed. the results revealed that glucose was the best carbon source and that the optimal concentration was 30 g liter(-1). as for the fermenting parameters, considerably large amounts of gellan gum were yielded by an 8-h-old culture and a 4% inoculum at 200 rpm on a rot ... | 2006 | 16672479 |
| population dynamics within a microbial consortium during growth on diesel fuel in saline environments. | the diversity and dynamics of a bacterial community extracted from an exploited oil field with high natural soil salinity near comodoro rivadavia in patagonia (argentina) were investigated. community shifts during long-term incubation with diesel fuel at four salinities between 0 and 20% nacl were monitored by single-strand conformation polymorphism community fingerprinting of the pcr-amplified v4-v5 region of the 16s rrna genes. information obtained by this qualitative approach was extended by ... | 2006 | 16672500 |
| utilizing ultrafiltration to remove alkaline phosphatase from clinical analyzer water. | alkaline phosphatase (alp) conjugated to antibodies is often used in enzyme immunoassays (eias). these assays are notably sensitive to experimental conditions. a possible source of interference is bacterial alp, which is released when bacterial contamination occurs in clinical analyzers. preliminary experiments led to the selection of a detection kit, alp source, and specific types of tubes for collecting water samples and performing assays. the release of alp from various strains of bacteria id ... | 2006 | 16681431 |
| author's reply to comment on "biological removal of polychlorinated dibenzo-p-dioxins from incinerator fly ash by sphingomonas wittichii rw1" by rolf u. halden. | 2006 | 16712898 | |
| biodesulfurization of alkylated forms of dibenzothiophene and benzothiophene by sphingomonas subarctica t7b. | sphingomonas subarctica t7b was isolated from soil in toyotomi, hokkaido, japan as an organism capable of desulfurizing aromatic hydrocarbons in light gas oil (lgo) through enrichment culture. s. subarctica t7b could grow on mineral salt sulfur-free (mssf) medium with the n-tetradecane oil phase containing dibenzothiophene (dbt), alkyl dibenzothiophenes (alkyl dbts) or alkyl benzothiophenes (alkyl bts) as the sole sulfur source and desulfurize these compounds, but could not utilize the tetradeca ... | 2006 | 16716940 |
| bioremediation of halogenated compounds: comparison of dehalogenating bacteria and improvement of catalyst stability. | five bacterial strains were compared for halogenated compounds conversion in aqueous media. depending on the strain, the optimal temperature for dehalogenase activity of resting cells varied from 30 to 45 degrees c, while optimal ph raised from 8.4 to 9.0. the most effective dehalogenase activity for 1-chlorobutane conversion was detected with rhodococcus erythropolis ncimb13064 and escherichia coli bl21 (de3) (dhaa). the presence of 2-chlorobutane or propanal in the aqueous media could inhibit ... | 2006 | 16723151 |
| structural basis for the enantiospecificities of r- and s-specific phenoxypropionate/alpha-ketoglutarate dioxygenases. | (r)- and (s)-dichlorprop/alpha-ketoglutarate dioxygenases (rdpa and sdpa) catalyze the oxidative cleavage of 2-(2,4-dichlorophenoxy)propanoic acid (dichlorprop) and 2-(4-chloro-2-methyl-phenoxy)propanoic acid (mecoprop) to form pyruvate plus the corresponding phenol concurrent with the conversion of alpha-ketoglutarate (alphakg) to succinate plus co2. rdpa and sdpa are strictly enantiospecific, converting only the (r) or the (s) enantiomer, respectively. homology models were generated for both e ... | 2006 | 16731970 |
| potential of a 16s rrna-based taxonomic microarray for analyzing the rhizosphere effects of maize on agrobacterium spp. and bacterial communities. | bacterial diversity is central to ecosystem sustainability and soil biological function, for which the role of roots is important. the high-throughput analysis potential of taxonomic microarray should match the breadth of bacterial diversity. here, the power of this technology was evidenced through methodological verifications and analysis of maize rhizosphere effect based on a 16s rrna-based microarray developed from the prototype of h. sanguin et al. (environ. microbiol. 8:289-307, 2006). the ... | 2006 | 16751545 |
| analysis of amino acid residues involved in catalysis of polyethylene glycol dehydrogenase from sphingopyxis terrae, using three-dimensional molecular modeling-based kinetic characterization of mutants. | polyethylene glycol dehydrogenase (pegdh) from sphingopyxis terrae (formerly sphingomonas terrae) is composed of 535 amino acid residues and one flavin adenine dinucleotide per monomer protein in a homodimeric structure. its amino acid sequence shows 28.5 to 30.5% identity with glucose oxidases from aspergillus niger and penicillium amagasakiense. the adp-binding site and the signature 1 and 2 consensus sequences of glucose-methanol-choline oxidoreductases are present in pegdh. based on three-di ... | 2006 | 16751555 |
| engineering a beta-carotene ketolase for astaxanthin production. | a new beta-carotene ketolase gene (crtw) was cloned from an environmental isolate sphingomonas sp. dc18. a robust and reliable color screen was developed for protein engineering to improve its activity on hydroxylated carotenoids for astaxanthin production. localized random mutagenesis was performed on the crtw gene including the upstream ribosomal binding site (rbs). six mutations (h96l, r203w, a205v, a208v, f213l and a215t) in the crtw gene were isolated multiple times that showed improved ast ... | 2006 | 16890469 |
| genetic labelling and application of the isoproturon-mineralizing sphingomonas sp. strain srs2 in soil and rhizosphere. | to construct a luxab-labelled sphingomonas sp. strain srs2 maintaining the ability to mineralize the herbicide isoproturon and usable for monitoring the survival and distribution of strain srs2 on plant roots in laboratory systems. | 2006 | 16910932 |
| effects of a small electric current on sterilization of a dental unit water line. | in the present study, water was circulated in a simulated dental unit water line with electrifying a small current. the morphology of the biofilm developed on inner surface of the water line and the number of heterotrophic bacteria were investigated to elucidate the effect of a low level electric current on the biofilms formation associated with bacteria reproduction. destruction and malconformation of biofilms by electrification was observed using sem, in addition to deformation and hypertrophy ... | 2006 | 16913572 |
| production and rheological characterization of biopolymer of sphingomonas capsulata atcc 14666 using conventional and industrial media. | this work was aimed at the production and rheological characterization of biopolymer by sphingomonas capsulata atcc 14666, using conventional and industrial media. the productivity reached the maximum of 0.038 g/l x h, at 208 rpm and 4% (w/v) of sucrose. for this condition, different concentrations of industrial medium were tested (2.66, 4, 6, and 8%). the best productivity was obtained using pretreated molasses 8% (w/v) (0.296 g/l x h), residue of textured soybean protein 6% (wt/v) (0.244 g/l x ... | 2006 | 16915702 |