Publications

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
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
survey of environmental biocontamination on board the international space station.	the international space station (iss) is an orbital living and working environment extending from the original zarya control module built in 1998. the expected life span of the completed station is around 10 years and during this period it will be constantly manned. it is inevitable that the iss will also be home to an unknown number of microorganisms. this survey reports on microbiological contamination in potable water, air, and on surfaces inside the iss. the viable counts in potable water di ...	2006	16364606
influence of growth phase on the phospholipidic fatty acid composition of two marine bacterial strains in pure and mixed cultures.	this in vitro study was conducted in order to determine the effects of hydrocarbons and growth phase on the phospholipid ester-linked fatty acid composition of two marine sedimentary hydrocarbon-degrading bacteria. these two strains, namely corynebacterium sp. and sphingomonas sp. 2mpii, were cultivated on either a simple soluble substrate (ammonium acetate) or a hydrocarbon (respectively n-eicosane and phenanthrene). the incubations were stopped at different times corresponding to point of lag ...	2006	16380233
biotransformation of 1,2,3-tri- and 1,2,3,4,7,8-hexachlorodibenzo-p- dioxin by sphingomonas wittichii strain rw1.	sphingomonas wittichii rw1 is able to catabolize 1,2,3,4-tetrachlorodibenzo-p-dioxin (h. b. hong, y. s. chang, i. h. nam, p. fortnagel, and s. schmidt, appl. environ. microbiol. 68:2584-2588, 2002). here we demonstrate the aerobic bacterial catabolism of the ubiquitous toxic diaryl ether pollutant 1,2,3,4,7,8-hexachlorodibenzo-p-dioxin by this strain. the products of this biotransformation were identified as tetrachlorocatechol and 2-methoxy-3,4,5,6-tetrachlorophenol by comparing mass spectra re ...	2006	16391032
slow-release inoculation allows sustained biodegradation of gamma-hexachlorocyclohexane.	this study investigated the feasibility of a slow-release inoculation approach as a bioaugmentation strategy for the degradation of lindane (gamma-hexachlorocyclohexane [gamma-hch]). slow-release inoculation of sphingomonas sp. gamma 1-7 was established in both liquid and soil slurry microcosms using open-ended silicone tubes in which the bacteria are encapsulated in a protective nutrient-rich matrix. the capacity of the encapsulated cells to degrade lindane under aerobic conditions was evaluate ...	2006	16391099
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
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
characterization of four rhodococcus alcohol dehydrogenase genes responsible for the oxidation of aromatic alcohols.	four genes were isolated and characterized for alcohol dehydrogenases (adhs) catalyzing the oxidation of aromatic alcohols such as benzyl alcohol to their corresponding aldehydes, one from o-xylene-degrading rhodococcus opacus tkn14 and the other three from n-alkane-degrading rhodococcus erythropolis pr4. various aromatic alcohols were bioconverted to their corresponding carboxylic acids using escherichia coli cells expressing each of the four adh genes together with an aromatic aldehyde dehydro ...	2006	16292529
characterization of the novel hch-degrading strain, microbacterium sp. itrc1.	a gram-positive microbacterium sp. strain, itrc1, that was able to degrade the persistent and toxic hexachlorocyclohexane (hch) isomers was isolated and characterized. the itrc1 strain has the capacity to degrade all four major isomers of hch present in both liquid cultures and aged contaminated soil. dna fragments corresponding to the two initial genes involved in gamma-hch degradative pathway, encoding enzymes for gamma-pentachlorocyclohexene hydrolytic dehalogenase (linb) and a 2,5-dichloro-2 ...	2006	16315057
efficient production of 2-pyrone 4,6-dicarboxylic acid as a novel polymer-based material from protocatechuate by microbial function.	sphingomonas paucimobilis syk-6, which can degrade various low molecular weight compounds derived from plant polyphenols such as lignin, lignan, and tannin, metabolizes these substances via 2-pyrone-4,6-dicarboxylic acid (pdc). we focused on this metabolic intermediate as a potential raw material for novel, bio-based polymers. we cloned the ligab and ligc genes of syk-6, which respectively encode protocatechuate 4,5-dioxygenase and 4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase, into a ...	2006	16322989
distribution and phylogeny of hexachlorocyclohexane-degrading bacteria in soils from spain.	hexachlorocyclohexane (hch)-degrading bacteria are believed to mediate natural attenuation of hch contamination and have potential for active bioremediation processes. this study addressed the very limited understanding of the distribution, diversity and substrate specificity of such bacteria from 13 soil samples, varying in levels of hch contamination, from four sites in spain. hexachlorocyclohexane removal occurred in 16 of 36 enrichment cultures. hexachlorocyclohexane-degrading populations we ...	2006	16343322
composition of microbial communities in hexachlorocyclohexane (hch) contaminated soils from spain revealed with a habitat-specific microarray.	microarray technology was used to characterize and compare hexachlorocyclohexane (hch) contaminated soils from spain. a library of 2,290 hypervariable 16s rrna gene sequences was prepared with serial analysis of ribosomal sequence tags (sarst) from a composite of contaminated and uncontaminated soils. by designing hybridization probes specific to the 100 most abundant ribosomal sequence tags (rsts) in the composite library, the rst array was designed to be habitat-specific and predicted to monit ...	2006	16343328
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
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
isolation and physiological characterization of the pentachlorophenol degrading bacterium sphingomonas chlorophenolica.	many chlorophenols tend to persist in the environment, and they may become public health hazards. among chlorophenols, pentachlorophenol (pcp) is a priority pollutant that has been used widely as a general biocide in commercial wood treatment. owing to the rapid industrial growth, serious soil and water pollutions by chlorophenols has been reported in taiwan. in this study, 10 indigenous pcp-degrading bacterial strains were isolated from a pcp-degrading mixed culture, and the potential of both t ...	2006	16005492
the degradation of alpha-quaternary nonylphenol isomers by sphingomonas sp. strain ttnp3 involves a type ii ipso-substitution mechanism.	the degradation of radiolabeled 4(3',5'-dimethyl-3'-heptyl)-phenol [nonylphenol (np)] was tested with resting cells of sphingomonas sp. strain ttnp3. concomitantly to the degradation of np, a metabolite identified as hydroquinone transiently accumulated and short-chain organic acids were then produced at the expense of hydroquinone. two other radiolabeled isomers of np, 4(2',6'-dimethyl-2'-heptyl)-phenol and 4(3',6'-dimethyl-3'-heptyl)-phenol, were synthesized. in parallel experiments, the 4(2', ...	2006	16091931
expression of glycosylated haloalkane dehalogenase linb in pichia pastoris.	heterologous expression of the bacterial enzyme haloalkane dehalogenase linb from sphingomonas paucimobilis ut26 in methylotrophic yeast pichia pastoris is reported. the haloalkane dehalogenase gene linb was subcloned into the ppiczalphaa vector and integrated into the genome of p. pastoris. the recombinant linb secreted from the yeast was purified to homogeneity and biochemically characterized. the deglycosylation experiment and mass spectrometry measurements showed that the recombinant linb ex ...	2006	16216524
[presence of the microbiological risk in umbrian sawmills].	the purpose of this study was to quantify and identify the airborne microbial contamination in umbria sawmills. in this paper we reported the preliminary results of our analysis. microbial contaminants (fungi and bacteria) were assessed with passive (ima standard) and active (sas microbial sampler) methods. there were significant differences of bacterial and/or fungal cfu/m3 values between the outdoor and indoor environments during the normal sawmills activity. staphylococcus, sphingomonas, past ...	2006	17380948
characterization of alkylphenol degradation gene cluster in pseudomonas putida mt4 and evidence of oxidation of alkylphenols and alkylcatechols with medium-length alkyl chain.	alkylphenols (aps) are ubiquitous contaminants in aquatic environments and have endocrine disrupting and toxic effects on aquatic organisms. to investigate biodegradation mechanisms of aps, an ap degradation gene cluster was cloned from a butylphenol (bp)-degrading bacterium, pseudomonas putida mt4. the gene cluster consisted of 13 genes named bupba1a2a3a4a5a6cehifg. from the nucleotide sequences, bupa1a2a3a4a5a6 were predicted to encode a multicomponent phenol hydroxylase (ph), whereas bupbcehi ...	2006	17116584
molecular diversity studies of bacterial communities of oil polluted microbial mats from the etang de berre (france).	the biodiversity of microbial mats inhabiting the oil-contaminated lagoon etang de berre was determined by molecular approaches. the fingerprint of denaturing gradient gel electrophoresis (dgge) and automatic ribosomal intergenic spacer analysis (arisa) of mats exposed to different pollution levels showed specific microbial communities for each site but similar diversity richness. species composition of the mats were compared by constructing 16s rrna libraries. amplified rdna restriction analysi ...	2006	17117996
bacterial diversity in the active stage of a bioremediation system for mineral oil hydrocarbon-contaminated soils.	soils contaminated with mineral oil hydrocarbons are often cleaned in off-site bioremediation systems. in order to find out which bacteria are active during the degradation phase in such systems, the diversity of the active microflora in a degrading soil remediation system was investigated by small-subunit (ssu) rrna analysis. two sequential rna extracts from one soil sample were generated by a procedure incorporating bead beating. both extracts were analysed separately by generating individual ...	2006	17074900
statistical approach to optimization of fermentative production of gellan gum from sphingomonas paucimobilis atcc 31461.	gellan gum, a high-molecular-weight anionic linear polysaccharide produced by pure-culture fermentation from sphingomonas paucimobilis atcc 31461, has elicited industrial interest in recent years as a high-viscosity biogum, a suspending agent, a gelling agent, and an agar substitute in microbial media. in this paper we report on the optimization of gellan gum production using a statistical approach. in the first step, the one factor-at-a-time method was used to investigate the effect of medium c ...	2006	17046526
directed evolution of a non-heme-iron-dependent extradiol catechol dioxygenase: identification of mutants with intradiol oxidative cleavage activity.	the non-heme-iron(ii)-dependent extradiol catechol dioxygenases catalyse the oxidative cleavage of substituted catechols found on bacterial aromatic degradation pathways. the reaction mechanism of the extradiol dioxygenases is believed to proceed through the same proximal hydroperoxide intermediate as the iron(iii)-dependent intradiol catechol dioxygenases. directed evolution was carried out on members of the class iii extradiol catechol dioxygenases, by using 1) error-prone polymerase chain rea ...	2006	17051653
characterization of a naphthalene dioxygenase endowed with an exceptionally broad substrate specificity toward polycyclic aromatic hydrocarbons.	in sphingomonas chy-1, a single ring-hydroxylating dioxygenase is responsible for the initial attack of a range of polycyclic aromatic hydrocarbons (pahs) composed of up to five rings. the components of this enzyme were separately purified and characterized. the oxygenase component (ht-phni) was shown to contain one rieske-type [2fe-2s] cluster and one mononuclear fe center per alpha subunit, based on epr measurements and iron assay. steady-state kinetic measurements revealed that the enzyme had ...	2006	17014090
blooms of single bacterial species in a coastal lagoon of the southwestern atlantic ocean.	we investigated seasonal differences in community structure and activity (leucine incorporation) of the planktonic bacterial assemblage in the freshwater and brackish-water zones of a shallow coastal lagoon of the southwestern atlantic ocean. alphaproteobacteria formed the dominant microbial group in both zones throughout the sampling period. after an intrusion of marine water, members of the sar11 lineage became abundant in the brackish-water zone. these bacteria were apparently distributed ove ...	2006	17021206
[construction of double-labelled carbofuran-degrading bacterium sphingomonas sp. cds-1].	the genomic dna of a carbofuran-degrading bacterium sphingomonas sp. cds-1 was digested by sau3al and ligated to probe-gfp digested by bamhi, and the product was transformed to the e. coli dh5alpha competent cells. fifty positive clones that could emit green fluorescence under uv were selected from about 1 x 10(4) clones grown on selective plates amplb. one clone f7 with the strongest fluorescence was selected, the recombinant plasmid pf7 from this clone was digested with ecor i & hind iii and t ...	2006	17037065
removal of cyanobacteria, cyanotoxins, heterotrophic bacteria and endotoxins at an operating surface water treatment plant.	the removal of cyanobacteria, hepatotoxins produced by them (microcystins), phytoplankton, heterotrophic bacteria and endotoxins were monitored at a surface water treatment plant with coagulation, clarification, sand filtration, ozonation, slow sand filtration and chlorination as the treatment process. coagulation-sand filtration reduced microcystins by 1.2-2.4, and endotoxins by 0.72-2.01 log10 units. ozonation effectively removed the residual microcystins. the treatment process reduced phytopl ...	2006	17037128
degradability of dimethyl terephthalate by variovorax paradoxus t4 and sphingomonas yanoikuyae dos01 isolated from deep-ocean sediments.	two strains of bacteria were isolated from deep-ocean sediments of the south china sea using enrichment culturing technique and they were identified as sphingomonas yanoikuyae dos01 (ay878409) and variovorax paradoxus t4 (ay878410) based on 16s rrna gene sequences. s. yanoikuyae dos01 was only capable of transforming dimethyl terephthalate (dmtp) to monomethyl terephthalate (mmtp) without further degradation while v. paradoxus t4 exhibited ability in mineralizing dmtp as the sole source of carbo ...	2006	16955363
description of sphingobium fuliginis sp. nov., a phenanthrene-degrading bacterium from a fly ash dumping site, and reclassification of sphingomonas cloacae as sphingobium cloacae comb. nov.	a phenanthrene-degrading bacterium, strain tkp(t), was isolated from a fly ash dumping site of the thermal power plant in panki, kanpur, india, by an enrichment culture method using phenanthrene as the sole source of carbon and energy. phylogenetic analysis based on 16s rrna gene sequences indicated that the strain belonged to the genus sphingobium, as it showed highest sequence similarity to sphingobium herbicidovorans dsm 11019(t) (97.3 %) and sphingomonas cloacae jcm 10874(t) (96.5 %), compar ...	2006	16957112
sphingomonas dokdonensis sp. nov., isolated from soil.	a gram-negative, rod-shaped, sphingomonas-like bacterial strain, ds-4(t), was isolated from soil of dokdo, korea, and its taxonomic position was investigated using a polyphasic approach. strain ds-4(t) grew optimally on trypticase soy agar medium without nacl at ph 6.0-6.5 and 25 degrees c. it contained q-10 as the predominant ubiquinone and c(18 : 1)omega7c, c(16 : 0), c(14 : 0) 2-oh and c(16 : 1)omega7c and/or iso-c(15 : 0) 2-oh as the major fatty acids. sphingoglycolipid, phosphatidylcholine, ...	2006	16957115
identification and quantification of uncultivated proteobacteria associated with pyrene degradation in a bioreactor treating pah-contaminated soil.	uncultivated bacteria associated with the degradation of pyrene in a bioreactor treating soil contaminated with polycyclic aromatic hydrocarbons (pah) were identified by dna-based stable-isotope probing (sip) and quantified by real-time quantitative pcr. most of the 16s rrna gene sequences recovered from (13)c-enriched dna fractions clustered phylogenetically within three separate groups of beta- and gamma-proteobacteria unassociated with described genera and were designated "pyrene groups 1, 2 ...	2006	16958754
novel upper meta-pathway extradiol dioxygenase gene diversity in polluted soil.	for the determination of the catabolic community diversity that is related to biodegradation potential, we developed a protocol for the assessment of catabolic marker genes in polluted soils. primers specific to upper pathway extradiol dioxygenase genes were designed which amplified a 469-bp product from sphingomonas sp. hv3. the constructed primers were used in pcr amplification of upper pathway ring cleavage genes from dna directly isolated from a mineral oil polluted landfill site, a mineral ...	2006	16958914
linear 3-hydroxybutyrate tetramer (hb4) produced by sphingomonas sp. is characterized as a growth promoting factor for some rhizomicrofloral composers.	sphingomonas spp. of alpha-proteobacteria often play a role in assisting the development of microfloral communities under adverse soil conditions. using a frateuria sp. as an indicator for bacterial growth assay, we investigated the bacterial growth-promoting factor in the culture fluids of sphingomonas sp. ec-k085. this factor was successfully isolated and identified as linear (r,r,r,r)-3-hydroxybutyrate tetramer (hb4), having a hydroxy-end and a carboxy-end group. when 28 mug of hb4 was charge ...	2006	16960351
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
natural killer t cells recognize diacylglycerol antigens from pathogenic bacteria.	natural killer t (nkt) cells recognize glycosphingolipids presented by cd1d molecules and have been linked to defense against microbial infections. previously defined foreign glycosphingolipids recognized by nkt cells are uniquely found in nonpathogenic sphingomonas bacteria. here we show that mouse and human nkt cells also recognized glycolipids, specifically a diacylglycerol, from borrelia burgdorferi, which causes lyme disease. the b. burgdorferi-derived, glycolipid-induced nkt cell prolifera ...	2006	16921381
genetic diversity of dioxygenase genes in polycyclic aromatic hydrocarbon-degrading bacteria isolated from mangrove sediments.	to investigate the diversity of dioxygenase genes involved in polycyclic aromatic hydrocarbon (pah)-degradation, a total of 32 bacterial strains were isolated from surface mangrove sediments, from the genera mycobacterium, sphingomonas, terrabacter, sphingopyxis, sphingobium and rhodococcus. two sets of pcr primers were constructed to detect the nida-like and nahac-like sequences of the alpha subunit of the pah ring-hydroxylating dioxygenase. pcr amplified the dna fragments from all gram-positiv ...	2006	16923069
cloning, expression, purification, crystallization and preliminary structure determination of glucose-1-phosphate uridylyltransferase (ugpg) from sphingomonas elodea atcc 31461 bound to glucose-1-phosphate.	the cloning, expression, purification, crystallization and preliminary crystallographic analysis of glucose-1-phosphate uridylyltransferase (ugpg) from sphingomonas elodea atcc 31461 bound to glucose-1-phosphate are reported. diffraction data sets were obtained from seven crystal forms in five different space groups, with highest resolutions ranging from 4.20 to 2.65 a. the phase problem was solved for a p2(1) crystal form using multiple isomorphous replacement with anomalous scattering from an ...	2006	16946483
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
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
microbial degradation of nonylphenol and other alkylphenols--our evolving view.	because the endocrine disrupting effects of nonylphenol (np) and octylphenol became evident, the degradation of long-chain alkylphenols (ap) by microorganisms was intensively studied. most np-degrading bacteria belong to the sphingomonads and closely related genera, while np metabolism is not restricted to defined fungal taxa. growth on np and its mineralization was demonstrated for bacterial isolates, whereas ultimate degradation by fungi still remains unclear. while both bacterial and fungal d ...	2006	16826376
multisubstrate biodegradation kinetics for binary and complex mixtures of polycyclic aromatic hydrocarbons.	biodegradation kinetics were studied for binary and complex mixtures of nine polycyclic aromatic hydrocarbons (pahs): naphthalene, 1-methylnaphthalene, 2-methylnaphthalene, 2-ethylnaphthalene, phenanthrene, anthracene, pyrene, fluorene, and fluoranthene. discrepancies between the observed biodegradation rates and those predicted by a sole-substrate model indicate that significant substrate interactions occurred in both the binary and complex-mixture experiments. for all compounds except naphthal ...	2006	16833134
removal and biodegradation of polycyclic aromatic hydrocarbons by selenastrum capricornutum.	the removal and degradation of a mixture of polycyclic aromatic hydrocarbons (pahs), namely phenanthrene (phe), fluoranthene (fla), and pyrene (pyr), by a green microalgal species, selenastrum capricornutum, at different initial cell densities were studied. the pah removal efficiency increased with the initial cell density, and 96% of phe, 100% of fla, and 100% of pyr in the medium were removed by live s. capricornutum at the density of 1 x 10(7) cells/ml in 4 d, whereas less than 50% of pahs we ...	2006	16833137
bacterial decontamination of duwl biofilm using oxygenal 6.	the aim of this study was bacteriological assessment of the dental unit waterlines (duwl) biofilm - concentration and composition of the aerobe and facultative anaerobe bacterial microflora, and evaluation of the influence of a disinfecting product, oxygenal 6, on the biofilm composition. tubing fragments were taken from 25 units twice, before and after disinfection, and bacterial suspension of the biofilm was obtained from the samples. the bacterial flora was determined with the plate culture m ...	2006	16841887
functional and transcriptional analyses of the initial oxygenase genes for acenaphthene degradation from sphingomonas sp. strain a4.	sphingomonas sp. strain a4 is capable of utilizing acenaphthene as its sole carbon and energy source. to isolate the genes responsible for acenaphthene degradation, transposon mutagenesis was performed on strain a4 and four mini-tn5-inserted mutants lacking the ability to utilize acenaphthene were isolated. in three of the four mini-tn5 inserted mutants, the mini-tn5s were inserted into the same locus (within about 16 kb) as the arha1a2 genes, which had previously been identified as the genes en ...	2006	16849808
postoperative endophthalmitis caused by sphingomonas paucimobilis.	we present a case in which a new organism, sphingomonas paucimobilis, caused endophthalmitis after phacoemulsification in a 73-year-old woman. the case shows a recurrent acute endophthalmitis with complete resolution only after vitrectomy. this organism has not been described as a cause of endophthalmitis and was resistant to initial medical management. we also describe an interaction between this organism and a co-infective organism that may account for the unusual clinical course.	2006	16857516
cutting edge: impaired glycosphingolipid trafficking and nkt cell development in mice lacking niemann-pick type c1 protein.	niemann-pick type c1 (npc1) is a late endosomal/lysosomal transmembrane protein involved in the cellular transport of glycosphingolipids and cholesterol that is mutated in a majority of patients with niemann-pick c neurodegenerative disease. we found that npc1-deficient mice lacked valpha14-jalpha18 nkt cells, a major population of cd1d-restricted t cells that is conserved in humans. npc1-deficient mice also exhibited marked defects in the presentation of sphingomonas cell wall ags to nkt cells ...	2006	16785493
caver: a new tool to explore routes from protein clefts, pockets and cavities.	the main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent.	2006	16792811
gram-negative bacteria from patients seeking medical advice in stockholm after the tsunami catastrophe.	microbiological cultures from 229 patients seeking medical advice in stockholm after the tsunami catastrophe of december 2004 were analysed at the clinical microbiology laboratory, karolinska university hospital, stockholm, sweden. gram-negative bacilli were the most common findings from wound cultures. common human pathogens such as escherichia coli, proteus species, klebsiella spp., and pseudomonas aeruginosa were isolated. more rare species of gram-negative bacilli, e.g. myroides odoratus, sp ...	2006	16798691
identification and functional analysis of the genes for naphthalenesulfonate catabolism by sphingomonas xenophaga bn6.	sphingomonas xenophaga bn6 degrades various (substituted) naphthalenesulfonates to the corresponding (substituted) salicylates. a gene cluster was identified on the plasmid pbn6 which coded for several enzymes participating in the degradative pathway for naphthalenesulfonates. a dna fragment of 16 915 bp was sequenced which contained 17 orfs. the genes encoding the 1,2-dihydroxynaphthalene dioxygenase, 2-hydroxychromene-2-carboxylate isomerase, and 2'-hydroxybenzalpyruvate aldolase of the naphth ...	2006	16804169
cloning and expression of the gene for periplasmic poly(vinyl alcohol) dehydrogenase from sphingomonas sp. strain 113p3, a novel-type quinohaemoprotein alcohol dehydrogenase.	a gene for periplasmic poly(vinyl alcohol) (pva) dehydrogenase (pvadh) was cloned, based on the n-terminal amino acid sequence of the purified pvadh from sphingomonas sp. 113p3 and the sequence of the gene for pvadh (pvaa, genbank accession no. ab190288). the recombinant pvadh tagged with hexahistidine was expressed in escherichia coli and purified to homogeneity. the recombinant enzyme had the same characteristics as the purified enzyme from sphingomonas sp. strain 113p. in addition to pva, the ...	2006	16804170
bacterial community in ancient siberian permafrost as characterized by culture and culture-independent methods.	the microbial composition of ancient permafrost sediments from the kolyma lowland of northeast eurasia was examined through culture and culture-independent approaches. these sediments have been continuously frozen for 5,000 to 2-3 million years. a total of 265 bacteria 16s rrna gene sequences were amplified from the permafrost total-community genomic dna and screened by amplified ribosomal 16s rrna restriction analysis. members of three major lineages were found: gamma-proteobacteria (mostly xan ...	2006	16805696
characterization of hydrocarbonoclastic bacterial communities from mangrove sediments in guanabara bay, brazil.	hydrocarbonoclastic bacterial communities inhabiting mangrove sediments were characterized by combining molecular and culture-dependent approaches. surface sediments were collected at two sampling sites in guanabara bay (rio de janeiro, brazil) and used to inoculate in vitro enrichment cultures containing crude oil to obtain hydrocarbonoclastic bacterial consortia. in parallel, in situ mesocosms (located in the guapimirim mangrove) were contaminated with petroleum. comparison of bacterial commun ...	2006	16815684
purification and characterization of an arene cis-dihydrodiol dehydrogenase endowed with broad substrate specificity toward polycyclic aromatic hydrocarbon dihydrodiols.	initial reactions involved in the bacterial degradation of polycyclic aromatic hydrocarbons (pahs) include a ring-dihydroxylation catalyzed by a dioxygenase and a subsequent oxidation of the dihydrodiol products by a dehydrogenase. in this study, the dihydrodiol dehydrogenase from the pah-degrading sphingomonas strain chy-1 has been characterized. the bphb gene encoding pah dihydrodiol dehydrogenase (pddh) was cloned and overexpressed as a his-tagged protein. the recombinant protein was purified ...	2006	16820465
purification and characterization of two enantioselective alpha-ketoglutarate-dependent dioxygenases, rdpa and sdpa, from sphingomonas herbicidovorans mh.	alpha-ketoglutarate-dependent (r)-dichlorprop dioxygenase (rdpa) and alpha-ketoglutarate-dependent (s)-dichlorprop dioxygenase (sdpa), which are involved in the degradation of phenoxyalkanoic acid herbicides in sphingomonas herbicidovorans mh, were expressed and purified as his6-tagged fusion proteins from escherichia coli bl21(de3)(plyss). rdpa and sdpa belong to subgroup ii of the alpha-ketoglutarate-dependent dioxygenases and share the specific motif hxdx(24)tx(131)hx(10)r. amino acids his-11 ...	2006	16820480
improvement in production and quality of gellan gum by sphingomonas paucimobilis under high dissolved oxygen tension levels.	the effect of agitation rate and dissolved oxygen tension (dot) on growth and gellan production by sphingomonas paucimobilis was studied. higher cell growth of 5.4 g l(-1) was obtained at 700 rpm but maximum gellan (15 g l(-1)) was produced at 500 rpm. dot levels above 20% had no effect on cell growth but gellan yield was increased to 23 g l(-1 )with increase in dot level to 100%. higher dot levels improved the viscosity and molecular weight of the polymer with change in acetate and glycerate co ...	2006	16820976
[isolation, identification and characteristics of a fenpropathrin-degrading bacterium jql4-5].	a bacterium capable of utilizing fenpropathrin as sole carbon source was isolated from activated sludge collected from wastewater treating system of a pesticide manufacturer. this bacterium was identified as sphingomonas sp. according to its physiological & biochemical analysis and the similarity analysis of its 16s rdna sequence (genbank accession no. dq177525). this bacterium could degrade 99.8% of 20 mg/l fenpropathrin in 24h. the optimal ph and temperature for the degradation were 7.0 and 30 ...	2006	17256618
[analysis of the degrading products of carbofuran by sphingomonas sp. with gc/ms and gc/ftir].	in different degrading phases, the degrading products of carbofuran by cds-1(sphingomonas sp. ) were extracted by acetone. according to the analysis of gas chromatography/mass spectrometry (gc/ms), carbofuran-7-phenol was identified as the initial degrading product, and an unknown metabolite with molecular weight of 182 was determined as 2-hydroxyl-3-tertiarybutylalcohol-phenol, which was the next degrading product of carbofuran-7-phenol. according to the analysis of gc/ms and gas chromatography ...	2006	17112053
[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
16s rdna phylogeny and distribution of lin genes in novel hexachlorocyclohexane-degrading sphingomonas strains.	hexachlorocyclohexane (hch) is a highly recalcitrant pesticide that persists in soils. three novel hch-degrading strains (ds2, ds2-2 and ds3-1) were isolated after enrichment from hch-contaminated soil from germany. these strains efficiently degraded the alpha-, gamma- and delta-isomers of hch, while strain ds3-1 also degraded beta-hch. based on 16s rdna analysis, strain ds3-1 was closely related to sphingomonas taejonensis, while strains ds2 and ds2-2 were closely related to sphingomonas flava ...	2005	16104856
ecochemical studies of interrelationships between epiphytic bacteria and host plants via secondary metabolites.	the plant surface, which is representative of the phylloplane and rhizoplane, is a characteristic habitat for microorganisms. in this review, the ecological roles of phytoepiphytic bacteria will be described. the phylloplane and rhizoplane, which are adjacent to the atmosphere and soil sphere respectively, accumulate topically and/or selectively release secondary metabolites that are specific to the plant genera and species which reside within these regions. some epiphytes have abilities to deca ...	2005	16116269
a second 5-carboxyvanillate decarboxylase gene, ligw2, is important for lignin-related biphenyl catabolism in sphingomonas paucimobilis syk-6.	a lignin-related biphenyl compound, 5,5'-dehydrodivanillate (ddva), is degraded to 5-carboxyvanillate (5cva) by the enzyme reactions catalyzed by ddva o-demethylase (ligx), meta-cleavage oxygenase (ligz), and meta-cleavage compound hydrolase (ligy) in sphingomonas paucimobilis syk-6. 5cva is then transformed to vanillate by a nonoxidative 5cva decarboxylase and is further degraded through the protocatechuate 4,5-cleavage pathway. a 5cva decarboxylase gene, ligw, was isolated from syk-6 (x. peng, ...	2005	16151081
recovery of microbially mediated processes in soil augmented with a pentachlorophenol-mineralizing bacterium.	specific physiological groups can be used to evaluate the recovery of soil microbial communities following disturbance. in this study, soil was contaminated with pentachlorophenol (pcp) to assess the resiliency of microorganisms responsible for carbon and nitrogen cycling. methane fluxes were monitored in soil microcosms to evaluate the effects of contamination and augmentation on microbial populations involved in carbon cycling. the addition of a pcp-mineralizing bacterium, sphingomonas chlorop ...	2005	16152961
hexachlorocyclohexane-degrading bacterial strains sphingomonas paucimobilis b90a, ut26 and sp+, having similar lin genes, represent three distinct species, sphingobium indicum sp. nov., sphingobium japonicum sp. nov. and sphingobium francense sp. nov., and reclassification of [sphingomonas] chungbukensis as sphingobium chungbukense comb. nov.	three strains of sphingomonas paucimobilis, b90a, ut26 and sp+, isolated from different geographical locations, were found to degrade hexachlorocyclohexane. phylogenetic analysis based on 16s rrna gene sequences indicated that these strains do not fall in a clade that includes the type strain, sphingomonas paucimobilis atcc 29837(t), but form a coherent cluster with [sphingomonas] chungbukensis imsnu 11152(t) followed by sphingobium chlorophenolicum atcc 33790(t). the three strains showed low dn ...	2005	16166696
formation of catechols via removal of acid side chains from ibuprofen and related aromatic acids.	although ibuprofen [2-(4-isobutylphenyl)-propionic acid] is one of the most widely consumed drugs in the world, little is known regarding its degradation by environmental bacteria. sphingomonas sp. strain ibu-2 was isolated from a wastewater treatment plant based on its ability to use ibuprofen as a sole carbon and energy source. a slight preference toward the r enantiomer was observed, though both ibuprofen enantiomers were metabolized. a yellow color, indicative of meta-cleavage, accumulated t ...	2005	16204529
recognition of bacterial glycosphingolipids by natural killer t cells.	natural killer t (nkt) cells constitute a highly conserved t lymphocyte subpopulation that has the potential to regulate many types of immune responses through the rapid secretion of cytokines. nkt cells recognize glycolipids presented by cd1d, a class i-like antigen-presenting molecule. they have an invariant t-cell antigen receptor (tcr) alpha-chain, but whether this invariant tcr recognizes microbial antigens is still controversial. here we show that most mouse and human nkt cells recognize g ...	2005	15791257
exogenous and endogenous glycolipid antigens activate nkt cells during microbial infections.	cd1d-restricted natural killer t (nkt) cells are innate-like lymphocytes that express a conserved t-cell receptor and contribute to host defence against various microbial pathogens. however, their target lipid antigens have remained elusive. here we report evidence for microbial, antigen-specific activation of nkt cells against gram-negative, lipopolysaccharide (lps)-negative alpha-proteobacteria such as ehrlichia muris and sphingomonas capsulata. we have identified glycosylceramides from the ce ...	2005	15791258
direct evidence for sphingomonas sp. a1 periplasmic proteins as macromolecule-binding proteins associated with the abc transporter: molecular insights into alginate transport in the periplasm.	a gram-negative bacterium, sphingomonas sp. a1, has a macromolecule (alginate) import system consisting of a pit on the cell surface and an alginate-specific atp-binding cassette importer in the inner membrane. transport of alginate from the pit to the abc importer is probably mediated by two periplasmic binding protein homologues (algq1 and algq2). here we describe characteristics of binding of algq1 and algq2 to alginate and its oligosaccharides through surface plasmon resonance biosensor anal ...	2005	15794643
diversity of carbazole-degrading bacteria having the car gene cluster: isolation of a novel gram-positive carbazole-degrading bacterium.	twenty-seven carbazole-utilizing bacterial strains were isolated from environmental samples, and were classified into 14 groups by amplified ribosomal dna restriction analysis. southern hybridization analyses showed that 3 and 17 isolates possessed the car gene homologs of pseudomonas resinovorans ca10 and sphingomonas sp. strain ka1, respectively. of the 17 isolates, 2 isolates also have the homolog of the caraa gene of sphingomonas sp. strain cb3. while the genome of one isolate, a gram-positi ...	2005	15796992