Publications

diethyl phthalate in compost: ecotoxicological effects and response of the microbial community.	there is a great need to understand the environmental impacts of organic pollutants on soil health. phthalates are widely used in consumables and can be found extensively. we studied the toxicity of diethyl phthalate (dep), spiked in a compost plant growth substrate, by means of the acute toxicity flash test and on the basis of the germination and plant growth of radish seedlings. the response of the microbial community to dep in the growth substrate was studied by pcr-dgge (denaturing gradient ...	2007	17258270
dominance of sphingomonads in a copper-exposed biofilm community for groundwater treatment.	the structure, biological activity and microbial biodiversity of a biofilm used for the removal of copper from groundwater were studied and compared with those of a biofilm grown under copper-free conditions. a laboratory-scale submerged fixed biofilter was fed with groundwater (2.3 l h(-1)) artificially polluted with cu(ii) (15 mg l(-1)) and amended with sucrose (150 mg l(-1)) as carbon source. between 73 and 90 % of the cu(ii) was removed from water during long-term operation (over 200 days). ...	2007	17259604
sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity.	an aerobic, gram-negative, yellow-pigmented, non-motile bacterium, designated strain kmm 3882t, was isolated from a marine bivalve (anadara broughtoni) collected from peter the great bay, sea of japan, and was subjected to phenotypic and phylogenetic analyses. strain kmm 3882t was found to exert a remarkable inhibitory activity against a number of gram-positive micro-organisms. phylogenetic analysis based on 16s rrna gene sequences placed strain kmm 3882t within the genus sphingomonas, as an ind ...	2007	17267979
design of sphingomonad-detecting probes for a dna array, and its application to investigate the behavior, distribution, and source of rhizospherous sphingomonas and other sphingomonads inhabiting an acid sulfate soil paddock in kalimantan, indonesia.	throughout central and south kalimantan, indonesia, strongly acidic soil (ph 2.1-3.7) is widely distributed, and the local acidic soil-tolerant plants, including local rice varieties, often possess sphingomonads in their rhizosphere and rhizoplane. to investigate the behavior of sphingomonads inhabiting the rhizosphere of such acid-tolerant plants, we designed 13 different dna array probes (each of 72 mer) specific to a group of sphingomonads, using a hypervariable v6 region of the 16s rrna gene ...	2007	17284854
optimisation of the long-term efficacy of dental chair waterline disinfection by the identification and rectification of factors associated with waterline disinfection failure.	although many studies have highlighted the problem of biofilm growth in dental chair unit waterlines (duws), no long-term studies on the efficacy of duw disinfection using a large number of dental chair units (dcus) have been reported.	2007	17303302
isolation of a chlorpyrifos-degrading bacterium, sphingomonas sp. strain dsp-2, and cloning of the mpd gene.	a highly effective chlorpyrifos-degrading bacterium strain dsp-2 was isolated from the polluted treatment system of a chlorpyrifos manufacturer. this strain was preliminarily identified as sphingomonas sp. based on its morphological, physiological and biochemical tests as well as 16s rdna analysis. it utilized chlorpyrifos as its sole source of carbon for growth, by hydrolyzing chlorpyrifos to 3,5,6-trichloro-2-pyridinol (tcp). it could also utilize parathion, parathion-methyl, fenitrothion and ...	2007	17306510
17beta-estradiol-degrading bacteria isolated from activated sludge.	fourteen phylogenetically diverse 17beta-estradiol-degrading bacteria (strains kc1-14) were isolated from activated sludge of a wastewater treatment plant. these isolates widely distributed among eight different genera--aminobacter (strains kc6 and kc7), brevundimonas (strain kc12), escherichia (strain kc13), flavobacterium (strain kc1), microbacterium (strain kc5), nocardioides (strain kc3), rhodococcus (strain kc4), and sphingomonas (strains kc8-kc11 and kc14)--of three phyla: proteobacteria, ...	2007	17310711
molecular analysis of bacterial diversity in kerosene-based drilling fluid from the deep ice borehole at vostok, east antarctica.	decontamination of ice cores is a critical issue in phylogenetic studies of glacial ice and subglacial lakes. at the vostok drill site, a total of 3650 m of ice core have now been obtained from the east antarctic ice sheet. the ice core surface is coated with a hard-to-remove film of impure drilling fluid comprising a mixture of aliphatic and aromatic hydrocarbons and foranes. in the present study we used 16s rrna gene sequencing to analyze the bacterial content of the vostok drilling fluid samp ...	2007	17313578
decolorisation and detoxification of direct blue-15 by a bacterial consortium.	studies were carried out on decolorisation and biotransformation of the dye direct blue-15 into 3,3'-dimethoxybenzidine (o'-dianisidine) and a sulphonated derivative by a five-member bacterial consortium. chromatographic studies revealed further complete biodegradation of 3,3'-dimethoxybenzidine coupled with release of ammonia, but the recalcitrant sulphonated derivative persisted. the microorganisms identified in the mixed consortium by 16s rdna sequence analysis were alcaligenes faecalis, sphi ...	2007	17321737
microorganisms isolated from the water phase of tropospheric clouds at the puy de dôme: major groups and growth abilities at low temperatures.	this work constitutes the first large report on aerobic cultivable microorganisms present in cloud water. seven cloud-event samples were collected at the puy de dôme summit, and cultivation was performed leading to the isolation of 71 bacterial, 42 fungal and 15 yeast strains. most of the fungi isolated were of cladosporium or trametes affiliation, and yeasts were of cryptococcus affiliation. bacteria, identified on the basis of their 16s rrna gene sequence, were found to belong to actinobacteri ...	2007	17328765
cometabolic degradation of dibenzofuran and dibenzothiophene by a newly isolated carbazole-degrading sphingomonas sp. strain.	a carbazole-utilizing bacterium was isolated by enrichment from petroleum-contaminated soil. the isolate, designated sphingomonas sp. strain xldn2-5, could utilize carbazole (ca) as the sole source of carbon, nitrogen, and energy. washed cells of strain xldn2-5 were shown to be capable of degrading dibenzofuran (dbf) and dibenzothiophene (dbt). examination of metabolites suggested that xldn2-5 degraded dbf to 2-hydroxy-6-(2-hydroxyphenyl)-6-oxo-2,4-hexadienic acid and subsequently to salicylic a ...	2007	17337542
structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from sphingobium yanoikuyae b1.	the initial step involved in oxidative hydroxylation of monoaromatic and polyaromatic compounds by the microorganism sphingobium yanoikuyae strain b1 (b1), previously known as sphingomonas yanoikuyae strain b1 and beijerinckia sp. strain b1, is performed by a set of multiple terminal rieske non-heme iron oxygenases. these enzymes share a single electron donor system consisting of a reductase and a ferredoxin (bpdo-fb1). one of the terminal rieske oxygenases, biphenyl 2,3-dioxygenase (bpdo-ob1), ...	2007	17349044
effect of the mycorrhizosphere on the genotypic and metabolic diversity of the bacterial communities involved in mineral weathering in a forest soil.	to date, several bacterial species have been described as mineral-weathering agents which improve plant nutrition and growth. however, the possible relationships between mineral-weathering potential, taxonomic identity, and metabolic ability have not been investigated thus far. in this study, we characterized a collection of 61 bacterial strains isolated from scleroderma citrinum mycorrhizae, the mycorrhizosphere, and the adjacent bulk soil in an oak forest. the ability of bacteria to weather bi ...	2007	17351101
culturable leaf-associated bacteria on tomato plants and their potential as biological control agents.	culturable leaf-associated bacteria inhabiting a plant have been considered as promising biological control agent (bca) candidates because they can survive on the plant. we investigated the relationship between bacterial groups of culturable leaf-associated bacteria on greenhouse- and field-grown tomato leaves and their antifungal activities against tomato diseases in vitro and in vivo. in addition, the isolated bacteria were analyzed for n-acyl-homoserine lactone (ahl) and indole-3-acetic acid ...	2007	17356949
endogenous sphingolipid metabolites related to the growth in sphingomonas chungbukensis.	sphingolipids are present in animals, plants, fungi, yeasts and some bacteria. in mammalian cells sphingolipids act as lipid mediators for cell growth, differentiation, apoptosis and angiogenesis. in contrast, in bacteria the biological significance of sphingolipids has not been fully elucidated and sphingolipid metabolism has not been investigated. the aim of this study was to compare the pattern of sphingolipid metabolites in hit-t15 beta cells originating from hamster pancreas to that in the ...	2007	17424937
parameters controlling the gene-targeting frequency at the sphingomonas species rrn site and expression of the methyl parathion hydrolase gene.	to investigate the key parameters controlling the exogenous methyl parathion hydrolase (mph) gene mpd-targeting frequency at the ribosomal rna operon (rrn) site of sphingomonas species which has a wide range of biotechnological applications.	2007	17578423
bacterial synthesis of poly(hydroxybutyrate- co-hydroxyvalerate) using carbohydrate-rich mahua (madhuca sp.) flowers.	the objective of the present work was to utilize an unrefined natural substrate namely mahua (madhuca sp.) flowers, as a carbon source for the production of bacterial polyhydroxyalkanoate (pha) copolymer by bacillus sp-256.	2007	17584466
elucidation of the ipso-substitution mechanism for side-chain cleavage of alpha-quaternary 4-nonylphenols and 4-t-butoxyphenol in sphingobium xenophagum bayram.	recently we showed that degradation of several nonylphenol isomers with alpha-quaternary carbon atoms is initiated by ipso-hydroxylation in sphingobium xenophagum bayram (f. l. p. gabriel, a. heidlberger, d. rentsch, w. giger, k. guenther, and h.-p. e. kohler, j. biol. chem. 280:15526-15533, 2005). here, we demonstrate with 18o-labeling experiments that the ipso-hydroxy group was derived from molecular oxygen and that, in the major pathway for cleavage of the alkyl moiety, the resulting nonanol ...	2007	17369338
isolation and characterization of a novel bacterium, sphingomonas bisphenolicum strain ao1, that degrades bisphenol a.	bisphenol a (2,2-bis(4-hydroxyphenyl) propane, bpa), which is used as a synthetic resin material or a plasticizer, is a pollutant that possesses endocrine-disrupting activity. bioremediation of bpa is used to decrease its polluting effects, and here we report a novel bacterial strain ao1, which is able to degrade bpa. this strain was isolated using enrichment cultivation from a soil sample from a vegetable-growing field; the sample was one of 500 soil samples collected across japan. strain ao1 d ...	2007	16821103
evaluation of pyrrolidonyl arylamidase for the identification of nonfermenting gram-negative rods.	to evaluate the activity of pyrrolidonyl arylamidase (pyr) for the differentiation and identification of nonfermenting gram negative rods (nfgnr), 293 isolates were tested. a 24 h culture of each test organism was prepared. from this a 108-109 cfu/ml suspension was added to 0.25 ml of sterile physiologic solution. a pyr disk was then added and the test was incubated for 30 minutes at 35-37 degrees c, at environmental atmosphere. reading was done by adding 1 drop of cinnamaldehyde reagent. strain ...	2007	16822636
contribution to the detection and identification of oxidation metabolites of nonylphenol in sphingomonas sp. strain ttnp3.	sphingomonas sp. strain ttnp3 has been previously described as a bacterium that is capable of degrading the technical mixture of nonylphenol (np) isomers and also the 4(3',5'-dimethyl-3'-heptyl)-phenol single isomer of np. until recently, 3,5-dimethyl-3-heptanol was the only reported metabolite of 4(3',5'-dimethyl-3'-heptyl)-phenol. a short time ago, the detection of an intracellular metabolite resulting from the oxidation of 4(3',5'-dimethyl-3'-heptyl)-phenol which was identified as 2(3,5-dimet ...	2007	16821104
effect of heavy metals on the biodegradation of dibenzofuran in liquid medium.	the effect of heavy metals on the degradation of dibenzofuran by sphingomonas wittichii rw1 was determined in liquid cultures. the results showed that 10mg/l cadmium, mercury and copper not only affected the growth of rw1 with dibenzofuran but also the ability of resting cells to degrade this compound. growth and degradation were strongly inhibited by mercury, even at 1mg/l, while the inhibitory effect of cadmium and copper at the same concentration or at 5mg/l were negligible. in contrast, arse ...	2007	16879920
optimization of nutrients for gellan gum production by sphingomonas paucimobilis atcc-31461 in molasses based medium using response surface methodology.	a molasses based medium for the production of gellan by sphingomonas paucimobilis atcc-31461 was developed. placket-burman design criterion was applied to study the effect of various nutrient supplements on gellan production using molasses. among the 20 variables tested, molasses, tryptone, casaminoacid, disodium hydrogen orthophosphate and manganese chloride showed significant effect on gellan production. a central composite design was applied to determine the optimum concentrations of the sign ...	2007	16707262
a gene linb2 responsible for the conversion of beta-hch and 2,3,4,5,6-pentachlorocyclohexanol in sphingomonas sp. bhc-a.	commercial formulations of hexachlorocyclohexane (hch) consist of a mixture of four isomers: alpha, beta, gamma, and delta. all four isomers are toxic and recalcitrant pollutants. beta-hch is more problematic due to its longer persistence in the environment. sphingomonas sp. bhc-a was able to degrade not only alpha-, gamma-, and delta-hch but also beta-hch. to clone a gene responsible for the degradation of beta-hch, a tn5 mutation was introduced into bhc-a, and one mutant bhc-a45 defective in b ...	2007	16977465
microbial aspects of the interaction between soil depth and biodegradation of the herbicide isoproturon.	factors controlling change in biodegradation rate of the pesticide isoproturon with soil depth were investigated in a field with sandy-loam soil. soil was sampled at five depths between 0-10 and 70-80 cm. degradation rate declined progressively down the soil profile, with degradation slower, and relative differences in degradation rate between soil depths greater, in intact cores relative to sieved soil. neither the maximum rate of degradation, or sorption, changed with soil depth, indicating th ...	2007	16996107
biodegradation rates of 2-methylisoborneol (mib) and geosmin through sand filters and in bioreactors.	taste and odour (t&o) causing compounds, in particular, 2-methylisoborneol (mib) and geosmin, are a problem for water authorities as they are recalcitrant to conventional water treatment. in this study, biological sand filtration was shown to be an effective process for the complete removal of mib and geosmin, with removal shown to be predominantly through biodegradation. in addition, mib and geosmin were also effectively degraded in batch bioreactor experiments using biofilm sourced from one of ...	2007	17005238
study of substrate inhibition by electrophoretically mediated microanalysis in partially filled capillary.	substrate inhibition is a common phenomenon in enzyme kinetics. we report here for the first time its study by a combination of the electrophoretically mediated microanalysis (emma) methodology with a partial filling technique. in this setup, the part of capillary is filled with the buffer best for the enzymatic reaction whereas, the rest of the capillary is filled with the background electrolyte optimal for separation of substrates and products. in the case of haloalkane dehalogenase, a model e ...	2007	17010980
novel bacterial sulfur oxygenase reductases from bioreactors treating gold-bearing concentrates.	the microbial community and sulfur oxygenase reductases of metagenomic dna from bioreactors treating gold-bearing concentrates were studied by 16s rrna library, real-time polymerase chain reaction (rt-pcr), conventional cultivation, and molecular cloning. results indicated that major bacterial species were belonging to the genera acidithiobacillus, leptospirillum, sulfobacillus, and sphingomonas, accounting for 6.3, 66.7, 18.8, and 8.3%, respectively; the sole archaeal species was ferroplasma sp ...	2007	17111141
isolation of bacteria able to grow on both polyethylene glycol (peg) and polypropylene glycol (ppg) and their peg/ppg dehydrogenases.	two bacterial consortia growing on a random copolymer of ethylene glycol and propylene glycol units were obtained by enrichment cultures from various microbial samples. six major strains included in both consortia were purified and identified as sphingomonads, pseudomonas sp. and stenotrophomonas maltophilia. three of them (sphingobium sp. strain ek-1, sphingopyxis macrogoltabida strain ey-1, and pseudomonas sp. strain pe-2) utilized both peg and polypropylene glycol (ppg) as a sole carbon sourc ...	2007	17043822
simultaneous biodegradation of methyl parathion and carbofuran by a genetically engineered microorganism constructed by mini-tn5 transposon.	a genetically engineered microorganism (gem) capable of simultaneous degrading methyl parathion (mp) and carbofuran was successfully constructed by random insertion of a methyl parathion hydrolase gene (mpd) into the chromosome of a carbofuran degrading sphingomonas sp. cds-1 with the mini-transposon system. the gem constructed was relatively stable and cell viability and original degrading characteristic was not affected compared with the original recipient cds-1. the effects of temperature, in ...	2007	17091349
cyclodextrin-linked alginate beads as supporting materials for sphingomonas cloacae, a nonylphenol degrading bacteria.	calcium alginate beads covalently linked with alpha-cyclodextrin (alpha-cd-alginate beads) were prepared and examined for their ability to serve as a supporting matrix for bacterial degradation of nonylphenol, an endocrine disruptor. column chromatographic experiment using alpha-cd-alginate beads with diameter of 657+/-82 microm and with degree of cd substitution of 0.16 showed a strong affinity for nonylphenol adsorption. although addition of alpha-cd (2.7-27 mm) to the culture broth of sphingo ...	2007	17055261
deproteinization of gellan gum produced by sphingomonas paucimobilis atcc 31461.	deproteinization is a technical bottleneck in the purification of viscous water-soluble polysaccharides. the aim of this work is to provide an appropriate approach to deproteinize crude gellan gum. several methods of deproteinization were investigated, including sevag method, alkaline protease, papain and neutral protease. the results revealed that sevag method had high deproteinization efficiency (87.9%), but it showed dissatisfactory recovery efficiency of gellan gum (28.6%), which made it les ...	2007	17069918
enhanced degradation of a mixture of polycyclic aromatic hydrocarbons by a defined microbial consortium in a two-phase partitioning bioreactor.	biological treatment methods are effective at destroying polycyclic aromatic hydrocarbons (pahs), and some of the highest rates of pah degradation have been achieved using two-phase-partitioning bioreactors (tppbs). tppbs consist of a cell-containing aqueous phase and a biocompatible and immiscible organic phase that partitions toxic and/or recalcitrant substrates to the cells based on their metabolic demand and on maintaining the thermodynamic equilibrium of the system. in this study, the degra ...	2007	16758271
molecular microbial diversity of a soil sample and detection of ammonia oxidizers from cape evans, mcmurdo dry valley, antarctica.	the aim of our study was to estimate the uncultured eubacterial diversity of a soil sample collected below a dead seal, cape evans, mcmurdo, antarctica by an ssu rdna gene library approach. our study by sequencing of clones from ssu rdna gene library approach revealed high diversity in the soil sample from antarctica. more than 50% of clones showed homology to cytophaga-flavobacterium-bacteroides group; sequences also belonged to alpha, beta, gamma proteobacteria, thermus-deinococcus and high gc ...	2007	16517136
[contamination with sphingomonas paucimobilis: about seven cases isolated in conservation and transport mediums of corneal grafts].	from september to december 2004, contaminations were found in fifteen conservation and transport mediums of corneal grafts at the tissue bank of brest, including seven by sphingomonas paucimobilis. the pulsed-field gel electrophoresis made it possible to establish the genotypic profiles of each strain and to compare them. similarities were found between certain strains of the contaminated mediums and those of the thermostated double boiler of the tissue bank. the link between the contamination a ...	2007	16631318
aerobic degradation of diethyl phthalate by sphingomonas sp.	an aerobic diethyl phthalate (dep) degrading bacterium, dep-ad1, was isolated from activated sludge. based on its 16s rdna sequence, this isolate was identified belonging to sphingomonas genus with 99% similarity to sphingomonas sp. strain c28242 and 98% similarity to s. capsulate. the specific degradation rate of dep was concentration dependent with a maximum of 14 mg-dep/(lh). results of degradation tests showed that dep-ad1 could also degrade monoethyl phthalate (mep), dimethyl phthalate (dmp ...	2007	16563747
identification of opda, a gene involved in biodegradation of the endocrine disrupter octylphenol.	octylphenol (op) is an estrogenic detergent breakdown product. structurally similar nonylphenols are transformed via type ii ispo substitution, resulting in the production of hydroquinone and removal of the branched side chain. nothing is known, however, about the gene(s) encoding this activity. we report here on our efforts to clone the gene(s) encoding op degradation activity from sphingomonas sp. strain pwe1, which we isolated for its ability to grow on op. a fosmid library of pwe1 dna yielde ...	2007	17890335
microbial degradation of the biocide polyhexamethylene biguanide: isolation and characterization of enrichment consortia and determination of degradation by measurement of stable isotope incorporation into dna.	to isolate micro-organisms capable of utilizing polyhexamethylene biguanide (phmb) as a sole source of nitrogen, and to demonstrate biodegradation of the biocide.	2007	17897221
characterization of ligv essential for catabolism of vanillin by sphingomonas paucimobilis syk-6.	the vanillin dehydrogenase gene (ligv), which conferred the ability to transform vanillin into vanillate on escherichia coli, was isolated from sphingomonas paucimobilis syk-6. the ligv gene consists of a 1,440-bp open reading frame encoding a polypeptide with a molecular mass of 50,301 da. the deduced amino acid sequence of ligv showed about 50% identity with the known vanillin dehydrogenases of pseudomonas vanillin degraders. the gene product of ligv (ligv) produced in e. coli preferred nad+ t ...	2007	17928721
use of plate-wash samples to monitor the fates of culturable bacteria in mercury- and trichloroethylene-contaminated soils.	with the ultimate aim of developing bioremediation technology that use the optimum bacterial community for each pollutant, we performed polymerase chain reaction (pcr)-denaturing gradient gel electrophoresis (dgge) and phylogenetic analysis and identified communities of culturable bacteria in hgcl(2)- and trichloroethylene (tce)-contaminated soil microcosms. pcr-dgge band patterns were similar at 0 and 1 ppm hgcl(2), but changes in specific bands occurred at 10 ppm hgcl(2). band patterns appeari ...	2007	17940764
isolation of bacterial endophytes from germinated maize kernels.	the germination of surface-sterilized maize kernels under aseptic conditions proved to be a suitable method for isolation of kernel-associated bacterial endophytes. bacterial strains identified by partial 16s rrna gene sequencing as pantoea sp., microbacterium sp., frigoribacterium sp., bacillus sp., paenibacillus sp., and sphingomonas sp. were isolated from kernels of 4 different maize cultivars. genus pantoea was associated with a specific maize cultivar. the kernels of this cultivar were ofte ...	2007	17668041
aerobic degradation of lindane (gamma-hexachlorocyclohexane) in bacteria and its biochemical and molecular basis.	gamma-hexachlorocyclohexane (gamma-hch, also called gamma-bhc and lindane) is a halogenated organic insecticide that causes serious environmental problems. the aerobic degradation pathway of gamma-hch was extensively revealed in bacterial strain sphingobium japonicum (formerly sphingomonas paucimobilis) ut26. gamma-hch is transformed to 2,5-dichlorohydroquinone through sequential reactions catalyzed by lina, linb, and linc, and then 2,5-dichlorohydroquinone is further metabolized by lind, line, ...	2007	17634937
[microbial diversity in scorpion intestine (buthus martensii karsch)].	scorpion is an important officinal animal, and has a high nutritional value. in this study, the culture-independent and culture-dependent methods were used to investigate the microbial diversity in the scorpion's intestine. results based on culture-independent method showed the bacteria to be related to alpha, beta, gamma-proteobacteria. bacteria isolated by the culture-dependent method were high g + c, gram-positive bacteria. the genera enterobacter, serratia and ochrobactrum were detected by b ...	2007	18062268
a novel pathway for the biodegradation of gamma-hexachlorocyclohexane by a xanthomonas sp. strain ich12.	to isolate gamma-hexachlorocyclohexane (hch)-degrading bacteria from contaminated soil and characterize the metabolites formed and the genes involved in the degradation pathway.	2007	17578411
changes in bacterial populations and in biphenyl dioxygenase gene diversity in a polychlorinated biphenyl-polluted soil after introduction of willow trees for rhizoremediation.	the aim of this study was to analyze the structural and functional changes occurring in a polychlorinated-biphenyl (pcb)-contaminated soil ecosystem after the introduction of a suitable host plant for rhizoremediation (salix viminalis). we have studied the populations and phylogenetic distribution of key bacterial groups (alpha- and betaproteobacteria, acidobacteria, and actinobacteria) and the genes encoding iron-sulfur protein alpha (ispalpha) subunits of the toluene/biphenyl dioxygenases in s ...	2007	17693557
biological pretreatment with two bacterial strains for enzymatic hydrolysis of office paper.	the cellulose-hydrolyzing strains, sphingomonas paucimobilis mk1 and bacillus circulans mk2, were separated from soil and were grown together in a single culture plate. growth b. circulans mk2 in liquid culture required symbiosis with s. paucimobilis mk1. biological pretreatment with the combined strain suspension after the liquid culture improved enzymatic hydrolysis of office paper from municipal wastes. sugar recovery by s. paucimobilis mk1 (51%) was 1.4 times higher than that of the untreate ...	2007	17487532
enhanced degradation of benzo[a]pyrene by mycobacterium sp. in conjunction with green alga.	previous work in this laboratory has confirmed that the bacteria mycobacterium sp. strain rjgii.135 and sphingomonas yanoikuyae strain b1 and the green alga selanastrum capricornutum strain utex 1648 degrade benzo[a]pyrene (bap) to various bap intermediates. s. capricornutum was first grown with bap for 4 days. the organic extract of this media was then introduced into separate cultures of strain rjgii.135 and strain b1; separate cultures were grown with bap for comparison. cultures grown with b ...	2007	17555789
purification and characterization of a three-component salicylate 1-hydroxylase from sphingomonas sp. strain chy-1.	in the bacterial degradation of polycyclic aromatic hydrocarbons (pahs), salicylate hydroxylases catalyze essential reactions at the junction between the so-called upper and lower catabolic pathways. unlike the salicylate 1-hydroxylase from pseudomonads, which is a well-characterized flavoprotein, the enzyme found in sphingomonads appears to be a three-component fe-s protein complex, which so far has not been characterized. here, the salicylate 1-hydroxylase from sphingomonas sp. strain chy-1 wa ...	2007	17905882
isolation, identification, and degradation characteristics of phenazine-1-carboxylic acid-degrading strain sphingomonas sp. dp58.	a phenazine-1-carboxylic acid (pca)-degrading bacterium, strain dp58, was isolated from pimiento rhizosoil. based on morphology, physiologic tests, 16s rdna sequence, and phylogenetic characteristics, it was identified as sphingomonas sp. the pca-degradation experiments were conducted both in luria-bertani and inorganic salt medium at 28 degrees c. the relationship between bacterium growth and pca degradation suggested that strain dp58 could use pca as the sole source of carbon and nitrogen and ...	2007	17700987
differential responses of eubacterial, mycobacterium, and sphingomonas communities in polycyclic aromatic hydrocarbon (pah)-contaminated soil to artificially induced changes in pah profile.	recent reports suggest that mycobacterium is better adapted to soils containing poorly bioavailable polycyclic aromatic hydrocarbons (pahs) compared to sphingomonas. to study this hypothesis, artificial conditions regarding pah profile and pah bioavailability were induced in two pah-contaminated soils and the response of the eubacterial, mycobacterium, and sphingomonas communities to these changed conditions was monitored during laboratory incubation. soil k3663 with a relatively high proportion ...	2007	17766819
biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (pcbs).	bacteria and functional genes associated with biphenyl (bp) degradation in the root zone of an austrian pine (pinus nigra l.) growing naturally in polychlorinated-bp (pcb)-contaminated soil were identified using stable isotope probing (sip) integrated with comprehensive functional gene analyses. sip revealed 75 different genera that derived carbon from 13c-bp, with pseudonocardia, kribella, nocardiodes and sphingomonas predominating carbon acquisition. rhodococcus spp. were not detected with sip ...	2007	18043623
removal of organic load from olive washing water by an aerated submerged biofilter and profiling of the bacterial community involved in the process.	the present work aims to use a biofilter technology (aerated submerged filters) for the aerobic transformation at laboratory-scale of olive washing water (oww) generated in the first steps of olive oil processing, as well as the genetic profiling and identification to the species level of the bacteria involved in the formation of the biofilm, by means of tgge. chemical parameters, such as biological oxygen demand at five days (bod5) and chemical oxygen demand (cod), decreased markedly (up to 90 ...	2007	18051300
two bacterial entophytes eliciting both plant growth promotion and plant defense on pepper (capsicum annuum l.).	plant growth-promoting rhizobacteria (pgpr) have the potential to be used as microbial inoculants to reduce disease incidence and severity and to increase crop yield. some of the pgpr have been reported to be able to enter plant tissues and establish endophytic populations. here, we demonstrated an approach to screen bacterial endophytes that have the capacity to promote the growth of pepper seedlings and protect pepper plants against a bacterial pathogen. initially, out of 150 bacterial isolate ...	2007	18051359
degradation of carbazole by microbial cells immobilized in magnetic gellan gum gel beads.	polycyclic aromatic heterocycles, such as carbazole, are environmental contaminants suspected of posing human health risks. in this study, we investigated the degradation of carbazole by immobilized sphingomonas sp. strain xldn2-5 cells. four kinds of polymers were evaluated as immobilization supports for sphingomonas sp. strain xldn2-5. after comparison with agar, alginate, and kappa-carrageenan, gellan gum was selected as the optimal immobilization support. furthermore, fe(3)o(4) nanoparticles ...	2007	17827304
unique diversity of carotenoid-producing bacteria isolated from misasa, a radioactive site in japan.	we obtained carotenoid-producing microorganisms at a high frequency from water samples collected at misasa (tottori, japan), a region known for its high natural radioactivity content. a comprehensive 16s rrna gene-based phylogenetic analysis revealed that the 104 potential carotenoid producers isolated from misasa could be classified into 38 different species belonging to seven bacterial classes (flavobacteria, sphingobacteria, alpha-proteobacteria, gamma-proteobacteria, deinococci, actinobacter ...	2007	17828533
ipso-substitution: a general biochemical and biodegradation mechanism to cleave alpha-quaternary alkylphenols and bisphenol a.	sphingobium xenophagum bayram is capable of metabolizing 4-alkoxyphenols and endocrine disruptive alpha-quaternary 4-nonylphenols by an ipso-substitution mechanism that involves ring hydroxylation at the site of the substituent. here, we show that bayram's ipso-hydroxylating activity was able to transform also bisphenol a (= dimethyl-4,4'-methylenediphenol; bpa) and 4-isopropylphenol. we identified six metabolites when resting cells of strain bayram were incubated with bpa. they were unambiguous ...	2007	17886831
identification of bacteria from clinical samples using bartonella alpha-proteobacteria growth medium.	in an effort to overcome historical problems associated with the isolation of bartonella species from animal and human blood samples, our laboratory developed a novel, chemically modified, insect-based, liquid culture medium (bartonella alpha-proteobacteria growth medium, bapgm). in this study, we describe the isolation of non-bartonella bacteria from aseptically obtained human blood and tissue samples that were inoculated into bapgm pre-enrichment culture medium, and were obtained during attemp ...	2007	17889384
nosocomial outbreak of sphingomonas paucimobilis bacteremia in a hemato/oncology unit.	nosocomial sphingomonas paucimobilis infections can arise from contaminated water and the contaminated hands of hospital staff. within a 1-month period, we isolated six s. paucimobilis strains, including four from blood cultures of four patients and two from hospital environment specimens including tap water and a bathtub in a hemato/oncology unit. we described here these strains' molecular epidemiological analyses by pulsed-field gel electrophoresis (pfge) and antibiotic susceptibilities by e-t ...	2007	18032843
overlaps between the various biodegradation pathways in sphingomonas subarctica sa1.	a bacterium capable to grow on sulfanilic acid as sole carbon, nitrogen and sulfur source has been isolated. a unique feature of this strain is that it contains the full set of enzymes necessary for the biodegradation of sulfanilic acid. taxonomical analysis identified our isolate as sphingomonas subaretica sa1 sp. the biodegradation pathway of sulfanilic acid was investigated at the molecular level. screening the substrate specificity of the strain disclosed its capacity to degrade six analogou ...	2007	18297793
isolation of hexachlorocyclohexane-degrading sphingomonas sp. by dehalogenase assay and characterization of genes involved in gamma-hch degradation.	to screen and identify bacteria from contaminated soil samples which can degrade hexachlorocyclohexane (hch)-isomers based on dechlorinase enzyme activity and characterize genes and metabolites.	2008	18042212
activity and viability of polycyclic aromatic hydrocarbon-degrading sphingomonas sp. lb126 in a dc-electrical field typical for electrobioremediation measures.	there has been growing interest in employing electro-bioremediation, a hybrid technology of bioremediation and electrokinetics for the treatment of contaminated soil. knowledge however on the effect of weak electrokinetic conditions on the activity and viability of pollutant-degrading microorganisms is scarce. here we present data about the influence of direct current (dc) on the membrane integrity, adenosine triphosphate (atp) pools, physico-chemical cell surface properties, degradation kinetic ...	2008	21261821
rhizoremediation of lindane by root-colonizing sphingomonas.	we used a two-step enrichment approach to isolate root-colonizing hexachlorocyclohexane (hch)-degrading microorganisms. the first step consists of the use of classical liquid enrichment to isolate γ-hch degraders. the γ-hch-degrading microbes were attached in mass to corn seeds sown in soil with γ-hch, and after plant development we rescued bacteria growing on root tips. bacteria were then subjected to a second enrichment round in which growth on liquid medium with γ-hch and inoculation of corn ...	2008	21261825
metabolic degradation of phenazine-1-carboxylic acid by the strain sphingomonas sp. dp58: the identification of two metabolites.	the biotransformation of phenazine-1-carboxylic acid (pca) by pca-degrading strain sphingomonas sp. dp58 yielded small quantities of metabolites and was demonstrated for the first time. the metabolites were isolated by using preparative high-performance liquid chromatography (hplc). in addition, these were subsequently characterized by gas chromatography (gc)-mass spectrum (ms) after n,o-bis(trimethylsilyl)trifluoroacetamide (bstfa) derivatization and (1)h-nuclear magnetic resonance (nmr). they ...	2008	18097645
sphingomonas insulae sp. nov., isolated from soil.	a gram-negative, motile and rod-shaped sphingomonas-like bacterial strain, ds-28(t), was isolated from the soil of dokdo, korea, and was subjected to a polyphasic taxonomic study. it grew optimally at around ph 6.5 and 25 degrees c in the presence of 0-0.5% nacl. it contained q-10 as the predominant ubiquinone and c(18:1)omega7c, c(14:0) 2-oh and c(16:0) as the major fatty acids. major polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. th ...	2008	18175714
isolation and characterization of phenanthrene-degrading strains sphingomonas sp. zp1 and tistrella sp. zp5.	two bacteria strains sphingomonas sp. strain zp1 and tistrella sp. strain zp5 were identified as phenanthrene-degrading ones, based on gram staining, oxydase reaction, biochemical tests, fame analysis, g+c content and 16s rdna gene sequence analysis. we isolated these two bacteria strains sphingomonas sp. zp1 and tistrella sp. zp5 from soil samples contaminated with polycyclic aromatic hydrocarbon (pah)-containing waste from oil refinery field in shanghai, china. strain sphingomonas sp. zp1 was ...	2008	17850962
different bacterial groups for biodegradation of three- and four-ring pahs isolated from a hong kong mangrove sediment.	mangrove sediments have been found to degrade three- to four-ring pahs extensively. in the present study, 11 strains from 4 genera mycobacterium (3 strains), sphingomonas (5), terrabacter (2) and rhodococcus (1) were isolated from a single surface sediment sample of a hong kong mangrove swamp, among which the terrabacter strains were isolated to grow with fluoranthene for the first time. although all four genera could degrade three- and four-ring pahs, their in situ activities in natural sedimen ...	2008	17868985
de novo synthesis of a d-galacturonic acid thioglycoside as key to the total synthesis of a glycosphingolipid from sphingomonas yanoikuyae.	a concise synthesis of a differentially protected d-galacturonic acid (d-gala) thioglycoside and the construction of a potent immunomodulating glycosphingolipid are described. the key steps of the synthesis are an evans aldol reaction between a c4 aldehyde and a pmb-protected glycolyloxazolidinone as well as a tandem-pmb-deprotection/cyclization to thioglycosides. the key glycosylation step is optimized by varying the anomeric leaving group, the activating agent, and the solvent system.	2008	18363404
severe hypoglycemia associated with use of trimethoprim/sulfamethoxazole in a patient with chronic renal insufficiency.		2008	18364403
optimization of gellan gum production by sphingomonas paucimobilis atcc 31461 with nonionic surfactants using central composite design.	the effect of nonionic surfactants on gellan production by sphingomonas paucimobilis was studied by the addition of 0.5, 0.75, 1.0, 1.25 and 1.5 g/l surfactants to shake flask culture. the nonionic surfactants tween 80, tween 40 and triton x-100 improved gellan production by s. paucimobilis, and the maximum yield (10.44 g/l) was obtained with triton x-100 at 0.75 g/l compared with that of the control fermentation (8.63 g/l) without surfactant. the do profiles associated with gellan production in ...	2008	18397769
multi-factors on biodegradation kinetics of polycyclic aromatic hydrocarbons (pahs) by sphingomonas sp. a bacterial strain isolated from mangrove sediment.	biodegradation of polycyclic aromatic hydrocarbons (pahs) in contaminated sediment is an attractive remediation technique and its success depends on biodegradation kinetics, and the optimal condition for the pah-degrading isolates; however, information on this aspect is still scarce. the effects of multi-factors on biodegradation of phenanthrene, a 3-ring model pah, in contaminated sediment slurry by sphingomonas sp. a bacterial strain isolated from surface mangrove sediment, were investigated u ...	2008	18433800
isolation and characterization of marine bacterial strain degrading fucoidan from korean undaria pinnatifida sporophylls.	in spite of an increasing interest in fucoidans as biologically active compounds, no convenient commercial sources with fucoidanase activity are yet available. a marine bacterial strain that showed confluent growth on a minimal medium containing fucoidan, prepared from korean undaria pinnatifida sporophylls, as the sole carbon source was isolated and identified based on a 16s rdna sequence analysis as a strain of sphingomonas paucimobilis, and named sphingomonas paucimobilis pf-1. the strain dep ...	2008	18467852
molecular cloning and characterization of cytochrome p450 and ferredoxin genes involved in bisphenol a degradation in sphingomonas bisphenolicum strain ao1.	to clone and characterize the genes bisda and bisdb, encoding ferredoxin(bisd) (fd(bisd)) and cytochrome p450(bisd) (p450(bisd)), respectively, from the bisphenol a (bpa) degrading sphingomonas bisphenolicum strain ao1.	2008	18492046
identification and organization of genes for diutan polysaccharide synthesis from sphingomonas sp. atcc 53159.	a cluster of genes for diutan polysaccharide synthesis was isolated from a library of sphingomonas sp. atcc 53159 genomic dna by complementation of glucosyl-isoprenylphosphate transferase-deficient mutants of sphingomonas elodea atcc 31461 (producing gellan) and xanthomonas campestris (producing xanthan). the synthesis of polysaccharide in these strains shares a common first step, transfer of glucose-1-phosphate from udp-glucose to the isoprenylphosphate lipid. the cluster of 24 genes was compar ...	2008	18210176
microbial diversity of soil bacteria in agricultural field contaminated with heavy metals.	in this study we evaluated the bacterial diversity in a soil sample from a site next to a chemical industrial factory previously contaminated with heavy metals. analysis of 16s rdna sequences amplified from dna directly extracted from the soil revealed 17 different bacterial types (genera and/or species). they included polyangium spp., sphingomonas spp., variovorax spp., hafina spp., clostridia, acidobacteria, the enterics and some uncultured strains. microbes able to tolerate high concentration ...	2008	18595405
factors influencing the electrokinetic dispersion of pah-degrading bacteria in a laboratory model aquifer.	despite growing interest in the electro-bioremediation of contaminated soil it is still largely unknown to which degree weak electric fields influence the fate of contaminant-degrading microorganisms in the sub-surface. here we evaluate the factors influencing the electrokinetic transport and deposition of fluorene-degrading sphingomonas sp. lb126 in a laboratory model aquifer exposed to a direct current (dc) electric field (1 v cm(-1)) typically used in electro-bioremediation measures. the infl ...	2008	18607588
molecular characterization of the bacterial communities in the different compartments of a full-scale reverse-osmosis water purification plant.	the origin, structure, and composition of biofilms in various compartments of an industrial full-scale reverse-osmosis (ro) membrane water purification plant were analyzed by molecular biological methods. samples were taken when the ro installation suffered from a substantial pressure drop and decreased production. the bacterial community of the ro membrane biofilm was clearly different from the bacterial community present at other locations in the ro plant, indicating the development of a speci ...	2008	18621875
novel methylotrophic bacteria isolated from the river thames (london, uk).	enrichment and elective culture for methylotrophs from sediment of the river thames in central london yielded a diversity of pure cultures representing several genera of gram-negative and gram-positive bacteria, which were mainly of organisms not generally regarded as typically methylotrophic. substrates leading to successful isolations included methanol, monomethylamine, dimethylamine, trimethylamine, methanesulfonate and dimethylsulfone. several isolates were studied in detail and shown by the ...	2008	18681896
the screening, characterization, and use of omega-laurolactam hydrolase: a new enzymatic synthesis of 12-aminolauric acid.	several omega-laurolactam degrading microorganisms were isolated from soil samples. these strains were capable of growing in a medium containing omega-laurolactam as sole source of carbon and nitrogen. among them, five strains (t7, t31, u124, u224, and u238) were identified as cupriavidus sp. t7, acidovorax sp. t31, cupriavidus sp. u124, rhodococcus sp. u224, and sphingomonas sp. u238, respectively. the omega-laurolactam hydrolyzing enzyme from rhodococcus sp. u224 was purified to homogeneity, a ...	2008	18685217
biodegradation of dimethyl phthalate by sphingomonas sp. isolated from phthalic-acid-degrading aerobic granules.	phthalic acid esters (paes) contamination in water, air, and soil is one of the major environmental concerns in many countries. besides the pae biodegradation process, the pae degrading bacteria have become one of the focuses of study. this study reports the successful isolation of one kind of indigenous bacterium pa-02 from phthalic acid (pa)-degrading aerobic granules. based on its 16s ribosomal dna sequence, isolate pa-02 was identified as sphingomonas genus with 100% similarity to sphingomon ...	2008	18751698
modified sublimation to isolate phenanthrene-degrading bacteria of the genera sphingomonas and burkholderia from xiamen oil port.	sublimation was developed by alley and brown (2000) in order to isolate bacterial strains that were capable of degrading water insoluble compounds. in this study, sublimation was modified by the use of nutritional agar plates, instead of mineral salt agar, to isolate phenanthrene-degrading bacteria from a mixed culture that had been enriched under the selective pressure of high phenanthrene content. five strains were obtained with different morphology and degradation ability. based on the 16s rd ...	2008	18502449
substrate recognition by family 7 alginate lyase from sphingomonas sp. a1.	sphingomonas sp. a1 alginate lyase a1-ii', a member of polysaccharide lyase family 7, shows a broad substrate specificity acting on poly alpha-l-guluronate (poly(g)), poly beta-d-mannuronate (poly(m)) and the heteropolymer (poly(mg)) in alginate molecules. a1-ii' with a glove-like beta-sandwich as a basic scaffold forms a cleft covered with two lid loops (l1 and l2). here, we demonstrate the loop flexibility for substrate binding and structural determinants for broad substrate recognition and ca ...	2008	18514736
interactions among buffelgrass, phenanthrene and phenanthrene-degrading bacteria in gnotobiotic microcosms.	an experiment was undertaken in gnotobiotic microcosms to determine the role of buffelgrass (cenchrus ciliaris) and a phenanthrene-degrading bacterium (strain pm600) in the degradation of phenanthrene. the gram-negative bacterium was identified as a sphingomonas sp. by 16s rrna gene sequence analysis and as s. paucimobilis by biochemical tests (api 20 ne strips). its yellow pigment corresponded to nostoxanthin and its cellular fatty acids were typical of the genus sphingomonas. moreover, it was ...	2008	18569317
metabolism of the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (rdx) in a contaminated vadose zone.	the aim of this study was to explore biodegradation potential of hexahydro-1,3,5-trinitro-1,3,5-triazine (rdx) in a deep contaminated unsaturated zone over israel's coastal aquifer. while anaerobic biodegradation potential was observed throughout the profile down to the water table at a depth of 45m, aerobic biodegradation was limited to the surface of the unsaturated zone. traces of nitroso-rdx intermediates were detected in the soil samples, indicating possible in situ activity. polymerase cha ...	2008	18774159
protein engineering of improved prolyl endopeptidases for celiac sprue therapy.	due to their unique ability to cleave immunotoxic gluten peptides endoproteolytically, prolyl endopeptidases (peps) are attractive oral therapeutic candidates for protecting celiac sprue patients from the toxic effects of dietary gluten. enhancing the activity and stability of peps under gastric conditions (low ph, high pepsin concentration) is a challenge for protein engineers. using a combination of sequence- and structure-based approaches together with machine learning algorithms, we have ide ...	2008	18836204
[relationship between soil fungistasis and bacterial community structure].	as a natural attribute of clean and healthy soil, fungistasis is an important indicator of soil quality, and has positive ecological significance to the inhibition of plant disease eruption caused by soil-borne fungal pathogens. in this study, soil samples (0-15 cm) were collected from the abandoned land at shenyang experimental station of ecology, chinese academy of sciences, to which pesticides and fertilizers have never been applied for nearly 10 years. a series of soil samples with gradient ...	2008	18839921
[recognition and analysis on primary metabolites of nonylphenol].	in order to discuss the nonylphenol (np) biodegradability effect in the wastewater treatment process, the primary metabolites and route of np had been analyzed in the molecular level by the interpretation of gas chromatography mass spectrometry (gc-ms) and the two experimental methods. a method was that activated sludge degraded two types of simulating sewage comparatively. type-1 wastewater was made up of water, glucose, peptone and inorganic salts, and type-2 sewage was mixed up of np and type ...	2008	18637365
cloning and overexpression of alkaline phosphatase phok from sphingomonas sp. strain bsar-1 for bioprecipitation of uranium from alkaline solutions.	cells of sphingomonas sp. strain bsar-1 constitutively expressed an alkaline phosphatase, which was also secreted in the extracellular medium. a null mutant lacking this alkaline phosphatase activity was isolated by tn5 random mutagenesis. the corresponding gene, designated phok, was cloned and overexpressed in escherichia coli strain bl21(de3). the resultant e. coli strain ek4 overexpressed cellular activity 55 times higher and secreted extracellular phok activity 13 times higher than did bsar- ...	2008	18641147
characterization of the gut bacterial community in manduca sexta and effect of antibiotics on bacterial diversity and nematode reproduction.	the tobacco hornworm, manduca sexta, is a model lepidopteran insect used to study the pathogenic and mutualistic phases of entomopathogenic nematodes (epns) and their bacterial symbionts. while intestinal microbial communities could potentially compete with the epn and its bacterial partner for nutrient resources of the insect, the microbial gut community had not been characterized previously. here, we show that the midgut of m. sexta raised on an artificial diet contained mostly gram-positive c ...	2008	18647359
cloning and characterization of phosphoglucomutase and phosphomannomutase derived from sphingomonas chungbukensis dj77.	the enzymes phosphoglucomutase (pgm) and phosphomannomutase (pmm) play an important role in the synthesis of extracellular polysaccharide. by colony hybridization of the fosmid library of sphingomonas chungbukensis dj77, an open reading frame (orf-1) of 1,626 nucleotides, whose predicted product is highly homologous with other pgm proteins from several bacterial species, was identified. an additional open reading frame (orf-2) of 1,437 nucleotides was identified, and its encoded protein shows a ...	2008	18664520
decolorization of anthraquinone dye intermediate and its accelerating effect on reduction of azo acid dyes by sphingomonas xenophaga in anaerobic-aerobic process.	decolorization of 1-aminoanthraquinone-2-sulfonic acid (asa-2) and its accelerating effect on the reduction of azo acid dyes by sphingomonas xenophaga qyy were investigated. the study showed that asa-2 could be efficiently decolorized by strain qyy under aerobic conditions according to the analysis of total organic carbon removal and uv-vis spectra changes. moreover, strain qyy was able to reduce azo acid dyes under anaerobic conditions. the effects of various operating conditions such as carbon ...	2008	18074231
the negative interaction between the degradation of phenanthrene and tricyclazole in medium, soil and soil/compost mixture.	to assess the co-catabolism of phenanthrene and tricyclazole in different samples, the interaction during the degradation of phenanthrene and tricyclazole were investigated in medium, soil and soil/spent mushroom compost (smc) mixture. generally, tricyclazole showed a negative influence on the activity of phenanthrene dioxygenase and it inhibited the degradation of phenanthrene prominently, both in cultures of phenanthrene catabolic isolates (sphingomonas paucimobilis zx4 and the mixed flora m1) ...	2008	18189158
characterization of two compatible small plasmids from sphingobium yanoikuyae.	we isolated and characterized two small cryptic indigenous plasmids, pyan-1 (4,896 bp) and pyan-2 (4,687 bp), from sphingobium yanoikuyae, and developed a versatile system that permitted genetic manipulation of the genus sphingomonas. nucleotide sequencing of both plasmids revealed that they contained moba, mobs, and repa genes, which are predicted to encode proteins associated with mobilization and replication, in common. transformation with each plasmid harboring the antibiotic resistance gene ...	2008	18391447
crystal structure of a novel bacterial cell-surface flagellin binding to a polysaccharide.	bacterial flagellins are generally self-assembled into extracellular flagella for cell motility. however, the flagellin homologue p5 is found on the cell surface of sphingomonas sp. a1 (strain a1) and binds tightly to the alginate polysaccharide. to assimilate alginate, strain a1 forms a mouthlike pit on the cell surface and concentrates the polymer in the pit. p5 is a candidate receptor that recognizes extracellular alginate and controls pit formation. to improve our understanding of the struct ...	2008	18189419
diversity of endophytic bacterial communities in poplar grown under field conditions.	bacterial endophytes may be important for plant health and other ecologically relevant functions of poplar trees. the composition of endophytic bacteria colonizing the aerial parts of poplar was studied using a multiphasic approach. the terminal restriction fragment length polymorphism analysis of 16s rrna genes demonstrated the impact of different hybrid poplar clones on the endophytic community structure. detailed analysis of endophytic bacteria using cultivation methods in combination with cl ...	2008	18199082
discovery of a bacterial gene cluster for catabolism of the plant hormone indole 3-acetic acid.	the isolation and annotation of an 8994-bp dna fragment from pseudomonas putida 1290, which conferred upon p. putida kt2440 the ability to utilize the plant hormone indole 3-acetic acid (iaa) as a sole source of carbon and energy, is described. this iac locus (for indole 3-acetic acid catabolism) was identified through analysis of a plasposon mutant of p. putida 1290 that was no longer able to grow on iaa or indole 3-acetaldehyde and was unable to protect radish roots from stunting by exogenousl ...	2008	18205812
bacterial diversity in synovial fluids of patients with tmd determined by cloning and sequencing analysis of the 16s ribosomal rna gene.	the purpose of this study was to examine the presence of bacteria in synovial fluids from patients with temporomandibular joint disorder (tmd) by polymerase chain reaction (pcr) targeting the 16s ribosomal rna (rrna) gene, followed by cloning and sequencing.	2008	18206402
effect of rhamnolipids on degradation of anthracene by two newly isolated strains, sphingomonas sp. 12a and pseudomonas sp. 12b.	anthracene is a pah that is not readily degraded, plus its degradation mechanism is still not clear. thus, two strains of bacteria-degrading bacteria were isolated from longterm petroleum-polluted soil and identified as sphingomonas sp. 12a and pseudomonas sp. 12b by a 16s rrna sequence analysis. to further enhance the anthracene-degrading ability of the two strains, the biosurfactants produced by pseudomonas aeruginosa w3 were used, which were characterized as rhamnolipids. it was found that th ...	2008	18239418
effect of electrokinetic transport on the vulnerability of pah-degrading bacteria in a model aquifer.	there has been increasing interest in employing electro-bioremediation, a hybrid technology of bioremediation and electrokinetics, to overcome the low bioavailability of hydrophobic organic contaminants (hoc) by homogenizing sorption-retarded hoc and immobilised microorganisms. present electro-remediation approaches mainly aim at macroscale pollutant extraction and tend to neglect possible impacts of direct current (dc) on the physiology of microorganisms. the effect of weak electric fields (x = ...	2008	18253840
biodegradation potential and bacterial diversity of a petrochemical wastewater treatment plant in iran.	an activated sludge treatment was evaluated for its effectiveness in cleaning up a petrochemical wastewater in iran. for assessing biodegradation potential of activated sludge, seven characteristics of wastewater (temperature, ph, dissolved oxygen, chemical oxygen demand, concentrations of ethylene dichloride, vinyl chloride, and total hydrocarbons) were monitored during six months. it was shown that dominant pollutants in order of magnitude were normal-alkanes (c(10)-c(21)), aromatics, and poly ...	2008	18255283
superchannel of bacteria: biological significance and new horizons.	sphingomonas species a1 is a newly identified pit-forming bacterium that directly incorporates a macromolecule (alginate) into its cytoplasm through a pit-dependent transport system, which we termed a superchannel. a pit is a novel, high-dimensional organ acquired through the fluidity and reconstitution of cell surface molecules, including flagellin, and through cooperation with the transport machinery in the cells, which confers upon bacterial cells a more efficient way to secure and assimilate ...	2008	18256495