Publications

utilizing ultrafiltration to remove alkaline phosphatase from clinical analyzer water.	alkaline phosphatase (alp) conjugated to antibodies is often used in enzyme immunoassays (eias). these assays are notably sensitive to experimental conditions. a possible source of interference is bacterial alp, which is released when bacterial contamination occurs in clinical analyzers. preliminary experiments led to the selection of a detection kit, alp source, and specific types of tubes for collecting water samples and performing assays. the release of alp from various strains of bacteria id ...	2006	16681431
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
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
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
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 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
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
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
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
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
polyphosphate accumulation among denitrifying bacteria in activated sludge.	bacterial polyphosphate accumulation and denitrification are important processes in biological removal of nutrients from wastewater. it has been suggested that phosphorus accumulators are able to denitrify. however, the bacteria known as the most important phosphorus accumulators, belonging to the genus acinetobacter are generally not known to denitrify. to clarify how commonly both physiological traits are present in the same organism, we screened 165 isolates from activated sludge and wastewat ...	1995	16887523
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
novel organization of catechol meta pathway genes in the nitrobenzene degrader comamonas sp. js765 and its evolutionary implication.	the catechol meta cleavage pathway is one of the central metabolic pathways for the degradation of aromatic compounds. a novel organization of the pathway genes, different from that of classical soil microorganisms, has been observed in sphingomonas sp hv3 and pseudomonas sp. dj77. in a comamonas sp. js765, cdoe encoding catechol 2,3-dioxygenase shares a common ancestry only with tdnc of a pseudomonas putida strain, while codg encoding 2-hydroxymuconic semialdehyde dehydrogenase shows a higher d ...	2007	16947040
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
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
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
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
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
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
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
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
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
[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
measurement of biodegradability parameters for single unsubstituted and methylated polycyclic aromatic hydrocarbons in liquid bacterial suspensions.	substrate depletion experiments were conducted to characterize aerobic biodegradation of 20 single polycyclic aromatic hydrocarbons (pahs) by induced sphingomonas paucimobilis strain epa505 in liquid suspensions. pahs consisted of low molecular weight, unsubstituted, and methyl-substituted homologs. a material balance equation containing the andrews kinetic model, an extension of the monod model accounting for substrate inhibition, was numerically fitted to batch depletion data to estimate extan ...	2007	17115446
kinetics of biodegradation of binary and ternary mixtures of pahs.	the kinetics of biodegradation of mixtures of polycyclic aromatic hydrocarbons (pahs) by sphingomonas paucimobilis strain epa505 were investigated. the investigation focused on three- and four-ring pahs, specifically 2-methylphenanthrene, fluoranthene, and pyrene. uptake rates in aerobic batch suspended cultivations were measured for the individual pahs and their binary and ternary mixtures. it was observed that kinetics were influenced by the mixture composition and the kinetic properties of th ...	2007	17115447
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
the recent evolution of pentachlorophenol (pcp)-4-monooxygenase (pcpb) and associated pathways for bacterial degradation of pcp.	man-made polychlorinated phenols such as pentachlorophenol (pcp) have been used extensively since the 1920s as preservatives to prevent fungal attack on wood. during this time, they have become serious environmental contaminants. despite the recent introduction of pcp in the environment on an evolutionary time scale, pcp-degrading bacteria are present in soils worldwide. the initial enzyme in the pcp catabolic pathway of numerous sphingomonads, pcp-4-monooxygenase (pcpb), catalyzes the para-hydr ...	2007	17123025
the catalytic pocket of the ring-hydroxylating dioxygenase from sphingomonas chy-1.	ring-hydroxylating dioxygenases are multicomponent bacterial enzymes that catalyze the first step in the oxidative degradation of aromatic hydrocarbons. the dioxygenase from sphingomonas chy-1 is unique in that it can oxidize a wide range of polycyclic aromatic hydrocarbons (pahs). with a crystal structure similar to that of the seven other known dioxygenases, its catalytic domain features the largest hydrophobic substrate binding cavity characterized so far. molecular modeling studies indicated ...	2007	17157819
the sphingomonas plasmid pcar3 is involved in complete mineralization of carbazole.	we determined the complete 254,797-bp nucleotide sequence of the plasmid pcar3, a carbazole-degradative plasmid from sphingomonas sp. strain ka1. a region of about 65 kb involved in replication and conjugative transfer showed similarity to a region of plasmid pnl1 isolated from the aromatic-degrading novosphingobium aromaticivorans strain f199. the presence of many insertion sequences, transposons, repeat sequences, and their remnants suggest plasticity of this plasmid in genetic structure. alth ...	2007	17172338
genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds.	lignins are the most abundant aromatic compounds in nature, and their decomposition is essential to the terrestrial carbon cycle. white rot fungi secreting phenol oxidases are assumed to be involved in the initial degradation of native lignin, whereas bacteria play a main role in the mineralization of lignin-derived low-molecular-weight compounds in soil. there are a number of reports on the degradation pathways for lignin-derived aromatic compounds, but their catabolism has not been enzymatical ...	2007	17213657
biodegradation of bisphenol a and related compounds by sphingomonas sp. strain bp-7 isolated from seawater.	a bacterium capable of assimilating 2,2-bis(4-hydroxyphenyl)propane (bisphenol a), strain bp-7, was isolated from offshore seawater samples on a medium containing bisphenol a as sole source of carbon and energy, and identified as sphingomonas sp. strain bp-7. other strains, pseudomonas sp. strain bp-14, pseudomonas sp. strain bp-15, and strain no. 24a, were also isolated from bisphenol a-enrichment culture of the seawater. these strains did not degrade bisphenol a, but accelerated the degradatio ...	2007	17213659
influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons by sphingomonas sp. strain pheb4.	the influence of growth medium on cometabolic degradation of polycyclic aromatic hydrocarbons (pahs) was investigated when sphingomonas sp. strain pheb4 isolated from surface mangrove sediments was grown in either phenanthrene-containing mineral salts medium (pmsm) or nutrient broth (nb). the nb-grown culture exhibited a more rapid cometabolic degradation of single and mixed non-growth substrate pahs compared to the pmsm-grown culture. the concentrations of pah metabolites were also lower in nb- ...	2007	17216444
description of sphingosinicella xenopeptidilytica sp. nov., a beta-peptide-degrading species, and emended descriptions of the genus sphingosinicella and the species sphingosinicella microcystinivorans.	a gram-negative, rod-shaped bacterium, strain 3-2w4(t), was isolated from the aeration tank of a wastewater treatment plant in zurich and was found to have the exceptional capacity to degrade synthetic beta-peptides. 16s rrna gene sequence analysis showed that strain 3-2w4(t) is closely related to sphingosinicella microcystinivorans y2(t), but dna-dna hybridization experiments between these two strains revealed that they belong to two different species. the two strains displayed different finger ...	2007	17220451
changes to the structure of sphingomonas spp. communities associated with biodegradation of the herbicide isoproturon in soil.	the phenyl-urea herbicide isoproturon is a major contaminant of surface and ground-water in agricultural catchments. earlier work suggested that within-field spatial variation of isoproturon degradation rate resulted from interactions between catabolizing sphingomonas spp. and ph. in the current study, changes to the structure of sphingomonas communities during isoproturon catabolism were investigated using sphingomonas-specific 16s rrna gene primers. growth-linked catabolism at high-ph (>7.5) s ...	2007	17241244
[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
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
plant carbohydrate scavenging through tonb-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria.	tonb-dependent receptors (tbdrs) are outer membrane proteins mainly known for the active transport of iron siderophore complexes in gram-negative bacteria. analysis of the genome of the phytopathogenic bacterium xanthomonas campestris pv. campestris (xcc), predicts 72 tbdrs. such an overrepresentation is common in xanthomonas species but is limited to only a small number of bacteria. here, we show that one xcc tbdr transports sucrose with a very high affinity, suggesting that it might be a sucro ...	2007	17311090
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
integrated response to inducers by communication between a catabolic pathway and its regulatory system.	efficient gene regulation of metabolic pathways implies that the profile of molecules inducing the pathway matches that of the molecules that are metabolized. gratuitous induction, a well-known phenomenon in catabolic pathways, is the consequence of differences in the substrate and inducer profiles. this phenomenon is particularly evident in pathways for biodegradation of organic contaminants that can be induced by a variety of molecules similar to the real substrates. analysis of the regulation ...	2007	17351041
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
role of dissolved humic acids in the biodegradation of a single isomer of nonylphenol by sphingomonas sp.	this study shows the important role of humic acids in the degradation of (14)c and (13)c labeled isomer of np by sphingomonas sp. strain ttnp3 and the detoxification of the resulting metabolites. due to the association of np with humic acids, its solubility in the medium was enhanced and the extent of mineralization of nonylphenol increased from 20% to above 35%. this was accompanied by the formation of significant amounts of np residues bound to the humic acids, which also occurred via abiotic ...	2007	17367841
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
[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 estrogen-degrading bacteria isolated from an artificial sandy aquifer with ultrafiltered secondary effluent as the medium.	this study investigated the aerobic and anoxic biodegradation of four estrogens [estrone (e1), estradiol (e2), estriol (e3), and the synthetic 17 alpha-ethinylestradiol (ee2)] in microcosms constructed with marine sand and ulftrafiltered (uf) secondary effluent. three estrogen-degrading bacteria, lhj1, lhj3, and cyh, were isolated. based on gram-stain morphology and 16s rrna sequence homology, lhj1 and lhj3 belong to the genus acinetobacter and agromyces, respectively; cyh matched to 95% with th ...	2007	17396255
characterization of a c-c bond hydrolase from sphingomonas wittichii rw1 with novel specificities towards polychlorinated biphenyl metabolites.	sphingomonas wittichii rw1 degrades chlorinated dibenzofurans and dibenzo-p-dioxins via meta cleavage. we used inverse pcr to amplify dxnb2, a gene encoding one of three meta-cleavage product (mcp) hydrolases identified in the organism that are homologues of bphd involved in biphenyl catabolism. purified dxnb2 catalyzed the hydrolysis of 8-oh 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate (hopda) approximately six times faster than for hopda at saturating substrate concentrations. moreover, the speci ...	2007	17416660
limits of propidium iodide as a cell viability indicator for environmental bacteria.	viability measurements of individual bacteria are applied in various scopes of research and industry using approaches where propidium iodide (pi) serves as dead cell indicator. the reliability of pi uptake as a cell viability indicator for dead (pi permeable) and viable (pi impermeable) bacteria was tested using two soil bacteria, the gram(-) sphingomonas sp. lb126 and the gram(+) mycobacterium frederiksbergense lb501t.	2007	17421025
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
the complex of sphingomonas elodea atcc 31461 glucose-1-phosphate uridylyltransferase with glucose-1-phosphate reveals a novel quaternary structure, unique among nucleoside diphosphate-sugar pyrophosphorylase members.	gellan gum is a widely used commercial material, available in many different forms. its economic importance has led to studies into the biosynthesis of exopolysaccharide gellan gum, which is industrially prepared in high yields using sphingomonas elodea atcc 31461. glucose-1-phosphate uridylyltransferase mediates the reversible conversion of glucose-1-phosphate and utp into udp-glucose and pyrophosphate, which is a key step in the biosynthetic pathway of gellan gums. here we present the x-ray cr ...	2007	17434970
potential of the adhesion of bacteria isolated from drinking water to materials.	heterotrophic bacteria (11 genera, 14 species, 25 putative strains) were isolated from drinking water, identified either biochemically or by partial 16s rdna gene sequencing and their adherence characteristics were determined by two methods: i. thermodynamic prediction of adhesion potential by measuring hydrophobicity (contact angle measurements) and ii. by measuring adherence to eight different substrata (asi 304 and 316 stainless steel, copper, polyvinyl chloride, polypropylene, polyethylene, ...	2007	17440920
the crystal structure of the ring-hydroxylating dioxygenase from sphingomonas chy-1.	the ring-hydroxylating dioxygenase (rhd) from sphingomonas chy-1 is remarkable due to its ability to initiate the oxidation of a wide range of polycyclic aromatic hydrocarbons (pahs), including pahs containing four- and five-fused rings, known pollutants for their toxic nature. although the terminal oxygenase from chy-1 exhibits limited sequence similarity with well characterized rhds from the naphthalene dioxygenase family, the crystal structure determined to 1.85 a by molecular replacement rev ...	2007	17451434