| frequency of horizontal gene transfer of a large catabolic plasmid (pjp4) in soil. | limited work has been done to assess the bioremediation potential of transfer of plasmid-borne degradative genes from introduced to indigenous organisms in the environment. here we demonstrate the transfer by conjugation of the catabolic plasmid pjp4, using a model system with donor and recipient organisms. the donor organism was alcaligenes eutrophus jmp134 and the recipient organism was variovorax paradoxus isolated from a toxic waste site. plasmid pjp4 contains genes for mercury resistance an ... | 1994 | 7993092 |
| degradation of homovanillate by a strain of variovorax paradoxus via ring hydroxylation. | a newly isolated strain of variovorax paradoxus could grow on homovanillate and several monohydroxylated phenylacetic acids. during growth on homovanillate, the organism formed separate nad(p)h-dependent hydroxylases with activity towards 4-hydroxyphenylacetic acid and homovanillate. homovanillate hydroxylase catalysed a typical monooxygenase reaction and had little activity towards 4-hydroxyphenylacetic acid gc-ms and tlc analysis suggested that homovanillate was 1-hydroxylated to yield a dihyd ... | 1995 | 8586270 |
| polaromonas vacuolata gen. nov., sp. nov., a psychrophilic, marine, gas vacuolate bacterium from antarctica. | several strains of a novel heterotrophic gas vacuolate bacterium were isolated from antarctic marine waters. the results of phylogenetic analyses in which 16s ribosomal dan sequencing was used, coupled with phenotypic tests, indicated that strain 34-p(t) (t = type strain) belongs to a new genus and species of the beta subgroup of the proteobacteria, for which the name polaromonas vacuolata is proposed. although the other four strains studied probably belong to this new species, dna-dna hybridiza ... | 1996 | 8782696 |
| pristine environments harbor a new group of oligotrophic 2,4-dichlorophenoxyacetic acid-degrading bacteria. | 2,4-dichlorophenoxyacetic acid (2,4-d)-degrading bacteria were isolated from pristine environments which had no history of 2,4-d exposure. by using 2,4-d dye indicator medium or 14c-labeled 2,4-d medium, six strains were isolated from eight enrichment cultures capable of degrading 2,4-d. phylogenetic analyses based on 16s ribosomal dna (rdna) sequencing and physiological properties revealed that one isolate from hawaiian volcanic soil could be classified in the genus variovorax (a member of the ... | 1997 | 9172346 |
| phylogenetic characterization of bacteria in the subsurface microbial culture collection. | the subsurface microbial culture collection (smcc) was established by the u.s. dept. of energy (doe) and contains nearly 10,000 strains of microorganisms (mostly bacteria) isolated from terrestrial subsurface environments. selected groups of bacterial isolates from three sample sites situated above geochemically and hydrologically different subsurface environments have been characterized by phylogenetic analysis of 16s ribosomal rna (rrna) gene nucleotide sequences. among these isolates were mem ... | 1997 | 9299704 |
| biodegradation of metal-edta complexes by an enriched microbial population. | a mixed culture utilizing edta as the sole carbon source was isolated from a mixed inoculum of water from the river mersey (united kingdom) and sludge from an industrial effluent treatment plant. fourteen component organisms were isolated from the culture, including representatives of the genera methylobacterium, variovorax, enterobacter, aureobacterium, and bacillus. the mixed culture biodegraded metal-edta complexes slowly; the biodegradability was in the order fe > cu > co > ni > cd. by incor ... | 1998 | 9546167 |
| bacterial isolates degrading aliphatic polycarbonates. | bacteria that degrade an aliphatic polycarbonate, poly(hexamethylene carbonate), were isolated from river water in ibaraki. prefecture, japan, after enrichment in liquid medium containing poly(hexamethylene carbonate) suspensions as carbon source, and dilution to single cells. four of the strains, 35l, wff52, 61a and 61b2, degraded poly(hexamethylene carbonate) on agar plate containing suspended poly(hexamethylene carbonate). degradation of poly(hexamethylene carbonate) was confirmed by gel perm ... | 1998 | 9570117 |
| microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer. | microbial community composition associated with benzene oxidation under in situ fe(iii)-reducing conditions in a petroleum-contaminated aquifer located in bemidji, minn., was investigated. community structure associated with benzene degradation was compared to sediment communities that did not anaerobically oxidize benzene which were obtained from two adjacent fe(iii)-reducing sites and from methanogenic and uncontaminated zones. denaturing gradient gel electrophoresis of 16s rdna sequences ampl ... | 1999 | 10388703 |
| calorimetrically recognized maximum yield of poly-3-hydroxybutyrate (phb) continuously synthesized from toxic substrates. | the broader usage of poly-beta-hydroxybutyrate (phb), for instance as bulk plastics, calls for cheap raw materials and greater overall process efficiency. the bacterial synthesis is generally induced and promoted by the limitation of growth via nitrogen, oxygen or phosphate depletion with the simultaneous excess and higher concentration of the carbon substrate. consequently, toxic substrates have been considered unsuitable for phb synthesis. nevertheless, a single-stage continuous process for pr ... | 2000 | 10682283 |
| response of soybean rhizosphere communities to human hygiene water addition as determined by community level physiological profiling (clpp) and terminal restriction fragment length polymorphism (trflp) analysis. | in this report, we describe an experiment conducted at kennedy space center in the biomass production chamber (bpc) using soybean plants for purification and processing of human hygiene water. specifically, we tested whether it was possible to detect changes in the root-associated bacterial assemblage of the plants and ultimately to identify the specific microorganism(s) which differed when plants were exposed to hygiene water and other hydroponic media. plants were grown in hydroponics media co ... | 2000 | 10689173 |
| effect of field inoculation with sinorhizobium meliloti l33 on the composition of bacterial communities in rhizospheres of a target plant (medicago sativa) and a non-target plant (chenopodium album)-linking of 16s rrna gene-based single-strand conformation polymorphism community profiles to the diversity of cultivated bacteria. | fourteen weeks after field release of luciferase gene-tagged sinorhizobium meliloti l33 in field plots seeded with medicago sativa, we found that the inoculant also occurred in bulk soil from noninoculated control plots. in rhizospheres of m. sativa plants, s. meliloti l33 could be detected in noninoculated plots 12 weeks after inoculation, indicating that growth in the rhizosphere preceded spread into bulk soil. to determine whether inoculation affected bacterial diversity, 1,119 bacteria were ... | 2000 | 10919821 |
| sulfolane degradation by mixed cultures and a bacterial isolate identified as a variovorax sp. | sulfolane (tetrahydrothiophene-1,1-dioxide) is used in the sulfinol process for natural gas sweetening. at many sour-gas processing plants spills, landfills and leakage from unlined surface storage ponds have contaminated groundwaters with sulfolane. due to its high water solubility and mobility in aquifers, sulfolane poses a risk for off-site contamination. this study investigated the aerobic biodegradation of sulfolane by two mixed microbial enrichment cultures and by three bacterial isolates. ... | 2000 | 10985750 |
| metabolism of acyl-homoserine lactone quorum-sensing signals by variovorax paradoxus. | acyl-homoserine lactones (acyl-hsls) serve as dedicated cell-to-cell signaling molecules in many species of the class proteobacteria. we have addressed the question of whether these compounds can be degraded biologically. a motile, rod-shaped bacterium was isolated from soil based upon its ability to utilize n-(3-oxohexanoyl)-l-homoserine lactone as the sole source of energy and nitrogen. the bacterium was classified as a strain of variovorax paradoxus. the v. paradoxus isolate was capable of gr ... | 2000 | 11092851 |
| analysis of bacterial communities in the rhizosphere of chrysanthemum via denaturing gradient gel electrophoresis of pcr-amplified 16s rrna as well as dna fragments coding for 16s rrna. | the effect of developing chrysanthemum roots on the presence and activity of bacterial populations in the rhizosphere was examined by using culture-independent methods. nucleic acids were extracted from rhizosphere soil samples associated with the bases of roots or root tips of plants harvested at different stages of development. pcr and reverse transcriptase (rt) pcr were used to amplify 16s ribosomal dna (rdna) and 16s rrna, respectively, and the products were subjected to denaturing gradient ... | 2001 | 11133442 |
| identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl-polluted moorland soil. | the presumptive metabolically active members of a bacterial community in a moorland soil in germany, highly polluted with polychlorinated biphenyls (pcbs), were identified by sequencing of cloned reverse transcription-polymerase chain reaction (rt-pcr) amplification products of 16s rrna generated from total rna extracts. analysis of the 16s rrna clone library revealed a considerable diversity of metabolically active bacteria in the soil, despite the acidic ph and high concentrations of pcbs. clo ... | 1999 | 11207739 |
| characterization of plant growth promoting rhizobacteria isolated from polluted soils and containing 1-aminocyclopropane-1-carboxylate deaminase. | fifteen bacterial strains containing 1-aminocyclopropane-1-carboxylate (acc) deaminase were isolated from the rhizoplane of pea (pisum sativum l.) and indian mustard (brassica juncea l.) grown in different soils and a long-standing sewage sludge contaminated with heavy metals. the isolated strains were characterized and assigned to various genera and species, such as pseudomonas brassicacearum, pseudomonas marginalis, pseudomonas oryzihabitans, pseudomonas putida, pseudomonas sp., alcaligenes xy ... | 2001 | 11547884 |
| xenophilus azovorans gen. nov., sp. nov., a soil bacterium that is able to degrade azo dyes of the orange ii type. | the taxonomy of strain kf46ft, which was isolated previously after an aerobic enrichment with the azo compound 1-(4'-carboxyphenylazo)-2-naphthol as the sole source of energy and carbon, was investigated by a polyphasic approach. the organism contained a quinone system with ubiquinone q-8 and 2-hydroxyputrescine and putrescine as the major polyamines, suggesting that strain kf46ft belonged to the beta-subclass of the proteobacteria. the polar lipid profile consisted mainly of phosphatidylethanol ... | 2001 | 11594616 |
| relationships within the proteobacteria of plant pathogenic acidovorax species and subspecies, burkholderia species, and herbaspirillum rubrisubalbicans by sequence analysis of 16s rdna, numerical analysis and determinative tests. | sequence data for 16s rdna of the type strains of acidovorax avenae subsp. avenae, a. avenae subsp. cattleyae, a. avenae subsp. citrulli, a. konjaci and herbaspirillum rubrisubalbicans were compared with genbank library accessions of burkholderia spp., comamonas sp., ralstonia solanacearum and variovorax sp. maximum parsimony analysis produced two clusters: 1. acidovorax spp., comamonas sp., and variovorax sp. (all in the comamonadaceae), and 2. burkholderia spp., ralstonia solanacearum, and her ... | 2001 | 11827206 |
| bacterial diversity associated with subalpine fir (abies lasiocarpa) ectomycorrhizae following wildfire and salvage-logging in central british columbia. | to assess the effect of fire and salvage logging on the diversity of mycorrhizal-bacterial communities, bacteria associated with cenococcum, thelephora, tomentella, russulaceae, and e-strain ectomycorrhizae (ecm) of abies lasiocarpa seedlings were characterized using two approaches. first, bacteria were isolated and characterized by biolog, gas chromatography fatty acid methyl ester (gc-fame), and amplified 16s rdna restriction analysis (ardra). the bacterial communities retrieved from ecm from ... | 2002 | 12224560 |
| identification and characterization of a new gene from variovorax paradoxus iso1 encoding n-acyl-d-amino acid amidohydrolase responsible for d-amino acid production. | an n-acyl-d-amino acid amidohydrolase (n-d-aaase) was identified in cell extracts of a strain, iso1, isolated from an environment containing n-acetyl-d-methionine. the bacterium was classified as variovorax paradoxus by phylogenetic analysis. the gene was cloned and sequenced. the gene consisted of a 1467-bp orf encoding a polypeptide of 488 amino acids. the v. paradoxusn-d-aaase showed significant amino acid similarity to the n-acyl-d-amino acid amidohydrolases of the two eubacteria alcaligenes ... | 2002 | 12354118 |
| degradation of polycyclic aromatic hydrocarbons at low temperature under aerobic and nitrate-reducing conditions in enrichment cultures from northern soils. | the potential for biodegradation of polycyclic aromatic hydrocarbons (pahs)at low temperature and under anaerobic conditions is not well understood, but such biodegradation would be very useful for remediation of polluted sites. biodegradation of a mixture of 11 different pahs with two to five aromatic rings, each at a concentration of 10 micro g/ml, was studied in enrichment cultures inoculated with samples of four northern soils. under aerobic conditions, low temperature severely limited pah b ... | 2003 | 12514005 |
| bacteria associated with cysts of the soybean cyst nematode (heterodera glycines). | the soybean cyst nematode (scn), heterodera glycines, causes economically significant damage to soybeans (glycine max) in many parts of the world. the cysts of this nematode can remain quiescent in soils for many years as a reservoir of infection for future crops. to investigate bacterial communities associated with scn cysts, cysts were obtained from eight scn-infested farms in southern ontario, canada, and analyzed by culture-dependent and -independent means. confocal laser scanning microscopy ... | 2003 | 12514048 |
| synergistic degradation of linuron by a bacterial consortium and isolation of a single linuron-degrading variovorax strain. | the bacterial community composition of a linuron-degrading enrichment culture and the role of the individual strains in linuron degradation have been determined by a combination of methods, such as denaturing gradient gel electrophoresis of the total 16s rrna gene pool, isolation and identification of strains, and biodegradation assays. three strains, variovorax sp. strain wdl1, delftia acidovorans wdl34, and pseudomonas sp. strain wdl5, were isolated directly from the linuron-degrading culture. ... | 2003 | 12620840 |
| respiration of 13c-labeled substrates added to soil in the field and subsequent 16s rrna gene analysis of 13c-labeled soil dna. | our goal was to develop a field soil biodegradation assay using (13)c-labeled compounds and identify the active microorganisms by analyzing 16s rrna genes in soil-derived (13)c-labeled dna. our biodegradation approach sought to minimize microbiological artifacts caused by physical and/or nutritional disturbance of soil associated with sampling and laboratory incubation. the new field-based assay involved the release of (13)c-labeled compounds (glucose, phenol, caffeine, and naphthalene) to soil ... | 2003 | 12620850 |
| microbial consortia that degrade 2,4-dnt by interspecies metabolism: isolation and characterisation. | two consortia, isolated by selective enrichment from a soil sample of a nitroaromatic-contaminated site, degraded 2,4-dnt as their sole nitrogen source without accumulating one or more detectable intermediates. though originating from the same sample, the optimised consortia had no common members, indicating that selective enrichment resulted in different end points. consortium 1 and consortium 2 contained four and six bacterial species respectively, but both had two members that were able to co ... | 2003 | 12801097 |
| novel bacteria degrading n-acylhomoserine lactones and their use as quenchers of quorum-sensing-regulated functions of plant-pathogenic bacteria. | bacteria degrading the quorum-sensing (qs) signal molecule n-hexanoylhomoserine lactone were isolated from a tobacco rhizosphere. twenty-five isolates degrading this homoserine lactone fell into six groups according to their genomic rep-pcr and rrs pcr-rflp profiles. representative strains from each group were identified as members of the genera pseudomonas, comamonas, variovorax and rhodococcus: all these isolates degraded n-acylhomoserine lactones other than the hexanoic acid derivative, albei ... | 2003 | 12904538 |
| microbial characterization of the mars odyssey spacecraft and its encapsulation facility. | microbial characterization of the mars odyssey spacecraft and the kennedy space center spacecraft assembly and encapsulation facility ii (saef-ii) was carried out by both culture-based and molecular methods. the most dominant cultivable microbes were species of bacillus, with comamonads, microbacteria and actinomycetales also represented. several spore-forming isolates were resistant to gamma-radiation, uv, h2o2 and desiccation, and one acinetobacter radioresistens isolate and several aureobasid ... | 2003 | 14510851 |
| searching for nitrile hydratase using the consensus-degenerate hybrid oligonucleotide primers strategy. | consensus-degenerate oligonucleotide hybrid primers (codehop) were designed by using the www-implemented strategy, based on multiple alignments of nitrile hydratase (nhase) alpha subunit, available from embl database. these primers were successfully tested with known nhase-producing bacterial strains such as agrobacterium tumefaciens dsm 9674, rhodococcus erythropolis dsm 9675, r. erythropolis 9685 and r. erythropolis 11397 and also allowed amplification from organisms not previously referenced ... | 2004 | 15162394 |
| identification and characterization of a novel d-amidase gene from variovorax paradoxus and its expression in escherichia coli. | the gene for the newly described d-amidase from variovorax paradoxus (krieg et al. 2002) was cloned and functionally expressed in escherichia coli. since native enzyme was available in minute amounts only, we determined the n-terminal sequence of the enzyme and utilized the universal genomewalker approach to make use of the common internal sequence of the amidase signature family. the high gc content of the gene made it necessary to employ an appropriate dna polymerase in the amplification react ... | 2005 | 15480636 |
| unique kinetic properties of phenol-degrading variovorax strains responsible for efficient trichloroethylene degradation in a chemostat enrichment culture. | a chemostat enrichment of soil bacteria growing on phenol as the sole carbon source has been shown to exhibit quite high trichloroethylene (tce)-degrading activities. to identify the bacterial populations responsible for the high tce-degrading activity, a multidisciplinary survey of the chemostat enrichment was conducted by employing molecular-ecological and culture-dependent approaches. three chemostat enrichment cultures were newly developed under different phenol-loading conditions (0.25, 0.7 ... | 2005 | 15691947 |
| elucidating the key member of a linuron-mineralizing bacterial community by pcr and reverse transcription-pcr denaturing gradient gel electrophoresis 16s rrna gene fingerprinting and cultivation. | a bacterial community from danish agricultural soil was enriched with linuron [n-(3,4-dichlorophenyl)-n'-methoxy-n'-methylurea] as the sole carbon and nitrogen source. the community mineralized [ring-u-14c]linuron completely to 14co2 and 14c-biomass. denaturing gradient gel electrophoresis analysis and cultivation revealed that a variovorax sp. was responsible for the mineralization activity. | 2005 | 16000836 |
| degradation of simazine by microorganisms isolated from soils of spanish olive fields. | the capability of the microbial flora isolated from an olive field soil from andalusia to mineralize simazine has been analyzed. from this soil, a group of bacteria capable of degrading 60 mg simazine litre(-1) in less than a week has been isolated. these microorganisms showed a low capacity for degrading this herbicide to carbon dioxide. when total dna was isolated from this group of bacteria, we were able to detect by pcr the presence of only the atzc and the trzn genes. some components of thi ... | 2005 | 16007568 |
| isolation and molecular detection of methylotrophic bacteria occurring in the human mouth. | diverse methylotrophic bacteria were isolated from the tongue, and supra- and subgingival plaque in the mouths of volunteers and patients with periodontitis. one-carbon compounds such as dimethylsulfide in the mouth are likely to be used as growth substrates for these organisms. methylotrophic strains of bacillus, brevibacterium casei, hyphomicrobium sulfonivorans, methylobacterium, micrococcus luteus and variovorax paradoxus were characterized physiologically and by their 16s rrna gene sequence ... | 2005 | 16011760 |
| horizontal gene transfer of atrazine-degrading genes (atz) from agrobacterium tumefaciens st96-4 padp1::tn5 to bacteria of maize-cultivated soil. | the plasmid padp1::tn5 derived from padp1[atr+] carrying a tn5 transposon conferring kanamycin and streptomycin resistances was constructed and introduced in agrobacterium tumefaciens st96-4. this genetically modified strain was inoculated (approximately 10(8) cfu g(-1)) in potted soils planted with maize and treated or not with atrazine (1.5 mg kg(-1)). bulk and maize rhizosphere soils were sampled 39 days after planting to look for soil indigenous bacteria that had acquired padp1::tn5. four tr ... | 2005 | 16032656 |
| extracellular dna in single- and multiple-species unsaturated biofilms. | the extracellular polymeric substances (eps) of bacterial biofilms form a hydrated barrier between cells and their external environment. better characterization of eps could be useful in understanding biofilm physiology. the eps are chemically complex, changing with both bacterial strain and culture conditions. previously, we reported that pseudomonas aeruginosa unsaturated biofilm eps contains large amounts of extracellular dna (edna) (r. e. steinberger, a. r. allen, h. g. hansma, and p. a. hol ... | 2005 | 16151131 |
| diversity of n-acyl homoserine lactone-producing and -degrading bacteria in soil and tobacco rhizosphere. | in gram-negative bacteria, quorum-sensing (qs) communication is mostly mediated by n-acyl homoserine lactones (n-ahsl). the diversity of bacterial populations that produce or inactivate the n-ahsl signal in soil and tobacco rhizosphere was investigated by restriction fragment length polymorphism (rflp) analysis of amplified 16s dna and dna sequencing. such analysis indicated the occurrence of n-ahsl-producing strains among the alpha-, beta- and gamma-proteobacteria, including genera known to pro ... | 2005 | 16232294 |
| molecular characterization of the nonphotosynthetic partner bacterium in the consortium "chlorochromatium aggregatum". | phototrophic consortia represent valuable model systems for the study of signal transduction and coevolution between different bacteria. the phototrophic consortium "chlorochromatium aggregatum" consists of a colorless central rod-shaped bacterium surrounded by about 20 green-pigmented epibionts. although the epibiont was identified as a member of the green sulfur bacteria, and recently isolated and characterized in pure culture, the central colorless bacterium has been identified as a member of ... | 2005 | 16269785 |
| hydrocarbon contamination changes the bacterial diversity of soil from around scott base, antarctica. | a combination of culture-independent and culturing methods was used to determine the impacts of hydrocarbon contamination on the diversity of bacterial communities in coastal soil from ross island, antarctica. while numbers of culturable aerobic heterotrophic microbes were 1-2 orders of magnitude higher in the hydrocarbon-contaminated soil than control soil, the populations were less diverse. members of the divisions fibrobacter/acidobacterium, cytophaga/flavobacterium/bacteroides, deinococcus/t ... | 2004 | 16329936 |
| cooperative catabolic pathways within an atrazine-degrading enrichment culture isolated from soil. | atrazine degradation previously has been shown to be carried out by individual bacterial species or by relatively simple consortia that have been isolated using enrichment cultures. here, the degradative pathway for atrazine was examined for a complex 8-membered enrichment culture. the species composition of the culture was determined by pcr-dgge. the bacterial species included agrobacterium tumefaciens, caulobacter crescentus, pseudomonas putida, sphingomonas yaniokuyae, nocardia sp., rhizobium ... | 2005 | 16329946 |
| aerobic biodegradation of 2,2'-dithiodibenzoic acid produced from dibenzothiophene metabolites. | dibenzothiophene is a sulfur heterocycle found in crude oils and coal. the biodegradation of dibenzothiophene through the kodama pathway by pseudomonas sp. strain bt1d leads to the formation of three disulfides: 2-oxo-2-(2-thiophenyl)ethanoic acid disulfide, 2-oxo-2-(2-thiophenyl)ethanoic acid-2-benzoic acid disulfide, and 2,2'-dithiodibenzoic acid. when provided as the carbon and sulfur source in liquid medium, 2,2'-dithiodibenzoic acid was degraded by soil enrichment cultures. two bacterial is ... | 2006 | 16391083 |
| production of (r)-3-amino-3-phenylpropionic acid and (s)-3-amino-3-phenylpropionic acid from (r,s)-n-acetyl-3-amino-3-phenylpropionic acid using microorganisms having enantiomer-specific amidohydrolyzing activity. | (r)-3-amino-3-phenylpropionic acid ((r)-beta-phe) and (s)-3-amino-3-phenylpropionic acid ((s)-beta-phe) are key compounds on account of their use as intermediates in synthesizing pharmaceuticals. enantiomerically pure non-natural amino acids are generally prepared by enzymatic resolution of the racemic n-acetyl form, but despite the intense efforts this method could not be used for preparing enantiomerically pure beta-phe, because the effective enzyme had not been found. therefore, screening for ... | 2006 | 16428826 |
| biodegradation of 3-nitrotyrosine by burkholderia sp. strain js165 and variovorax paradoxus js171. | the cascade of reactive nitrogen species generated from nitric oxide causes modification of proteins, lipids, and nucleic acids in a wide range of organisms. 3-nitrotyrosine is one of the most common products of the action of reactive nitrogen species on proteins. although a great deal is known about the formation of 3-nitrotyrosine, the subsequent metabolism of this compound is a mystery. variovorax paradoxus js171 and burkholderia sp. strain js165 were isolated from soil slurries when 3-nitrot ... | 2006 | 16461647 |
| utilization of capsaicin and vanillylamine as growth substrates by capsicum (hot pepper)-associated bacteria. | capsaicin contributes to the organoleptic attributes of hot peppers. here, we show that capsaicin is utilized as a growth nutrient by certain bacteria. enrichment cultures utilizing capsaicin were successfully initiated using capsicum-derived plant material or leaves of tomato (a related solanaceae) as inocula. no other sources of inoculum examined yielded positive enrichments. of 25 isolates obtained from enrichments: all utilized 8-methylnonanoic acid; nine were found capable of degrading caps ... | 2006 | 16478462 |
| microbial production of optically active beta-phenylalanine through stereoselective degradation of racemic beta-phenylalanine. | the ability to produce (r)- or (s)-beta-phenylalanine from racemic beta-phenylalanine through stereoselective degradation was screened for. variovorax sp. jh2 and arthrobacter sp. the faculty of agriculture, kyoto university (aku) 638 were found to be potential catalysts for (r)- and (s)-beta-phenylalanine production respectively. on 192 h cultivation of variovorax sp. in medium containing 1.0% (w/v) racemic beta-phenylalanine, 0.46% (w/v) (r)-beta-phenylalanine with an enantiomeric purity of 99 ... | 2006 | 16880592 |
| arsenic-resistant proteobacterium from the phyllosphere of arsenic-hyperaccumulating fern (pteris vittata l.) reduces arsenate to arsenite. | an arsenic-resistant bacterium, asrb1, was isolated from the fronds of pteris vittata grown in a site contaminated with copper chromium arsenate. the bacterium exhibited resistance to arsenate, arsenite, and antimony in the culture medium. asrb1, like pseudomonas putida, grew on macconkey and xylose-lactose-desoxycholate agars and utilized citrate but, unlike p. putida, was positive for indole test and negative for oxidase test. a phylogenetic analysis of the 16s rrna gene showed that asrb1 is a ... | 2006 | 16917527 |
| 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 |
| structure and kinetics of phosphonopyruvate hydrolase from variovorax sp. pal2: new insight into the divergence of catalysis within the pep mutase/isocitrate lyase superfamily. | phosphonopyruvate (p-pyr) hydrolase (pph), a member of the phosphoenolpyruvate (pep) mutase/isocitrate lyase (pepm/icl) superfamily, hydrolyzes p-pyr and shares the highest sequence identity and functional similarity with pepm. recombinant pph from variovorax sp. pal2 was expressed in escherichia coli and purified to homogeneity. analytical gel filtration indicated that the protein exists in solution predominantly as a tetramer. the pph ph rate profile indicates maximal activity over a broad ph ... | 2006 | 16981709 |
| genetic rearrangement of the atzab atrazine-degrading gene cassette from padp1::tn5 to the chromosome of variovorax sp. md1 and md2. | we report the characterization of the rearrangement phenomena responsible for the movement of the atrazine-degrading atza and b genes from padp1::tn5 to the chromosome of variovorax sp. md1 and md2. long pcrs and southern blot analyses revealed that the two genes forming a gene cassette moved in a unique rearrangement event. it also revealed that the boundaries of the plasmid sequence inserted in the chromosome correspond to is1071or to sequences close to is1071. it suggests that this genetic re ... | 2007 | 17188820 |
| isolation and characterization of hydrogen-oxidizing bacteria induced following exposure of soil to hydrogen gas and their impact on plant growth. | in many legumes, the nitrogen fixing root nodules produce h2 gas that diffuses into soil. it has been demonstrated that such exposure of soil to h2 can promote plant growth. to assess whether this may be due to h2-oxidizing microorganisms, bacteria were isolated from soil treated with h2 under laboratory conditions and from soils collected adjacent to h2 producing soybean nodules. nineteen isolates of h2-oxidizing bacteria were obtained and all exhibited a half-saturation coefficient (ks) for h2 ... | 2007 | 17222141 |
| desulfurization of aromatic sulfonates by rhizosphere bacteria: high diversity of the asfa gene. | the plant growth-promoting effect of pseudomonas putida s-313 is associated with its ability to desulfurize arylsulfonates. to understand this further, other plant-associated bacteria able to desulfurize a range of arylsulfonates were isolated from the rhizospheres of winter and spring barley. the isolates belonged to the beta-proteobacteria, including bacteria from the variovorax paradoxus group and from the acidovorax genus. they desulfurized toluenesulfonate to p-cresol, and were found to con ... | 2007 | 17222151 |
| heavy metal resistance and genotypic analysis of metal resistance genes in gram-positive and gram-negative bacteria present in ni-rich serpentine soil and in the rhizosphere of alyssum murale. | forty-six bacterial cultures, including one culture collection strain, thirty from the rhizosphere of alyssum murale and fifteen from ni-rich soil, were tested for their ability to tolerate arsenate, cadmium, chromium, zinc, mercury, lead, cobalt, copper, and nickel in their growth medium. the resistance patterns, expressed as minimum inhibitory concentrations, for all cultures to the nine different metal ions were surveyed by using the agar dilution method. a large number of the cultures were r ... | 2007 | 17276484 |
| isolation of maize soil and rhizosphere bacteria with antagonistic activity against aspergillus flavus and fusarium verticillioides. | bacterial isolates from mississippi maize field soil and maize rhizosphere samples were evaluated for their potential as biological control agents against aspergillus flavus and fusarium verticillioides. isolated strains were screened for antagonistic activities in liquid coculture against a. flavus and on agar media against a. flavus and f. verticillioides. we identified 221 strains that inhibited growth of both fungi. these bacteria were further differentiated by their production of extracellu ... | 2007 | 17685333 |
| selection and characterization of aerobic bacteria capable of degrading commercial mixtures of low-ethoxylated nonylphenols. | isolation and characterization of new bacterial strains capable of degrading nonylphenol ethoxylates (npneo) with a low ethoxylation degree, which are particularly recalcitrant to biodegradation. | 2008 | 17850311 |
| characterization of novel linuron-mineralizing bacterial consortia enriched from long-term linuron-treated agricultural soils. | linuron-mineralizing cultures were enriched from two linuron-treated agricultural soils in the presence and absence of a solid support. the cultures contained linuron-degrading bacteria, which coexisted with bacteria degrading either 3,4-dichloroaniline (3,4-dca) or n,o-dimethylhydroxylamine (n,o-dmha), two common metabolites in the linuron degradation pathway. for one soil, the presence of a solid support enriched for linuron-degrading strains phylogenetically related to but different from thos ... | 2007 | 17991021 |
| identification of diazotrophs in the culturable bacterial community associated with roots of lasiurus sindicus, a perennial grass of thar desert, india. | lasiurus sindicus is a highly nutritive, drought-tolerant, perennial grass that is endemic to the thar desert of rajasthan, india. analysis of 16s rrna coding genes of the bacterial isolates enriched in nitrogen-free semisolid medium, from the surface-sterilized roots of l. sindicus, showed predominance of gram-negative over gram-positive bacteria. according to comparative sequence analysis of 16s rdna sequence data, gram-positive bacteria with low gc content (staphylococcus warneri and bacillus ... | 2007 | 17264993 |
| 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 |
| variovorax soli sp. nov., isolated from greenhouse soil. | a gram-negative, rod-shaped, non-spore-forming bacterium, strain gh9-3(t), isolated from greenhouse soil, was investigated in a polyphasic study. the novel organism grew at 10-35 degrees c, 0-3 % nacl and ph 5-9. it had ubiquinone 8 (q-8) as the predominant isoprenoid quinone and possessed c(16 : 0), summed feature 3, c(17 : 0) cyclo and c(18 : 1) omega7c as the major fatty acids (together representing 87.4 % of the total). the dna g+c content was 67.1 mol%. 16s rrna gene sequence analysis of st ... | 2006 | 17158995 |
| characterization of biofilm formation on a humic material. | biofilms are major sites of carbon cycling in streams. therefore, it is crucial to improve knowledge about biofilms' structure and microbial composition to understand their contribution in the self-purification of surface water. the present work intends to study biofilm formation in the presence of humic substances (hss) as a carbon source. two biofilm flowcells were operated in parallel; one with synthetic stream water, displaying a background carbon concentration of 1.26+/-0.84 mg l(-1), the o ... | 2008 | 18712549 |
| gene cloning of alpha-methylserine aldolase from variovorax paradoxus and purification and characterization of the recombinant enzyme. | the alpha-methylserine aldolase gene from variovorax paradoxus strains aj110406, nbrc15149, and nbrc15150 was cloned and expressed in escherichia coli. formaldehyde release activity from alpha-methyl-l-serine was detected in the cell-free extract of e.coli expressing the gene from three strains. the recombinant enzyme from v. paradoxus nbrc15150 was purified. the vmax and km of the enzyme for the formaldehyde release reaction from alpha-methyl-l-serine were 1.89 micromol min(-1) mg(-1) and 1.2 m ... | 2008 | 18838814 |
| purification and gene cloning of alpha-methylserine aldolase from ralstonia sp. strain aj110405 and application of the enzyme in the synthesis of alpha-methyl-l-serine. | by screening microorganisms that are capable of assimilating alpha-methyl-dl-serine, we detected alpha-methylserine aldolase in ralstonia sp. strain aj110405, variovorax paradoxus aj110406, and bosea sp. strain aj110407. a homogeneous form of this enzyme was purified from ralstonia sp. strain aj110405, and the gene encoding the enzyme was cloned and expressed in escherichia coli. the enzyme appeared to be a homodimer consisting of identical subunits, and its molecular mass was found to be 47 kda ... | 2008 | 18952881 |
| 3-mercaptopropionate dioxygenase, a cysteine dioxygenase homologue, catalyzes the initial step of 3-mercaptopropionate catabolism in the 3,3-thiodipropionic acid-degrading bacterium variovorax paradoxus. | the thioether 3,3-thiodipropionic acid can be used as precursor substrate for biotechnological synthesis of 3-mercaptopropionic acid-containing polythioesters. therefore, the hitherto unknown catabolism of this compound was elucidated to engineer novel and improved polythioester biosynthesis pathways in the future. bacteria capable of using 3,3-thiodipropionic acid as the sole source of carbon and energy for growth were enriched from the environment. from eleven isolates, tbea3, tbea6, and sfwt ... | 2009 | 19001372 |
| biodegradation of methyl tert-butyl ether by cold-adapted mixed and pure bacterial cultures. | an aerobic mixed bacterial culture (cl-emc-1) capable of utilizing methyl tert-butyl ether (mtbe) as the sole source of carbon and energy with a growth temperature range of 3 to 30 degrees c and optimum of 18 to 22 degrees c was enriched from activated sludge. transient accumulation of tert-butanol (tba) occurred during utilization of mtbe at temperatures from 3 degrees c to 14 degrees c, but tba did not accumulate above 18 degrees c. the culture utilized mtbe at a concentration of up to 1.5 g l ... | 2007 | 17146651 |
| rhizosphere bacteria containing 1-aminocyclopropane-1-carboxylate deaminase increase yield of plants grown in drying soil via both local and systemic hormone signalling. | decreased soil water availability can stimulate production of the plant hormone ethylene and inhibit plant growth. strategies aimed at decreasing stress ethylene evolution might attenuate its negative effects. an environmentally benign (nonchemical) method of modifying crop ethylene relations - soil inoculation with a natural root-associated bacterium variovorax paradoxus 5c-2 (containing the enzyme 1-aminocyclopropane-1-carboxylate (acc) deaminase that degrades the ethylene precursor acc), was ... | 2009 | 19121036 |
| constitutive mineralization of low concentrations of the herbicide linuron by a variovorax sp. strain. | the mineralization of the herbicide linuron at concentrations of microg and mg l(-1) was studied in liquid batch experiments with variovorax sp. strain srs16. the strain was highly efficient at mineralizing a range of linuron concentrations (0.002-10 mg l(-1)) with 20-60% of the added (14)c-ring-labeled linuron metabolized to (14)co(2) within hours to days depending on the initial linuron concentration and incubation period. at mg l(-1) linuron concentrations the mineralization activity by srs16 ... | 2009 | 19187207 |
| expression of the phosphonoalanine-degradative gene cluster from variovorax sp. pal2 is induced by growth on phosphonoalanine and phosphonopyruvate. | the phosphonopyruvate hydrolase (pala) found in variovorax sp., pal2, is a novel carbon-phosphorus bond cleavage enzyme, which is expressed even in the presence of high levels of phosphate, thus permitting phosphonopyruvate to be used as the sole carbon and energy source. analysis of the regions adjacent to the pala gene revealed the presence of the five structural genes that constitute the 2-amino-3-phosphonopropionic acid (phosphonoalanine)-degradative operon. reverse transcriptase-pcr (rt-pcr ... | 2009 | 19191873 |
| evaluation of biocontrol activity of rhizobacteria from beta vulgaris against heterodera schachtii. | one hundred fifty rhizobacteria isolated from roots of swiss chard grown in a soil suppressive to the sugar beet cyst nematode, heterodera schachtii, were tested for their influence on the nematode's ability to hatch and infect roots. two screening systems were used that focused on the ability of bacteria to inhibit either nematode hatching or root infection. most of the bacterial strains reduced hatching in vitro compared to the control, while with 5% of the strains there were 0% hatch. seven p ... | 1999 | 19270875 |
| coordinated surface activities in variovorax paradoxus eps. | variovorax paradoxus is an aerobic soil bacterium frequently associated with important biodegradative processes in nature. our group has cultivated a mucoid strain of variovorax paradoxus for study as a model of bacterial development and response to environmental conditions. colonies of this organism vary widely in appearance depending on agar plate type. | 2009 | 19523213 |
| demonstrating formation of potentially persistent transformation products from the herbicides bromoxynil and ioxynil using liquid chromatography-tandem mass spectrometry (lc-ms/ms). | it is shown that potentially persistent transformation products can be formed from the herbicides bromoxynil (3,5-dibromo-4-hydroxybenzonitrile) and ioxynil (3,5-diiodo-4-hydroxybenzonitrile), and possible leaching to groundwater is discussed. a similar process to the formation of bam (2,6-dichlorobenzamide) from the herbicide dichlobenil (2,6-dichlorobenzonitrile) can be anticipated as bromoxynil and ioxynil are analogues of dichlobenil and they are degraded by the enzymes nitrilase, nitrile hy ... | 2007 | 17125153 |
| variovorax dokdonensis sp. nov., isolated from soil. | a gram-negative, motile and oval- or rod-shaped bacterial strain, ds-43t, was isolated from soil from dokdo, korea, and its taxonomic position was investigated by using a polyphasic approach. the strain grew optimally at ph 7.0-8.0 and at 30 degrees c in the presence of 0.5 % (w/v) nacl. strain ds-43t had q-8 as the predominant ubiquinone and c(16 : 0), c(16 : 1)omega7c and/or iso-c(15 : 0) 2-oh, c(18 : 1)omega7c and c(17 : 0) cyclo as the major fatty acids, which are consistent with the corresp ... | 2006 | 16585700 |
| biphenyl-metabolizing bacteria in the rhizosphere of horseradish and bulk soil contaminated by polychlorinated biphenyls as revealed by stable isotope probing. | dna-based stable isotope probing in combination with terminal restriction fragment length polymorphism was used in order to identify members of the microbial community that metabolize biphenyl in the rhizosphere of horseradish (armoracia rusticana) cultivated in soil contaminated with polychlorinated biphenyls (pcbs) compared to members of the microbial community in initial, uncultivated bulk soil. on the basis of early and recurrent detection of their 16s rrna genes in clone libraries construct ... | 2009 | 19700551 |
| bacterial growth and biofilm production on pyrene. | enrichment cultures inoculated with arctic soil yielded a biofilm that grew on pyrene and phenanthrene. in a 60-day period, the biofilm degraded 20 microg ml(-1) pyrene or 39 microg ml(-1) phenanthrene. single colonized pyrene crystals (approximately 1.5x0.75x0.35 mm) yielded 10(11) culturable heterotrophs and 10(5) biofilm propagules. analysis of ribosomal intergenic spacers identified six phylotypes in a clone library from the pyrene biofilm. analysis of 16s rrna gene sequences indicated that ... | 2002 | 19709207 |
| microbial succession during a field evaluation of phenol and toluene as the primary substrates for trichloroethene cometabolism. | microbial community composition and succession were studied in an aquifer that was amended with phenol, toluene, and chlorinated aliphatic hydrocarbons to evaluate the effectiveness of these aromatic substrates for stimulating trichloroethene (tce) bioremediation. samples were taken after the previous year's field studies, which used phenol as the primary substrate, and after three successive monthly treatments of phenol plus 1,1-dichloroethene (1,1-dce) plus tce, phenol plus tce, and toluene pl ... | 1997 | 16535576 |
| the rhizosphere bacterium variovorax paradoxus 5c-2 containing acc deaminase does not increase systemic aba signaling in maize (zea mays l.). | | 2009 | 19816130 |
| characterization of an isoproturon mineralizing bacterial culture enriched from a french agricultural soil. | the phenylurea herbicide isoproturon, 3-(4-isopropylphenyl)-1,1-dimethylurea (ipu), was found to be rapidly mineralized by a bacterial culture isolated from an agricultural soil regularly exposed to ipu. molecular analysis of the bacterial culture by dna fingerprinting, cloning and sequencing of the 16s rrna genes revealed that it consisted of six different members among whom the dominant was related to sphingomonas sp. six bacterial strains belonging to genera ancylobacter, pseudomonas, stenotr ... | 2009 | 19836052 |
| genetic and phenotypic diversity of parathion-degrading bacteria isolated from rice paddy soils. | three parathion-degrading bacteria and eight pairs of bacteria showing syntrophic metabolism of parathion were isolated from rice field soils, and their genetic and phenotypic characteristics were investigated. the three isolates and eight syntrophic pairs were able to utilize parathion as a sole source of carbon and energy, producing p-nitrophenol as the intermediate metabolite during the complete degradation of parathion. analysis of 16s rrna gene sequence indicated that the isolates were rela ... | 2009 | 20075637 |
| proteomic study of linuron and 3,4-dichloroaniline degradation by variovorax sp. wdl1: evidence for the involvement of an aniline dioxygenase-related multicomponent protein. | a proteomic approach was used to explore the metabolism of the phenylurea herbicide linuron and 3,4-dichloroaniline (3,4-dca) in variovorax sp. wdl1. this bacterium grows on linuron as sole source of carbon, nitrogen and energy, while it transiently accumulates 3,4-dca as a metabolite. differential protein expression analysis of variovorax sp. wdl1 grown in a heterotrophic medium in the presence and absence of linuron or 3,4-dca was conducted using 2-d page. selected up- and downregulated protei ... | 2010 | 20146937 |
| utilization of homoserine lactone as a sole source of carbon and energy by soil arthrobacter and burkholderia species. | homoserine lactone (hsl) is a ubiquitous product of metabolism. it is generated by all known biota during the editing of certain mischarged aminoacyl-trna reactions, and is also released as a product of quorum signal degradation by bacterial species expressing acyl-hsl acylases. little is known about its environmental fate over long or short periods of time. the mammalian enzyme paraoxonase, which has no known homologs in bacteria, has been reported to degrade hsl via a lactonase mechanism. cert ... | 2006 | 16341844 |
| control of continuous polyhydroxybutyrate synthesis using calorimetry and flow cytometry. | the substrate-carbon flow can be controlled in continuous bioreactor cultures by the medium composition, for example, by the c/n ratio. the carbon distribution is optimal when a maximum fraction flows into the desired product and the residual is just sufficient to compensate for the dilution of the microbial catalyst. undershooting of the latter condition is reflected immediately by changes in the gibbs energy dissipation and cellular states. two calorimetric measurement principles were applied ... | 2006 | 16245347 |
| assessment of mtbe biodegradation pathways by two-dimensional isotope analysis in mixed bacterial consortia under different redox conditions. | the fuel oxygenate, methyl tert-butyl ether (mtbe), although now widely banned or substituted, remains a persistent groundwater contaminant. multidimensional compound-specific isotope analysis (csia) of carbon and hydrogen is being developed for determining the extent of mtbe loss due to biodegradation and can also potentially distinguish between different biodegradation pathways. carbon and hydrogen isotopic fractionation factors were determined for mtbe degradation in aerobic and anaerobic lab ... | 2010 | 20582586 |
| microbial community structure and trichloroethylene degradation in groundwater. | trichloroethylene (tce) is a prevalent contaminant of groundwater that can be cometabolically degraded by indigenous microbes. groundwater contaminated with tce from a us department of energy site in ohio was used to characterize the site-specific impact of phenol on the indigenous bacterial community for use as a possible remedial strategy. incubations of 14c-tce-spiked groundwater amended with phenol showed increased tce mineralization compared with unamended groundwater. community structure w ... | 2005 | 16121220 |
| bacteria from drinking water supply and their fate in gastrointestinal tracts of germ-free mice: a phylogenetic comparison study. | microorganisms in drinking water sources may colonize in gastrointestinal (gi) tracts and this phenomenon may pose a potential health risk especially to immunocompromised population. the microbial community diversity of the drinking water was compared with the gi tracts of the mice using phylogenetic and statistical analyses of 16s rrna gene sequences. a group of germ-free mice were fed with drinking water from public water supply that passed through an automated watering system with documented ... | 2010 | 20705313 |
| purification, characterization, gene cloning and nucleotide sequencing of d: -stereospecific amino acid amidase from soil bacterium: delftia acidovorans. | the d-amino acid amidase-producing bacterium was isolated from soil samples using an enrichment culture technique in medium broth containing d-phenylalanine amide as a sole source of nitrogen. the strain exhibiting the strongest activity was identified as delftia acidovorans strain 16. this strain produced intracellular d-amino acid amidase constitutively. the enzyme was purified about 380-fold to homogeneity and its molecular mass was estimated to be about 50 kda, on sodium dodecyl sulfate poly ... | 2005 | 15959727 |
| aerobic degradation of mercaptosuccinate by the gram-negative bacterium variovorax paradoxus strain b4. | the gram-negative bacterium variovorax paradoxus strain b4 was isolated from soil under mesophilic and aerobic conditions to elucidate the so far unknown catabolism of mercaptosuccinate (ms). during growth with ms this strain released significant amounts of sulfate into the medium. tn5::mob-induced mutagenesis was successfully employed and yielded nine independent mutants incapable of using ms as a carbon source. in six of these mutants, tn5::mob insertions were mapped in a putative gene encodin ... | 2010 | 21075928 |
| complete genome sequence of the metabolically versatile plant growth-promoting endophyte variovorax paradoxus s110. | variovorax paradoxus is a microorganism of special interest due to its diverse metabolic capabilities, including the biodegradation of both biogenic compounds and anthropogenic contaminants. v. paradoxus also engages in mutually beneficial interactions with both bacteria and plants. the complete genome sequence of v. paradoxus s110 is composed of 6,754,997 bp with 6,279 predicted protein-coding sequences within two circular chromosomes. genomic analysis has revealed multiple metabolic features f ... | 2010 | 21183664 |
| a molecular toolbox to estimate the number and diversity of variovorax in the environment: application in soils treated with the phenylurea herbicide linuron. | real-time pcr and pcr-denaturing gradient gel electrophoresis (dgge) approaches that specifically target the variovorax 16s rrna gene were developed to estimate the number and diversity of variovorax in environmental ecosystems. pcr primers suitable for both methods were selected as such that the enclosed sequence showed maximum polymorphism. pcr specificity was maximized by combining pcr with a targeted endonuclease treatment of template dna to eliminate 16s rrna genes of the closely related ac ... | 2011 | 21204875 |
| isolation and identification of soil bacteria growing at the expense of arbuscular mycorrhizal fungi. | soil-microorganism symbioses are of fundamental importance for plant adaptation to the environment. research in microbial ecology has revealed that some soil bacteria are associated with arbuscular mycorrhizal fungi (amf). however, these interactions may be much more complex than originally thought. to assess the type of bacteria associated with amf, we initially isolated spores of glomus irregulare from an agrostis stolonifera rhizosphere. the spores were washed with sterile water and plated on ... | 2011 | 21219415 |
| seasonal change in bacterial flora and biomass in mountain snow from the tateyama mountains, japan, analyzed by 16s rrna gene sequencing and real-time pcr. | the bacterial flora and biomass in mountain snow from the tateyama mountains, toyama prefecture, japan, one of the heaviest snowfall regions in the world, were analyzed by amplified ribosomal dna restriction analysis followed by 16s rrna gene sequencing and dna quantification by real-time pcr. samples of surface snow collected in various months during the melting season contained a psychrophilic bacterium, cryobacterium psychrophilum, and two psychrotrophic bacteria, variovorax paradoxus and jan ... | 2005 | 15640179 |
| relative quantitative pcr to assess bacterial community dynamics during biodegradation of diesel and biodiesel fuels under various aeration conditions. | the degradation of diesel fuel, b20 blend and biodiesel in liquid cultures by a seven-member bacterial consortium was compared under conditions with full aeration or with limited aeration with nitrate added as main electron acceptor. community dynamics was assessed employing real-time pcr and the ddct method for relative quantification. biodegradation rates increased with increasing biodiesel content, but were significantly reduced under conditions with nitrate. despite large variations in biode ... | 2010 | 21239170 |
| flow calorimetry and dielectric spectroscopy to control the bacterial conversion of toxic substrates into polyhydroxyalcanoates. | the microbial conversion of toxic substrates into valuable products in continuous culture requires the equivalent of a tight rope walk between formation of the desired product and intoxication of the microbial catalyst. the condition of the latter is reflected immediately by changes in heat flow rate and beta-dispersion in an electrical rf field. therefore, these were applied to the example of the continuous growth-associated synthesis of polyhydroxyalcanoates (pha) from phenol by the bacterial ... | 2004 | 14760695 |
| multiple dna extractions coupled with stable-isotope probing of anthracene-degrading bacteria in contaminated soil. | in many of the dna-based stable-isotope probing (sip) studies published to date in which soil communities were investigated, a single dna extraction was performed on the soil sample, usually using a commercial dna extraction kit, prior to recovering the (13)c-labeled (heavy) dna by density-gradient ultracentrifugation. recent evidence suggests, however, that a single extraction of a soil sample may not lead to representative recovery of dna from all of the organisms in the sample. to determine w ... | 2011 | 21398486 |
| aerobic cometabolism of trichloroethene and cis-dichloroethene with benzene and chlorinated benzenes as growth substrates. | using inoculum from a microcosm study that exhibited aerobic transformation of cis-1,2-dichloroethene (cdce) and trichloroethene (tce) commensurate with biodegradation of monoaromatic compounds, enrichment cultures were developed by providing benzene, chlorobenzene (cb), dichlorobenzene (dcb) isomers and 1,2,4-trichlorobenzene as carbon and energy sources. isolates that grow on benzene, cb, 1,2-dcb and 1,3-dcb were identified as rhodococcus, ralstonia, variovorax and ralstonia spp., respectively ... | 2011 | 21531438 |
| molecular definition of vaginal microbiota in east african commercial sex workers. | resistance to hiv infection in a cohort of commercial sex workers (csw) living in nairobi, kenya is linked to mucosal and anti-inflammatory factors that may be influenced by vaginal microbiota. since bacterial vaginosis (bv), a polymicrobial dysbiosis characterized by low levels of protective lactobacillus organisms, is an established risk factor for hiv infection, we investigated whether vaginal microbiology was associated with hiv-exposed seronegative (hesn) or hiv-seropositive (hiv+) status i ... | 2011 | 21531840 |
| [diversity of siderophore-producing endophytic bacteria of cymbidium goeringii roots]. | in order to obtain the effective plant growth-promoting bacteria, we studied the diversity of siderophore-producing endophytic bacteria in the roots of cymbidium goeringii. | 2011 | 21574379 |
| bacterial populations associated with the oxidation and reduction of arsenic in an unsaturated soil. | microbial populations responsible for the oxidation and reduction of as were examined in unsaturated (aerobic) soil columns treated with 75 microm arsenite [as(iii)] or 250 microm arsenate [as(v)]. arsenite [as(iii)] was rapidly oxidized to as(v) via microbial activity, whereas no apparent reduction of as(v) was observed in the column experiments. eight aerobic heterotrophic bacteria with varying as redox phenotypes were isolated from the same columns. three isolates, identified as agrobacterium ... | 2004 | 14740724 |
| comparison of subsurface and surface soil bacterial communities in california grassland as assessed by terminal restriction fragment length polymorphisms of pcr-amplified 16s rrna genes. | the integrated biomass beneath the surface horizon in unsaturated soils is large and potentially important in nutrient and carbon cycling. compared to surface soils, the ecology of these subsurface soils is weakly understood, particularly in terms of the composition of bacterial communities. we compared soil bacterial communities along two vertical transects by terminal restriction fragment length polymorphisms (trflps) of pcr-amplified 16s rrna genes to determine how surface and deep bacterial ... | 2003 | 14708746 |
| biotransformation of the neonicotinoid insecticide thiacloprid by the bacterium variovorax boronicumulans strain j1 and mediation of the major metabolic pathway by nitrile hydratase. | a neonicotinoid insecticide thiacloprid-degrading bacterium strain j1 was isolated from soil and identified as variovorax boronicumulans by 16s rrna gene sequence analysis. liquid chromatography-mass spectrometry and nuclear magnetic resonance analysis indicated the major pathway of thiacloprid (thi) metabolism by v. boronicumulans j1 involved hydrolysis of the n-cyanoimino group to form an n-carbamoylinino group containing metabolite, thi amide. resting cells of v. boronicumulans j1 degraded ... | 2011 | 22148554 |
| the purification and characterization of phosphonopyruvate hydrolase, a novel carbon-phosphorus bond cleavage enzyme from variovorax sp pal2. | phosphonopyruvate hydrolase, a novel bacterial carbon-phosphorus bond cleavage enzyme, was purified to homogeneity by a series of chromatographic steps from cell extracts of a newly isolated environmental strain of variovorax sp. pal2. the enzyme was inducible in the presence of phosphonoalanine or phosphonopyruvate; unusually, its expression was independent of the phosphate status of the cell. the native enzyme had a molecular mass of 63 kda with a subunit mass of 31.2 kda. activity of purified ... | 2003 | 12697754 |
| a novel hydrolase identified by genomic-proteomic analysis of phenylurea herbicide mineralization by variovorax sp. strain srs16. | the soil bacterial isolate variovorax sp. strain srs16 mineralizes the phenylurea herbicide linuron. the proposed pathway initiates with hydrolysis of linuron to 3,4-dichloroaniline (dca) and n,o-dimethylhydroxylamine, followed by conversion of dca to krebs cycle intermediates. differential proteomic analysis showed a linuron-dependent upregulation of several enzymes that fit into this pathway, including an amidase (liba), a multicomponent chloroaniline dioxygenase, and enzymes associated with a ... | 2011 | 22003008 |
| High-sensitivity stable-isotope probing by a quantitative terminal restriction fragment length polymorphism protocol. | Stable-isotope probing (SIP) has proved a valuable cultivation-independent tool for linking specific microbial populations to selected functions in various natural and engineered systems. However, application of SIP to microbial populations with relatively minor buoyant density increases, such as populations that utilize compounds as a nitrogen source, results in reduced resolution of labeled populations. We therefore developed a tandem quantitative PCR (qPCR)-TRFLP (terminal restriction fragmen ... | 2012 | 22038597 |
| variovorax defluvii sp. nov., isolated from sewage flowing into river geumho in south korea. | a polyphasic taxonomic study was carried out on 2c1-b(t) and 2c-21, two strains isolated from the sewage flowing into river geumho in korea.the cells of strains were gram-negative, non-spore-forming, motile and oval or rod-shaped bacteria. comparative 16s rrna gene sequence studies showed a clear affiliation of these two bacteria into the betaproteobacteria, which were most closely related to variovorax boronicumulans kctc 22010(t), variovorax dokdonensis kctc 12544(t), variovorax ginsengisoli k ... | 2011 | 21948092 |