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nitrogen removal characteristics of pseudomonas putida y-9 capable of heterotrophic nitrification and aerobic denitrification at low temperature.the cold-adapted bacterium pseudomonas putida y-9 was investigated and exhibited excellent capability for nitrogen removal at 15°c. the strain capable of heterotrophic nitrification and aerobic denitrification could efficiently remove ammonium, nitrate, and nitrite at an average removal rate of 2.85 mg, 1.60 mg, and 1.83 mg nl(-1 )h(-1), respectively. strain y-9 performed nitrification in preference to denitrification when ammonium and nitrate or ammonium and nitrite coexisted in the solution. m ...201728293626
bacterial effects and interfacial inactivation mechanism of nzvi/pd on pseudomonas putida strain.with the introduction of nano zero valent iron (nzvi) technology into our environment, its potential environmental risk to environmental microorganisms has attracted considerable attention. in this study, pseudomonas putida was chosen as a typical strain to study the bacterial toxicity of nzvi/pd. the cfu assay results indicated that nzvi/pd was toxic to p. putida cells but the toxicity decreased with an increase in do. the experiments isolated by dialysis bag and flow cytometry analysis suggest ...201728285239
production of polyhydroxyalkanoates from sludge palm oil using pseudomonas putida s12.polyhydroxyalkanoates (phas) are biodegradable plastics produced by bacteria, but their use in diverse applications is prohibited by high production costs. to reduce these costs, the conversion of phas from crude sludge palm oil (spo) as an inexpensive renewable raw material by pseudomonas strains was tested. pseudomonasputida s12 was found to produce the highest yield (~41%) of elastomeric medium-chain-length (mcl)-phas from spo. the mcl-pha characteristics were analyzed by gas-chromatography/m ...201728274100
cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces.mounting evidence suggests that natural microbial communities exhibit a high level of spatial organization at the micrometric scale that facilitate ecological interactions and support biogeochemical cycles. microbial patterns are difficult to study definitively in natural environments due to complex biodiversity, observability and variable physicochemical factors. here, we examine how trophic dependencies give rise to self-organized spatial patterns of a well-defined bacterial consortium grown o ...201728262696
ultrasonic disruption of pseudomonas putida for the release of arginine deiminase: kinetics and predictive models.the responses of the ultrasound-mediated disruption of pseudomonas putida kt2440 were modelled as the function of biomass concentration in the cell suspension; the treatment time of sonication; the duty cycle and the acoustic power of the sonicator. for the experimental data, the response surface (rsm), the artificial neural network (ann) and the support vector machine (svm) models were compared for their ability to predict the performance parameters. the satisfactory prediction of the unseen da ...201728260664
high performance and prospective application of xanthate-modified thiourea chitosan sponge-combined pseudomonas putida and talaromyces amestolkiae biomass for pb(ii) removal from wastewater.biosorption using microbes has been proved to be an efficient technology to remove heavy metals from wastewater, whereas the imperfections in mechanical property and separation limit their practical application. in this study, pseudomonas putida i3 and talaromyces amestolkiae pb respectively combined with xanthate-modified thiourea chitosan sponge (pxtcs and txtcs) were synthesized to investigate the pb(ii) removal ability from solutions. the prepared biosorbents possessed a three-dimensional ma ...201728258997
potential microbial contamination during sampling of permafrost soil assessed by tracers.drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. we also present ...201728230151
a facile approach for surface alteration of pseudomonas putida i3 by supplying k2so4 into growth medium: enhanced removal of pb(ii) from aqueous solution.a new sight of obtaining a high efficient biosorbent by supplying specific salts into bacterial growth medium was investigated in this study for pb(ii). among a series of salts including na2so4, na2s2o3, kcl, and k2so4, the highest pb(ii) removal efficiency was observed by psychrotrophilic pseudomonas putida i3 grown in the presence of 30g/l k2so4 (ksi3-30) with biosorption capacity of 62.89mg/g under cold condition (15°c), which was increased by 42.35% as compared to control (without any additi ...201728219053
structure of a lov protein in apo-state and implications for construction of lov-based optical tools.unique features of light-oxygen-voltage (lov) proteins like relatively small size (~12-19 kda), inherent modularity, highly-tunable photocycle and oxygen-independent fluorescence have lately been exploited for the generation of optical tools. structures of lov domains reported so far contain a flavin chromophore per protein molecule. here we report two new findings on the short lov protein w619_1-lov from pseudomonas putida. first, the apo-state crystal structure of w619_1-lov at 2.5 å resolutio ...201728211532
complete genome sequence of the polychlorinated biphenyl-degrading bacterium pseudomonas putida kf715 (nbrc 110667) isolated from biphenyl-contaminated soil.pseudomonas putida kf715 (nbrc 110667) utilizes biphenyl as a sole source of carbon and degrades polychlorinated biphenyls (pcbs). here, we report a complete genome sequence of the kf715 strain, which comprises a circular chromosome and four plasmids. biphenyl catabolic genes were located on the largest plasmid, pkf715a.201728209826
quantifying bacterial attachment and detachment using leaching solutions of various ionic strengths after bacterial pulse.in this study, we quantified the attachment and detachment of bacteria during transport in order to elucidate the contributions of reversible attachment on bacterial breakthrough curves. the first set of breakthrough experiment was performed for a laboratory sand column using leaching solutions of deionized water and mineral salt medium (msm) of 200 mm with reference to kcl solution by employing pseudomonas putida as a model bacterium. in the second set of experiment, the ionic strengths of leac ...201728197984
carbon source-dependent inducible metabolism of veratryl alcohol and ferulic acid in pseudomonas putida csv86.pseudomonas putida csv86 degrades lignin-derived metabolic intermediates, viz, veratryl alcohol, ferulic acid, vanillin, and vanillic acid, as the sole sources of carbon and energy. strain csv86 also degraded lignin sulfonate. cell respiration, enzyme activity, biotransformation, and high-pressure liquid chromatography (hplc) analyses suggest that veratryl alcohol and ferulic acid are metabolized to vanillic acid by two distinct carbon source-dependent inducible pathways. vanillic acid was furth ...201728188206
pathogen cross-transmission via building sanitary plumbing systems in a full scale pilot test-rig.the who consensus document on the epidemiology of the sars epidemic in 2003, included a report on a concentrated outbreak in one hong kong housing block which was considered a 'super-spreading event'. the who report conjectured that the sanitary plumbing system was one transmission route for the virus. empty u-traps allowed the aerosolised virus to enter households from the sewerage system. no biological evidence was presented. this research reports evidence that pathogens can be aerosolised and ...201728187135
acc deaminase-containing plant growth-promoting rhizobacteria protect papaver somniferum from downy mildew.the aim of this study was to determine whether acc (1-aminocyclopropane-1-carboxylic acid) deaminase-containing bacterial treatments could enhance the tolerance of poppy (papaver somniferum l.) plants against biotic stress of downy mildew caused by peronospora sp.201728186676
medium chain length polyhydroxyalkanoates biosynthesis in pseudomonas putida mt-2 is enhanced by co-metabolism of glycerol/octanoate or fatty acids mixtures.the synthesis of medium chain length polyhydroxyalkanoates (mcl-phas) by pseudomonas putida mt-2 was investigated under nitrogen-rich then deficient conditions with glycerol/octanoate or long-chain fatty acids (lcfas) as carbon sources. when mixed, glycerol and octanoate were co-assimilated regardless of nitrogen availability but provided that glycerol uptake has been already triggered under non-limiting nutrient conditions. this concomitant consumption allowed to enhance mcl-phas accumulation ( ...201728174083
a two-column flash chromatography approach to pyoverdin production from pseudomonas putida gb1.our knowledge of the biological and environmental reactivity of siderophores is limited by the difficulty and cost of obtaining reasonable quantities by purification or synthesis. in this note, we describe a modified procedure for the low-cost, mg-scale purification of pyoverdin-type siderophores using a dual-flash chromatography (reverse-phase absorption and size exclusion) approach.201728161587
itraq-based quantitative proteomic analysis of the global response to 17β-estradiol in estrogen-degradation strain pseudomonas putida sjte-1.microorganism degradation is efficient to remove the steroid hormones like 17β-estradiol (e2); but their degradation mechanism and metabolic network to these chemicals are still not very clear. here the global responses of the estrogen-degradation strain pseudomonas putida sjte-1 to 17β-estradiol and glucose were analyzed and compared using the itraq (isobaric tags for relative and absolute quantization) strategy combined with lc-ms/ms (liquid chromatography-tandem mass spectrometry). 78 protein ...201728155874
structure and biochemistry of phenylacetaldehyde dehydrogenase from the pseudomonas putida s12 styrene catabolic pathway.phenylacetaldehyde dehydrogenase catalyzes the nad(+)-dependent oxidation of phenylactealdehyde to phenylacetic acid in the styrene catabolic and detoxification pathway of pseudomonas putida (s12). here we report the structure and mechanistic properties of the n-terminally histidine-tagged enzyme, npadh. the 2.83 å x-ray crystal structure is similar in fold to sheep liver cytosolic aldehyde dehydrogenase (aldh1), but has unique set of intersubunit interactions and active site tunnel for substrat ...201728153386
rapid proteomics to prospect and validate novel bacterial metabolism induced by environmental burden.understanding the pathophysiology of genes and enzymes involved in caffeine metabolism can have extracurricular benefits, such as providing distinct methylxanthines as intermediates for pharmaceutical synthesis, and also improve environmental waste remediation. the strains pseudomonas putida cbb5 and ces may provide insights into these applications because they may both be induced to degrade caffeine, yet the latter thrives in concentrations >8.0gl(-1); threefold higher than any other bacteria. ...201728137573
proteins with chads (conserved histidine α-helical domains) are attached to polyphosphate granules in vivo and constitute a novel family of polyphosphate-associated proteins (phosins).on the basis of bioinformatic evidence, we suspected that proteins with a cyth (cyab thiamine triphosphatase) domain and/or a chad (conserved histidine α-helical domain) motif might represent polyphosphate (polyp) granule-associated proteins. we found no evidence of polyp targeting by proteins with cyth domains. in contrast, two chad motif-containing proteins from ralstonia eutropha h16 (a0104 and b1017) that were expressed as fusions with enhanced yellow fluorescent protein (eyfp) colocalized w ...201728130300
global transcriptional responses to osmotic, oxidative, and imipenem stress conditions in pseudomonas putida.bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. in this study, the transcriptional response of pseudomonas putida kt2440 to osmotic, oxidative, and imipenem stress conditions at two time points was investigated via identification of differentially expressed mrnas and small rnas (srnas). a total of 440 srna transcripts were detected, of which 10% correspond to previously annotated srnas, 40% to novel intergenic transcripts, and 50% ...201728130298
microbial biotransformation of five pyrrolidinophenone-type psychoactive substances in wastewater and a wastewater isolated pseudomonas putida strain.wastewater-based epidemiology (wbe) employs the analysis of wastewater to detect and quantify drug use and discharge within a community. in this work, transformation products (tp) by microbes in the environment were identified after incubations in wastewater and an isolated microbial strain. the microbial strain was isolated from an enrichment culture of wastewater supplemented with 3,4-methylenedioxy-pyrovalerone, and identified by matrix assisted laser desorption - time of flight mass spectrom ...201728092435
pathway-consensus approach to metabolic network reconstruction for pseudomonas putida kt2440 by systematic comparison of published models.over 100 genome-scale metabolic networks (gsmns) have been published in recent years and widely used for phenotype prediction and pathway design. however, gsmns for a specific organism reconstructed by different research groups usually produce inconsistent simulation results, which makes it difficult to use the gsmns for precise optimal pathway design. therefore, it is necessary to compare and identify the discrepancies among networks and build a consensus metabolic network for an organism. here ...201728085902
the pseudomonas putida t6ss is a plant warden against phytopathogens.bacterial type vi secretion systems (t6sss) are molecular weapons designed to deliver toxic effectors into prey cells. these nanomachines have an important role in inter-bacterial competition and provide advantages to t6ss active strains in polymicrobial environments. here we analyze the genome of the biocontrol agent pseudomonas putida kt2440 and identify three t6ss gene clusters (k1-, k2- and k3-t6ss). besides, 10 t6ss effector-immunity pairs were found, including putative nucleases and pore-f ...201728045455
active antibacterial and antifouling surface coating via a facile one-step enzymatic cross-linking.prevention of microbial contamination of surfaces is one of the biggest challenges for biomedical applications. establishing a stable, easily produced, highly antibacterial surface coating offers an efficient solution but remains a technical difficulty. here, we report on a new approach to create an in situ hydrogel film-coating on glass surfaces made by enzymatic cross-linking under physiological conditions. the cross-linking is catalyzed by horseradish peroxidase (hrp)/glucose oxidase (god)-co ...201728005352
plant defence induced by pgpr against spodoptera litura in tomato (solanum lycopersicum l.).the research conducted including its rationale: spodoptera litura is the major pest of tomato causing significant reduction in tomato yield. application of plant growth promoting rhizobacteria(pgpr) prevent use of chemical fertilizer and synthetic pesticides through enhancement of plant growth and yield and induction of systemic resistance. present investigation is an attempt to evaluate the role of pgpr, pseudomonas putida and rothia sp. on the physiology and yield of tomato fruit infested with ...201728004873
phylogenetic analysis reveals the taxonomically diverse distribution of the pseudomonas putida group.pseudomonas putida is well-known for degradation activities for a variety of compounds and its infections have been reported. thus, p. putida includes both clinical and nonclinical isolates. to date, no reports have examined the phylogenetic relationship between clinical and nonclinical isolates of the p. putida group. in this study, fifty-nine strains of p. putida group containing twenty-six clinical, and thirty-three nonclinical, isolates, were subjected to phylogenetic and taxonomic analyses ...201727989998
mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens.there is a paucity of data regarding the microbial constituents of tobacco products and their impacts on public health. moreover, there has been no comparative characterization performed on the bacterial microbiota associated with the addition of menthol, an additive that has been used by tobacco manufacturers for nearly a century. to address this knowledge gap, we conducted bacterial community profiling on tobacco from user- and custom-mentholated/non-mentholated cigarette pairs, as well as a c ...201728202080
highly efficient simultaneous adsorption and biodegradation of a highly-concentrated anionic dye by a high-surface-area carbon-based biocomposite.mesoporous high-surface-area activated carbon (mhsa-ac), which has a honeycomb structure, was produced from coconut shells by simultaneous chemical and physical activation and used for the rapid adsorption of an anionic dye, namely acid orange 10 (ao10), from water. owing to its porosity and high brunauer-emmett-teller surface area (2283.91 m(2)g(-1)), mhsa-ac is a highly efficient adsorbent. it also has good biocompatibility and is a good immobilization carrier; the grooves on the mhsa-ac surfa ...201728365499
draft genome sequence of pseudomonas putida strain gm4fr, an endophytic bacterium isolated from festuca rubra l.pseudomonas putida gm4fr is an endophytic bacterium isolated from aerial plant tissues of festuca rubra l. functional annotation of the draft genome (7.1 mb) revealed 6,272 predicted protein-encoding genes. the genome provides insights into the biocontrol and plant growth-promoting potential of p. putida gm4fr.201728360162
deconvolution of gene expression noise into spatial dynamics of transcription factor-promoter interplay.gene expression noise is not only the mere consequence of stochasticity, but also a signal that reflects the upstream physical dynamics of the cognate molecular machinery. soil bacteria facing recalcitrant pollutants exploit noise of catabolic promoters to deploy beneficial phenotypes such as metabolic bet-hedging and/or division of biochemical labour. although the role of upstream promoter-regulator interplay in the origin of this noise is little understood, its specifications are probably ciph ...201728355056
isolation and characteristics of sulfentrazone-degrading bacteria.this study aimed to isolate and characterize bacteria able to use sulfentrazone in the commercial formulation as their sole carbon source. the isolation of the potential sulfentrazone-degrading bacteria was made from soil samples with a recent history of herbicide application and from isolates identified through rdna sequencing. subsequently, we assessed the growth of the isolates and their sulfentrazone degradation ability using high-performance liquid chromatography. twenty-six potential sulfe ...201727820678
effect of rhamnolipid solubilization on hexadecane bioavailability: enhancement or reduction?in this study, liquid culture systems containing rhamnolipid-solubilized, separate-phase, and multi-state hexadecane as the carbon source were employed for examining the effect of rhamnolipid solubilization on the bioavailability of hexadecane. experimental results showed that the uptake of rhamnolipid-solubilized hexadecane by pseudomonas aeruginosa atcc 9027, a rhamnolipid producing strain, was enhanced compared to the uptake of mass hexadecane as a separate phase, indicating rhamnolipid solub ...201727773441
fleq of pseudomonas putida kt2440 is a multimeric cyclic diguanylate binding protein that differentially regulates expression of biofilm matrix components.the intracellular signal molecule cyclic di-gmp (c-di-gmp) is an important element in regulation of biofilm formation by bacteria. in pseudomonas aeruginosa, fleq functions as a c-di-gmp-dependent transcriptional regulator of expression of flagellar genes and the exopolysaccharide (eps) pel, a component of the biofilm extracellular matrix. in the plant-beneficial bacterium pseudomonas putida kt2440, a mutation in fleq reduces biofilm formation and colonization of plant surfaces. using isothermal ...201727503246
bacteria can proliferate in thawed cryoprecipitate stored at room temperature for longer than 4 h.although key coagulation factor activities are maintained in thawed cryoprecipitate stored for up to 24 h at ambient temperature, several jurisdictions limit such storage to 4-6 h. here, we separately spiked thawed cryoprecipitate units with four bacterial strains: staphylococcus epidermidis, serratia liquefaciens, pseudomonas putida and pseudomonas aeruginosa. no strains grew in the first 4 h of storage, but by 24 h, three of four exhibited up to 1000-fold proliferation. pathogen inactivation t ...201728382701
indole-induced activities of β-lactamase and efflux pump confer ampicillin resistance in pseudomonas putida kt2440.indole, which is widespread in microbial communities, has received attention because of its effects on bacterial physiology. pseudomonas putida and pseudomonas aeruginosa can acquire ampicillin (amp) resistance during growth on indole-amp agar. transcriptome, mutant, and inhibitor studies have suggested that amp resistance induced by indole can be attributed to increased gene expression of ttgab encoding two genes of rnd-type multidrug efflux operons and an ampc encoding β-lactamase. expression, ...201728352264
dna polymerases imuc and dinb are involved in dna alkylation damage tolerance in pseudomonas aeruginosa and pseudomonas putida.translesion dna synthesis (tls), facilitated by low-fidelity polymerases, is an important dna damage tolerance mechanism. here, we investigated the role and biological function of tls polymerase imuc (former dnae2), generally present in bacteria lacking dna polymerase v, and tls polymerase dinb in response to dna alkylation damage in pseudomonas aeruginosa and p. putida. we found that tls dna polymerases imuc and dinb ensured a protective role against n- and o-methylation induced by n-methyl-n'- ...201728118378
novel insights into biosynthesis and uptake of rhamnolipids and their precursors.the human pathogenic bacterium pseudomonas aeruginosa produces rhamnolipids, glycolipids with functions for bacterial motility, biofilm formation, and uptake of hydrophobic substrates. rhamnolipids represent a chemically heterogeneous group of secondary metabolites composed of one or two rhamnose molecules linked to one or mostly two 3-hydroxyfatty acids of various chain lengths. the biosynthetic pathway involves rhamnosyltransferase i encoded by the rhlab operon, which synthesizes 3-(3-hydroxya ...201727988798
fusion proteins of an enoate reductase and a baeyer-villiger monooxygenase facilitate the synthesis of chiral lactones.nature uses the advantages of fusion proteins for multi-step reactions to facilitate the metabolism in cells as the conversion of substrates through intermediates to the final product can take place more rapidly and with less side-product formation. in a similar fashion, also for enzyme cascade reactions, the fusion of biocatalysts involved can be advantageous. in the present study, we investigated fusion of an alcohol dehydrogenase (adh), an enoate reductase (ered) and a baeyer-villiger monooxy ...201727289001
continuous multistep synthesis of perillic acid from limonene by catalytic biofilms under segmented flow.the efficiency of biocatalytic reactions involving industrially interesting reactants is often constrained by toxification of the applied biocatalyst. here, we evaluated the combination of biologically and technologically inspired strategies to overcome toxicity-related issues during the multistep oxyfunctionalization of (r)-(+)-limonene to (r)-(+)-perillic acid. pseudomonas putida gs1 catalyzing selective limonene oxidation via the p-cymene degradation pathway and recombinant pseudomonas taiwan ...201727530691
expression of the phosphodiesterase bifa facilitating swimming motility is partly controlled by flia in pseudomonas putida kt2440.flagella-mediated motility is an important capability of many bacteria to survive in nutrient-depleted and harsh environments. decreasing the intracellular cyclic di-gmp (c-di-gmp) level by overexpression of phosphodiesterase bifa promotes flagellar-mediated motility and induces planktonic lifestyle in pseudomonas. the mechanism that regulates expression of bifa gene was poorly studied. here we showed that expression of bifa was partly controlled by flagellar sigma factor flia (σ(28) ) in pseudo ...201727663176
performance of an ultraviolet mutagenetic polyphosphate-accumulating bacterium pz2 and its application for wastewater treatment in a newly designed constructed wetland.total phosphorus (tp) removal performance and application for wastewater treatment of polyphosphate-accumulating bacteria (pab) in constructed wetlands (cws) were investigated. in this study, a novel isolated ultraviolet (uv) mutant pz2 with phosphate-accumulating ability was screened from domestic wastewater and identified as pseudomonas putida by 16s ribosomal dna (rdna) sequencing analysis. the tp removal performance of pz2 in the synthetic wastewater reached the highest of 93.95 % within 45  ...201727659999
toxicity evaluation of selected ammonium-based ionic liquid forms with mcpp and dicamba moieties on pseudomonas putida.combination of the hydrophilic herbicidal anion with hydrophobic, antimicrobial ammonium cation allows to obtain compounds in ionic liquid form with better properties then conventional herbicides. both cation and anion can be modified by selection of herbicide and the length of alkyl chains in cation structure. however the knowledge of their potential toxic effects are still limited. furthermore, the relation between hydrophobicity associated with the length of alkyl chains and toxicity for ioni ...201727716584
structural basis for the transcriptional repressor nicr2 in nicotine degradation from pseudomonas.nicotine is an environmental toxicant in tobacco wastes, imposing severe hazards for the health of human and other mammalians. nicr2, a tetr-like repressor from pseudomonas putida s16, plays a critical role in regulating nicotine degradation. here, we determined the crystal structures of nicr2 and its complex with the inducer 6-hydroxy-3-succinoyl-pyridine (hsp). the n-terminal domain of nicr2 contains a conserved helix-turn-helix (hth) dna-binding motif, while the c-terminal domain contains a c ...201727741553
characterization of a novel blaimp gene, blaimp-58, using whole genome sequencing in a pseudomonas putida isolate detected in denmark.a multidrug-resistant strain of pseudomonas putida was isolated from the urine of a 65-year-old women hospitalized for serious clinical conditions. using whole genome sequencing a novel blaimp gene, blaimp-58 was discovered and characterized.201727771209
global transcriptional response of solvent-sensitive and solvent-tolerant pseudomonas putida strains exposed to toluene.pseudomonas putida strains are generally recognized as solvent tolerant, exhibiting varied sensitivity to organic solvents. pan-genome analysis has revealed that 30% of genes belong to the core-genome of pseudomonas. accessory and unique genes confer high degree of adaptability and capabilities for the degradation and synthesis of a wide range of chemicals. for the use of these microbes in bioremediation and biocatalysis, it is critical to understand the mechanisms underlying these phenotypic di ...201727768818
biochemical and genetic bases of indole-3-acetic acid (auxin phytohormone) degradation by the plant-growth-promoting rhizobacterium paraburkholderia phytofirmans psjn.several bacteria use the plant hormone indole-3-acetic acid (iaa) as a sole carbon and energy source. a cluster of genes (named iac) encoding iaa degradation has been reported in pseudomonas putida 1290, but the functions of these genes are not completely understood. the plant-growth-promoting rhizobacterium paraburkholderia phytofirmans psjn harbors iac gene homologues in its genome, but with a different gene organization and context than those of p. putida 1290. the iac gene functions enable p ...201727795307
host range of the conjugative transfer system of incp-9 naphthalene-catabolic plasmid nah7 and characterization of its orit region and relaxase.nah7 and pww0 from gammaproteobacterial pseudomonas putida strains are incp-9 conjugative plasmids that carry the genes for degradation of naphthalene and toluene, respectively. although such genes on these plasmids are well-characterized, experimental investigation of their conjugation systems remains at a primitive level. to clarify these conjugation systems, in this study, we investigated the nah7-encoded conjugation system by (i) analyzing the origin of its conjugative transfer (orit)-contai ...201727742684
ecological risk assessment of pharmaceuticals in the receiving environment of pharmaceutical wastewater in pakistan.the pharmaceutical industry of pakistan is growing with an annual growth rate of 10%. besides this growth, this industry is not complying with environmental standards, and discharging its effluent into domestic wastewater network. only limited information is available about the occurrence of pharmaceutical compounds (pcs) in the environmental matrices of pakistan that has motivated us to aim at the occurrence and ecological risk assessment of 11 pcs of different therapeutic classes in the wastew ...201727810578
influence of ph on dynamics of microbial enhanced oil recovery processes using biosurfactant producing pseudomonas putida: mathematical modelling and numerical simulation.in present work, the influence of reservoir ph conditions on dynamics of microbial enhanced oil recovery (meor) processes using pseudomonas putida was analysed numerically from the developed mathematical model for meor processes. further, a new strategy to improve the meor performance has also been proposed. it is concluded from present study that by reversing the reservoir ph from highly acidic to low alkaline condition (ph 5-8), flow and mobility of displaced oil, displacement efficiency, and ...201727836230
metabolic engineering to expand the substrate spectrum of pseudomonas putida toward sucrose.sucrose is an important disaccharide used as a substrate in many industrial applications. it is a major component of molasses, a cheap by-product of the sugar industry. unfortunately, not all industrially relevant organisms, among them pseudomonas putida, are capable of metabolizing sucrose. we chose a metabolic engineering approach to circumvent this blockage and equip p. putida with the activities necessary to consume sucrose. therefore, we constructed a pair of broad-host range mini-transposo ...201728349670
the impact of succinate trace on pww0 and ortho-cleavage pathway transcription in pseudomonas putida mt-2 during toluene biodegradation.toluene is a pollutant catabolised through the interconnected pww0 (tol) and ortho-cleavage pathways of pseudomonas putida mt-2, while upon succinate and toluene mixtures introduction in batch cultures grown on m9 medium, succinate was previously reported as non-repressing. the effect of a 40 times lower succinate concentration, as compared to literature values, was explored through systematic real-time qpcr monitoring of transcriptional kinetics of the key tol pu, pm and ortho-cleavage pbenr, p ...201728347959
saponaria officinalis l. extract: surface active properties and impact on environmental bacterial strains.plant-derived surfactants are characterised by low toxicity, high biodegradability and environmental compatibility. they therefore have many applications; for instance, they can be used in bioremediation to accelerate biodegradation processes, especially of hydrophobic pollutants. this paper analyses the properties of an extract from saponaria officinalis l. containing saponins and its impact on bacterial strains isolated from soil, as well as its potential for application in hydrocarbon bioreme ...201727918965
functional components of the bacterial czccba efflux system reduce cadmium uptake and accumulation in transgenic tobacco plants.cadmium (cd) is a toxic trace element released into the environment by industrial and agricultural practices, threatening the health of plants and contaminating the food/feed chain. biotechnology can be used to develop plant varieties with a higher capacity for cd accumulation (for use in phytoremediation programs) or a lower capacity for cd accumulation (to reduce cd levels in food and feed). here we generated transgenic tobacco plants expressing components of the pseudomonas putida czccba effl ...201727902938
methods for the isolation of genes encoding novel pha metabolism enzymes from complex microbial communities.development of different phas as alternatives to petrochemically derived plastics can be facilitated by mining metagenomic libraries for diverse pha cycle genes that might be useful for synthesis of bio-plastics. the specific phenotypes associated with mutations of the pha synthesis pathway genes in sinorhizobium meliloti and pseudomonas putida, allows the use of powerful selection and screening tools to identify complementing novel pha synthesis genes. identification of novel genes through thei ...201727900694
a high-throughput microtiter plate assay for the discovery of active and enantioselective amino alcohol-specific transaminases.chiral vicinal amino alcohols are important chiral building blocks and intermediates in the pharmaceutical industry. the transaminase (tam) catalyzed kinetic resolution of racemic amino alcohols provides a straightforward approach to access these important compounds. this study describes the development of a novel microtiter plate assay to screen vicinal amino alcohol-specific tams using a tetrazolium red-based colorimetric assay to monitor the rate of α-hydroxy ketone formation at 510 nm. this ...201727899283
application of the freeze-dried bioluminescent bioreporter pseudomonas putida mt-2 kg1206 to the biomonitoring of groundwater samples from monitoring wells near gasoline leakage sites.this study examined the applicability of a freeze-dried bioluminescent bioreporter, pseudomonas putida mt-2 kg1206 (called kg1206), to the biomonitoring of groundwater samples. samples were collected from the monitoring wells of gas station tanks or old pipeline leakage sites in korea. in general, the freeze-dried strain in the presence of pure inducer chemicals showed low bioluminescence activity and a different activity order compared with that of the subcultured strain. the effects of kno3 as ...201727853856
cellshape: a user-friendly image analysis tool for quantitative visualization of bacterial cell factories inside.visualization of the intracellular constituents of individual bacteria while performing as live biocatalysts is in principle doable through more or less sophisticated fluorescence microscopy. unfortunately, rigorous quantitation of the wealth of data embodied in the resulting images requires bioinformatic tools that are not widely extended within the community-let alone that they are often subject to licensing that impedes software reuse. in this context we have developed cellshape, a user-frien ...201727492366
delignification and enhanced gas release from soil containing lignocellulose by treatment with bacterial lignin degraders.the aim of the study was to isolate bacterial lignin-degrading bacteria from municipal solid waste soil, and to investigate whether they could be used to delignify lignocellulose-containing soil, and enhance methane release.201728393443
controlling the regioselectivity of baeyer-villiger monooxygenases by mutation of active-site residues.baeyer-villiger monooxygenase (bvmo)-mediated regiodivergent conversions of asymmetric ketones can lead to the formation of "normal" or "abnormal" lactones. in a previous study, we were able to change the regioselectivity of a bvmo by mutation of the active-site residues to smaller amino acids, which thus created more space. in this study, we demonstrate that this method can also be used for other bvmo/substrate combinations. we investigated the regioselectivity of 2-oxo-δ(3) -4,5,5-trimethylcyc ...201728504873
suppression of enteric bacteria by bacteriophages: importance of phage polyvalence in the presence of soil bacteria.bacteriophages are widely recognized for their importance in microbial ecology and bacterial control. however, little is known about how phage polyvalence (i.e., broad host range) affects bacterial suppression and interspecies competition in environments harboring enteric pathogens and soil bacteria. here we compare the efficacy of polyvalent phage pef1 versus coliphage t4 in suppressing a model enteric bacterium (e. coli k-12) in mixtures with soil bacteria (pseudomonas putida f1 and bacillus s ...201728414441
structural characterization of pyoverdines produced by pseudomonas putida kt2440 and pseudomonas taiwanensis vlb120.the previously unknown sequences of several pyoverdines (pvd) produced by a biotechnologically-relevant bacterium, namely, pseudomonas taiwanensis vlb120, were characterized by high performance liquid chromatography (hplc)-high resolution mass spectrometry (hrms). the same structural characterization scheme was checked before by analysis of pseudomonas sp. putida kt2440 samples with known pvds. a new sample preparation strategy based on solid-phase extraction was developed, requiring significant ...201728631237
presence of vim-positive pseudomonas species in chickens and their surrounding environment.metallo-β-lactamase gene blavim was identified on the chromosome of four pseudomonas sp. isolates from a chicken farm, including one pseudomonas aeruginosa isolate from a swallow (yanornis martini), one pseudomonas putida isolate from a fly, and two p. putida isolates from chickens. the four isolates shared two variants of blavim-carrying genomic contexts that resemble the corresponding regions of clinical metallo-β-lactamase-producing pseudomonas spp. our study suggests that the surveillance of ...201728438943
draft genome sequence of acinetobacter johnsonii c6, an environmental isolate engaging in interspecific metabolic interactions.acinetobacter johnsonii c6 originates from creosote-polluted groundwater and performs ecological and evolutionary interactions with pseudomonas putida in biofilms. the draft genome of a. johnsonii c6 is 3.7 mbp and was shaped by mobile genetic elements. it reveals genes facilitating the biodegradation of aromatic hydrocarbons and resistance to antimicrobials and metals.201728428290
in vitro selection and identification of potential probiotics isolated from the gastrointestinal tract of nile tilapia, oreochromis niloticus.fish gut bacteria can be used as probiotics for aquaculture. the aim of this study is to screen and identify beneficial probiotic bacteria from the gut of nile tilapia, oreochromis niloticus. nine out of one hundred thirty-five isolates were non-pathogenic through intraperitoneal injection and had antibacterial activities with at least a strain from the five isolated fish pathogens, aeromonas sobria, aeromonas hydrophila, pseudomonas aeruginosa, pseudomonas putida, and staphylococcus aureus. fur ...201728819794
evaluation of nutrients removal (no3-n, nh3-n and po4-p) with chlorella vulgaris, pseudomonas putida, bacillus cereus and a consortium of these microorganisms in the treatment of wastewater effluents.in this research removal of nh3-n, no3-n and po4-p nutrients from municipal wastewater was studied, using chlorella vulgaris, pseudomonas putida, bacillus cereus and an artificial consortium of them. the objective is to analyze the performance of these microorganisms and their consortium, which has not been previously studied for nutrient removal in municipal wastewater. a model wastewater was prepared simulating the physicochemical characteristics found at the wastewater plant in chapala, mexic ...201728708609
molecular investigation on the binding of cd(ii) by the binary mixtures of montmorillonite with two bacterial species.bacteria-phyllosilicate complexes are commonly found in natural environments and are capable of immobilizing trace metals. however, the molecular binding mechanisms of heavy metals to these complex aggregates still remain poorly understood. this study investigated cd adsorption on gram-positive bacillus subtilis, gram-negative pseudomonas putida and their binary mixtures with montmorillonite using surface complexation model, cd k-edge extended x-ray absorption fine structure (exafs) spectroscopy ...201728754562
dual infection by burkholderia cepaciaand pseudomonas putida in an infective endocarditis case.infective endocarditis is rarely caused by burkholderia cepacia. pseudomonas putidahas not been reported to cause infective endocarditis so far. this is the first case of infective endocarditis being reported, that is caused by pseudomonas putidaand burkholderia cepaciain an immunocompetent host with no predisposing factors. aortic valve replacement surgery was carried out and antibiotics were given, to which the patient responded well and recovered.201728689527
igm-mediated autoimmune responses to oxidative specific epitopes, but not nitrosylated adducts, are significantly decreased in pregnancy: association with bacterial translocation, perinatal and lifetime major depression and the tryptophan catabolite (trycat) pathway.immunoglubulin (ig)m responses directed to oxidative specific epitopes (oses) and nitric oxide (no)-adducts are significantly associated with major depression and physio-somatic symptoms. end of term serum igm responses to oses and no-adducts were assayed in pregnant women with (n = 24) and without prenatal depression (n = 25) as well as in 24 non-pregnant women. associations of igm/iga responses to gram-negative gut commensal bacteria (leaky gut index) and iga/igm responses to tryptophan catabo ...201728600633
a versatile one-step crispr-cas9 based approach to plasmid-curing.plasmids are widely used and essential tools in molecular biology. however, plasmids often impose a metabolic burden and are only temporarily useful for genetic engineering, bio-sensing and characterization purposes. while numerous techniques for genetic manipulation exist, a universal tool enabling rapid removal of plasmids from bacterial cells is lacking.201728764701
construction and optimization of a heterologous pathway for protocatechuate catabolism in escherichia coli enables bioconversion of model aromatic compounds.the production of biofuels from lignocellulose yields a substantial lignin byproduct stream that currently has few applications. biological conversion of lignin-derived compounds into chemicals and fuels has the potential to improve the economics of lignocellulose-derived biofuels, but few microbes are able both to catabolize lignin-derived aromatic compounds and generate valuable products. while escherichia coli has been engineered to produce a variety of fuels and chemicals, it is incapable of ...201728733280
developing a genetically encoded, cross-species biosensor for detecting ammonium and regulating biosynthesis of cyanophycin.responding to nitrogen status is essential for all living organisms. bacteria have evolved various complex and exquisite regulatory systems to control nitrogen metabolism. however, natural nitrogen regulatory systems, owing to their complexity, often function only in their original hosts and do not respond properly when transferred to another species. by harnessing the lactococcus glnra system, we developed a genetically encoded, cross-species ammonium biosensor that displays a dynamic range up ...201728683543
a novel programmable lysozyme-based lysis system in pseudomonas putida for biopolymer production.cell lysis is crucial for the microbial production of industrial fatty acids, proteins, biofuels, and biopolymers. in this work, we developed a novel programmable lysis system based on the heterologous expression of lysozyme. the inducible lytic system was tested in two gram-negative bacterial strains, namely escherichia coli and pseudomonas putida kt2440. before induction, the lytic system did not significantly arrest essential physiological parameters in the recombinant e. coli (ecpi) and p. p ...201728663596
de novo biosynthesis of glutarate via α-keto acid carbon chain extension and decarboxylation pathway in escherichia coli.microbial based bioplastics are promising alternatives to petroleum based synthetic plastics due to their renewability and economic feasibility. glutarate is one of the most potential building blocks for bioplastics. the recent biosynthetic routes for glutarate were mostly based on the l-lysine degradation pathway from pseudomonas putida that required lysine either by feeding or lysine overproduction via genetic manipulations. herein, we established a novel glutarate biosynthetic pathway by inco ...201728618222
interspecies cross-talk between co-cultured pseudomonas putida and escherichia coli.pseudomonas putida and escherichia coli are ubiquitous microorganisms that can be isolated from soil rhizosphere, the surface of vegetables, fresh waters and wastewaters - environments in which they likely co-exist. despite this, the potential interactions between these microbes have not been studied in detail. to analyse these interactions, we carried out rna-seq transcriptomic analysis of these microbes as monocultures and as co-cultures. our results show that co-culture of these microbes sign ...201728585781
synthetic biology of polyhydroxyalkanoates (pha).microbial polyhydroxyalkanoates (pha) are a family of biodegradable and biocompatible polyesters which have been extensively studied using synthetic biology and metabolic engineering methods for improving production and for widening its diversity. synthetic biology has allowed pha to become composition controllable random copolymers, homopolymers, and block copolymers. recent developments showed that it is possible to establish a microbial platform for producing not only random copolymers with c ...201728567487
identification of two secondary acyltransferases of lipid a in pseudomonas putida kt2442.identify the secondary acyltransferases of lipid a in pseudomonas putida.201728557109
mqsr/mqsa toxin/antitoxin system regulates persistence and biofilm formation in pseudomonas putida kt2440.bacterial toxin/antitoxin (ta) systems have received increasing attention due to their prevalence, diverse structures, and important physiological functions. in this study, we identified and characterized a type ii ta system in a soil bacterium pseudomonas putida kt2440. this ta system belongs to the mqsr/mqsa family. we found that pp_4205 (mqsr) greatly inhibits cell growth in p. putida kt2440 and escherichia coli, the antitoxin pp_4204 (mqsa) neutralizes the toxicity of the toxin mqsr, and the ...201728536573
continuous supply of glucose and glycerol enhances biotransformation of ricinoleic acid to (e)-11-(heptanoyloxy) undec-9-enoic acid in recombinant escherichia coli.this study aimed at the development of biotransformation strategies with feeding of energy sources for bioconversion of ricinoleic acid to (e)-11-(heptanoyloxy) undec-9-enoic acid (11-houa), a key intermediate of brassylic acid, by recombinant escherichia coli overexpressing an alcohol dehydrogenase from micrococcus luteus and a baeyer-villiger monooxygenase from pseudomonas putida kt2440. feeding of glucose or glycerol facilitated both the preparation of high-density cell biocatalyst and supply ...201728536060
characterisation of a 3-hydroxypropionic acid-inducible system from pseudomonas putida for orthogonal gene expression control in escherichia coli and cupriavidus necator.3-hydroxypropionic acid (3-hp) is an important platform chemical used as a precursor for production of added-value compounds such as acrylic acid. metabolically engineered yeast, escherichia coli, cyanobacteria and other microorganisms have been developed for the biosynthesis of 3-hp. attempts to overproduce this compound in recombinant pseudomonas denitrificans revealed that 3-hp is consumed by this microorganism using the catabolic enzymes encoded by genes hpdh, hbdh and mmsa. 3-hp-inducible s ...201728496205
cleaning and disinfection of biofilms composed of listeria monocytogenes and background microbiota from meat processing surfaces.surfaces of food processing premises are exposed to regular cleaning and disinfection (c&d) regimes, using biocides that are highly effective against bacteria growing as planktonic cells. however, bacteria growing in surface associated communities (biofilms) are typically more tolerant towards c&d than their individual free cells counterparts, and survival of pathogens such as listeria monocytogenes may be affected by interspecies interactions within biofilms. in this study, pseudomonas and acin ...201728667108
the antibacterial activity and mechanism of ginkgolic acid c15:1.the present study investigated the antibacterial activity and underlying mechanisms of ginkgolic acid (ga) c15:1 monomer using green fluorescent protein (gfp)-labeled bacteria strains.201728088196
metabolic pathway for a new strain pseudomonas synxantha lsh-7': from chemotaxis to uptake of n-hexadecane.bacteria can use n-hexadecane as a carbon source, but it remains incompletely understood whether n-hexadecane is transformed into metabolic intermediates prior to cellular uptake or not. we newly isolated a strain identified as pseudomonas synxantha lsh-7' and conducted chemotaxis experiment of this bacterial strain towards n-hexadecane, hexadecanol and hexadecanoic acid with qualitative assays respectively. furthermore, we described the identification of extracellular alkane hydroxylase and alc ...201728051099
enhanced heterologous protein productivity by genome reduction in lactococcus lactis nz9000.the implementation of novel chassis organisms to be used as microbial cell factories in industrial applications is an intensive research field. lactococcus lactis, which is one of the most extensively studied model organisms, exhibits superior ability to be used as engineered host for fermentation of desirable products. however, few studies have reported about genome reduction of l. lactis as a clean background for functional genomic studies and a model chassis for desirable product fermentation ...201728049473
isolation and identification of phyllospheric bacteria possessing antimicrobial activity from astragalus obtusifolius, prosopis juliflora, xanthium strumarium and hippocrepis unisiliqousa.the widespread utilization of antimicrobial compounds has caused emergence of resistant microorganisms in the world. hence, the research to probe the products with antimicrobial features has led to finding natural habitats and discovering new pharmaceutical products.201728090278
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