Publications

h2-driven biotransformation of n-octane to 1-octanol by a recombinant pseudomonas putida strain co-synthesizing an o2-tolerant hydrogenase and a p450 monooxygenase.	an in vivo biotransformation system is presented that affords the hydroxylation of n-octane to 1-octanol on the basis of nadh-dependent cyp153a monooxygenase and nad(+)-reducing hydrogenase heterologously synthesized in a bacterial host. the hydrogenase sustains h2-driven nadh cofactor regeneration even in the presence of o2, the co-substrate of monooxygenase.	2015	26394141
a quick rhizobacterial selection tests for the remediation of copper contaminated soils.	the main objective of the study is to develop and improve quick bacterial tests to select the best candidates for the bioaugmentation of metal-contaminated soil, coupled with phytoextraction.	2015	26042640
biocompatibility of low molecular weight polymers for two-phase partitioning bioreactors.	two phase partitioning bioreactors (tppbs) improve the efficiency of fermentative processes by limiting the exposure of microorganisms to toxic solutes by sequestering them into a non-aqueous phase (nap). a potential limitation of this technology, when using immiscible organic solvents as the nap, is the cytoxicity that these materials may exert on the microbes. an improved tppb configuration is one in which polymeric naps are used to replace organic solvents in order to take advantage of their ...	2015	26032439
mechanisms of solvent resistance mediated by interplay of cellular factors in pseudomonas putida.	a number of microorganisms have the ability to thrive in the presence of a range of toxic solvents. tolerance to these chemicals is a multifactorial process, meaning that bacterial cells use a set of physiological and gene expression changes to overcome the damage imparted by these chemicals. this review focuses mainly on issues related to tolerance to aromatic hydrocarbons and butanol in pseudomonas, although other microorganisms are also discussed. pseudomonas putida strains contain a circular ...	2015	25934123
plant growth-promoting effects of native pseudomonas strains on mentha piperita (peppermint): an in vitro study.	plant growth-promoting rhizobacteria (pgpr) affect growth of host plants through various direct and indirect mechanisms. three native pgpr (pseudomonas putida) strains isolated from rhizospheric soil of a mentha piperita (peppermint) crop field near córdoba, argentina, were characterised and screened in vitro for plant growth-promoting characteristics, such as indole-3-acetic acid (iaa) production, phosphate solubilisation and siderophore production, effects of direct inoculation on plant growth ...	2015	26012535
dynamics of suspended and attached aerobic toluene degraders in small-scale flow-through sediment systems under growth and starvation conditions.	the microbially mediated reactions, that are responsible for field-scale natural attenuation of organic pollutants, are governed by the concurrent presence of a degrading microbial community, suitable energy and carbon sources, electron acceptors, as well as nutrients. the temporal lack of one of these essential components for microbial activity, arising from transient environmental conditions, might potentially impair in situ biodegradation. this study presents results of small scale flow-throu ...	2015	26009808
effects of impurities in biodiesel-derived glycerol on growth and expression of heavy metal ion homeostasis genes and gene products in pseudomonas putida ls46.	biodiesel production-derived waste glycerol (wg) was previously investigated as potential carbon source for medium chain length polyhydroxyalkanoate (mcl-pha) production by pseudomonas putida ls46. in this study, we evaluated the effect of impurities in the wg on p. putida ls46 physiology during exponential growth and corresponding changes in transcription and protein expression profiles compared with cells grown on pure, reagent grade glycerol. high concentration of metal ions, such as na(+), a ...	2015	26002633
understanding of real alternative redox partner of streptomyces peucetius doxa: prediction and validation using in silico and in vitro analyses.	streptomyces peucetius atcc27952 contains the cytochrome p450 monoxygenase doxa that is responsible for the hydroxylation of daunorubicin into doxorubicin. although s. peucetius atcc27952 contains several potential redox partners, the most suitable endogenous electron-transport system is still unclear; therefore, we conducted a study of potential redox partners using accelrys discovery studio 3.5. recombinant doxa along with its redox partners from s. peucetius fdx1, fdr2, and fdx3, and the puti ...	2015	26334717
cellulose derived graphenic fibers for capacitive desalination of brackish water.	we describe a simple and inexpensive cellulose-derived and layer-by-layer stacked carbon fiber network electrode for capacitive deionization (cdi) of brackish water. the microstructure and chemical composition were characterized using spectroscopic and microscopic techniques; electrochemical/electrical performance was evaluated by cyclic voltammetry and 4-probe electrical conductivity and surface area by brunauer-emmett-teller analysis, respectively. the desalination performance was investigated ...	2015	26305260
tn7-based device for calibrated heterologous gene expression in pseudomonas putida.	the soil bacterium pseudomonas putida is increasingly attracting considerable interest as a platform for advanced metabolic engineering through synthetic biology approaches. however, genomic context, gene copy number, and transcription/translation interplay often introduce considerable uncertainty to the design of reliable genetic constructs. in this work, we have established a standardized heterologous expression device in which the promoter strength is the only variable; the remaining paramete ...	2015	26133359
label-free quantification reveals major proteomic changes in pseudomonas putida f1 during the exponential growth phase.	the physiological adaptation to stationary growth by pseudomonas putida f1, a model organism for the degradation of aromatic compounds, was investigated by proteome-wide label-free quantification.the data unveiled that entrance to the stationary phase did not involve an abrupt switch within the p. putida f1 proteome, but rather an ongoing adaptation that started already during the mid-exponential growth phase. the proteomic adaptations involved a clear increase in amino acid degradation capabili ...	2015	26122999
evaluation of an eventual ecotoxicity induced by textile effluents using a battery of biotests.	textile industry is considered as one of the important factors of the economic growth in tunisia. however, this prominent role has certainly some drawbacks mainly represented by the huge amounts of textile wastewaters generated that become a real menace to nature. many previous studies showed the purifying potential of some activated sludge and bacteria (pseudomonas putida) to decolourize textile effluents. however, in many cases, decolourization of wastewaters is not necessary associated with d ...	2015	26087930
[the role of mineral phosphorus compounds in naphthalene biodegradation by pseudomonas putida].	the effect of phosphate concentration in the culture medium on the growth and naphthalene degradation by pseudomonas putida bs 3701 was studied. the limiting concentration of phosphate was 0.4 mm and 0.1 mm under cultivation in media with naphthalene and glucose, respectively the phosphate deficiency correlated with a decrease in the activities of naphthalene dioxygenase and salicylate hydroxylase and with salicylate accumulation in the culture medium. we suggest that this fact indicates the imp ...	2015	26027355
pseudomonas alkylphenolica sp. nov., a bacterial species able to form special aerial structures when grown on p-cresol.	pseudomonas sp. kl28t is an aerobic, rod-shaped bacterium that was isolated from the soil of changwon, south korea, based on its ability to grow in the presence of linear alkylphenols (c1-c5). despite several studies on strain kl28t, it could not be assigned to any known species in the genus pseudomonas. the name 'pseudomonas alkylphenolia' was proposed for kl28t, but the strain had not until now been characterized taxonomically and the name currently has no standing in the bacterial nomenclatur ...	2015	26276124
photosynthetic aeration in biological wastewater treatment using immobilized microalgae-bacteria symbiosis.	chlorella vulgaris encapsulated in alginate beads were added into a bioreactor treating synthetic wastewater using pseudomonas putida. a symbiotic co2/o2 gas exchange was established between the two microorganisms for photosynthetic aeration of wastewater. during batch operation, glucose removal efficiency in the bioreactor improved from 50% in 12 h without aeration to 100% in 6 h, when the bioreactor was aerated photosynthetically. during continuous operation, the bioreactor was operated at a l ...	2015	26266755
crude oil biodegradation aided by biosurfactants from pseudozyma sp. nii 08165 or its culture broth.	the aim of this work was to evaluate the biosurfactants produced by the yeast pseudozyma sp. nii 08165 for enhancing the degradation of crude oil by a model hydrocarbon degrading strain, pseudomonas putida mtcc 1194. pseudozyma biosurfactants were supplemented at various concentrations to the p. putida culture medium containing crude oil as sole carbon source. supplementation of the biosurfactants enhanced the degradation of crude oil by p. putida; the maximum degradation of hydrocarbons was obs ...	2015	25985416
oxidative stress in bacteria (pseudomonas putida) exposed to nanostructures of silicon carbide.	silicon carbide (sic) nanostructures produced by combustion synthesis can cause oxidative stress in the bacterium pseudomonas putida. the results of this study showed that sic nanostructures damaged the cell membrane, which can lead to oxidative stress in living cells and to the loss of cell viability. as a reference, micrometric sic was also used, which did not exhibit toxicity toward cells. oxidative stress was studied by analyzing the activity of peroxidases, and the expression of the glucose ...	2015	25965002
nhej enzymes ligd and ku participate in stationary-phase mutagenesis in pseudomonas putida.	under growth-restricting conditions bacterial populations can rapidly evolve by a process known as stationary-phase mutagenesis. bacterial nonhomologous end-joining (nhej) system which consists of the dna-end-binding enzyme ku and the multifunctional dna ligase ligd has been shown to be important for survival of bacteria especially during quiescent states, such as late stationary-phase populations or sporulation. in this study we provide genetic evidence that nhej enzymes participate in stationa ...	2015	25942369
isolation of a diphenylamine-degrading bacterium and characterization of its metabolic capacities, bioremediation and bioaugmentation potential.	the antioxidant diphenylamine (dpa) is used in fruit-packaging plants for the control of the physiological disorder apple scald. its use results in the production of dpa-contaminated wastewater which should be treated before finally discharged. biological treatment systems using tailored-made microbial inocula with specific catabolic activities comprise an appealing and sustainable solution. this study aimed to isolate dpa-degrading bacteria, identify the metabolic pathway of dpa and evaluate th ...	2015	26260839
evaluation of phosphate-solubilizing bacteria on the growth and grain yield of rice (oryza sativa l.) cropped in northern iran.	this study aimed to evaluate the efficiency of four phosphate-solubilizing bacteria (psb) on the growth and yield of rice under different soil conditions.	2015	26294004
structural characterization of multiple pyoverdines secreted by two pseudomonas strains using liquid chromatography-high resolution tandem mass spectrometry with varying dissociation energies.	high-affinity iron (fe)-scavenging molecules, or siderophores, are secreted by microorganisms to acquire and compete for fe. pyoverdine (pvd), the primary siderophore produced by pseudomonas, consists of a dihydroxyquinoline-type chromophore, a peptide chain of variable length and conformation, and a side chain composed of a dicarboxylic acid or its monoamide derivative. elucidation of the pvd structures secreted by different pseudomonas strains is an important step toward understanding their fe ...	2015	25895945
an upp-based markerless gene replacement method for genome reduction and metabolic pathway engineering in pseudomonas mendocina nk-01 and pseudomonas putida kt2440.	a markerless gene replacement method was adapted by combining a suicide plasmid, pex18tc, with a counterselectable marker, the upp gene encoding uracil phosphoribosyltransferase (uprtase), for the medium-chain length polyhydroxyalkanoates (pha(mcl))-producing strain pseudomonas mendocina nk-01. an nk-01 5-fluorouracil (5-fu) resistant background strain was first constructed by deleting the chromosomal upp gene. the suicide plasmid pex18tc, carrying a functional allele of the upp gene of p. mendo ...	2015	25828098
solvent resistance pumps of pseudomonas putida s12: applications in 1-naphthol production and biocatalyst engineering.	the solvent resistance capacity of pseudomonas putida s12 was applied by using the organism as a host for biocatalysis and through cloning and expressing solvent resistant pump genes into escherichia coli. p. putida s12 expressing toluene ortho mononooxygenase (tom-green) was used for 1-naphthol production in a water-organic solvent biphasic system. application of p. putida s12 improved 1-naphthol production per gram cell dry weight by approximately 42% compared to e. coli. moreover, p. putida s ...	2015	26143210
quantitative analysis of chemotaxis towards toluene by pseudomonas putida in a convection-free microfluidic device.	chemotaxis has been shown to be beneficial for the migration of soil-inhabiting bacteria towards industrial chemical pollutants, which they degrade. many studies have demonstrated the importance of this microbial property under various circumstances; however, few quantitative analyses have been undertaken to measure the two essential parameters that characterize the chemotaxis of bioremediation bacteria: the chemotactic sensitivity coefficient χ(0) and the chemotactic receptor constant k(c). the ...	2015	25408100
development of recombinant methioninase to target the general cancer-specific metabolic defect of methionine dependence: a 40-year odyssey.	all tested cancer cell types are methionine dependent in that the cells arrest and eventually die when deprived of methionine, a condition that is generally nontoxic to normal cells. methionine dependence is the only known general metabolic defect in cancer. methionine-deprived cancer cells arrest at the s/g2 phase, an unusual position for cell cycle arrest. in order to exploit the cancer-specific metabolic defect of methionine dependence, methioninases were developed.	2015	25439528
anthranilate degradation by a cold-adapted pseudomonas sp.	an alpine soil bacterium pseudomonas sp. strain pamc 25931 was characterized as eurypsychrophilic (both psychrophilic and mesotolerant) with a broad temperature range of 5-30 °c both for anthranilate (2-aminobenzoate) degradation and concomitant cell growth. two degradative gene clusters (antabc and catbca) were detected from a fosmid clone in the pamc 25931 genomic library; each cluster was confirmed to be specifically induced by anthranilate. when expressed in escherichia coli, the recombinant ...	2015	23720227
biodegradation of hexachlorobenzene by a constructed microbial consortium.	a consortium comprised of an engineered escherichia coli dh5α and a natural pentachlorophenol (pcp) degrader, sphingobium chlorophenolicum atcc 39723, was assembled for degradation of hexachlorobenzene (hcb), a persistent organic pollutant. the engineered e. coli strain, harbouring a gene cassette (cama (+) camb (+) camc) that encodes the f87w/y96f/l244a/v247l mutant of cytochrome p-450cam (cyp101), oxidised hcb to pcp. the resulting pcp was then further completely degraded by atcc 39723. the re ...	2015	25532745
application of internal standard method in recombinant luminescent bacteria test.	mercury and its organic compounds have been of severe concern worldwide due to their damage to the ecosystem and human health. the development of effective and affordable technology to monitor and signal the presence of bioavailable mercury is an urgent need. the mer gene is a mercury-responsive resistant gene, and a mercury-sensing recombinant luminescent bacterium using the mer gene was constructed in this study. the mer operon from marine pseudomonas putida strain sp1 was amplified and fused ...	2015	26354701
biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyalkanoates) by recombinant escherichia coli from glucose.	the polyhydroxyalkanoate (pha) copolymers consisting of short-chain-length (scl) and medium-chain-length (mcl) monomers have various properties ranging from stiff to flexible depending on the molar fraction of the monomer compositions. it has been reported that phag, which is first known as a (r)-3-hydroxyacyl-acyl carrier protein (acp)-coa transferase, actually functions as a 3-hydroxyacyl-acp thioesterase, and the product of pp0763 gene from pseudomonas putida kt2440 has a (r)-3-hydroxyacyl (3 ...	2015	25732207
enzyme fusion for whole-cell biotransformation of long-chain sec-alcohols into esters.	enzyme fusion was investigated as a strategy to improve productivity of a two-step whole-cell biocatalysis. the biotransformation of long-chain sec-alcohols into esters by an alcohol dehydrogenase (adh) and baeyer-villiger monooxygenases (bvmos) was used as the model reaction. the recombinant escherichia coli, expressing the fusion enzymes between the adh of micrococcus luteus nctc2665 and the bvmo of pseudomonas putida kt2440 or rhodococcus jostii rha1, showed significantly greater bioconversio ...	2015	25636834
isolation of oxygenase genes for indigo-forming activity from an artificially polluted soil metagenome by functional screening using pseudomonas putida strains as hosts.	metagenomes contain the dna from many microorganisms, both culturable and non-culturable, and are a potential resource of novel genes. in this study, a 5.2-gb metagenomic dna library was constructed from a soil sample (artificially polluted with four aromatic compounds, i.e., biphenyl, phenanthrene, carbazole, and 3-chlorobenzoate) in escherichia coli by using a broad-host-range cosmid vector. the resultant library was introduced into naphthalene-degrading pseudomonas putida-derived strains havi ...	2015	25573469
expression levels of chaperones influence biotransformation activity of recombinant escherichia coli expressing micrococcus luteus alcohol dehydrogenase and pseudomonas putida baeyer-villiger monooxygenase.	we demonstrated for the first time that the archaeal chaperones (i.e., γ-prefoldin and thermosome) can stabilize enzyme activity in vivo. ricinoleic acid biotransformation activity of recombinant escherichia coli expressing micrococcus luteus alcohol dehydrogenase and the pseudomonas putida kt2440 baeyer-villiger monooxygenase improved significantly with co-expression of γ-prefoldin or recombinant themosome originating from the deep-sea hyperthermophile archaea methanocaldococcus jannaschii. fur ...	2015	25545273
quantitative polymerase chain reaction for microbial growth kinetics of mixed culture system.	microbial growth kinetics is often used to optimize environmental processes owing to its relation to the breakdown of substrate (contaminants). however, the quantification of bacterial populations in the environment is difficult owing to the challenges of monitoring a specific bacterial population within a diverse microbial community. conventional methods are unable to detect and quantify the growth of individual strains separately in the mixed culture reactor. this work describes a novel quanti ...	2015	26165316
biomimetic ferrichrome: structural motifs for switching between narrow- and broad-spectrum activities in p. putida and e. coli.	a series of novel ferrichrome (fc) analogs was designed based on the x-ray structure of fc in the fhua transporter of escherichia coli. two strategies were employed: the first strategy optimized the overall size and relative orientation of h-bonding interactions. the second strategy increased h-bonding interactions by introducing external h-donors onto analogs' backbone. tris-amino templates were coupled to succinic or aspartic acid, and the second carboxyl was used for hydroxamate construction. ...	2015	26459799
immobilization of escherichia coli cells expressing 4-oxalocrotonate tautomerase for improved biotransformation of β-nitrostyrene.	the enzyme 4-oxalocrotonate tautomerase (4-ot) encoded by the xylh gene is a part of the degradation pathway of aromatic compounds in pseudomonas putida mt-2. 4-ot was described to catalyze michael-type addition of acetaldehyde to β-nitrostyrene, and the whole cell system based on recombinantly expressed 4-ot has been developed previously. in this study biocatalytic process based on escherichia coli whole cells expressing 4-ot was significantly improved using immobilization and ex situ product r ...	2015	26410191
the production of ω-hydroxy palmitic acid using fatty acid metabolism and cofactor optimization in escherichia coli.	hydroxylated fatty acids (hfas) are used as important precursors for bulk and fine chemicals in the chemical industry. here, to overproduce long-chain (c16-c18) fatty acids and hydroxy fatty acid, their biosynthetic pathways including thioesterase (lreu_0335) from lactobacillus reuteri dsm20016, β-hydroxyacyl-acp dehydratase (fabz) from escherichia coli, and a p450 system (i.e., cyp153a from marinobacter aquaeolei vt8 and cama/camb from pseudomonas putida atcc17453) were overexpressed. acyl-coa ...	2015	25957153
phenotypic knockouts of selected metabolic pathways by targeting enzymes with camel-derived nanobodies (v(hh)s).	surveying the dynamics of metabolic networks of gram-negative bacteria often requires the conditional shutdown of enzymatic activities once the corresponding proteins have been produced. we show that given biochemical functions can be entirely suppressed in vivo with camel antibodies (vhhs, nanobodies) that target active sites of cognate enzymes expressed in the cytoplasm. as a proof of principle, we raised vhhs against 2,5-dihydroxypyridine dioxygenase (nicx) of pseudomonas putida, involved in ...	2015	25887637
making variability less variable: matching expression system and host for oxygenase-based biotransformations.	variability in whole-cell biocatalyst performance represents a critical aspect for stable and productive bioprocessing. in order to investigate whether and how oxygenase-catalyzed reactions are affected by such variability issues in solvent-tolerant pseudomonas, different inducers, expression systems, and host strains were tested for the reproducibility of xylene and styrene monooxygenase catalyzed hydroxylation and epoxidation reactions, respectively. significantly higher activity variations we ...	2015	25877162
construction of a novel phenol synthetic pathway in escherichia coli through 4-hydroxybenzoate decarboxylation.	phenol is a bulk chemical with lots of applications in the chemical industry. fermentative production of phenol had been realized in both pseudomonas putida and escherichia coli by recruiting tyrosine phenol-lyase (tpl). the tpl pathway needs tyrosine as the direct precursor for phenol production. in this work, a novel phenol synthetic pathway was created in e. coli by recruiting 4-hydroxybenzoate decarboxylase, which can convert 4-hydroxybenzoate to phenol and carbon dioxide. activating 3-deoxy ...	2015	25758959
improved n-butanol tolerance in escherichia coli by controlling membrane related functions.	as the increasing demand from both chemical and fuel markets, the interest in producing n-butanol using biological route has been rejuvenated to engineer an economical fermentation process, competing with the currently-dominant chemical synthesis. n-butanol has been traditionally produced from the abe fermentation of clostridium acetobutylicum. this system, however, is not economically feasible due to its limited efficiency and the lack of genetic modification tools for further improvements. alt ...	2015	25858152
extracellular expression of natural cytosolic arginine deiminase from pseudomonas putida and its application in the production of l-citrulline.	the pseudomonas putida arginine deiminase (adi), a natural cytosolic enzyme, and thermobifida fusca cutinase were co-expressed in escherichia coli, and the optimized cutinase gene was used for increasing its expression level. 90.9% of the total adi protein was released into culture medium probably through a nonspecific leaking mechanism caused by the co-expressed cutinase. the enzymatic properties of the extracellular adi were found to be similar to those of adi prepared by conventional cytosoli ...	2015	26233330
characterization of the ability to form biofilms by plant-associated pseudomonas species.	successful colonization is the initial step for plant-bacteria interactions; therefore, the development of strategies to improve adherence to plant surfaces is critically important for environmental bacteria. biofilm formation is thought to be one such strategy for bacteria to establish stable colonization on inert and living surfaces. although biofilms play potential roles in enabling persistent bacterial colonization, little attention has been paid to biofilms formed by plant-associated bacter ...	2015	25487118
comparison of biomass detachment from biofilms of two different pseudomonas spp. under constant shear conditions.	in the context of biofilm development, detachment is of practical importance when placed in a biofilm management perspective. the objective of the present study was to examine biofilm structure and biofilm detachment under controlled conditions for two distinct microorganisms grown under constant shear conditions. detached biofilm biomass was regularly collected and analysed over the course of 72 h biofilm growth by pseudomonas putida and pseudomonas fluorescens cells, and biofilm structural dev ...	2015	25563340
pseudomonads biodegradation of aromatic compounds in oil sands process-affected water.	aromatic naphthenic acids (nas) have been shown to be more toxic than the classical nas found in oil sands process-affected water (ospw). to reduce this toxicity, pseudomonas fluorescens and pseudomonas putida were used to determine their ability to biodegrade aromatic compounds including treatments considering the impacts of external carbon and iron addition. results showed that with added carbon p. fluorescens and p. putida have the capability of biodegrading these aromatics. in the presence o ...	2015	25828413
endophytic bacteria from piper tuberculatum jacq.: isolation, molecular characterization, and in vitro screening for the control of fusarium solani f. sp piperis, the causal agent of root rot disease in black pepper (piper nigrum l.).	endophytic bacteria have been found to colonize internal tissues in many different plants, where they can have several beneficial effects, including defense against pathogens. in this study, we aimed to identify endophytic bacteria associated with roots of the tropical piperaceae piper tuberculatum, which is known for its resistance to infection by fusarium solani f. sp piperis, the causal agent of black pepper (piper nigrum) root rot disease in the amazon region. based on 16s rrna gene sequence ...	2015	26214435
a novel d-mandelate dehydrogenase used in three-enzyme cascade reaction for highly efficient synthesis of non-natural chiral amino acids.	a novel nad(+)-dependent d-mandelate dehydrogenase was identified from lactobacillus brevis (lbdmdh). after purified to homogeneity, the optimum ph and temperature for oxidation of d-mandelate were ph 10.0 and 40 °c, and the km and kcat were 1.1 mm and 355 s(-1) respectively. employing the lbdmdh together with a mandelate racemase from pseudomonas putida and a leucine dehydrogenase (esleudh) from exiguobacterium sibiricum, we established a three-step one-pot domino reaction system for preparing ...	2015	25449542
diversity of small rnas expressed in pseudomonas species.	rna sequencing (rna-seq) has revealed several hundreds of previously undetected small rnas (srnas) in all bacterial species investigated, including strains of pseudomonas aeruginosa, pseudomonas putida and pseudomonas syringae. nonetheless, only little is known about the extent of conservation of expressed srnas across strains and species. in this study, we have used rna-seq to identify srnas in p. putida dot-t1e and pseudomonas extremaustralis 14-3b. this is the first strain of p. extremaustral ...	2015	25394275
genome-scale reconstruction of the metabolic network in pseudomonas stutzeri a1501.	pseudomonas stutzeri a1501 is an endophytic bacterium capable of nitrogen fixation. this strain has been isolated from the rice rhizosphere and provides the plant with fixed nitrogen and phytohormones. these interesting features encouraged us to study the metabolism of this microorganism at the systems-level. in this work, we present the first genome-scale metabolic model (ipb890) for p. stutzeri, involving 890 genes, 1135 reactions, and 813 metabolites. a combination of automatic and manual app ...	2015	26302703
isolation and characterisation of rhizosphere bacteria active against meloidogyne incognita, phytophthora nicotianae and the root knot-black shank complex in tobacco.	the use of dually antagonistic bacteria (dab) as alternatives to chemicals for biological control of disease complexes has received little attention. in this study targeting the meloidogyne incognita-phytophthora nicotianae complex, dab from the tobacco rhizosphere were identified and screened against the diseases caused by one or both pathogens in tobacco.	2015	24799254
isolation of carbapenem-resistant pseudomonas spp. from food.	pseudomonas spp. are ubiquitous in nature. carbapenem resistance in environmental isolates of members of this genus is thought to be rare but the exact resistance rate is unknown. in this study, carbapenem-resistant pseudomonas spp. were isolated from chicken and pork samples and the mechanisms underlying the carbapenem resistance in these strains were investigated. a total of 16 carbapenem-resistant pseudomonas aeruginosa, pseudomonas putida and pseudomonas otitidis isolates were recovered from ...	2015	27873658
the kinetic characterization and x-ray structure of a putative benzoylformate decarboxylase from m. smegmatis highlights the difficulties in the functional annotation of thdp-dependent enzymes.	benzoylformate decarboxylase (bfdc) is a thiamin diphosphate (thdp)-dependent enzyme that catalyzes the nonoxidative decarboxylation of benzoylformate. it is the penultimate enzyme in both the mandelate pathway and the d-phenylglycine degradation pathway. the thdp-dependent enzyme engineering database (teed) now lists more than 800 sequences annotated as bfdcs, including one from mycobacterium smegmatis (msbfdc). however, there is no evidence that either pathway for benzoylformate formation exis ...	2015	25936776
whole-cell-based identification of electrochemically active bacteria in microbial fuel cells by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.	electrochemically active bacteria (eab) that are capable of producing electricity from renewable biomass and organic wastes have been of particular interest in recent years. methods for selective enrichment, accurate identification and easy acquisition of eab fingerprints for phylogenetic characterization would facilitate utilization of these bioenergy-producing species in practical environmental engineering applications.	2015	26522312
specific gamma-aminobutyrate chemotaxis in pseudomonads with different lifestyle.	the pctc chemoreceptor of pseudomonas aeruginosa mediates chemotaxis with high specificity to gamma-aminobutyric acid (gaba). this compound is present everywhere in nature and has multiple functions, including being a human neurotransmitter or plant signaling compound. because p. aeruginosa is ubiquitously distributed in nature and able to infect and colonize different hosts, the physiological relevance of gaba taxis is unclear, but it has been suggested that bacterial attraction to neurotransmi ...	2015	25921834
the c-di-gmp phosphodiesterase bifa is involved in the virulence of bacteria from the pseudomonas syringae complex.	in a recent screen for novel virulence factors involved in the interaction between pseudomonas savastanoi pv. savastanoi and the olive tree, a mutant was selected that contained a transposon insertion in a putative cyclic diguanylate (c-di-gmp) phosphodiesterase-encoding gene. this gene displayed high similarity to bifa of pseudomonas aeruginosa and pseudomonas putida. here, we examined the role of bifa in free-living and virulence-related phenotypes of two bacterial plant pathogens in the pseud ...	2015	25385023
analysis of preference for carbon source utilization among three strains of aromatic compounds degrading pseudomonas.	soil isolates pseudomonas putida csv86, pseudomonas aeruginosa pp4 and pseudomonas sp. c5pp degrade naphthalene, phthalate isomers and carbaryl, respectively. strain csv86 displayed a diauxic growth pattern on phenylpropanoid compounds (veratraldehyde, ferulic acid, vanillin or vanillic acid) plus glucose with a distinct second lag-phase. the glucose concentration in the medium remained constant with higher cell respiration rates on aromatics and maximum protocatechuate 3,4-dioxygenase activity ...	2015	26316546
valvulopathy consistent with endocarditis in an argentine boa (boa constrictor occidentalis).	an argentine boa (boa constrictor occidentalis) of 5 yr 7 mo of age was presented for respiratory problems and regurgitation. radiographs revealed evidence of cardiomegaly and pneumonia. blood smear examination revealed the presence of intracytoplasmic inclusion bodies in peripheral lymphocytes, consistent with inclusion body disease. cultures of a tracheal wash sample resulted in growth of ochrobactrum intermedium and pseudomonas putida. echocardiographic examination revealed a large vegetative ...	2015	25831585
biofilms and extracellular polymeric substances mediate the transport of graphene oxide nanoparticles in saturated porous media.	understanding the fate and transport of graphene oxide nanoparticles (gonps) in the subsurface environments is of crucial importance since they may pose potential risks to the environment and human health. however, little is known about the significance of biofilm on mobility of gonps in the subsurface. here we investigated the transport of gonps in saturated sand coated with bacillus subtilis (gram-positive) and pseudomonas putida (gram-negative) biofilms, and their secreted extracellular polym ...	2015	26223021
variation in bacterial atp concentration during rapid changes in extracellular ph and implications for the activity of attached bacteria.	in this study we investigated the relationship between a rapid change in extracellular ph and the alteration of bacterial atp concentration. this relationship is a key component of a hypothesis indicating that bacterial bioenergetics - the creation of atp from adp via a proton gradient across the cytoplasmic membrane - can be altered by the physiochemical charge-regulation effect, which results in a ph shift at the bacteria's surface upon adhesion to another surface. the bacterial atp concentrat ...	2015	26037699
bacterial cell surface properties: role of loosely bound extracellular polymeric substances (lb-eps).	this study investigated the effect of loosely bound extracellular polymeric substances (lb-eps) on the comprehensive surface properties of four bacteria (bacillus subtilis, streptococcus suis, escherichia coli and pseudomonas putida). the removal of lb-eps from bacterial surfaces by high-speed centrifugation (12,000×g) was confirmed by sem images. viability tests showed that the percentages of viable cells ranged from 95.9% to 98.0%, and no significant difference was found after treatment (p>0.0 ...	2015	25805151
detoxification of the veterinary antibiotic chloramphenicol using electron beam irradiation.	electron beam irradiation has shown potential as an alternative process for the treatment of industrial effluents that contain toxic organic chemicals. this study investigated the effectiveness of electron beam in degrading chloramphenicol (cap) in aqueous solution. the degradation efficiency was 32.4% at 1 kgy, 86.9% at 5 kgy, and 100% at 10 kgy. the total organic carbon (toc) of cap in aqueous solution declined 4.6% at 1 kgy, 12.1% at 5 kgy, and 17.1% at 10 kgy of irradiation with electron bea ...	2015	25616384
contribution of arbuscular mycorrhizal fungi and/or bacteria to enhancing plant drought tolerance under natural soil conditions: effectiveness of autochthonous or allochthonous strains.	autochthonous microorganisms [a consortium of arbuscular-mycorrhizal (am) fungi and bacillus thuringiensis (bt)] were assayed and compared to rhizophagus intraradices (ri), bacillus megaterium (bm) or pseudomonas putida (psp) and non-inoculation on trifolium repens in a natural arid soil under drought conditions. the autochthonous bacteria bt and the allochthonous bacteria psp increased nutrients and the relative water content and decreased stomatal conductance, electrolyte leakage, proline and ...	2015	25462971
functional expression of l-lysine α-oxidase from scomber japonicus in escherichia coli for one-pot synthesis of l-pipecolic acid from dl-lysine.	l-pipecolic acid is a key component of biologically active molecules and a pharmaceutically important chiral building block. it can be stereoselectively produced from l-lysine by a two-step bioconversion involving l-lysine α-oxidase and ∆(1)-piperideine-2-carboxylae (pip2c) reductase. in this study, we focused on an l-lysine α-oxidase from scomber japonicus that was originally identified as an apoptosis-inducing protein (aip) and applied the enzyme to one-pot fermentation of l-pipecolic acid in ...	2015	25547835
pyrosequencing analysis of microbial community and food-borne bacteria on restaurant cutting boards collected in seri kembangan, malaysia, and their correlation with grades of food premises.	this study adopts the pyrosequencing technique to identify bacteria present on 26 kitchen cutting boards collected from different grades of food premises around seri kembangan, a city in malaysia. pyrosequencing generated 452,401 of total reads of otus with an average of 1.4×10(7) bacterial cells/cm(2). proteobacteria, firmicutes and bacteroides were identified as the most abundant phyla in the samples. taxonomic richness was generally high with >1000 operational taxonomic units (otus) observed ...	2015	25679309
the crystal structure of the versatile cytochrome p450 enzyme cyp109b1 from bacillus subtilis.	the crystal structure of the versatile cyp109b1 enzyme from bacillus subtilis has been solved at 1.8 å resolution. this is the first structure of an enzyme from this cyp family, whose members are prevalent across diverse species of bacteria. in the crystal structure the enzyme has an open conformation with an access channel leading from the heme to the surface. the substrate-free structure reveals the location of the key residues in the active site that are responsible for binding the substrate ...	2015	25587700
extraordinary solute-stress tolerance contributes to the environmental tenacity of mycobacteria.	mycobacteria are associated with a number of well-characterized diseases, yet we know little about their stress biology in natural ecosystems. this study focuses on the isolation and characterization of strains from yellowstone national park (ynp) and glacier national park (gnp; usa), the majority of those identified were mycobacterium parascrofulaceum, mycobacterium avium (ynp) or mycobacterium gordonae (gnp). generally, their windows for growth spanned a temperature range of > 60 °c; selected ...	2015	26059202
nicotine-degrading microorganisms and their potential applications.	nicotine-degrading microorganisms (ndms) are a special microbial group which can use nicotine as the sole carbon and nitrogen source for growth. since the 1950s, the bioconversion of nicotine by microbes has received increasing attention, and several ndms have been identified, such as arthrobacter nicotinovorans, microsporum gypseum, pellicularia filamentosa jts-208, and pseudomonas sp. 41. in recent years, increasing numbers of ndms have been isolated and identified from tobacco plantation soil ...	2015	25805341
purification and properties of glycine oxidase from pseudomonas putida kt2440.	glycine oxidase, encoded by the thio gene, participates in the biosynthesis of thiamin by providing glyoxyl imine to form the thiazole moiety of thiamin. we have purified and characterized thio from pseudomonas putida kt2440. it has a monomeric structure that is distinct from the homotetrameric thios from bacillus subtilis and geobacillus kaustophilus. the p. putida thio is unique in that glycine is its preferred substrate, which differs markedly from the b. subtilis and g. kaustophilus enzymes ...	2015	26875494
vanadium removal from ld converter slag using bacteria and fungi.	removal of vanadium from linz-donawits (ld) converter slag was investigated by means of three different species of microbial systems: acidithiobacillus thiooxidans (autotrophic bacteria), pseudomonas putida (heterotrophic bacteria) and aspergillus niger (fungi). the bioleaching process was carried out in both one-step and two-step process and the leaching efficiencies in both cases were compared. formation of inorganic and organic acids during the leaching process caused mobilization of vanadium ...	2015	25697901
development of a growth-dependent selection system for identification of l-threonine aldolases.	threonine aldolases (tas) are useful enzymes for the synthesis of β-hydroxy-α-amino acids due to their capability to catalyze asymmetric aldol reactions. starting from two prochiral compounds, an aldehyde and glycine, two chiral stereocenters were formed in a single step via c-c bond formation. owing to poor diastereoselectivity and low activity, the enzymatic synthesis of β-hydroxy-α-amino acids by tas is still a challenge. for identification of new tas, a growth-dependent selection system in p ...	2015	25616526
[oil biodegradation by microbial-plant associations].	the degradation of petroleum hydrocarbons by plant-microbial associations, as well as the peculiarities of the interaction between microorganisms in consortium and the associated plants, have been studied. it was shown that degrader microorganisms that are part of the consortium rhodococcus erythropolis s26, acinetobacter baumannii 1 b, acinetobacter baumannii 7, and pseudomonas putida f701 were effective in the degradation of oil and were good colonizers of plant roots (barley). the efficiency ...	2015	26027354
efficacy of lactoferricin b in controlling ready-to-eat vegetable spoilage caused by pseudomonas spp.	the microbial content of plant tissues has been reported to cause the spoilage of ca. 30% of chlorine-disinfected fresh vegetables during cold storage. the aim of this work was to evaluate the efficacy of antimicrobial peptides in controlling microbial vegetable spoilage under cold storage conditions. a total of 48 bacterial isolates were collected from ready-to-eat (rte) vegetables and identified as belonging to acinetobacter calcoaceticus, aeromonas media, pseudomonas cichorii, pseudomonas flu ...	2015	26453993
increasing antibiotic resistance in preservative-tolerant bacterial strains isolated from cosmetic products.	to ensure the microbiological quality, consumer safety and organoleptic properties of cosmetic products, manufacturers need to comply with defined standards using several preservatives and disinfectants. a drawback regarding the use of these preservatives is the possibility of generating cross-insusceptibility to other disinfectants or preservatives, as well as cross resistance to antibiotics. therefore, the objective of this study was to understand the adaptive mechanisms of enterobacter gergov ...	2015	26415667
genetic analysis of plant endophytic pseudomonas putida bp25 and chemo-profiling of its antimicrobial volatile organic compounds.	black pepper associated bacterium bp25 was isolated from root endosphere of apparently healthy cultivar panniyur-5 that protected black pepper against phytophthora capsici and radopholus similis - the major production constraints. the bacterium was characterized and mechanisms of its antagonistic action against major pathogens are elucidated. the polyphasic phenotypic analysis revealed its identity as pseudomonas putida. multi locus sequence typing revealed that the bacterium shared gene sequenc ...	2015	25801973
detection and characterization of a bacteriocin, putadicin t01, produced by pseudomonas putida isolated from hot spring water.	pseudomonas strains isolated from hot spring water were tested for bacteriocin-like substance (bls) production using a target panel of closely related microorganisms and other gram-positive and gram-negative bacteria. molecular identification was carried out through specific pcr and 16s rna sequence analysis. isolates were identified as brevundimonas diminuta and pseudomonas putida, the latter exhibited antimicrobial activity. pseudomonas putida strains produce an inhibitory substance against ot ...	2015	25556393
antioxidative enzyme profiling and biosorption ability of cupriavidus metallidurans ch34 and pseudomonas putida mt2 under cadmium stress.	cupriavidus metallidurans ch34 and pseudomonas putida mt2 were used as cadmium (cd)-resistant and -sensitive bacteria, respectively, to study their biosorption ability and their antioxidative enzymes. the minimal inhibitory concentration of c. metallidurans ch34 for cd was found to be 30 mm, and for p. putida mt2 it was 1.25 mm. the tube dilution method revealed the heavy-metal resistance pattern of c. metallidurans ch34 as ni(2+) (10 mm)>zn(2+) (4 mm)>cu(2+) (2 mm)>hg(2+) (1 mm)>cr(2+) (1 mm)>p ...	2015	23832807
influence of humic acid on the stability and bacterial toxicity of zinc oxide nanoparticles in water.	the present study investigated the stability of zinc oxide nanoparticles (zno nps) by the adsorption of humic acid (ha) and the mechanism of adsorption. the effect of humic acid on np toxicity was determined by escherichia coli (atcc 13534), e. coli (atcc 25922), and pseudomonas putida (mtcc 4910). the nanoparticles showed low zeta potential and were least stable in the absence of ha. however, the negative surface charge of the particles increased in the presence of ha (0-50mg/l) that reduced th ...	2015	26496792
biological treatment of cyanide by using klebsiella pneumoniae species.	in this study, optimization conditions for cyanide biodegradation by klebsiella pneumoniae strain were determined to be 25 °c, ph=7 and 150 rpm at the concentration of 0.5 mm potassium cyanide in the medium. additionally, it was found that k. pneumoniae strain is not only able to degrade potassium cyanide, but also to degrade potassium hexacyanoferrate(ii) trihydrate and sodium ferrocyanide decahydrate with the efficiencies of 85 and 87.5%, respectively. furthermore, this strain degraded potassi ...	2016	28115902
clinical relevance of molecular identification of microorganisms and detection of antimicrobial resistance genes in bloodstream infections of paediatric cancer patients.	bloodstream infections (bsis) are the major cause of mortality in cancer patients. molecular techniques are used for rapid diagnosis of bsi, allowing early therapy and improving survival. we aimed to establish whether real-time quantitative polymerase chain reaction (qpcr) could improve early diagnosis and therapy in paediatric cancer patients, and describe the predominant pathogens of bsi and their antimicrobial susceptibility.	2016	27585633
regulation of pyrroloquinoline quinone-dependent glucose dehydrogenase activity in the model rhizosphere-dwelling bacterium pseudomonas putida kt2440.	soil-dwelling microbes solubilize mineral phosphates by secreting gluconic acid, which is produced from glucose by a periplasmic glucose dehydrogenase (gdh) that requires pyrroloquinoline quinone (pqq) as a redox coenzyme. while gdh-dependent phosphate solubilization has been observed in numerous bacteria, little is known concerning the mechanism by which this process is regulated. here we use the model rhizosphere-dwelling bacterium pseudomonas putida kt2440 to explore gdh activity and pqq synt ...	2016	27287323
carbon sources for polyhydroxyalkanoates and an integrated biorefinery.	polyhydroxyalkanoates (phas) are a group of bioplastics that have a wide range of applications. extensive progress has been made in our understanding of phas' biosynthesis, and currently, it is possible to engineer bacterial strains to produce phas with desired properties. the substrates for the fermentative production of phas are primarily derived from food-based carbon sources, raising concerns over the sustainability of their production in terms of their impact on food prices. this paper give ...	2016	27447619
characterization of integrons and novel cassette arrays in bacteria from clinical isloates in china, 2000-2014.	rapid dissemination of antibiotic resistance genes among bacterial isolates is an increasing problem in china. integron, a conserved dna sequence, which is carried on episomal genetic structures, plays a very important role in development of antibiotic resistance. this systematic analysis was based on medline and embase databases. we summarized the distribution and proportion of different types of gene cassette arrays of integrons (including class 1, 2, 3 and atypical class 1 integron) from clin ...	2016	27533938
extremophiles in an antarctic marine ecosystem.	recent attempts to explore marine microbial diversity and the global marine microbiome have indicated a large proportion of previously unknown diversity. however, sequencing alone does not tell the whole story, as it relies heavily upon information that is already contained within sequence databases. in addition, microorganisms have been shown to present small-to-large scale biogeographical patterns worldwide, potentially making regional combinations of selection pressures unique. here, we focus ...	2016	27681902
regulation of the alkane hydroxylase cyp153 gene in a gram-positive alkane-degrading bacterium, dietzia sp. strain dq12-45-1b.	cyp153, one of the most common medium-chain n-alkane hydroxylases belonging to the cytochrome p450 superfamily, is widely expressed in n-alkane-degrading bacteria. cyp153 is also thought to cooperate with alkb in degrading various n-alkanes. however, the mechanisms regulating the expression of the protein remain largely unknown. in this paper, we studied cyp153 gene transcription regulation by the potential arac family regulator (cypr) located upstream of the cyp153 gene cluster in a broad-spect ...	2016	26567302
towards an enhanced understanding of plant-microbiome interactions to improve phytoremediation: engineering the metaorganism.	phytoremediation is a promising technology to clean-up contaminated soils based on the synergistic actions of plants and microorganisms. however, to become a widely accepted, and predictable remediation alternative, a deeper understanding of the plant-microbe interactions is needed. a number of studies link the success of phytoremediation to the plant-associated microbiome functioning, though whether the microbiome can exist in alternative, functional states for soil remediation, is incompletely ...	2016	27014254
volatile compounds emitted by pseudomonas aeruginosa stimulate growth of the fungal pathogen aspergillus fumigatus.	chronic lung infections with opportunistic bacterial and fungal pathogens are a major cause of morbidity and mortality especially in patients with cystic fibrosis. pseudomonas aeruginosa is the most frequently colonizing bacterium in these patients, and it is often found in association with the filamentous fungus aspergillus fumigatus. p. aeruginosa is known to inhibit the growth of a. fumigatus in situations of direct contact, suggesting the existence of interspecies communication that may infl ...	2016	26980832
rhizospheric bacteria of maize with potential for biocontrol of fusarium verticillioides.	the stalk, ear and root rot (serr) of maize caused by fusarium verticillioides (fv) severely impacts crop production in tropical and subtropical regions. the aim of the present work was to screen bacterial isolates in order to find novel native biocontrol agents against fv. a culturable bacterial collection consisting of 11,520 isolates enriched in firmicutes and proteobacteria was created from rhizosphere samples taken from serr symptomatic or asymptomatic maize plants. the complete collection ...	2016	27066355
functional metagenomics of a biostimulated petroleum-contaminated soil reveals an extraordinary diversity of extradiol dioxygenases.	a metagenomic library of a petroleum-contaminated soil was constructed in a fosmid vector that allowed heterologous expression of metagenomic dna. the library, consisting of 6.5 gb of metagenomic dna, was screened for extradiol dioxygenase (edo) activity using catechol and 2,3-dihydroxybiphenyl as the substrates. fifty-eight independent clones encoding extradiol dioxygenase activity were identified. forty-one different edo-encoding genes were identified. the population of edo genes was not domin ...	2016	26896130
linking microbial community and catabolic gene structures during the adaptation of three contaminated soils under continuous long-term pollutant stress.	three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (btex) for a period of 3 months. different from the soil from brazil (bra) and switzerland (sui), the czech republic (cze) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. bra and sui soil samples showed a clear succession of phylotypes. a rapid response to ...	2016	26850298
bacterial-plant-interactions: approaches to unravel the biological function of bacterial volatiles in the rhizosphere.	rhizobacteria produce an enormous amount of volatile compounds, however, the function of these metabolites is scarcely understood. investigations evaluating influences on plants performed in various laboratories using individually developed experimental setups revealed different and often contradictory results, e.g., ranging from a significant plant growth promotion to a dramatic suppression of plant development. in addition to these discrepancies, these test systems neglected properties and com ...	2016	26903987
variable effects of exposure to formulated microbicides on antibiotic susceptibility in firmicutes and proteobacteria.	microbicides are broad-spectrum antimicrobial agents that generally interact with multiple pharmacological targets. while they are widely deployed in disinfectant, antiseptic, and preservative formulations, data relating to their potential to select for microbicide or antibiotic resistance have been generated mainly by testing the compounds in much simpler aqueous solutions. in the current investigation, antibiotic susceptibility was determined for bacteria that had previously exhibited decrease ...	2016	27060123
potential of biological agents in decontamination of agricultural soil.	pesticides are widely used for the control of weeds, diseases, and pests of cultivated plants all over the world, mainly since the period after the second world war. the use of pesticides is very extensive to control harm of pests all over the globe. persistent nature of most of the synthetic pesticides causes serious environmental concerns. decontamination of these hazardous chemicals is very essential. this review paper elaborates the potential of various biological agents in decontamination o ...	2016	27293964
burns infection profile of singapore: prevalence of multidrug-resistant acinetobacter baumannii and the role of blood cultures.	with various changes implemented such as perioperative antibiotics for tangential excision, this retrospective study reviews the infection profile of burn patients at singapore's only centralized burns unit. worldwide, the appearance of multidrug-resistant (mdr) strains of acinetobacter baumannii (a. baumannii) continues to worsen patient outcomes. this study also surveys the role of blood cultures in burns at our unit.	2016	27574683
a microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor.	a whole-cell biosensor utilizing a transcription factor (tf) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires access to an expanded repertoire of tfs. using homology modeling and ligand docking for binding pocket identification, assisted by conservative mutations in the pocket, we engineered a novel specificity in an acinetobacter tf, pobr, to 'sense' a chemical p-nitrophenol (pnp) and measured the response via a fluoresce ...	2016	27536006
optical sensing of microbial life on surfaces.	the label-free detection of microbial cells attached to a surface is an active field of research. the field is driven by the need to understand and control the growth of biofilms in a number of applications, including basic research in natural environments, industrial facilities, and clinical devices, to name a few. despite significant progress in the ability to monitor the growth of biofilms and related living cells, the sensitivity and selectivity of such sensors are still a challenge. we beli ...	2016	26637605
a new physiological role for the dna molecule as a protector against drying stress in desiccation-tolerant microorganisms.	the dna molecule is associated with the role of encoding information required to produce rna which is translated into proteins needed by the cell. this encoding involves information transmission to offspring or to other organisms by horizontal transfer. however, despite the abundance of this molecule in both the cell and the environment, its physiological role seems to be restricted mainly to that of a coding and inheritance molecule. in this paper, we report a new physiological role for the dna ...	2016	28066383
antimicrobial activities of bacteria associated with the brown alga padina pavonica.	macroalgae belonging to the genus padina are known to produce antibacterial compounds that may inhibit growth of human- and animal pathogens. hitherto, it was unclear whether this antibacterial activity is produced by the macroalga itself or by secondary metabolite producing epiphytic bacteria. here we report antibacterial activities of epiphytic bacteria isolated from padina pavonica (peacocks tail) located on northern coast of tunisia. eighteen isolates were obtained in pure culture and tested ...	2016	27462308
recombinant ralstonia eutropha engineered to utilize xylose and its use for the production of poly(3-hydroxybutyrate) from sunflower stalk hydrolysate solution.	lignocellulosic raw materials have extensively been examined for the production of bio-based fuels, chemicals, and polymers using microbial platforms. since xylose is one of the major components of the hydrolyzed lignocelluloses, it is being considered a promising substrate in lignocelluloses based fermentation process. ralstonia eutropha, one of the most powerful and natural producers of polyhydroxyalkanoates (phas), has extensively been examined for the production of bio-based chemicals, fuels ...	2016	27260327
evaluation of a fully automated research prototype for the immediate identification of microorganisms from positive blood cultures under clinical conditions.	a clinical laboratory evaluation of an intrinsic fluorescence spectroscopy (ifs)-based identification system paired to a bact/alert virtuo microbial detection system (biomérieux, inc., durham, nc) was performed to assess the potential for fully automated identification of positive blood cultures. the prototype ifs system incorporates a novel method combining a simple microbial purification procedure with rapid in situ identification via spectroscopy. results were available within 15 min of a bot ...	2016	27094332
involvement of type vi secretion system in secretion of iron chelator pyoverdine in pseudomonas taiwanensis.	rice bacterial blight caused by xanthomonas oryzae pv. oryzae (xoo) is one of the most destructive rice diseases worldwide. therefore, in addition to breeding disease-resistant rice cultivars, it is desirable to develop effective biocontrol agents against xoo. here, we report that a soil bacterium pseudomonas taiwanensis displayed strong antagonistic activity against xoo. using matrix-assisted laser desorption/ionization imaging mass spectrometry, we identified an iron chelator, pyoverdine, secr ...	2016	27605490
integrated analysis of root microbiomes of soybean and wheat from agricultural fields.	root associated bacteria are critical for plant growth and health. understanding the composition and role of root microbiota is crucial toward agricultural practices that are less dependent on chemical fertilization, which has known negative effects on the environment and human health. here we analyzed the root-associated microbiomes of soybean and wheat under agricultural field conditions. we took samples from 11 different production fields across a large geographic area. we used 16s rrna pyros ...	2016	27312589