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water level changes affect carbon turnover and microbial community composition in lake sediments.due to climate change, many lakes in europe will be subject to higher variability of hydrological characteristics in their littoral zones. these different hydrological regimes might affect the use of allochthonous and autochthonous carbon sources. we used sandy sediment microcosms to examine the effects of different hydrological regimes (wet, desiccating, and wet-desiccation cycles) on carbon turnover. (13)c-labelled particulate organic carbon was used to trace and estimate carbon uptake into ba ...201626902802
genomic and phenotypic characterization of the species acinetobacter venetianus.crude oil is a complex mixture of hydrocarbons and other organic compounds that can produce serious environmental problems and whose removal is highly demanding in terms of human and technological resources. the potential use of microbes as bioremediation agents is one of the most promising fields in this area. members of the species acinetobacter venetianus have been previously characterized for their capability to degrade n-alkanes and thus may represent interesting model systems to implement ...201626902269
actinobacteria isolated from an underground lake and moonmilk speleothem from the biggest conglomeratic karstic cave in siberia as sources of novel biologically active compounds.actinobacteria isolated from unstudied ecosystems are one of the most interesting and promising sources of novel biologically active compounds. cave ecosystems are unusual and rarely studied. here, we report the isolation and characterization of ten new actinobacteria strains isolated from an ancient underground lake and moonmilk speleothem from the biggest conglomeratic karstic cave in siberia with a focus on the biological activity of the obtained strains and the metabolite dereplication of on ...201626901168
application of cinder gel-beads/reeds combination strategy for bioremediation of pyrene- and indeno(1,2,3-cd)pyrene-contaminated estuarine wetlands.pseudomonas putida pyr1 and acinetobacter baumannii inp1 isolated from liaohe estuarine wetlands were entrapped in cinder beads to make cinder gel-beads. they were combined with reeds for bioremediation of pyrene- and indeno(1,2,3-cd)pyrene-contaminated estuarine wetlands. the results showed that the removal percentages of pyrene and indeno(1,2,3-cd)pyrene (69.2 and 89.8 % respectively) in 40 days using cinder gel-beads/reeds were obviously higher than those using cinder gel-beads(52.6 and 70.0  ...201626897584
successful expression of the bordetella petrii nitrile hydratase activator p14k and the unnecessary role of ser115.the activator p14k is necessary for the activation of nitrile hydratase (nhase). however, it is hard to be expressed heterogeneously. although an n-terminal strep tagged p14k could be successfully expressed from pseudomonas putida, various strategies for the over-expression of p14k are needed to facilitate further application of nhase.201626897378
mechanisms of bacterial (serratia marcescens) attachment to, migration along, and killing of fungal hyphae.we have found a remarkable capacity for the ubiquitous gram-negative rod bacterium serratia marcescens to migrate along and kill the mycelia of zygomycete molds. this migration was restricted to zygomycete molds and several basidiomycete species. no migration was seen on any molds of the phylum ascomycota. s. marcescens migration did not require fungal viability or surrounding growth medium, as bacteria migrated along aerial hyphae as well.s. marcescens did not exhibit growth tropism toward zygo ...201626896140
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 ...201626896130
phenotypic heterogeneity and the evolution of bacterial life cycles.most bacteria live in colonies, where they often express different cell types. the ecological significance of these cell types and their evolutionary origin are often unknown. here, we study the evolution of cell differentiation in the context of surface colonization. we particularly focus on the evolution of a 'sticky' cell type that is required for surface attachment, but is costly to express. the sticky cells not only facilitate their own attachment, but also that of non-sticky cells. using i ...201626894881
anoxic metabolism and biochemical production in pseudomonas putida f1 driven by a bioelectrochemical system.pseudomonas putida is a promising host for the bioproduction of chemicals, but its industrial applications are significantly limited by its obligate aerobic character. the aim of this paper is to empower the anoxic metabolism of wild-type pseudomonas putida to enable bioproduction anaerobically, with the redox power from a bioelectrochemical system (bes).201626893611
electrochemical reduction of carbon dioxide to methanol by direct injection of electrons into immobilized enzymes on a modified electrode.we present results for direct bio-electrocatalytic reduction of co2 to c1 products using electrodes with immobilized enzymes. enzymatic reduction reactions are well known from biological systems where co2 is selectively reduced to formate, formaldehyde, or methanol at room temperature and ambient pressure. in the past, the use of such enzymatic reductions for co2 was limited due to the necessity of a sacrificial co-enzyme, such as nicotinamide adenine dinucleotide (nadh), to supply electrons and ...201626890322
biodegradation of ddt by stenotrophomonas sp. ddt-1: characterization and genome functional analysis.a novel bacterium capable of utilizing 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (ddt) as the sole carbon and energy source was isolated from a contaminated soil which was identified as stenotrophomonas sp. ddt-1 based on morphological characteristics, biolog gn2 microplate profile, and 16s rdna phylogeny. genome sequencing and functional annotation of the isolate ddt-1 showed a 4,514,569 bp genome size, 66.92% gc content, 4,033 protein-coding genes, and 76 rna genes including 8 rrna genes. ...201626888254
synthesis of chiral 2-alkanols from n-alkanes by a p. putida whole-cell biocatalyst.the cytochrome p450 monooxygenase cyp154a8 from nocardia farcinica was previously found to catalyze hydroxylation of linear alkanes (c7 -c9 ) with a high regio- and stereoselectivity. the objective of this study was to integrate cyp154a8 along with suitable redox partners into a whole-cell system for the production of chiral 2-alkanols starting from alkanes. both recombinant escherichia coli and pseudomonas putida whole-cell biocatalysts tested for this purpose showed the ability to produce chir ...201626887569
extraction method plays critical role in antibacterial activity of propolis-loaded hydrogels.extracted propolis has been used for a long time as a remedy. however, if the release rate of propolis is not controlled, the efficacy is reduced. to overcome this issue, extracted propolis was added to a cryogel system. propolis collected from southern brazil was extracted using different methods and loaded at different concentrations into polyvinyl alcohol (pva) and polyacrylic acid hydrogels as carrier systems. the material properties were investigated with a focus on the propolis release pro ...201626886307
characterization of mazf-mediated sequence-specific rna cleavage in pseudomonas putida using massive parallel sequencing.under environmental stress, microbes are known to alter their translation patterns using sequence-specific endoribonucleases that we call rna interferases. however, there has been limited insight regarding which rnas are specifically cleaved by these rna interferases, hence their physiological functions remain unknown. in the current study, we developed a novel method to effectively identify cleavage specificities with massive parallel sequencing. this approach uses artificially designed rnas co ...201626885644
contributions of sinorhizobium meliloti transcriptional regulator dksa to bacterial growth and efficient symbiosis with medicago sativa.the stringent response, mediated by the (p)ppgpp synthetase rela and the rna polymerase-binding protein dksa, is triggered by limiting nutrient conditions. for some bacteria, it is involved in regulation of virulence. we investigated the role of two dksa-like proteins from the gram-negative nitrogen-fixing symbiont sinorhizobium meliloti in free-living culture and in interaction with its host plant medicago sativa the two paralogs, encoded by the genes smc00469 and smc00049, differ in the consti ...201626883825
biocontrol agents promote growth of potato pathogens, depending on environmental conditions.there is a pressing need to understand and optimize biological control so as to avoid over-reliance on the synthetic chemical pesticides that can damage environmental and human health. this study focused on interactions between a novel biocontrol-strain, bacillus sp. jc12gb43, and potato-pathogenic phytophthora and fusarium species. in assays carried out in vitro and on the potato tuber, the bacterium was capable of near-complete inhibition of pathogens. this bacillus was sufficiently xerotolera ...201626880001
characterization of rhamnolipids by liquid chromatography/mass spectrometry after solid-phase extraction.rhamnolipids are surface-active agents with a broad application potential that are produced in complex mixtures by bacteria of the genus pseudomonas. analysis from fermentation broth is often characterized by laborious sample preparation and requires hyphenated analytical techniques like liquid chromatography coupled to mass spectrometry (lc-ms) to obtain detailed information about sample composition. in this study, an analytical procedure based on chromatographic method development and characte ...201626879646
a biobrick™-compatible vector for allelic replacement using the xyle gene as selection marker.circular plasmid-mediated homologous recombination is commonly used for marker-less allelic replacement, exploiting the endogenous recombination machinery of the host. common limitations of existing methods include high false positive rates due to mutations in counter-selection genes, and limited applicability to specific strains or growth media. finally, solutions compatible with physical standards, such as the biobrick™, are not currently available, although they proved to be successful in the ...201626877712
a preliminary study on the antibacterial mechanism of tegillarca granosa hemoglobin by derived peptides and peroxidase activity.the blood clam, tegillarca granosa, is one of the few bivalve molluscs containing hemoglobin (hb). in the present study, we purified two types of t. granosa hemoglobin, tg-hbi and tg-hbii, using size exclusion chromatography and measured their antibacterial and peroxidase activities. we also tested antibacterial activities of peptides prepared by trypsin digestion of purified tg-hb and reversed-phase high-performance liquid chromatography purification. purified tg-hbi and tg-hbii showed antibact ...201626876330
genetic engineering and heterologous expression of the disorazol biosynthetic gene cluster via red/et recombineering.disorazol, a macrocyclic polykitide produced by the myxobacterium sorangium cellulosum so ce12 and it is reported to have potential cytotoxic activity towards several cancer cell lines, including multi-drug resistant cells. the disorazol biosynthetic gene cluster (dis) from sorangium cellulosum (so ce12) was identified by transposon mutagenesis and cloned in a bacterial artificial chromosome (bac) library. the 58-kb dis core gene cluster was reconstituted from bacs via red/et recombineering and ...201626875499
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 ...201526875494
data on the standardization of a cyclohexanone-responsive expression system for gram-negative bacteria.engineering of robust microbial cell factories requires the use of dedicated genetic tools somewhat different from those traditionally used for laboratory-adapted microorganisms. we have edited and formatted the chnr/p chnb regulatory node of acinetobacter johnsonii to ease the targeted engineering of ectopic gene expression in gram-negative bacteria. the proposed compositional standard was thoroughly verified with a monomeric and superfolder green fluorescent protein (msf•gfp) in escherichia co ...201626870759
assay of blood and synovial fluid of patients with rheumatoid arthritis for staphylococcus aureus enterotoxin d: absence of bacteria but presence of its toxin.rheumatoid arthritis (ra) is the most common chronic inflammatory disease. the staphylococcal superantigens are considered as the causative agent of ra disease.201526870313
structural and kinetic characterization of the 4-carboxy-2-hydroxymuconate hydratase from the gallate and protocatechuate 4,5-cleavage pathways of pseudomonas putida kt2440.the bacterial catabolism of lignin and its breakdown products is of interest for applications in industrial processing of ligno-biomass. the gallate degradation pathway ofpseudomonas putidakt2440 requires a 4-carboxy-2-hydroxymuconate (chm) hydratase (galb), which has a 12% sequence identity to a previously identified chm hydratase (ligj) fromsphingomonassp. syk-6. the structure of galb was determined and found to be a member of the pig-ln-acetylglucosamine deacetylase family; galb is structural ...201626867578
persistence of nasal colonization with human pathogenic bacteria and associated antimicrobial resistance in the german general population.the nares represent an important bacterial reservoir for endogenous infections. this study aimed to assess the prevalence of nasal colonization by different important pathogens, the associated antimicrobial susceptibility and risk factors. we performed a prospective cohort study among 1878 nonhospitalized volunteers recruited from the general population in germany. participants provided nasal swabs at three time points (each separated by 4-6 months). staphylococcus aureus, enterobacteriaceae and ...201526862431
persistence of nasal colonization with human pathogenic bacteria and associated antimicrobial resistance in the german general population.the nares represent an important bacterial reservoir for endogenous infections. this study aimed to assess the prevalence of nasal colonization by different important pathogens, the associated antimicrobial susceptibility and risk factors. we performed a prospective cohort study among 1878 nonhospitalized volunteers recruited from the general population in germany. participants provided nasal swabs at three time points (each separated by 4-6 months). staphylococcus aureus, enterobacteriaceae and ...201526862431
high resolution structures of periplasmic glucose-binding protein of pseudomonas putida csv86 reveal structural basis of its substrate specificity.periplasmic substrate-binding proteins (sbps) bind to the specific ligand with high affinity and mediate their transport into the cytoplasm via the cognate inner membrane atp-binding cassette proteins. because of low sequence identities, understanding the structural basis of substrate recognition by sbps has remained very challenging. there are several structures available for the ligand-bound sugar sbps, but very few unliganded structures are reported. no structural data are available for sugar ...201626861882
integrated foam fractionation for heterologous rhamnolipid production with recombinant pseudomonas putida in a bioreactor.heterologeous production of rhamnolipids in pseudomonas putida is characterized by advantages of a non-pathogenic host and avoidance of the native quorum sensing regulation in pseudomonas aeruginosa. yet, downstream processing is a major problem in rhamnolipid production and increases in complexity at low rhamnolipid titers and when using chemical foam control. this leaves the necessity of a simple concentrating and purification method. foam fractionation is an elegant method for in situ product ...201626860613
effect of solid boundaries on swimming dynamics of microorganisms in a viscoelastic fluid.we numerically study the effect of solid boundaries on the swimming behavior of a motile microorganism in viscoelastic media. understanding the swimmer-wall hydrodynamic interactions is crucial to elucidate the adhesion of bacterial cells to nearby substrates which is precursor to the formation of the microbial biofilms. the microorganism is simulated using a squirmer model that captures the major swimming mechanisms of potential, extensile, and contractile types of swimmers, while neglecting th ...201426855446
hydrogen isotope fractionation as a tool to identify aerobic and anaerobic pah biodegradation.aerobic and anaerobic polycyclic aromatic hydrocarbon (pah) biodegradation was characterized by compound specific stable isotope analysis (csia) of the carbon and hydrogen isotope effects of the enzymatic reactions initiating specific degradation pathways, using naphthalene and 2-methylnaphtalene as model compounds. aerobic activation of naphthalene and 2-methylnaphthalene by pseudomonas putida ncib 9816 and pseudomonas fluorescens atcc 17483 containing naphthalene dioxygenases was associated wi ...201626855125
metabolic engineering of pseudomonas putida kt2440 for complete mineralization of methyl parathion and γ-hexachlorocyclohexane.agricultural soils are often cocontaminated with multiple pesticides. unfortunately, microorganisms isolated from natural environments do not possess the ability to simultaneously degrade different classes of pesticides. currently, we can use the approaches of synthetic biology to create a strain endowed with various catabolic pathways that do not exist in a natural microorganism. here, we describe the metabolic engineering of a biosafety pseudomonas putida strain kt2440 for complete mineralizat ...201626854500
effect of fermented broth from lactic acid bacteria on pathogenic bacteria proliferation.in this study, the effect that 5 fermented broths of lactic acid bacteria (lab) strains have on the viability or proliferation and adhesion of 7 potentially pathogenic microorganisms was tested. the fermented broth from lactococcus lactis c660 had a growth inhibitory effect on escherichia coli k92 that reached of 31%, 19% to pseudomonas fluorescens, and 76% to staphylococcus epidermidis. the growth of staph. epidermidis was negatively affected to 90% by lc. lactis 11454 broth, whereas the growth ...201626851857
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 ...201626850298
a microbial transformation using bacillus subtilis b7-s to produce natural vanillin from ferulic acid.bacillus subtilis strain b7-s screened from18 strains is an aerobic, endospore-forming, model organism of gram-positive bacteria which is capable to form vanillin during ferulic acid bioconversion. the bioconversion of ferulic acid to vanillin by bacillus subtilis b7-s (b. subtilis b7-s) was investigated. based on our results, the optimum bioconversion conditions for the production of vanillin by b. subtilis b7-s can be summarized as follows: temperature 35 °c; initial ph 9.0; inoculum volume 5% ...201626841717
comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating rhodococcus opacus pd630.lignin-derived (e.g. phenolic) compounds can compromise the bioconversion of lignocellulosic biomass to fuels and chemicals due to their toxicity and recalcitrance. the lipid-accumulating bacterium rhodococcus opacus pd630 has recently emerged as a promising microbial host for lignocellulose conversion to value-added products due to its natural ability to tolerate and utilize phenolics. to gain a better understanding of its phenolic tolerance and utilization mechanisms, we adaptively evolved r. ...201626837573
biodegradation of chlorpyrifos by bacterial genus pseudomonas.chlorpyrifos is an organophosphorus pesticide commonly used in agriculture. it is noxious to a variety of organisms that include living soil biota along with beneficial arthropods, fish, birds, humans, animals, and plants. exposure to chlorpyrifos may cause detrimental effects as delayed seedling emergence, fruit deformities, and abnormal cell division. contamination of chlorpyrifos has been found about 24 km from the site of its application. there are many physico-chemical and biological approa ...201626837064
carbonate precipitation through microbial activities in natural environment, and their potential in biotechnology: a review.calcium carbonate represents a large portion of carbon reservoir and is used commercially for a variety of applications. microbial carbonate precipitation, a by-product of microbial activities, plays an important metal coprecipitation and cementation role in natural systems. this natural process occurring in various geological settings can be mimicked and used for a number of biotechnologies, such as metal remediation, carbon sequestration, enhanced oil recovery, and construction restoration. in ...201626835451
minion analysis and reference consortium: phase 1 data release and analysis.the advent of a miniaturized dna sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools. the minion™ access programme (map) was initiated by oxford nanopore technologies™ in april 2014, giving public access to their usb-attached miniature sequencing device. the minion analysis and reference consortium (marc) was formed by a subset of map participants, with the aim of evaluating and providing standard protocols and re ...201526834992
the toxin grat inhibits ribosome biogenesis.most bacteria encode numerous chromosomal toxin-antitoxin (ta) systems that are proposed to contribute to stress tolerance, as they are able to shift the cells to a dormant state. toxins act on a variety of targets with the majority attacking the translational apparatus. intriguingly, the toxicity mechanisms of even closely related toxins may differ essentially. here, we report on a new type of ta toxin that inhibits ribosome biogenesis. grat of the grata system has previously been described in ...201626833678
sulfide consumption in sulfurimonas denitrificans and heterologous expression of its three sulfide-quinone reductase homologs.sulfurimonas denitrificans is a sulfur-oxidizing epsilonproteobacterium. it has been reported to grow with sulfide and to harbor genes that encode sulfide-quinone reductases (sqrs) (catalyze sulfide oxidation). however, the actual sulfide concentrations at which s. denitrificans grows and whether its sqrs are functional remain enigmatic. here, we illustrate the sulfide concentrations at which s. denitrificans exhibits good growth, namely, 0.18 mm to roughly 1.7 mm. around 2.23 mm, sulfide appear ...201626833414
l-hydroxyproline and d-proline catabolism in sinorhizobium meliloti.sinorhizobium meliloti forms n2-fixing root nodules on alfalfa, and as a free-living bacterium, it can grow on a very broad range of substrates, including l-proline and several related compounds, such as proline betaine, trans-4-hydroxy-l-proline (trans-4-l-hyp), and cis-4-hydroxy-d-proline (cis-4-d-hyp). fourteen hyp genes are induced upon growth of s. meliloti on trans-4-l-hyp, and of those, hypmnpq encodes an abc-type trans-4-l-hyp transporter and hypre encodes an epimerase that converts tran ...201626833407
study on wastewater toxicity using toxtrak™ method.toxtrak™ method is an analytical tool for the measurement of toxicity of drinking water, wastewater and natural water. it is based upon the estimation of the inhibitive effect on bacterial respiration processes. the main aim of this work was to test the applicability of toxtrak™ method in the assessment of wastewater toxicity in a full-scale wwtp in poland. in order to achieve it, the study was divided into two parts. first, the validation of toxtrak™ method was performed. second, wastewater tox ...201626832868
psamm: a portable system for the analysis of metabolic models.the genome-scale models of metabolic networks have been broadly applied in phenotype prediction, evolutionary reconstruction, community functional analysis, and metabolic engineering. despite the development of tools that support individual steps along the modeling procedure, it is still difficult to associate mathematical simulation results with the annotation and biological interpretation of metabolic models. in order to solve this problem, here we developed a portable system for the analysis ...201626828591
identification of a conserved 5'-drp lyase activity in bacterial dna repair ligase d and its potential role in base excision repair.bacillus subtilis is one of the bacterial members provided with a nonhomologous end joining (nhej) system constituted by the dna-binding ku homodimer that recruits the atp-dependent dna ligase d (bsuligd) to the double-stranded dna breaks (dsbs) ends. bsuligd has inherent polymerization and ligase activities that allow it to fill the short gaps that can arise after realignment of the broken ends and to seal the resulting nicks, contributing to genome stability during the stationary phase and ger ...201626826709
characterization of sxt/r391 integrative and conjugative elements in proteus mirabilis isolates from food-producing animals in china.sxt/r391 integrative and conjugative elements (ices) were detected in 8 out of 125 proteus mirabilis isolates from food-producing animals in china. whole-genome sequencing revealed that seven ices were identical to icepmijpn1, carrying the cephalosporinase gene blacmy-2. another one, designated icepmichn1, carried five resistance genes. all eight ices could be transferred to escherichia coli via conjugation. the results highlight the idea that animal farms are important reservoir of the sxt/r391 ...201626824957
a multi-substrate approach for functional metagenomics-based screening for (hemi)cellulases in two wheat straw-degrading microbial consortia unveils novel thermoalkaliphilic enzymes.functional metagenomics is a promising strategy for the exploration of the biocatalytic potential of microbiomes in order to uncover novel enzymes for industrial processes (e.g. biorefining or bleaching pulp). most current methodologies used to screen for enzymes involved in plant biomass degradation are based on the use of single substrates. moreover, highly diverse environments are used as metagenomic sources. however, such methods suffer from low hit rates of positive clones and hence the dis ...201626822785
specific gene loci of clinical pseudomonas putida isolates.pseudomonas putida are ubiquitous inhabitants of soils and clinical isolates of this species have been seldom described. clinical isolates show significant variability in their ability to cause damage to hosts because some of them are able to modulate the host's immune response. in the current study, comparisons between the genomes of different clinical and environmental strains of p. putida were done to identify genetic clusters shared by clinical isolates that are not present in environmental ...201626820467
a pseudomonas putida double mutant deficient in butanol assimilation: a promising step for engineering a biological biofuel production platform.biological production in heterologous hosts is of interest for the production of the c4 alcohol (butanol) and other chemicals. however, some hurdles need to be overcome in order to achieve an economically viable process; these include avoiding the consumption of butanol and maintaining tolerance to this solvent during production. pseudomonas putida is a potential host for solvent production; in order to further adapt p. putida to this role, we generated mini-tn5 mutant libraries in strain bird-1 ...201626818251
pqsbc, a condensing enzyme in the biosynthesis of the pseudomonas aeruginosa quinolone signal: crystal structure, inhibition, and reaction mechanism.pseudomonas aeruginosaproduces a number of alkylquinolone-type secondary metabolites best known for their antimicrobial effects and involvement in cell-cell communication. in the alkylquinolone biosynthetic pathway, the β-ketoacyl-(acyl carrier protein) synthase iii (fabh)-like enzyme pqsbc catalyzes the condensation of octanoyl-coenzyme a and 2-aminobenzoylacetate (2-aba) to form the signal molecule 2-heptyl-4(1h)-quinolone. pqsbc, a potential drug target, is unique for its heterodimeric arrang ...201626811339
threonine aldolases: perspectives in engineering and screening the enzymes with enhanced substrate and stereo specificities.threonine aldolases have emerged as a powerful tool for asymmetric carbon-carbon bond formation. these enzymes catalyse the unnatural aldol condensation of different aldehydes and glycine to produce highly valuable β-hydroxy-α-amino acids with complete stereocontrol at the α-carbon and moderate specificity at the β-carbon. a range of microbial threonine aldolases has been recently recombinantly produced by several groups and their biochemical properties were characterized. numerous studies have ...201626810201
mechanistic understanding of reduced agnp phytotoxicity induced by extracellular polymeric substances.a knowledge gap concerning the potential effects of extracellular polymeric substances (eps), a common organic material but highly variable in their composition of microbial origin, on the fate and phytotoxicity of silver nanoparticles (agnp) still remains. a 48-h root elongation toxicity test showed that agnp toxicity to wheat triticum aestivum l. was dramatically alleviated by eps isolated from pseudomonas putida, as revealed by 7-59% increase in relative root elongation (rre), 8-99% increase ...201626808239
comparisons of the transferability of plasmids pcar1, pb10, r388, and nah7 among pseudomonas putida at different cell densities.the transferability of plasmids pcar1, pb10, r388, and nah7 was compared using the same donor-recipient system at different cell density combinations in liquid or on a solid surface. pcar1 was efficiently transferred in liquid, whereas the other plasmids were preferentially transferred on a solid surface. difference of liquid or solid affected the transfer frequency especially at lower cell densities.201626806196
engineering synthetic bacterial consortia for enhanced desulfurization and revalorization of oil sulfur compounds.the 4s pathway is the most studied bioprocess for the removal of the recalcitrant sulfur of aromatic heterocycles present in fuels. it consists of three sequential functional units, encoded by the dszabcd genes, through which the model compound dibenzothiophene (dbt) is transformed into the sulfur-free 2-hydroxybiphenyl (2hbp) molecule. in this work, a set of synthetic dsz cassettes were implanted in pseudomonas putida kt2440, a model bacterial "chassis" for metabolic engineering studies. the co ...201626802977
mechanism-specific and whole-organism ecotoxicity of mono-rhamnolipids.biosurfactants like rhamnolipids are promising alternatives to chemical surfactants in a range of applications. a wider use requires an analysis of their environmental fate and their ecotoxicological potential. in the present study mono-rhamnolipids produced by a recombinant pseudomonas putida strain were analyzed using the green toxicology concept for acute and mechanism-specific toxicity in an ecotoxicological test battery. acute toxicity tests with the invertebrate daphnia magna and with zebr ...201626802344
pseudomonas putida kt2440 markerless gene deletion using a combination of λ red recombineering and cre/loxp site-specific recombination.pseudomonas putida kt2440 is a saprophytic, environmental microorganism that plays important roles in the biodegradation of environmental toxic compounds and production of polymers, chemicals and secondary metabolites. gene deletion of kt2440 usually involves cloning of the flanking homologous fragments of the gene of interest into a suicide vector followed by transferring into kt2440 via triparental conjugation. selection and counterselection steps are then employed to generate gene deletion mu ...201626802072
unusual poly-3-hydroxyalkanoates (phas) biosynthesis behavior of pseudomonas putida bet001 and delftia tsuruhatensis bet002 isolated from palm oil mill effluent.pseudomonas putida bet001 and delftia tsuruhatensis bet002, isolated from palm oil mill effluent, accumulated poly (3-hydroxyalkanoates) (pha) when grown on aliphatic fatty acids, sugars and glycerol. the substrates were supplied at 20:1 c/n mole ratio. among c-even n-alkanoic acids, myristic acid gave the highest pha content 26 and 28 wt% in p. putida and d. tsuruhatensis respectively. among c-odd n-alkanoic acids, undecanoic gave the highest pha content at 40 wt% in p. putida and 46 wt% in d. ...201626800648
sulfoxides, analogues of l-methionine and l-cysteine as pro-drugs against gram-positive and gram-negative bacteria.the problem of resistance to antibiotics requires the development of new classes of broad-spectrum antimicrobial drugs. the concept of pro-drugs allows researchers to look for new approaches to obtain effective drugs with improved pharmacokinetic and pharmacodynamic properties. thiosulfinates, formed enzymatically from amino acid sulfoxides upon crushing cells of genus allium plants, are known as antimicrobial compounds. the instability and high reactivity of thiosulfinates complicate their use ...201526798500
direct detection of burkholderia cepacia in susceptible pharmaceutical products using semi-nested pcr.burkholderia cepaciahas recently received a considerable attention as one of the major risks in susceptible pharmaceutical products. this microorganism can easily propagate and cause vast and severe contamination, especially to the water supplies for pharmaceutical companies. moreover, it proliferates within the products and can cause severe infections for humans. therefore, fast and sensitive detection of these bacteria is of a great demand. the present study introduces improved application of ...201626797972
silver nanoparticles formation by extracellular polymeric substances (eps) from electroactive bacteria.microbial extracellular polymeric substances (eps) excreted from microorganisms were a complex natural biological polymer mixture of proteins and polysaccharides, which played an important roles in the transport of metals, such as ag(+). electroactive bacteria, is an important class of environmental microorganisms, which can use iron or manganese mineral as terminal electron acceptors to generate energy for biosynthesis and cell maintenance. in this work, the eps extracted of three electroactive ...201626797954
terpene arms race in the seiridium cardinale - cupressus sempervirens pathosystem.the canker-causing fungus seiridium cardinale is the major threat to cupressus sempervirens worldwide. we investigated the production of terpenes by canker-resistant and susceptible cypresses inoculated with s. cardinale, the effect of these terpenes on fungal growth, and the defensive biotransformation of the terpenes conducted by the fungus. all infected trees produced de novo terpenes and strongly induced terpenic responses, but the responses were stronger in the canker-resistant than the sus ...201626796122
engineering cell factories for producing building block chemicals for bio-polymer synthesis.synthetic polymers are widely used in daily life. due to increasing environmental concerns related to global warming and the depletion of oil reserves, the development of microbial-based fermentation processes for the production of polymer building block chemicals from renewable resources is desirable to replace current petroleum-based methods. to this end, strains that efficiently produce the target chemicals at high yields and productivity are needed. recent advances in metabolic engineering h ...201626794242
study of the aminoglycoside subsistence phenotype of bacteria residing in the gut of humans and zoo animals.recent studies indicate that next to antibiotic resistance, bacteria are able to subsist on antibiotics as a carbon source. here we evaluated the potential of gut bacteria from healthy human volunteers and zoo animals to subsist on antibiotics. nine gut isolates of escherichia coli and cellulosimicrobium sp. displayed increases in colony forming units (cfu) during incubations in minimal medium with only antibiotics added, i.e., the antibiotic subsistence phenotype. furthermore, laboratory strain ...201526793182
study of the aminoglycoside subsistence phenotype of bacteria residing in the gut of humans and zoo animals.recent studies indicate that next to antibiotic resistance, bacteria are able to subsist on antibiotics as a carbon source. here we evaluated the potential of gut bacteria from healthy human volunteers and zoo animals to subsist on antibiotics. nine gut isolates of escherichia coli and cellulosimicrobium sp. displayed increases in colony forming units (cfu) during incubations in minimal medium with only antibiotics added, i.e., the antibiotic subsistence phenotype. furthermore, laboratory strain ...201526793182
cd(ii) sorption on montmorillonite-humic acid-bacteria composites.soil components (e.g., clays, bacteria and humic substances) are known to produce mineral-organic composites in natural systems. herein, batch sorption isotherms, isothermal titration calorimetry (itc), and cd k-edge exafs spectroscopy were applied to investigate the binding characteristics of cd on montmorillonite(mont)-humic acid(ha)-bacteria composites. additive sorption and non-additive cd(ii) sorption behaviour is observed for the binary mont-bacteria and ternary mont-ha-bacteria composite, ...201626792640
biochemical properties of paracoccus denitrificans fnrp: reactions with molecular oxygen and nitric oxide.in paracoccus denitrificans, three crp/fnr family regulatory proteins, narr, nnrr and fnrp, control the switch between aerobic and anaerobic (denitrification) respiration. fnrp is a [4fe-4s] cluster-containing homologue of the archetypal o2 sensor fnr from e. coli and accordingly regulates genes encoding aerobic and anaerobic respiratory enzymes in response to o2, and also no, availability. here we show that fnrp undergoes o2-driven [4fe-4s] to [2fe-2s] cluster conversion that involves up to 2 o ...201626790880
uncovering the transmembrane metal binding site of the novel bacterial major facilitator superfamily-type copper importer ccoa.uptake and trafficking of metals and their delivery to their respective metalloproteins are important processes. cells need precise control of each step to avoid exposure to excessive metal concentrations and their harmful consequences. copper (cu) is a required micronutrient used as a cofactor in proteins. however, in large amounts, it can induce oxidative damage; hence, cu homeostasis is indispensable for cell survival. biogenesis of respiratory heme-cu oxygen (hco) reductases includes inserti ...201626787831
insights into the function of a second, nonclassical ahp peroxidase, ahpa, in oxidative stress resistance in bacillus subtilis.organisms growing aerobically generate reactive oxygen-containing molecules, such as hydrogen peroxide (h2o2). these reactive oxygen molecules damage enzymes and dna and may even cause cell death. in response, bacillus subtilis produces at least nine potential peroxide-scavenging enzymes, two of which appear to be the primary enzymes responsible for detoxifying peroxides during vegetative growth: a catalase (encoded by kata) and an alkylhydroperoxide reductase (ahp, encoded by ahpc). ahpc uses t ...201626787766
the frurba operon is necessary for group a streptococcal growth in fructose and for resistance to neutrophil killing during growth in whole human blood.bacterial pathogens rely on the availability of nutrients for survival in the host environment. the phosphoenolpyruvate-phosphotransferase system (pts) is a global regulatory network connecting sugar uptake with signal transduction. since the fructose pts has been shown to impact virulence in several streptococci, including the human pathogen streptococcus pyogenes(the group a streptococcus[gas]), we characterized its role in carbon metabolism and pathogenesis in the m1t1 strain 5448. growth in ...201626787724
a hospital-wide outbreak of serratia marcescens, and ishikawa's "fishbone" analysis to support outbreak control.a nosocomial outbreak of serratia marcescens in respiratory samples predominantly from patients in a surgical intensive care unit is reported. most of these patients were cardiac surgical patients. initially, a vigorous but inconclusive investigation was implemented on the basis of standardized (according the us centers for disease control and prevention) steps of outbreak investigation. then, a systemic quality management approach with "fishbone" analysis was added. as a consequence, plausible ...201626783861
pseudomonas putida strain fstm2 isolated from shark skin: a potential source of bacteriocin.bacteriocin-producing pseudomonas putida strain fstm2 isolated from shark showed broad range of antibacterial activity against all pathogens tested except bacillus subtilis atcc11774, mrsa n32064, proteus mirabilis atcc12453, enterococcus faecalis atcc14506, salmonella typhimurium atcc51312, salmonella mutan atcc25175, and aeromonas hydrophila wbf314. of the three growth media tested in this study, tsb was observed to support the bacteriocin activity the most. while the highest bacteriocin activ ...201326782985
biosafety test for plant growth-promoting bacteria: proposed environmental and human safety index (ehsi) protocol.plant growth-promoting bacteria (pgpb) colonize plants and enhance their growth by different mechanisms. some of these microorganisms may represent a potential threat to human, animal or plant health; however, their use might be approved in parts of europe if they have been recommended as plant growth enhancers. the current regulatory framework has resulted in a fragmented, contradictory system, and there is an urgent need to establish harmonized protocols for the predictability, efficiency, con ...201526779168
biosafety test for plant growth-promoting bacteria: proposed environmental and human safety index (ehsi) protocol.plant growth-promoting bacteria (pgpb) colonize plants and enhance their growth by different mechanisms. some of these microorganisms may represent a potential threat to human, animal or plant health; however, their use might be approved in parts of europe if they have been recommended as plant growth enhancers. the current regulatory framework has resulted in a fragmented, contradictory system, and there is an urgent need to establish harmonized protocols for the predictability, efficiency, con ...201526779168
bioaccumulation of nickel by e. sativa and role of plant growth promoting rhizobacteria (pgprs) under nickel stress.phytoremediation potential of plants can be enhanced in association with microbes. further, many plant growth-promoting rhizobacteria can improve growth under stress. the present study was conducted to investigate the effect of pseudomonas putida (p. putida) on nickel (ni) uptake and on growth of eruca sativa (e. sativa). three different levels of ni (low; 150 ug/g, medium; 250 ug/g and high; 500 ug/g) were applied to the soil containing e. sativa seedlings, with or without p. putida. ni-toxicit ...201626773835
occurrence and ecological risk assessment of fluoroquinolone antibiotics in hospital waste of lahore, pakistan.in the present study, wastewater and sludge samples of two major hospitals of lahore, pakistan were analyzed by developing an hplc-uv method for the possible occurrence of five frequently used fluoroquinolone antibiotics i.e. ofloxacin, ciprofloxacin, sparfloxacin, moxifloxacin and gemifloxacin. the highest detected concentration was for moxifloxacin in both wastewater (224 μg/l) and sludge samples (219 μg/kg. the highest concentration of ofloxacin, ciprofloxacin, sparfloxacin and gemifloxacin w ...201626773357
toxicity of titanium dioxide nanoparticles on pseudomonas putida.the increasing use of engineered nanoparticles (nps) in industrial and household applications will very likely lead to the release of such materials into the environment. as wastewater treatment plants (wwtps) are usually the last barrier before the water is discharged into the environment, it is important to understand the effects of these materials in the biotreatment processes, since the results in the literature are usually contradictory. we proposed the use of flow cytometry (fc) technology ...201626771160
comparative genomics between two xenorhabdus bovienii strains highlights differential evolutionary scenarios within an entomopathogenic bacterial species.bacteria of the genus xenorhabdus are symbionts of soil entomopathogenic nematodes of the genus steinernema. this symbiotic association constitutes an insecticidal complex active against a wide range of insect pests. within xenorhabdus bovienii species, the x. bovienii cs03 strain (xb cs03) is nonvirulent when directly injected into lepidopteran insects, and displays a low virulence when associated with its steinernema symbiont. the genome of xb cs03 was sequenced and compared with the genome of ...201626769959
a loop-mediated isothermal amplification assay and sample preparation procedure for sensitive detection of xanthomonas fragariae in strawberry.xanthomonas fragariae is a bacterium that causes angular leaf spot of strawberry. asymptomatic infection is common and contributes to the difficulties in disease management. the aim of this study was to develop a loop-mediated isothermal amplification (lamp) assay as an efficient method for detection of asymptomatic infections of x. fragariae. in addition, a new method of sample preparation was developed that allows sampling of a larger amount of plant tissue, hence increasing the detection rate ...201626766068
influence of oxygen transfer on pseudomonas putida effects on growth rate and biodesulfurization capacity.the growth rate and desulfurization capacity accumulated by the cells during the growth of pseudomonas putida kth2 under different oxygen transfer conditions in a stirred and sparged tank bioreactor have been studied. hydrodynamic conditions were changed using different agitation conditions. during the culture, several magnitudes associated to growth, such as the specific growth rate, the dissolved oxygen concentration and the carbon source consumption have been measured. experimental results in ...201626762940
use of antimicrobial food additives as potential dipping solutions to control pseudomonas spp. contamination in the frankfurters and ham.this study evaluated the effect of sodium diacetate and sodium lactate solutions for reducing the cell count of pseudomonas spp. in frankfurters and hams. a mixture of pseudomonas aeruginosa (nccp10338, nccp10250, and nccp11229), and pseudomonas fluorescens (kacc10323 and kacc10326) was inoculated on cooked frankfurters and ham. the inoculated samples were immersed into control (sterile distilled water), sodium diacetate (5 and 10%), sodium lactate (5 and 10%), 5% sodium diacetate + 5% sodium la ...201426761492
bacterial flagellar motility on hydrated rough surfaces controlled by aqueous film thickness and connectedness.recent studies have shown that rates of bacterial dispersion in soils are controlled by hydration conditions that define size and connectivity of the retained aqueous phase. despite the ecological implications of such constraints, microscale observations of this phenomenon remain scarce. here, we quantified aqueous film characteristics and bacterial flagellated motility in response to systematic variations in microhydrological conditions on porous ceramic surfaces that mimic unsaturated soils. w ...201626757676
the lona protease regulates biofilm formation, motility, virulence, and the type vi secretion system in vibrio cholerae.the presence of the lon protease in all three domains of life hints at its biological importance. the prokaryotic lon protease is responsible not only for degrading abnormal proteins but also for carrying out the proteolytic regulation of specific protein targets. posttranslational regulation by lon is known to affect a variety of physiological traits in many bacteria, including biofilm formation, motility, and virulence. here, we identify the regulatory roles of lona in the human pathogen vibri ...201626755629
lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome.cinnamoyl-coa reductase (ccr), an enzyme central to the lignin biosynthetic pathway, represents a promising biotechnological target to reduce lignin levels and to improve the commercial viability of lignocellulosic biomass. however, silencing of the ccr gene results in considerable flux changes of the general and monolignol-specific lignin pathways, ultimately leading to the accumulation of various extractable phenolic compounds in the xylem. here, we evaluated host genotype-dependent effects of ...201626755604
construction of a subunit-fusion nitrile hydratase and discovery of an innovative metal ion transfer pattern.metallochaperones are metal-binding proteins designed to deliver the appropriate metal to a target protein. the metal is usually transferred between different proteins. in this study, we discovered that metal was transferred between the same subunit of a mutant nitrile hydratase (nhase). various "activator proteins" mediate the trafficking of metal ions into nhases. we constructed fusion nhases by fusing the β- and α-subunits and/or the "activator proteins" of the nhase from pseudomonas putida. ...201626755342
the effect of root exudate 7,4'-dihydroxyflavone and naringenin on soil bacterial community structure.our goal was to investigate how root exudate flavonoids influence the soil bacterial community structure and to identify members of the community that change their relative abundance in response to flavonoid exudation. using a model system that approximates flavonoid exudation of medicago sativa roots, we treated a soil with 7,4'-dihydroxyflavone and naringenin in two separate experiments using three different rates: medium (equivalent to the exudation rate of 7,4'-dihydroxyflavone from m. sativ ...201626752410
structure of methionine γ-lyase from clostridium sporogenes.methionine γ-lyase (mgl) is a pyridoxal 5'-phosphate-dependent enzyme that catalyzes the γ-elimination reaction of l-methionine. the enzyme is a promising target for therapeutic intervention in some anaerobic pathogens and has attracted interest as a potential cancer treatment. the crystal structure of mgl from clostridium sporogenes has been determined at 2.37 å resolution. the fold of the protein is similar to those of homologous enzymes from citrobacter freundii, entamoeba histolytica, pseudo ...201626750487
a novel enterocin t1 with anti-pseudomonas activity produced by enterococcus faecium t1 from chinese tibet cheese.an enterocin-producing enterococcus faecium t1 was isolated from chinese tibet cheese. the enterocin was purified by sp-sepharose and reversed phase hplc. it was identified as unique from other reported bacteriocins based on molecular weight (4629 da) and amino acid compositions; therefore it was subsequently named enterocin t1. enterocin t1 was stable at 80-100 °c and over a wide ph range, ph 3.0-10.0. protease sensitivity was observed to trypsin, pepsin, papain, proteinase k, and pronase e. im ...201626745981
diffusion of bacterial cells in porous media.the chemotaxis signal transduction network regulates the biased random walk of many bacteria in favorable directions and away from harmful ones through modulating the frequency of directional reorientations. in mutants of diverse bacteria lacking the chemotaxis response, migration in classic motility agar, which constitutes a fluid-filled porous medium, is compromised; straight-swimming cells unable to tumble become trapped within the agar matrix. spontaneous mutations that restore spreading hav ...201626745427
pseudomonas putida attunes morphophysiological, biochemical and molecular responses in cicer arietinum l. during drought stress and recovery.drought is one of the most important abiotic stresses that adversely affect plant growth and yield potential. however, some drought resistant rhizosphere competent bacteria are known to improve plant health and promote growth during abiotic stresses. present study showed the role of pseudomonas putida mtcc5279 (ra) in ameliorating drought stress on cv. bg-362 (desi) and cv. bg-1003 (kabuli) chickpea cultivars under in vitro and green house conditions. polyethylene glycol-induced drought stress s ...201626744996
diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch.the effect of environmental conditions on the diversity and interactions of microbial communities has caused tremendous interest in microbial ecology. here, we found that with identical influents but differing operational parameters (mainly mixed liquor suspended solid (mlss) concentrations, solid retention time (srt) and dissolved oxygen (do) concentrations), two full-scale municipal wastewater treatment systems applying oxidation ditch (od) and membrane bioreactor (mbr) processes harbored a ma ...201626743465
effects of carbazole-degradative plasmid pcar1 on biofilm morphology in pseudomonas putida kt2440.bacteria typically form biofilms under natural conditions. to elucidate the effect of the carriage of carbazole-degradative plasmid pcar1 on biofilm formation by host bacteria, we compared the biofilm morphology, using confocal laser scanning microscopy, of three pcar1-free and pcar1-carrying pseudomonas hosts: p. putida kt2440, p. aeruginosa pao1 and p. fluorescens pf0-1. although pcar1 did not significantly affect biofilm formation by pao1 or pf0-1, pcar1-carrying kt2440 became filamentous and ...201626743211
pseudomonas putida stimulates primordia on agaricus bitorquis.casing layer is one step of agaricus bisporus cultivation where there is a competitive environment with a high number of microorganisms and diversity interacting with mycelia. it is suggested that a minimal community of these microorganisms would be necessary to stimulate fructification. however, a. bisporus is not able to produce primordia in sterile casing layers or petri dishes. thus, the objective of this study was to characterize bacterial microbiota of casing layers from a. bisporus cultiv ...201626742772
transport, retention, and long-term release behavior of zno nanoparticle aggregates in saturated quartz sand: role of solution ph and biofilm coating.the transport, retention, and long-term release of zinc oxide nanoparticle aggregates (denoted below as zno-nps) were investigated in saturated, bare and biofilm (pseudomonas putida) coated sand packed columns. almost complete retention of zno-nps occurred in bare and biofilm coated sand when the influent solution ph was 9 and the ionic strength (is) was 0.1 or 10 mm nacl, and the retention profiles were always hyper-exponential. increasing the solution is and biofilm coating produced enhanced r ...201626741396
insights into the stereospecificity of the d-specific dehalogenase from rhizobium sp. rc1 toward d- and l-2-chloropropionate.halogenated compounds are recalcitrant environmental pollutants prevalent in agricultural fields, waste waters and industrial by-products, but they can be degraded by dehalogenase-containing microbes. notably, 2-haloalkanoic acid dehalogenases are employed to resolve optically active chloropropionates, as exemplified by the d-specific dehalogenase from rhizobium sp. rci (dehd), which acts on d-2-chloropropionate but not on its l-enantiomer. the catalytic residues of this dehalogenase responsible ...201426740767
influence of ni(2+) on urease activity produced by biofilms of arthrobacter oxydans 1388.new tio2-based hybrid materials composed of an organic polymer, cellulose acetate butyrate and copolymer of acrylonitrile acrylamide (an + aa) were prepared. the effectiveness of immobilization of microbial strain arthrobacter oxydans 1388 on the newly synthesized hybrid membranes was investigated by biochemical methods. the obtained results revealed that the matrix more suitable for biofilm formation was composed of organic polymers without a metal component in the membrane composition. the inf ...201426740756
uptake and trans-membrane transport of petroleum hydrocarbons by microorganisms.petroleum-based products are a primary energy source in the industry and daily life. during the exploration, processing, transport and storage of petroleum and petroleum products, water or soil pollution occurs regularly. biodegradation of the hydrocarbon pollutants by indigenous microorganisms is one of the primary mechanisms of removal of petroleum compounds from the environment. however, the physical contact between microorganisms and hydrophobic hydrocarbons limits the biodegradation rate. t ...201426740752
systems biology of microbial exopolysaccharides production.exopolysaccharides (epss) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial epss find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. epss ...201526734603
endophytic cultivable bacteria of the metal bioaccumulator spartina maritima improve plant growth but not metal uptake in polluted marshes soils.endophytic bacterial population was isolated from spartina maritima tissues, a heavy metal bioaccumulator cordgrass growing in the estuaries of tinto, odiel, and piedras river (south west spain), one of the most polluted areas in the world. strains were identified and ability to tolerate salt and heavy metals along with plant growth promoting and enzymatic properties were analyzed. a high proportion of these bacteria were resistant toward one or several heavy metals and metalloids including as, ...201526733985
year-long metagenomic study of river microbiomes across land use and water quality.select bacteria, such as escherichia coli or coliforms, have been widely used as sentinels of low water quality; however, there are concerns regarding their predictive accuracy for the protection of human and environmental health. to develop improved monitoring systems, a greater understanding of bacterial community structure, function, and variability across time is required in the context of different pollution types, such as agricultural and urban contamination. here, we present a year-long s ...201526733955
metabolic engineering and comparative performance studies of synechocystis sp. pcc 6803 strains for effective utilization of xylose.wood sugars such as xylose can be used as an inexpensive carbon source for biotechnological applications. the model cyanobacterium synechocystis sp. pcc 6803 lacks the ability to catabolize wood sugars as an energy source. here, we generated four synechocystis strains that heterologously expressed xylab enzymes, which mediate xylose catabolism, either in combination with or without one of three xylose transporters, namely xyle, galp, or glf. except for glf, which is derived from the bacterium zy ...201526732758
efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner.the total number of known three-dimensional protein structures is rapidly increasing. consequently, the need for fast structural search against complete databases without a significant loss of accuracy is increasingly demanding. recently, topsearch, an ultra-fast method for finding rigid structural relationships between a query structure and the complete protein data bank (pdb), at the multi-chain level, has been released. however, comparable accurate flexible structural aligners to perform effi ...201626732380
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