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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
biotechnological production of limonene in microorganisms.this mini review describes novel, biotechnology-based, ways of producing the monoterpene limonene. limonene is applied in relatively highly priced products, such as fragrances, and also has applications with lower value but large production volume, such as biomaterials. limonene is currently produced as a side product from the citrus juice industry, but the availability and quality are fluctuating and may be insufficient for novel bulk applications. therefore, complementary microbial production ...201626915992
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
detection of substrate-dependent conformational changes in the p450 fold by nuclear magnetic resonance.cytochrome p450 monooxygenases typically catalyze the insertion of one atom of oxygen from o2 into unactivated carbon-hydrogen and carbon-carbon bonds, with concomitant reduction of the other oxygen atom to h2o by nad(p)h. comparison of the average structures of the camphor hydroxylase cytochrome p450(cam) (cyp101) obtained from residual dipolar coupling (rdc)-restrained molecular dynamics (md) in the presence and absence of substrate camphor shows structural displacements resulting from the ess ...201626911901
characterization of triclosan metabolism in sphingomonas sp. strain yl-jm2c.triclosan (tcs) is one of the most widespread emerging contaminants and has adverse impact on aquatic ecosystem, yet little is known about its complete biodegradation mechanism in bacteria. sphingomonas sp, strain yl-jm2c, isolated from activated sludge of a wastewater treatment plant, was very effective on degrading tcs. response surface methodology (rsm) was applied to optimize the conditions like temperature and ph. from rsm, the optimal tcs degradation conditions were found to be 30 °c and p ...201626912101
biochar treatment resulted in a combined effect on soybean growth promotion and a shift in plant growth promoting rhizobacteria.the application of biochar to soil is considered to have the potential for long-term soil carbon sequestration, as well as for improving plant growth and suppressing soil pathogens. in our study we evaluated the effect of biochar on the plant growth of soybeans, as well as on the community composition of root-associated bacteria with plant growth promoting traits. two types of biochar, namely, maize biochar (mbc), wood biochar (wbc), and hydrochar (htc) were used for pot experiments to monitor p ...201626941730
metabolic inhibition of meloxicam by specific cyp2c9 inhibitors in cunninghamella blakesleeana ncim 687: in silico and in vitro studies.specific inhibitors of cytochrome p4502c9 enzyme (cyp2c9) viz. clopidogrel, fenofibrate fluvoxamine and sertraline at concentration of 50, 100, 150 and 200 µm were employed to investigate the nature of enzyme involved in bioconversion of meloxicam to its main metabolite 5-oh methyl meloxicam by cunninghamella blakesleeana. virtual screening for interaction of specific cyp2c9 inhibitors with human cyp2c9 enzyme was performed by molecular docking using auto dock vina 4.2 version. the in silico stu ...201627026863
unravelling potential virulence factor candidates in xanthomonas citri. subsp. citri by secretome analysis.citrus canker is a major disease affecting citrus production in brazil. it's mainly caused by xanthomonas citri subsp. citri strain 306 pathotype a (xac). we analysed the differential expression of proteins secreted by wild type xac and an asymptomatic mutant for hrpb4 (δhrpb4) grown in nutrient broth (nb) and a medium mimicking growth conditions in the plant (xam1). this allowed the identification of 55 secreted proteins, of which 37 were secreted by both strains when cultured in xam1. in this ...201626925342
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
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
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
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
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
facilitation of co-metabolic transformation and degradation of monochlorophenols by pseudomonas sp. cf600 and changes in its fatty acid composition.in this study, co-metabolic degradation of monochlorophenols (2-cp, 3-cp, and 4-cp) by the pseudomonas sp. cf600 strain in the presence of phenol, sodium benzoate, and 4-hydroxybenzoic acid as an additional carbon source as well as the survival of bacteria were investigated. moreover, the changes in cellular fatty acid profiles of bacteria depending on co-metabolic conditions were analyzed. it was found that bacteria were capable of degrading 4-cp completely in the presence of phenol, and in the ...201626917860
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
stability of the graa antitoxin depends on growth phase, atp level, and global regulator mext.bacterial type ii toxin-antitoxin systems consist of a potentially poisonous toxin and an antitoxin that inactivates the toxic protein by binding to it. most of the toxins regulate stress survival, but their activation depends on the stability of the antitoxin that has to be degraded in order for the toxin to be able to attack its cellular targets. the degradation of antitoxins is usually rapid and carried out by atp-dependent protease lon or clp, which is activated under stress conditions. the ...201626668267
synthesis and evaluation of mannitol-based inhibitors for lipopolysaccharide biosynthesis.antibiotic resistance is a serious threat against humankind and the need for new therapeutics is crucial. without working antibiotics, diseases that we thought were extinct will come back. in this paper two new mannitol bisphosphate analogs, 1,6-dideoxy-1,6-diphosphoramidate mannitol and 1,6-dideoxy-1,6-dimethansulfonamide mannitol, have been synthesized and evaluated as potential inhibitors of the enzyme gmhb in the biosynthesis of lipopolysaccharides. 1,6-dideoxy-1,6-diphosphoramidate mannitol ...201626981280
novel rhizosphere soil alleles for the enzyme 1-aminocyclopropane-1-carboxylate deaminase queried for function with an in vivo competition assay.metagenomes derived from environmental microbiota encode a vast diversity of protein homologs. how this diversity impacts protein function can be explored through selection assays aimed to optimize function. while artificially generated gene sequence pools are typically used in selection assays, their usage may be limited because of technical or ethical reasons. here, we investigate an alternative strategy, the use of soil microbial dna as a starting point. we demonstrate this approach by optimi ...201626637602
a 2-hydroxypyridine catabolism pathway in rhodococcus rhodochrous strain py11.rhodococcus rhodochrous py11 (dsm 101666) is able to use 2-hydroxypyridine as a sole source of carbon and energy. by investigating a gene cluster (hpo) from this bacterium, we were able to reconstruct the catabolic pathway of 2-hydroxypyridine degradation. here, we report that in rhodococcus rhodochrous py11, the initial hydroxylation of 2-hydroxypyridine is catalyzed by a four-component dioxygenase (hpobcdf). a product of the dioxygenase reaction (3,6-dihydroxy-1,2,3,6-tetrahydropyridin-2-one) ...201626655765
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
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
hexr controls glucose-responsive genes and central carbon metabolism in neisseria meningitidis.neisseria meningitidis, an exclusively human pathogen and the leading cause of bacterial meningitis, must adapt to different host niches during human infection. n. meningitidis can utilize a restricted range of carbon sources, including lactate, glucose, and pyruvate, whose concentrations vary in host niches. microarray analysis of n. meningitidis grown in a chemically defined medium in the presence or absence of glucose allowed us to identify genes regulated by carbon source availability. most ...201626644430
characterization of a carbapenem-hydrolyzing enzyme, poxb, in pseudomonas aeruginosa pao1.pseudomonas aeruginosa is an opportunistic pathogen often associated with severe and life-threatening infections that are highly impervious to treatment. this microbe readily exhibits intrinsic and acquired resistance to varied antimicrobial drugs. resistance to penicillin-like compounds is commonplace and provided by the chromosomal ampc β-lactamase. a second, chromosomally encoded β-lactamase, poxb, has previously been reported in p. aeruginosa. in the present work, the contribution of this cl ...201626621621
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
epidemiologic and genotypic review of carbapenemase-producing organisms in british columbia, canada, between 2008 and 2014.carbapenemase-producing organisms (cpos) are a serious emerging problem for health care facilities worldwide. owing to their resistance to most antimicrobial therapies, cpos are difficult to treat and pose a challenge for infection prevention and control. since 2010, lab-based surveillance for cpos and pcr-based testing were implemented in british columbia (bc), canada. a review of cpos in bc from 2008 to march 2014 was done to characterize the resistance mechanisms and possible clonal strain tr ...201626607987
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 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
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
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
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
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
mvat family proteins encoded on incp-7 plasmid pcar1 and the host chromosome regulate the host transcriptome cooperatively but differently.mvat proteins are members of the h-ns family of proteins in pseudomonads. the incp-7 conjugative plasmid pcar1 carries an mvat-homologous gene, pmr. in pseudomonas putida kt2440 bearing pcar1, pmr and the chromosomally carried homologous genes, tura and turb, are transcribed at high levels, and pmr interacts with tura and turb in vitro. in the present study, we clarified how the three mvat proteins regulate the transcriptome of p. putida kt2440(pcar1). analyses performed by a modified chromatin ...201626590283
isolation of polyvalent bacteriophages by sequential multiple-host approaches.many studies on phage biology are based on isolation methods that may inadvertently select for narrow-host-range phages. consequently, broad-host-range phages, whose ecological significance is largely unexplored, are consistently overlooked. to enhance research on such polyvalent phages, we developed two sequential multihost isolation methods and tested both culture-dependent and culture-independent phage libraries for broad infectivity. lytic phages isolated from activated sludge were capable o ...201626590277
bromochloromethane, a methane analogue, affects the microbiota and metabolic profiles of the rat gastrointestinal tract.bromochloromethane (bcm), an inhibitor of methanogenesis, has been used in animal production. however, little is known about its impact on the intestinal microbiota and metabolic patterns. the present study aimed to investigate the effect of bcm on the colonic bacterial community and metabolism by establishing a wistar rat model. twenty male wistar rats were randomly divided into two groups (control and treated with bcm) and raised for 6 weeks. bacterial fermentation products in the cecum were d ...201626567308
substrate and cofactor range differences of two cysteine dioxygenases from ralstonia eutropha h16.cysteine dioxygenases (cdos), which catalyze the sulfoxidation of cysteine to cysteine sulfinic acid (csa), have been extensively studied in eukaryotes because of their roles in several diseases. in contrast, only a few prokaryotic enzymes of this type have been investigated. in ralstonia eutropha h16, two cdo homologues (cdoa and cdob) have been identified previously. in vivo studies showed that escherichia coli cells expressing cdoa could convert 3-mercaptopropionate (3mp) to 3-sulfinopropiona ...201626590284
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
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
highly active and stable large catalase isolated from a hydrocarbon degrading aspergillus terreus mtcc 6324.a hydrocarbon degrading aspergillus terreus mtcc 6324 produces a high level of extremely active and stable cellular large catalase (cat) during growth on n-hexadecane to combat the oxidative stress caused by the hydrocarbon degrading metabolic machinery inside the cell. a 160-fold purification with specific activity of around 66 × 10(5) u mg(-1) protein was achieved. the native protein molecular mass was 368 ± 5 kda with subunit molecular mass of nearly 90 kda, which indicates that the native ca ...201627057351
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
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
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
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
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
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
going beyond the control of quorum-sensing to combat biofilm infections.most bacteria attach to surfaces where they form a biofilm, cells embedded in a complex matrix of polymers. cells in biofilms are much better protected against noxious agents than free-living cells. as a consequence it is very difficult to control pathogens with antibiotics in biofilm infections and novel targets are urgently needed. one approach aims at the communication between cells to form and to maintain a biofilm, a process called quorum-sensing. water soluble small-sized molecules mediate ...201627025518
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
identification of genes conferring tolerance to lignocellulose-derived inhibitors by functional selections in soil metagenomes.the production of fuels or chemicals from lignocellulose currently requires thermochemical pretreatment to release fermentable sugars. these harsh conditions also generate numerous small-molecule inhibitors of microbial growth and fermentation, limiting production. we applied small-insert functional metagenomic selections to discover genes that confer microbial tolerance to these inhibitors, identifying both individual genes and general biological processes associated with tolerance to multiple ...201626546427
characterization of the vibrio fischeri fatty acid chemoreceptors, vfcb and vfcb2.bacteria use a wide variety of methyl-accepting chemotaxis proteins (mcps) to mediate their attraction to or repulsion from different chemical signals in their environment. the bioluminescent marine bacterium vibrio fischeri is the monospecific symbiont of the hawaiian bobtail squid, euprymna scolopes, and encodes a large repertoire of mcps that are hypothesized to be used during different parts of its complex, multistage lifestyle. here, we report the initial characterization of two such mcps f ...201626567312
understanding butanol tolerance and assimilation in pseudomonas putida bird-1: an integrated omics approach.pseudomonas putida bird-1 has the potential to be used for the industrial production of butanol due to its solvent tolerance and ability to metabolize low-cost compounds. however, the strain has two major limitations: it assimilates butanol as sole carbon source and butanol concentrations above 1% (v/v) are toxic. with the aim of facilitating bird-1 strain design for industrial use, a genome-wide mini-tn5 transposon mutant library was screened for clones exhibiting increased butanol sensitivity ...201626986205
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
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
the cytochrome p450 cyp6p4 is responsible for the high pyrethroid resistance in knockdown resistance-free anopheles arabiensis.pyrethroid insecticides are the front line vector control tools used in bed nets to reduce malaria transmission and its burden. however, resistance in major vectors such as anopheles arabiensis is posing a serious challenge to the success of malaria control. herein, we elucidated the molecular and biochemical basis of pyrethroid resistance in a knockdown resistance-free anopheles arabiensis population from chad, central africa. using heterologous expression of p450s in escherichia coli coupled w ...201626548743
molecular insights into toluene sensing in the tods/todt signal transduction system.tods is a sensor kinase that responds to various monoaromatic compounds, which either cause an agonistic or antagonistic effect on phosphorylation of its cognate response regulator todt, and controls tod operon expression in pseudomonas putida strains. we describe a molecular sensing mechanism of tods that is activated in response to toluene. the crystal structures of the tods per-arnt-sim (pas) 1 sensor domain (residues 43-164) and its complex with toluene (agonist) or 1,2,4-trimethylbenzene (a ...201626903514
occurrence, diversity and community structure of culturable atrazine degraders in industrial and agricultural soils exposed to the herbicide in shandong province, p.r. china.soil populations of bacteria rapidly degrading atrazine are critical to the environmental fate of the herbicide. an enrichment bias from the routine isolation procedure prevents studying the diversity of atrazine degraders. in the present work, we analyzed the occurrence, diversity and community structure of soil atrazine-degrading bacteria based on their direct isolation.201627821056
species diversity of environmental gim-1-producing bacteria collected during a long-term outbreak.reports of outbreaks concerning carbapenemase-producing gram-negative bacteria in which the main source of transmission is the hospital environment are increasing. this study describes the results of environmental sampling in a protracted polyspecies metallo-beta-lactamase gim-1 outbreak driven by plasmids and bacterial clones of enterobacter cloacae and pseudomonas aeruginosa in a tertiary care center. environmental sampling targeting wet locations (especially sinks) was carried out on a surgic ...201627060121
triton hodge test: improved protocol for modified hodge test for enhanced detection of ndm and other carbapenemase producers.accurate detection of carbapenemase-producing gram-negative bacilli is of utmost importance for the control of nosocomial spread and the initiation of appropriate antimicrobial therapy. the modified hodge test (mht), a carbapenem inactivation assay, has shown poor sensitivity in detecting the worldwide spread of new delhi metallo-β-lactamase (ndm). recent studies demonstrated that ndm is a lipoprotein anchored to the outer membrane in gram-negative bacteria, unlike all other known carbapenemases ...201626719442
resource recovery from wastewater by biological technologies: opportunities, challenges, and prospects.limits in resource availability are driving a change in current societal production systems, changing the focus from residues treatment, such as wastewater treatment, toward resource recovery. biotechnological processes offer an economic and versatile way to concentrate and transform resources from waste/wastewater into valuable products, which is a prerequisite for the technological development of a cradle-to-cradle bio-based economy. this review identifies emerging technologies that enable res ...201628111567
resource recovery from wastewater by biological technologies: opportunities, challenges, and prospects.limits in resource availability are driving a change in current societal production systems, changing the focus from residues treatment, such as wastewater treatment, toward resource recovery. biotechnological processes offer an economic and versatile way to concentrate and transform resources from waste/wastewater into valuable products, which is a prerequisite for the technological development of a cradle-to-cradle bio-based economy. this review identifies emerging technologies that enable res ...201628111567
disruption of the microbiota across multiple body sites in critically ill children.despite intense interest in the links between the microbiome and human health, little has been written about dysbiosis among icu patients. we characterized microbial diversity in samples from 37 children in a pediatric icu (picu). standard measures of alpha and beta diversity were calculated, and results were compared with data from adult and pediatric reference datasets.201628034303
a halotolerant bacterium bacillus licheniformis hsw-16 augments induced systemic tolerance to salt stress in wheat plant (triticum aestivum).certain plant growth promoting bacteria can protect associated plants from harmful effects of salinity. we report the isolation and characterization of 1-aminocyclopropane-1-carboxylic acid (acc) deaminase bacterium bacillus licheniformis hsw-16 capable of ameliorating salt (nacl) stress in wheat plants. the bacterium was isolated from the water of sambhar salt lake, rajasthan, india. the presence of acc deaminase activity was confirmed by enzyme assay and analysis of acds gene, a structural gen ...201628018415
phenotypic and molecular detection of the bla kpc gene in clinical isolates from inpatients at hospitals in são luis, ma, brazil.bacteria that produce klebsiella pneumoniae carbapenemases (kpcs) are resistant to broad-spectrum β-lactam antibiotics. the objective of this study was to phenotypically and genotypically characterize the antibiotic susceptibility to carbapenems of 297 isolates recovered from clinical samples obtained from inpatients at 16 hospitals in são luis (maranhão, brazil).201627927163
a dna-based real-time pcr assay for robust growth quantification of the bacterial pathogen pseudomonas syringae on arabidopsis thaliana.the interaction of pseudomonas syringae with arabidopsis is one of the most commonly used systems to study various bacterial-host interrelationships. currently, most studies are based on the growth quantification of the pathogen to characterize resistance or virulence targets. however, the standard available method for determining bacterial proliferation in planta is laborious and has several limitations.201627895701
the systematic investigation of the quorum sensing system of the biocontrol strain pseudomonas chlororaphis subsp. aurantiaca pb-st2 unveils auri to be a biosynthetic origin for 3-oxo-homoserine lactones.the shoot endophytic biocontrol strain pseudomonas chlororaphis subsp. aurantiaca pb-st2 produces a wide range of exoproducts, including enzymes and antibiotics. the production of exoproducts is commonly tightly regulated. in order to get a deeper insight into the regulatory network of pb-st2, the strain was systematically investigated regarding its quorum sensing systems, both on the genetic and metabolic level. the genome analysis of pb-st2 revealed the presence of four putative acyl homoserin ...201627861617
transcriptional responses of the bacterium burkholderia terrae bs001 to the fungal host lyophyllum sp. strain karsten under soil-mimicking conditions.in this study, the mycosphere isolate burkholderia terrae bs001 was confronted with the soil fungus lyophyllum sp. strain karsten on soil extract agar plates in order to examine its transcriptional responses over time. at the initial stages of the experiment (t1-day 3; t2-day 5), contact between both partner organisms was absent, whereas in the final stage (t3-day 8), the two populations made intimate physical contact. overall, a strong modulation of the strain bs001 gene expression patterns was ...201627844108
transcriptional responses of the bacterium burkholderia terrae bs001 to the fungal host lyophyllum sp. strain karsten under soil-mimicking conditions.in this study, the mycosphere isolate burkholderia terrae bs001 was confronted with the soil fungus lyophyllum sp. strain karsten on soil extract agar plates in order to examine its transcriptional responses over time. at the initial stages of the experiment (t1-day 3; t2-day 5), contact between both partner organisms was absent, whereas in the final stage (t3-day 8), the two populations made intimate physical contact. overall, a strong modulation of the strain bs001 gene expression patterns was ...201627844108
mycelia as a focal point for horizontal gene transfer among soil bacteria.horizontal gene transfer (hgt) is a main mechanism of bacterial evolution endowing bacteria with new genetic traits. the transfer of mobile genetic elements such as plasmids (conjugation) requires the close proximity of cells. hgt between genetically distinct bacteria largely depends on cell movement in water films, which are typically discontinuous in natural systems like soil. using laboratory microcosms, a bacterial reporter system and flow cytometry, we here investigated if and to which degr ...201627811990
the genome of the toluene-degrading pseudomonas veronii strain 1ydbtex2 and its differential gene expression in contaminated sand.the natural restoration of soils polluted by aromatic hydrocarbons such as benzene, toluene, ethylbenzene and m- and p-xylene (btex) may be accelerated by inoculation of specific biodegraders (bioaugmentation). bioaugmentation mainly involves introducing bacteria that deploy their metabolic properties and adaptation potential to survive and propagate in the contaminated environment by degrading the pollutant. in order to better understand the adaptive response of cells during a transition to con ...201627812150
draft genome sequences of four achromobacter ruhlandii strains isolated from cystic fibrosis patients.achromobacter species are being increasingly isolated from the respiratory tract of cystic fibrosis patients. recent reports indicate that achromobacter ruhlandii is a potential human pathogen in cystic fibrosis-related infections. here we report the draft genome of four a. ruhlandii strains isolated from cystic fibrosis patients in brazil. this report describes a. ruhlandii as a potential opportunistic pathogen in cystic fibrosis and provides a framework to for additional enquires into potentia ...201627812598
biofilm as a production platform for heterologous production of rhamnolipids by the non-pathogenic strain pseudomonas putida kt2440.although a transition toward sustainable production of chemicals is needed, the physiochemical properties of certain biochemicals such as biosurfactants make them challenging to produce in conventional bioreactor systems. alternative production platforms such as surface-attached biofilm populations could potentially overcome these challenges. rhamnolipids are a group of biosurfactants highly relevant for industrial applications. however, they are mainly produced by the opportunistic pathogen pse ...201627776509
biotransformation of ferulic acid to vanillin in the packed bed-stirred fermentors.we performed the biotransformation of ferulic acid to vanillin using bacillus subtilis (b. subtilis) in the stirring packed-bed reactors filled with carbon fiber textiles (cft). scanning electron microscope (sem), hplc, qrt-pcr and atp assay indicated that vanillin biotransformation is tightly related to cell growth, cellar activity and the extent of biofilm formation. the biotransformation was affected by hydraulic retention time (hrt), temperature, initial ph, stirring speed and ferulic acid c ...201627708366
bacterial selection for biological control of plant disease: criterion determination and validation.this study aimed to evaluate the biocontrol potential of bacteria isolated from different plant species and soils. the production of compounds related to phytopathogen biocontrol and/or promotion of plant growth in bacterial isolates was evaluated by measuring the production of antimicrobial compounds (ammonia and antibiosis) and hydrolytic enzymes (amylases, lipases, proteases, and chitinases) and phosphate solubilization. of the 1219 bacterial isolates, 92% produced one or more of the eight co ...201627765523
bacterial selection for biological control of plant disease: criterion determination and validation.this study aimed to evaluate the biocontrol potential of bacteria isolated from different plant species and soils. the production of compounds related to phytopathogen biocontrol and/or promotion of plant growth in bacterial isolates was evaluated by measuring the production of antimicrobial compounds (ammonia and antibiosis) and hydrolytic enzymes (amylases, lipases, proteases, and chitinases) and phosphate solubilization. of the 1219 bacterial isolates, 92% produced one or more of the eight co ...201627765523
pseudomonas fluorescens f113 can produce a second flagellar apparatus, which is important for plant root colonization.the genomic sequence of pseudomonas fluorescens f113 has shown the presence of a 41 kb cluster of genes that encode the production of a second flagellar apparatus. among 2,535 pseudomonads strains with sequenced genomes, these genes are only present in the genomes of f113 and other six strains, all but one belonging to the p. fluorescens cluster of species, in the form of a genetic island. the genes are homologous to the flagellar genes of the soil bacterium azotobacter vinelandii. regulation of ...201627713729
complex interplay between fleq, cyclic diguanylate and multiple σ factors coordinately regulates flagellar motility and biofilm development in pseudomonas putida.most bacteria alternate between a free living planktonic lifestyle and the formation of structured surface-associated communities named biofilms. the transition between these two lifestyles requires a precise and timely regulation of the factors involved in each of the stages that has been likened to a developmental process. here we characterize the involvement of the transcriptional regulator fleq and the second messenger cyclic diguanylate in the coordinate regulation of multiple functions rel ...201627636892
a highly efficient sorbitol dehydrogenase from gluconobacter oxydans g624 and improvement of its stability through immobilization.a sorbitol dehydrogenase (gosldh) from gluconobacter oxydans g624 (g. oxydans g624) was expressed in escherichia coli bl21(de3)-codonplus ril. the complete 1455-bp codon-optimized gene was amplified, expressed, and thoroughly characterized for the first time. gosldh exhibited km and kcat values of 38.9 mm and 3820 s(-1) toward l-sorbitol, respectively. the enzyme exhibited high preference for nadp(+) (vs. only 2.5% relative activity with nad(+)). gosldh sequencing, structure analyses, and bioche ...201627633501
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 ...201627605490
screen of non-annotated small secreted proteins of pseudomonas syringae reveals a virulence factor that inhibits tomato immune proteases.pseudomonas syringae pv. tomato dc3000 (ptodc3000) is an extracellular model plant pathogen, yet its potential to produce secreted effectors that manipulate the apoplast has been under investigated. here we identified 131 candidate small, secreted, non-annotated proteins from the ptodc3000 genome, most of which are common to pseudomonas species and potentially expressed during apoplastic colonization. we produced 43 of these proteins through a custom-made gateway-compatible expression system for ...201627603016
high quality draft genome sequences of pseudomonas fulva dsm 17717(t), pseudomonas parafulva dsm 17004(t) and pseudomonas cremoricolorata dsm 17059(t) type strains.pseudomonas has the highest number of species out of any genus of gram-negative bacteria and is phylogenetically divided into several groups. the pseudomonas putida phylogenetic branch includes at least 13 species of environmental and industrial interest, plant-associated bacteria, insect pathogens, and even some members that have been found in clinical specimens. in the context of the genomic encyclopedia of bacteria and archaea project, we present the permanent, high-quality draft genomes of t ...201627594974
expression, purification and characterization of an endoglucanase from serratia proteamaculans cdbb-1961, isolated from the gut of dendroctonus adjunctus (coleoptera: scolytinae).serratia proteamaculans cdbb-1961, a gut symbiont from the roundheaded pine beetle dendroctonus adjunctus, displayed strong cellulolytic activity on agar-plates with carboxymethyl cellulose (cmc) as carbon source. automatic genome annotation of s. proteamaculans made possible the identification of a single endoglucanase encoding gene, designated spr cel8a. the predicted protein, named spr cel8a shows high similarity (59-94 %) to endo-1,4-β-d-glucanases (ec 3.2.1.4) from the glycoside hydrolase f ...201627576896
fluorescent pseudomonas strains with only few plant-beneficial properties are favored in the maize rhizosphere.plant growth-promoting rhizobacteria (pgpr) enhance plant health and growth using a variety of traits. effective pgpr strains typically exhibit multiple plant-beneficial properties, but whether they are better adapted to the rhizosphere than pgpr strains with fewer plant-beneficial properties is unknown. here, we tested the hypothesis that strains with higher numbers of plant-beneficial properties would be preferentially selected by plant roots. to this end, the co-occurrence of 18 properties in ...201627610110
high quality draft genome sequence of the type strain of pseudomonas lutea ok2(t), a phosphate-solubilizing rhizospheric bacterium.pseudomonas lutea ok2(t) (=lmg 21974(t), cect 5822(t)) is the type strain of the species and was isolated from the rhizosphere of grass growing in spain in 2003 based on its phosphate-solubilizing capacity. in order to identify the functional significance of phosphate solubilization in pseudomonas plant growth promoting rhizobacteria, we describe here the phenotypic characteristics of strain ok2(t) along with its high-quality draft genome sequence, its annotation, and analysis. the genome is com ...201627555890
molecular cloning and functional expression of a δ9- fatty acid desaturase from an antarctic pseudomonas sp. a3.fatty acid desaturase enzymes play an essential role in the synthesis of unsaturated fatty acids. pseudomonas sp. a3 was found to produce a large amount of palmitoleic and oleic acids after incubation at low temperatures. using polymerase chain reaction (pcr), a novel δ9- fatty acid desaturase gene was isolated, cloned, and successfully expressed in escherichia coli. the gene was designated as pa3fad9 and has an open reading frame of 1,185 bp which codes for 394 amino acids with a predicted mole ...201627494717
a luxr homolog in a cottonwood tree endophyte that activates gene expression in response to a plant signal or specific peptides.homologs of the luxr acyl-homoserine lactone (ahl) quorum-sensing signal receptor are prevalent in proteobacteria isolated from roots of the eastern cottonwood tree, populus deltoides many of these isolates possess an orphan luxr homolog, closely related to oryr from the rice pathogen xanthomonas oryzae oryr does not respond to ahl signals but, instead, responds to an unknown plant compound. we discovered an oryr homolog, pipr, in the cottonwood endophyte pseudomonas sp. strain gm79. the genes a ...201627486195
effect of shear stress on pseudomonas aeruginosa isolated from the cystic fibrosis lung.chronic colonization of the lungs by pseudomonas aeruginosa is one of the major causes of morbidity and mortality in cystic fibrosis (cf) patients. to gain insights into the characteristic biofilm phenotype of p. aeruginosa in the cf lungs, mimicking the cf lung environment is critical. we previously showed that growth of the non-cf-adapted p. aeruginosa pao1 strain in a rotating wall vessel, a device that simulates the low fluid shear (ls) conditions present in the cf lung, leads to the formati ...201627486191
structural and catalytic characterization of a fungal baeyer-villiger monooxygenase.baeyer-villiger monooxygenases (bvmos) are biocatalysts that convert ketones to esters. due to their high regio-, stereo- and enantioselectivity and ability to catalyse these reactions under mild conditions, they have gained interest as alternatives to chemical baeyer-villiger catalysts. despite their widespread occurrence within the fungal kingdom, most of the currently characterized bvmos are from bacterial origin. here we report the catalytic and structural characterization of bvmoafl838 from ...201627472055
pcr-independent detection of bacterial species-specific 16s rrna at 10 fm by a pore-blockage sensor.a pcr-free, optics-free device is used for the detection of escherichia coli (e. coli) 16s rrna at 10 fm, which corresponds to ~100-1000 colony forming units/ml (cfu/ml) depending on cellular rrna levels. the development of a rapid, sensitive, and cost-effective nucleic acid detection platform is sought for the detection of pathogenic microbes in food, water and body fluids. since 16s rrna sequences are species specific and are present at high copy number in viable cells, these nucleic acids off ...201627455337
comparative genomic, proteomic and exoproteomic analyses of three pseudomonas strains reveals novel insights into the phosphorus scavenging capabilities of soil bacteria.bacteria that inhabit the rhizosphere of agricultural crops can have a beneficial effect on crop growth. one such mechanism is the microbial-driven solubilization and remineralization of complex forms of phosphorus (p). it is known that bacteria secrete various phosphatases in response to low p conditions. however, our understanding of their global proteomic response to p stress is limited. here, exoproteomic analysis of pseudomonas putida bird-1 (bird-1), pseudomonas fluorescens sbw25 and pseud ...201627233093
comparative genomic and functional analyses: unearthing the diversity and specificity of nematicidal factors in pseudomonas putida strain 1a00316.we isolated pseudomonas putida (p. putida) strain 1a00316 from antarctica. this bacterium has a high efficiency against meloidogyne incognita (m. incognita) in vitro and under greenhouse conditions. the complete genome of p. putida 1a00316 was sequenced using pacbio single molecule real-time (smrt) technology. a comparative genomic analysis of 16 pseudomonas strains revealed that although p. putida 1a00316 belonged to p. putida, it was phenotypically more similar to nematicidal pseudomonas fluor ...201627384076
source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities.horizontal gene transfer is a fundamental process in bacterial evolution that can accelerate adaptation via the sharing of genes between lineages. conjugative plasmids are the principal genetic elements mediating the horizontal transfer of genes, both within and between bacterial species. in some species, plasmids are unstable and likely to be lost through purifying selection, but when alternative hosts are available, interspecific plasmid transfer could counteract this and maintain access to pl ...201627385827
degradation pathways of 2- and 4-nitrobenzoates in cupriavidus sp. strain st-14 and construction of a recombinant strain, st-14::3nba, capable of degrading 3-nitrobenzoate.strain st-14, characterized as a member of the genus cupriavidus, was capable of utilizing 2- and 4-nitrobenzoates individually as sole sources of carbon and energy. biochemical studies revealed the assimilation of 2- and 4-nitrobenzoates via 3-hydroxyanthranilate and protocatechuate, respectively. screening of a genomic fosmid library of strain st-14 constructed in escherichia coli identified two gene clusters, onb and pob-pca, to be responsible for the complete degradation of 2-nitrobenzoate a ...201627208126
a de-novo genome analysis pipeline (denogap) for large-scale comparative prokaryotic genomics studies.comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. while there are number of excellent tools developed for performing this task, most scale poorly when faced with hundreds of genome sequences, and many require extensive manual curation.201627363390
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 ...201627312589
isolation of bdellovibrio sp. from soil samples in mexico and their potential applications in control of pathogens.in this study, two strains of bdellovibrio were isolated from soil samples using the culture-dependent technique and two members of the family enterobacteriaceae (klebsiella sp. and salmonella sp.) as prey. the bdellovibrio strains were bacteriolytic, plaque-forming, and highly motile gram-negative bacteria. we identified and confirmed the bdellovibrio strains using microscopy, pcr amplification, and sequencing of the 16s rrna gene. they were observed to be different strains based on hit locus a ...201627297185
meta-analysis reveals that the genus pseudomonas can be a better choice of biological control agent against bacterial wilt disease caused by ralstonia solanacearum.biological control agents (bcas) from different microbial taxa are increasingly used to control bacterial wilt caused by ralstonia solanacearum. however, a quantitative research synthesis has not been conducted on the role of bcas in disease suppression. therefore, the present study aimed to meta-analyze the impacts of bcas on both ralstonia wilt disease suppression and plant (host) growth promotion. the analysis showed that the extent of disease suppression by bcas varied widely among studies, ...201627298597
coordinated regulation of species-specific hydroxycinnamic acid degradation and siderophore biosynthesis pathways in agrobacterium fabrum.the rhizosphere-inhabiting species agrobacterium fabrum (genomospecies g8 of the agrobacterium tumefaciens species complex) is known to degrade hydroxycinnamic acids (hcas), especially ferulic acid and p-coumaric acid, via the novel a. fabrum hca degradation pathway. gene expression profiles of a. fabrum strain c58 were investigated in the presence of hcas, using a c58 whole-genome oligoarray. both ferulic acid and p-coumaric acid caused variations in the expression of more than 10% of the c58 g ...201627060117
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