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insights into functional and evolutionary analysis of carbaryl metabolic pathway from pseudomonas sp. strain c5pp.carbaryl (1-naphthyl n-methylcarbamate) is a most widely used carbamate pesticide in the agriculture field. soil isolate, pseudomonas sp. strain c5pp mineralizes carbaryl via 1-naphthol, salicylate and gentisate, however the genetic organization and evolutionary events of acquisition and assembly of pathway have not yet been studied. the draft genome analysis of strain c5pp reveals that the carbaryl catabolic genes are organized into three putative operons, 'upper', 'middle' and 'lower'. the seq ...201627924916
a metabolic widget adjusts the phosphoenolpyruvate-dependent fructose influx in pseudomonas putida.fructose uptake in the soil bacterium pseudomonas putida occurs through a canonical phosphoenolpyruvate (pep)-dependent sugar transport system (pts(fru)). the logic of the genetic circuit that rules its functioning is puzzling: the transcription of the frubka operon, encoding all the components of pts(fru), can escape the repression exerted by the catabolite repressor/activator protein cra solely in the presence of intracellular fructose-1-p, an agonist formed only when fructose has been already ...201627933319
properties of alternative microbial hosts used in synthetic biology: towards the design of a modular chassis.the chassis is the cellular host used as a recipient of engineered biological systems in synthetic biology. they are required to propagate the genetic information and to express the genes encoded in it. despite being an essential element for the appropriate function of genetic circuits, the chassis is rarely considered in their design phase. consequently, the circuits are transferred to model organisms commonly used in the laboratory, such as escherichia coli, that may be suboptimal for a requir ...201627903818
synthesis and functions of jasmonates in maize.of the over 600 oxylipins present in all plants, the phytohormone jasmonic acid (ja) remains the best understood in terms of its biosynthesis, function and signaling. much like their eicosanoid analogues in mammalian system, evidence is growing for the role of the other oxylipins in diverse physiological processes. ja serves as the model plant oxylipin species and regulates defense and development. for several decades, the biology of ja has been characterized in a few dicot species, yet the func ...201627916835
microscope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.the annotation of genomes from ngs platforms needs to be automated and fully integrated. however, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. this shortcoming limits the knowledge that can be extracted from genomes and metabolic models. launched in 2005, the microscope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and ...201627899624
microscope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.the annotation of genomes from ngs platforms needs to be automated and fully integrated. however, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. this shortcoming limits the knowledge that can be extracted from genomes and metabolic models. launched in 2005, the microscope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and ...201627899624
salicylic acid is involved in the basal resistance of tomato plants to citrus exocortis viroid and tomato spotted wilt virus.tomato plants expressing the nahg transgene, which prevents accumulation of endogenous salicylic acid (sa), were used to study the importance of the sa signalling pathway in basal defence against citrus exocortis viroid (cevd) or tomato spotted wilt virus (tswv). the lack of sa accumulation in the cevd- or tswv-infected nahg tomato plants led to an early and dramatic disease phenotype, as compared to that observed in the corresponding parental money maker. addition of acibenzolar-s-methyl, a ben ...201627893781
metabolic engineering of pseudomonas putida kt2440 for the production of para-hydroxy benzoic acid.para-hydroxy benzoic acid (phba) is the key component for preparing parabens, a common preservatives in food, drugs, and personal care products, as well as high-performance bioplastics such as liquid crystal polymers. pseudomonas putida kt2440 was engineered to produce phba from glucose via the shikimate pathway intermediate chorismate. to obtain the phba production strain, chorismate lyase ubic from escherichia coli and a feedback resistant 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase e ...201627965953
multiple and variable nhej-like genes are involved in resistance to dna damage in streptomyces ambofaciens.non-homologous end-joining (nhej) is a double strand break (dsb) repair pathway which does not require any homologous template and can ligate two dna ends together. the basic bacterial nhej machinery involves two partners: the ku protein, a dna end binding protein for dsb recognition and the multifunctional ligd protein composed a ligase, a nuclease and a polymerase domain, for end processing and ligation of the broken ends. in silico analyses performed in the 38 sequenced genomes of streptomyce ...201627965636
initiation of chromosomal replication in predatory bacterium bdellovibrio bacteriovorus.bdellovibrio bacteriovorus is a small gram-negative predatory bacterium that attacks other gram-negative bacteria, including many animal, human, and plant pathogens. this bacterium exhibits a peculiar biphasic life cycle during which two different types of cells are produced: non-replicating highly motile cells (the free-living phase) and replicating cells (the intracellular-growth phase). the process of chromosomal replication in b. bacteriovorus must therefore be temporally and spatially regul ...201627965633
whole-genome sequences of two manganese(ii)-oxidizing bacteria, bosea sp. strain biwako-01 and alphaproteobacterium strain u9-1i.this report describes the whole-genome sequences of two mn(ii)-oxidizing bacteria, filamentous mn oxide microparticle-forming bosea sp. strain biwako-01 and alphaproteobacterium strain u9-1i.201627881541
enhancing poly(3-hydroxyalkanoate) production in escherichia coli by the removal of the regulatory gene arca.recombinant escherichia coli is a desirable platform for the production of many biological compounds including poly(3-hydroxyalkanoates), a class of naturally occurring biodegradable polyesters with promising biomedical and material applications. although the controlled production of desirable polymers is possible with the utilization of fatty acid feedstocks, a central challenge to this biosynthetic route is the improvement of the relatively low polymer yield, a necessary factor of decreasing t ...201627878786
draft genome sequence of pseudomonas mosselii gil3, isolated from catfish and antagonistic against hypervirulent aeromonas hydrophila.pseudomonas mosselii gil3 was isolated from a catfish that survived from lethal challenge with hypervirulent aeromonas hydrophila (vah). when assayed in vitro, the bacterium showed antagonism against vah. sequence analysis revealed that the genome of p. mosselii gil3 encodes numerous aromatic metabolism pathways and proteins for biosynthesis of antimicrobial compounds.201627856595
two-step production of phenylpyruvic acid from l-phenylalanine by growing and resting cells of engineered escherichia coli: process optimization and kinetics modeling.phenylpyruvic acid (ppa) is widely used in the pharmaceutical, food, and chemical industries. here, a two-step bioconversion process, involving growing and resting cells, was established to produce ppa from l-phenylalanine using the engineered escherichia coli constructed previously. first, the biotransformation conditions for growing cells were optimized (l-phenylalanine concentration 20.0 g·l-1, temperature 35°c) and a two-stage temperature control strategy (keep 20°c for 12 h and increase the ...201627851793
mutation of the streptococcus gordonii thiol-disulfide oxidoreductase sdba leads to enhanced biofilm formation mediated by the ciarh two-component signaling system.streptococcus gordonii is a commensal inhabitant of human oral biofilms. previously, we identified an enzyme called sdba that played an important role in biofilm formation by s. gordonii. sdba is thiol-disulfide oxidoreductase that catalyzes disulfide bonds in secreted proteins. surprisingly, inactivation of sdba results in enhanced biofilm formation. in this study we investigated the basis for biofilm formation by the δsdba mutant. the results revealed that biofilm formation was mediated by the ...201627846284
adaptive evolution of phosphorus metabolism in prochlorococcus.inorganic phosphorus is scarce in the eastern mediterranean sea, where the high-light-adapted ecotype hli of the marine picocyanobacterium prochlorococcus marinus thrives. physiological and regulatory control of phosphorus acquisition and partitioning has been observed in hli both in culture and in the field; however, the optimization of phosphorus metabolism and associated gains for its phosphorus-limited-growth (plg) phenotype have not been studied. here, we reconstructed a genome-scale metabo ...201627868089
novel culturing techniques select for heterotrophs and hydrocarbon degraders in a subantarctic soil.the soil substrate membrane system (ssms) is a novel micro-culturing technique targeted at terrestrial soil systems. we applied the ssms to pristine and diesel fuel spiked polar soils, along with traditional solid media culturing and culture independent 454 tag pyrosequencing to elucidate the effects of diesel fuel on the soil community. the ssms enriched for up to 76% of the total soil diversity within high diesel fuel concentration soils, in contrast to only 26% of the total diversity for the ...201627827405
draft genome sequence of a multi-metal resistant bacterium pseudomonas putida ath-43 isolated from greenwich island, antarctica. 201627877169
bacterial genome engineering and synthetic biology: combating pathogens.the emergence and prevalence of multidrug resistant (mdr) pathogenic bacteria poses a serious threat to human and animal health globally. nosocomial infections and common ailments such as pneumonia, wound, urinary tract, and bloodstream infections are becoming more challenging to treat due to the rapid spread of mdr pathogenic bacteria. according to recent reports by the world health organization (who) and centers for disease control and prevention (cdc), there is an unprecedented increase in th ...201627814687
lapf and its regulation by fis affect the cell surface hydrophobicity of pseudomonas putida.the ability of bacteria to regulate cell surface hydrophobicity is important for the adaptation to different environmental conditions. the hydrophobicity of cell surface can be determined by several factors, including outer membrane and surface proteins. in this study, we report that an adhesin lapf influences cell surface hydrophobicity of pseudomonas putida. cells lacking lapf are less hydrophobic than wild-type cells in stationary growth phase. moreover, the overexpression of the global regul ...201627812186
partial least squares with structured output for modelling the metabolomics data obtained from complex experimental designs: a study into the y-block coding.partial least squares (pls) is one of the most commonly used supervised modelling approaches for analysing multivariate metabolomics data. pls is typically employed as either a regression model (pls-r) or a classification model (pls-da). however, in metabolomics studies it is common to investigate multiple, potentially interacting, factors simultaneously following a specific experimental design. such data often cannot be considered as a "pure" regression or a classification problem. nevertheless ...201627801817
the bacterial enhancer-dependent rna polymerase.transcription initiation is highly regulated in bacterial cells, allowing adaptive gene regulation in response to environment cues. one class of promoter specificity factor called sigma54 enables such adaptive gene expression through its ability to lock the rna polymerase down into a state unable to melt out promoter dna for transcription initiation. promoter dna opening then occurs through the action of specialized transcription control proteins called bacterial enhancer-binding proteins (bebps ...201627789741
heavy metal pollution from gold mines: environmental effects and bacterial strategies for resistance.mining activities can lead to the generation of large quantities of heavy metal laden wastes which are released in an uncontrolled manner, causing widespread contamination of the ecosystem. though some heavy metals classified as essential are important for normal life physiological processes, higher concentrations above stipulated levels have deleterious effects on human health and biota. bacteria able to withstand high concentrations of these heavy metals are found in the environment as a resul ...201627792205
coconut lethal yellowing diseases: a phytoplasma threat to palms of global economic and social significance.the recent discovery of bogia coconut syndrome in papua new guinea (png) is the first report of a lethal yellowing disease (lyd) in oceania. numerous outbreaks of lyds of coconut have been recorded in the caribbean and africa since the late nineteenth century and have caused the death of millions of palms across several continents during the twentieth century. despite the severity of economic losses, it was only in the 1970s that the causes of lyds were identified as phytoplasmas, a group of ins ...201627833616
synergistic nisin-polymyxin combinations for the control of pseudomonas biofilm formation.the emergence and dissemination of multi-drug resistant pathogens is a global concern. moreover, even greater levels of resistance are conferred on bacteria when in the form of biofilms (i.e., complex, sessile communities of bacteria embedded in an organic polymer matrix). for decades, antimicrobial peptides have been hailed as a potential solution to the paucity of novel antibiotics, either as natural inhibitors that can be used alone or in formulations with synergistically acting antibiotics. ...201627833601
depth and well type related to groundwater microbiological contamination.use of groundwater from private wells in households has increased considerably, owing to a better cost/benefit ratio than that of water provided by local utilities for a fee. however, this water is usually untreated, which makes it a vehicle for diseases. thus, monitoring this water is necessary to ensure its integrity and quality. we aimed to evaluate the physical, chemical, and microbiological parameters of untreated groundwater drawn from different types of wells, and the antimicrobial suscep ...201627775681
draft genome sequence of a pseudomonas sp. strain carrying blaimp-25 and blavim-2 carbapenemase genes from hospital sewage.pseudomonas strain wchp16 recovered from hospital sewage in west china hospital, chengdu, china was found to carry two carbapenemase genes blaimp-25 and blavim-2 here, we report its 5.7-mb draft genome sequence, comprising 141 contigs and an average 59.53% g+c content. the genome contained 5,504 coding sequences and 67 trna genes.201627795238
label-free, rapid and quantitative phenotyping of stress response in e. coli via ramanome.rapid profiling of stress-response at single-cell resolution yet in a label-free, non-disruptive and mechanism-specific manner can lead to many new applications. we propose a single-cell-level biochemical fingerprinting approach named "ramanome", which is the collection of single-cell raman spectra (scrs) from a number of cells randomly selected from an isogenic population at a given time and condition, to rapidly and quantitatively detect and characterize stress responses of cellular population ...201627756907
flhf is required for swarming motility and full pathogenicity of bacillus cereus.besides sporulation, bacillus cereus can undergo a differentiation process in which short swimmer cells become elongated and hyperflagellated swarmer cells that favor migration of the bacterial community on a surface. the functionally enigmatic flagellar protein flhf, which is the third paralog of the signal recognition particle (srp) gtpases ffh and ftsy, is required for swarming in many bacteria. previous data showed that flhf is involved in the control of the number and positioning of flagell ...201627807433
exported epoxide hydrolases modulate erythrocyte vasoactive lipids during plasmodium falciparum infection.erythrocytes are reservoirs of important epoxide-containing lipid signaling molecules, including epoxyeicosatrienoic acids (eets). eets function as vasodilators and anti-inflammatory modulators in the bloodstream. bioactive eets are hydrolyzed to less active diols (dihydroxyeicosatrienoic acids) by epoxide hydrolases (ehs). the malaria parasite plasmodium falciparum infects host red blood cells (rbcs) and exports hundreds of proteins into the rbc compartment. in this study, we show that two para ...201627795395
an apple fruit fermentation (aff) treatment improves the composition of the rhizosphere microbial community and growth of strawberry (fragaria × ananassa duch 'benihoppe') seedlings.plant growth can be promoted by the application of apple fruit fermentation (aff), despite unclear of the underlying mechanisms, the effects involved in aff on rhizosphere microorganisms have been hypothesized. we investigated the consequences of applying aff alone or in combination with bacillus licheniformis to strawberry tissue culture seedlings in vitro, the analyses of denaturing gradient gel electrophoresis (dgge) and 16s rdna were performed to determine aff effects on rhizosphere. moreove ...201627755580
determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering.protein function often depends on global, collective internal motions. however, the simultaneous quantitative experimental determination of the forms, amplitudes, and time scales of these motions has remained elusive. we demonstrate that a complete description of these large-scale dynamic modes can be obtained using coherent neutron-scattering experiments on perdeuterated samples. with this approach, a microscopic relationship between the structure, dynamics, and function in a protein, cytochrom ...201627757419
investigation into the mode of phosphate activation in the 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolase from pseudomonas putida f1.the 4-hydroxy-4-methyl-2-oxoglutarate (hmg)/4-carboxy-4-hydroxy-2-oxoadipate (cha) aldolase is the last enzyme of both the gallate and protocatechuate 4,5-cleavage pathways which links aromatic catabolism to central cellular metabolism. the enzyme is a class ii, divalent metal dependent, aldolase which is activated in the presence of inorganic phosphate (pi), increasing its turnover rate >10-fold. this phosphate activation is unique for a class ii aldolase. the aldolase pyruvate methyl proton ex ...201627741265
flavin-dependent redox transfers by the two-component diketocamphane monooxygenases of camphor-grown pseudomonas putida ncimb 10007.the progressive titres of key monooxygenases and their requisite native donors of reducing power were used to assess the relative contribution of various camphor plasmid (cam plasmid)- and chromosome-coded activities to biodegradation of (rac)-camphor at successive stages throughout growth of pseudomonas putida ncimb 10007 on the bicylic monoterpenoid. a number of different flavin reductases (frs) have the potential to supply reduced flavin mononucleotide to both 2,5- and 3,6-diketocamphane mono ...201627754389
draft genome sequence of the marine rhodobacteraceae strain o3.65, cultivated from oil-polluted seawater of the deepwater horizon oil spill.the marine alphaproteobacterium strain o3.65 was isolated from an enrichment culture of surface seawater contaminated with weathered oil (slicks) from the deepwater horizon (dwh) oil spill and belongs to the ubiquitous, diverse and ecological relevant roseobacter group within the rhodobacteraceae. here, we present a preliminary set of physiological features of strain o3.65 and a description and annotation of its draft genome sequence. based on our data we suggest potential ecological roles of th ...201627777651
cpxr activates mexab-oprm efflux pump expression and enhances antibiotic resistance in both laboratory and clinical nalb-type isolates of pseudomonas aeruginosa.resistance-nodulation-division (rnd) efflux pumps are responsible for multidrug resistance in pseudomonas aeruginosa. in this study, we demonstrate that cpxr, previously identified as a regulator of the cell envelope stress response in escherichia coli, is directly involved in activation of expression of rnd efflux pump mexab-oprm in p. aeruginosa. a conserved cpxr binding site was identified upstream of the mexa promoter in all genome-sequenced p. aeruginosa strains. cpxr is required to enhance ...201627736975
inhibition of xanthomonas fragariae, causative agent of angular leaf spot of strawberry, through iron deprivation.in commercial production settings, few options exist to prevent or treat angular leaf spot (als) of strawberry, a disease of economic importance and caused by the bacterial pathogen xanthomonas fragariae. in the process of isolating and identifying x. fragariae bacteria from symptomatic plants, we observed growth inhibition of x. fragariae by bacterial isolates from the same leaf macerates. identified as species of pseudomonas and rhizobium, these isolates were confirmed to suppress growth of x. ...201627790193
comprehensive genomic and phenotypic metal resistance profile of pseudomonas putida strain s13.1.2 isolated from a vineyard soil.trace metals are required in many cellular processes in bacteria but also induce toxic effects to cells when present in excess. as such, various forms of adaptive responses towards extracellular trace metal ions are essential for the survival and fitness of bacteria in their environment. a soil pseudomonas putida, strain s13.1.2 has been isolated from french vineyard soil samples, and shown to confer resistance to copper ions. further investigation revealed a high capacity to tolerate elevated c ...201627730570
molecular detection of acanthamoeba spp., naegleria fowleri and vermamoeba (hartmannella) vermiformis as vectors for legionella spp. in untreated and solar pasteurized harvested rainwater.legionella spp. employ multiple strategies to adapt to stressful environments including the proliferation in protective biofilms and the ability to form associations with free-living amoeba (fla). the aim of the current study was to identify legionella spp., acanthamoeba spp., vermamoeba (hartmannella) vermiformis and naegleria fowleri that persist in a harvested rainwater and solar pasteurization treatment system.201627724947
highly efficient and stable novel nanobiohybrid catalyst to avert 3,4-dihydroxybenzoic acid pollutant in water.the present study reported for the first time covalent immobilization of protocatechuate 3,4-dioxygenase (3,4-pod) onto functionalized multi-walled carbon nanotubes (f-mwcnt) for degrading the toxic 3,4-dihydroxybenzoic acid (3,4-dhba) pollutant in water. the f-mwcnts had a maximum 3,4-pod loading of 1060 μg/mg. immobilized 3,4 pod had 44% of relative structural changes to its free configurations. nevertheless, >90% of relative activity and about 50% of catalytic efficiency were retained to the ...201627721429
metabolic engineering of corynebacterium glutamicum for enhanced production of 5-aminovaleric acid.5-aminovaleric acid (5ava) is an important five-carbon platform chemical that can be used for the synthesis of polymers and other chemicals of industrial interest. enzymatic conversion of l-lysine to 5ava has been achieved by employing lysine 2-monooxygenase encoded by the davb gene and 5-aminovaleramidase encoded by the dava gene. additionally, a recombinant escherichia coli strain expressing the davb and dava genes has been developed for bioconversion of l-lysine to 5ava. to use glucose and xy ...201627717386
flagellin flic phosphorylation affects type 2 protease secretion and biofilm dispersal in pseudomonas aeruginosa pao1.protein phosphorylation has a major role in controlling the life-cycle and infection stages of bacteria. proteome-wide occurrence of s/t/y phosphorylation has been reported for many prokaryotic systems. previously, we reported the phosphoproteome of pseudomonas aeruginosa and pseudomonas putida. in this study, we show the role of s/t phosphorylation of one motility protein, flic, in regulating multiple surface-associated phenomena of p. aeruginosa pao1. this is the first report of occurrence of ...201627701473
mitochondrial carriers link the catabolism of hydroxyaromatic compounds to the central metabolism in candida parapsilosis.the pathogenic yeast candida parapsilosis metabolizes hydroxyderivatives of benzene and benzoic acid to compounds channeled into central metabolism, including the mitochondrially localized tricarboxylic acid cycle, via the 3-oxoadipate and gentisate pathways. the orchestration of both catabolic pathways with mitochondrial metabolism as well as their evolutionary origin is not fully understood. our results show that the enzymes involved in these two pathways operate in the cytoplasm with the exce ...201627707801
disruption of pseudomonas putida by high pressure homogenization: a comparison of the predictive capacity of three process models for the efficient release of arginine deiminase.disruption of pseudomonas putida kt2440 by high-pressure homogenization in a french press is discussed for the release of arginine deiminase (adi). the enzyme release response of the disruption process was modelled for the experimental factors of biomass concentration in the broth being disrupted, the homogenization pressure and the number of passes of the cell slurry through the homogenizer. for the same data, the response surface method (rsm), the artificial neural network (ann) and the suppor ...201627699703
plant drought tolerance enhancement by trehalose production of desiccation-tolerant microorganisms.a collection of desiccation-tolerant xeroprotectant-producing microorganisms was screened for their ability to protect plants against drought, and their role as plant growth-promoting rhizobacteria was investigated in two different crops (tomato and pepper). the most commonly described biochemical mechanisms for plant protection against drought by microorganisms including the production of phytohormones, antioxidants and xeroprotectants were analyzed. in particular, the degree of plant protectio ...201627746776
harnessing host-vector microbiome for sustainable plant disease management of phloem-limited bacteria.plant health and productivity is strongly influenced by their intimate interaction with deleterious and beneficial organisms, including microbes, and insects. of the various plant diseases, insect-vectored diseases are of particular interest, including those caused by obligate parasites affecting plant phloem such as candidatus (ca.) phytoplasma species and several species of ca. liberibacter. recent studies on plant-microbe and plant-insect interactions of these pathogens have demonstrated that ...201627746788
draft genome sequences of four hospital-associated pseudomonas putida isolates.we present here the draft genome sequences of four pseudomonas putida isolates belonging to a single clone suspected for nosocomial transmission between patients and a bronchoscope in a tertiary hospital. the four genome sequences belong to a single lineage but contain differences in their mobile genetic elements.201627688339
activation of the glutamic acid-dependent acid resistance system in escherichia coli bl21(de3) leads to increase of the fatty acid biotransformation activity.the biosynthesis of carboxylic acids including fatty acids from biomass is central in envisaged biorefinery concepts. the productivities are often, however, low due to product toxicity that hamper whole-cell biocatalyst performance. here, we have investigated factors that influence the tolerance of escherichia coli to medium chain carboxylic acid (i.e., n-heptanoic acid)-induced stress. the metabolic and genomic responses of e. coli bl21(de3) and mg1655 grown in the presence of n-heptanoic acid ...201627681369
structural and histone binding ability characterization of the arb2 domain of a histone deacetylase hda1 from saccharomyces cerevisiae.hda1 is the catalytic core component of the h2b- and h3- specific histone deacetylase (hdac) complex from saccharomyces cerevisiae, which is involved in the epigenetic repression and plays a crucial role in transcriptional regulation and developmental events. though the n-terminal catalytic hdac domain of hda1 is well characterized, the function of the c-terminal arb2 domain remains unknown. in this study, we determine the crystal structure of the arb2 domain from s. cerevisiae hda1 at a resolut ...201627665728
antibiotic resistance of diverse bacteria from aquaculture in borneo.the administration of antimicrobials in aquaculture provides a selective pressure creating a reservoir of multiple resistant bacteria in the cultured fish and shrimps as well as the aquaculture environment. the objective of this study was to determine the extent of antibiotic resistance in aquaculture products and aquaculture's surrounding environment in sarawak, malaysian borneo. ninety-four identified bacterial isolates constituted of 17 genera were isolated from sediment, water, and cultured ...201627746817
transcriptomic analysis of the highly efficient oil-degrading bacterium acinetobacter venetianus rag-1 reveals genes important in dodecane uptake and utilization.the hydrocarbonoclastic bacterium acinetobacter venetianus rag-1 has attracted substantial attention due to its powerful oil-degrading capabilities and its potential to play an important ecological role in the cleanup of alkanes. in this study, we compare the transcriptome of the strain rag-1 grown in dodecane, the corresponding alkanol (dodecanol), and sodium acetate for the characterization of genes involved in dodecane uptake and utilization. comparison of the transcriptional responses of rag ...201627664055
biosynthesis of catechol melanin from glycerol employing metabolically engineered escherichia coli.melanins comprise a chemically-diverse group of polymeric pigments whose function is related to protection against physical and chemical stress factors. these polymers have current and potential applications in the chemical, medical, electronics and materials industries. the biotechnological production of melanins offers the possibility of obtaining these pigments in pure form and relatively low cost. in this study, escherichia coli strains were engineered to evaluate the production of melanin f ...201627659593
draft genome sequence of a diazotrophic, plant growth-promoting rhizobacterium of the pseudomonas syringae complex.we report here the draft genome sequence of pseudomonas syringae gr12-2, a nitrogen-fixing, plant growth-promoting bacterium, isolated from the rhizosphere of an arctic grass. the 6.6-mbp genome contains 5,676 protein-coding genes, including a nitrogen-fixation island similar to that in p. stutzeri.201627660794
identification and characterization of an aeromonas hydrophila oligopeptidase gene pepf negatively related to biofilm formation.bacterial biofilms are involved in adaptation to complex environments and are responsible for persistent bacterial infections. biofilm formation is a highly complex process during which multifarious genes work together regularly. in this study, we screened the ez-tn5 transposon mutant library to identify genes involved in biofilm formation of aeromonas hydrophila. a total of 24 biofilm-associated genes were identified, the majority of which encoded proteins related to cell structure, transcripti ...201627713736
identification of gefitinib off-targets using a structure-based systems biology approach; their validation with reverse docking and retrospective data mining.gefitinib, an egfr tyrosine kinase inhibitor, is used as fda approved drug in breast cancer and non-small cell lung cancer treatment. however, this drug has certain side effects and complications for which the underlying molecular mechanisms are not well understood. by systems biology based in silico analysis, we identified off-targets of gefitinib that might explain side effects of this drugs. the crystal structure of egfr-gefitinib complex was used for binding pocket similarity searches on a d ...201627653775
structure and catalytic mechanism of monodehydroascorbate reductase, mdhar, from oryza sativa l. japonica.ascorbic acid (asa) maintains redox homeostasis by scavenging reactive oxygen species from prokaryotes to eukaryotes, especially plants. the enzyme monodehydroascorbate reductase (mdhar) regenerates asa by catalysing the reduction of monodehydroascorbate, using nadh or nadph as an electron donor. the detailed recycling mechanism of mdhar remains unclear due to lack of structural information. here, we present the crystal structures of mdhar in the presence of cofactors, nicotinamide adenine dinuc ...201627652777
genome-based genetic tool development for bacillus methanolicus: theta- and rolling circle-replicating plasmids for inducible gene expression and application to methanol-based cadaverine production.bacillus methanolicus is a thermophilic methylotroph able to overproduce amino acids from methanol, a substrate not used for human or animal nutrition. based on our previous rna-seq analysis a mannitol inducible promoter and a putative mannitol activator gene mtlr were identified. the mannitol inducible promoter was applied for controlled gene expression using fluorescent reporter proteins and a flow cytometry analysis, and improved by changing the -35 promoter region and by co-expression of the ...201627713731
engineering of tm1459 from thermotoga maritima for increased oxidative alkene cleavage activity.oxidative cleavage of alkenes is a widely employed process allowing oxyfunctionalization to corresponding carbonyl compounds. recently, a novel biocatalytic oxidative alkene cleavage activity on styrene derivatives was identified in tm1459 from thermotoga maritima. in this work we engineered the enzyme by site-saturation mutagenesis of active site amino acids to increase its activity and to broaden its substrate scope. a high-throughput assay for the detection of the ketone products was successf ...201627713741
triclosan in water, implications for human and environmental health.triclosan (tcs) is a broad spectrum antibacterial agent present as an active ingredient in some personal care products such as soaps, toothpastes and sterilizers. it is an endocrine disrupting compound and its increasing presence in water resources as well as in biosolid-amended soils used in farming, its potential for bioaccumulation in fatty tissues and toxicity in aquatic organisms are a cause for concern to human and environmental health. tcs has also been detected in blood, breast milk, uri ...201627722057
biosynthesis and molecular actions of specialized 1,4-naphthoquinone natural products produced by horticultural plants.the 1,4-naphthoquinones (1,4-nqs) are a diverse group of natural products found in every kingdom of life. plants, including many horticultural species, collectively synthesize hundreds of specialized 1,4-nqs with ecological roles in plant-plant (allelopathy), plant-insect and plant-microbe interactions. numerous horticultural plants producing 1,4-nqs have also served as sources of traditional medicines for hundreds of years. as a result, horticultural species have been at the forefront of many b ...201627688890
physical forces shape group identity of swimming pseudomonas putida cells.the often striking macroscopic patterns developed by motile bacterial populations on agar plates are a consequence of the environmental conditions where the cells grow and spread. parameters such as medium stiffness and nutrient concentration have been reported to alter cell swimming behavior, while mutual interactions among populations shape collective patterns. one commonly observed occurrence is the mutual inhibition of clonal bacteria when moving toward each other, which results in a distinc ...201627695443
cloning, expression, and characterization of a peptidoglycan hydrolase from the burkholderia pseudomallei phage st79.the lytic phage st79 of burkholderia pseudomallei can lyse a broad range of its host including antibiotic resistant isolates from within using a set of proteins, holin, lysb, lysc and endolysin, a peptidoglycan (pg) hydrolase enzyme. the phage st79 endolysin gene identified as peptidase m15a was cloned, expressed and purified to evaluate its potential to lyse pathogenic bacteria. the molecular size of the purified enzyme is approximately 18 kda and the in silico study cited here indicated the pr ...201627637947
fine-tuning of amino sugar homeostasis by eiia(ntr) in salmonella typhimurium.the nitrogen-metabolic phosphotransferase system, pts(ntr), consists of the enzymes i(ntr), npr and iia(ntr) that are encoded by ptsp, ptso, and ptsn, respectively. due to the proximity of ptso and ptsn to rpon, the pts(ntr) system has been postulated to be closely related with nitrogen metabolism. to define the correlation between pts(ntr) and nitrogen metabolism, we performed ligand fishing with eiia(ntr) as a bait and revealed that d-glucosamine-6-phosphate synthase (glms) directly interacted ...201627628932
genomic, transcriptomic and proteomic analysis provide insights into the cold adaptation mechanism of the obligate psychrophilic fungus mrakia psychrophila.mrakia psychrophila is an obligate psychrophilic fungus. the cold adaptation mechanism of psychrophilic fungi remains unknown. comparative genomics analysis indicated that m. psychrophila had a specific codon usage preference, especially for codons of gly and arg and its major facilitator superfamily (mfs) transporter gene family was expanded. transcriptomic analysis revealed that genes involved in ribosome and energy metabolism were upregulated at 4°c, while genes involved in unfolded protein b ...201627633791
saccharomyces cerevisiae metabolism in ecological context.the architecture and regulation of saccharomyces cerevisiae metabolic network are among the best studied owing to its widespread use in both basic research and industry. yet, several recent studies have revealed notable limitations in explaining genotype-metabolic phenotype relations in this yeast, especially when concerning multiple genetic/environmental perturbations. apparently unexpected genotype-phenotype relations may originate in the evolutionarily shaped cellular operating principles bei ...201627634775
systems metabolic engineering of corynebacterium glutamicum for the production of the carbon-5 platform chemicals 5-aminovalerate and glutarate.the steadily growing world population and our ever luxurious life style, along with the simultaneously decreasing fossil resources has confronted modern society with the issue and need of finding renewable routes to accommodate for our demands. shifting the production pipeline from raw oil to biomass requires efficient processes for numerous platform chemicals being produced with high yield, high titer and high productivity.201627618862
architecture of class 1, 2, and 3 integrons from gram negative bacteria recovered among fruits and vegetables.the spread of antibiotic resistant bacteria throughout the food chain constitutes a public health concern. to understand the contribution of fresh produce in shaping antibiotic resistance bacteria and integron prevalence in the food chain, 333 antibiotic resistance gram negative isolates were collected from organic and conventionally produced fruits (pears, apples, and strawberries) and vegetables (lettuces, tomatoes, and carrots). although low levels of resistance have been detected, the bacter ...201627679611
the structure of the periplasmic sensor domain of the histidine kinase cuss shows unusual metal ion coordination at the dimeric interface.in bacteria, two-component systems act as signaling systems to respond to environmental stimuli. two-component systems generally consist of a sensor histidine kinase and a response regulator, which work together through histidyl-aspartyl phosphorelay to result in gene regulation. one of the two-component systems in escherichia coli, cuss-cusr, is known to induce expression of cuscfba genes at increased periplasmic cu(i) and ag(i) concentrations to help maintain metal ion homeostasis. cuss is a m ...201627583660
physiological response of escherichia coli o157:h7 sakai to dynamic changes in temperature and water activity as experienced during carcass chilling.enterohemeorrhagic escherichia coli is a leading cause of foodborne illness, with the majority of cases linked to foods of bovine origin. currently, no completely effective method for controlling this pathogen during carcass processing exists. understanding how this pathogen behaves under those stress conditions experienced on the carcass during chilling in cold air could offer opportunities for development or improvement of effective decontamination processes. therefore, we studied the growth k ...201627615263
occurrence and antimicrobial susceptibility of enteric rods and pseudomonads isolated from the dental prostheses biofilm.to determine the occurrence and the in vitro antimicrobial susceptibility of enteric rods and pseudomonads from the denture biofilm of 52 subjects at the center for dental specialties of sobral/ ceara, brazil.201627812616
identification of klebsiella pneumoniae carbapenemase-producing klebsiella oxytoca in clinical isolates in tehran hospitals, iran by chromogenic medium and molecular methods.production of carbapenemase, especially klebsiella pneumoniae carbapenemases (kpc), is one of the antibiotic resistance mechanisms of enterobacteriaceae such as klebsiella oxytoca. this study aimed to investigate and identify kpc-producing k. oxytoca isolates using molecular and phenotypic methods.201627812488
recent advances in synthetic biosafety.synthetically engineered organisms hold promise for a broad range of medical, environmental, and industrial applications. organisms can potentially be designed, for example, for the inexpensive and environmentally benign synthesis of pharmaceuticals and industrial chemicals, for the cleanup of environmental pollutants, and potentially even for biomedical applications such as the targeting of specific diseases or tissues. however, the use of synthetically engineered organisms comes with several r ...201627635235
interspecific bacterial interactions are reflected in multispecies biofilm spatial organization.interspecies interactions are essential for the persistence and development of any kind of complex community, and microbial biofilms are no exception. multispecies biofilms are structured and spatially defined communities that have received much attention due to their omnipresence in natural environments. species residing in these complex bacterial communities usually interact both intra- and interspecifically. such interactions are considered to not only be fundamental in shaping overall biomas ...201627630624
comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide.γ-hexachlorocyclohexane (γ-hch) is a recalcitrant man-made chlorinated pesticide. here, the complete genome sequences of four γ-hch-degrading sphingomonad strains, which are most unlikely to have been derived from one ancestral γ-hch degrader, were compared. together with several experimental data, we showed that (i) all the four strains carry almost identical lina to line genes for the conversion of γ-hch to maleylacetate (designated "specific" lin genes), (ii) considerably different genes are ...201627581378
primary succession of nitrogen cycling microbial communities along the deglaciated forelands of tianshan mountain, china.structural succession and its driving factors for nitrogen (n) cycling microbial communities during the early stages of soil development (0-44 years) were studied along a chronosequence in the glacial forelands of the tianshan mountain no.1 glacier in the arid and semi-arid region of central asia. we assessed the abundance and population of functional genes affiliated with n-fixation (nifh), nitrification (bacterial and archaeal amoa), and denitrification (nirk/s and nosz) in a glacier foreland ...201627625641
matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (maldi-tof ms) based microbial identifications: challenges and scopes for microbial ecologists.matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (maldi-tof ms) based biotyping is an emerging technique for high-throughput and rapid microbial identification. due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, maldi-tof ms has started replacing existing practices prevalent in clinical diagnosis. however, applicability of maldi-tof ms in the area of micr ...201627625644
molecular and structural considerations of tf-dna binding for the generation of biologically meaningful and accurate phylogenetic footprinting analysis: the lysr-type transcriptional regulator family as a study model.the goal of most programs developed to find transcription factor binding sites (tfbss) is the identification of discrete sequence motifs that are significantly over-represented in a given set of sequences where a transcription factor (tf) is expected to bind. these programs assume that the nucleotide conservation of a specific motif is indicative of a selective pressure required for the recognition of a tf for its corresponding tfbs. despite their extensive use, the accuracies reached with these ...201627567672
nitrogen regulation of the xyl genes of pseudomonas putida mt-2 propagates into a significant effect of nitrate on m-xylene mineralization in soil.the nitrogen species available in the growth medium are key factors determining expression of xyl genes for biodegradation of aromatic compounds by pseudomonas putida. nitrogen compounds are frequently amended to promote degradation at polluted sites, but it remains unknown how regulation observed in the test tube is propagated into actual catabolism of, e.g. m-xylene in soil, the natural habitat of this bacterium. to address this issue, we have developed a test-tube-to-soil model system that ex ...201627561962
immune modulation enables a specialist insect to benefit from antibacterial withanolides in its host plant.the development of novel plant chemical defenses and counter adaptations by herbivorous insect could continually drive speciation, producing more insect specialists than generalists. one approach to test this hypothesis is to compare closely related generalist and specialist species to reveal the associated costs and benefits of these different adaptive strategies. we use the specialized moth heliothis subflexa, which feeds exclusively on plants in the genus physalis, and its close generalist re ...201627561781
efficient reconstruction of predictive consensus metabolic network models.understanding cellular function requires accurate, comprehensive representations of metabolism. genome-scale, constraint-based metabolic models (gsms) provide such representations, but their usability is often hampered by inconsistencies at various levels, in particular for concurrent models. commgen, our tool for consensus metabolic model generation, automatically identifies inconsistencies between concurrent models and semi-automatically resolves them, thereby contributing to consolidate knowl ...201627563720
novel nad+-farnesal dehydrogenase from polygonum minus leaves. purification and characterization of enzyme in juvenile hormone iii biosynthetic pathway in plant.juvenile hormone iii is of great concern due to negative effects on major developmental and reproductive maturation in insect pests. thus, the elucidation of enzymes involved jh iii biosynthetic pathway has become increasing important in recent years. one of the enzymes in the jh iii biosynthetic pathway that remains to be isolated and characterized is farnesal dehydrogenase, an enzyme responsible to catalyze the oxidation of farnesal into farnesoic acid. a novel nad+-farnesal dehydrogenase of p ...201627560927
toxin yafq reduces escherichia coli growth at low temperatures.toxin/antitoxin (ta) systems reduce metabolism under stress; for example, toxin yafq of the yafq/dinj escherichia coli ta system reduces growth by cleaving transcripts with in-frame 5'-aaa-g/a-3' sites, and antitoxin dinj is a global regulator that represses its locus as well as controls levels of the stationary sigma factor rpos. here we investigated the influence on cell growth at various temperatures and found that deletion of the antitoxin gene, dinj, resulted in both reduced metabolism and ...201627557125
the diversity of mtdna rns introns among strains of ophiostoma piliferum, ophiostoma pluriannulatum and related species.based on previous studies, it was suspected that the mitochondrial rns gene within the ophiostomatales is rich in introns. this study focused on a collection of strains representing ophiostoma piliferum, ophiostoma pluriannulatum and related species that cause blue-stain; these fungi colonize the sapwood of trees and impart a dark stain. this reduces the value of the lumber. the goal was to examine the mtdna rns intron landscape for these important blue stain fungi in order to facilitate future ...201627610327
functional genomic analyses of enterobacter, anopheles and plasmodium reciprocal interactions that impact vector competence.malaria exerts a tremendous socioeconomic impact worldwide despite current control efforts, and novel disease transmission-blocking strategies are urgently needed. the enterobacter bacterium esp_z, which is naturally harboured in the mosquito midgut, can inhibit the development of plasmodium parasites prior to their invasion of the midgut epithelium through a mechanism that involves oxidative stress. here, a multifaceted approach is used to study the tripartite interactions between the mosquito, ...201627549662
comparative genomics and metabolic analysis reveals peculiar characteristics of rhodococcus opacus strain m213 particularly for naphthalene degradation.the genome of rhodococcus opacus strain m213, isolated from a fuel-oil contaminated soil, was sequenced and annotated which revealed a genome size of 9,194,165 bp encoding 8680 putative genes and a g+c content of 66.72%. among the protein coding genes, 71.77% were annotated as clusters of orthologous groups of proteins (cogs); 55% of the cogs were present as paralog clusters. pulsed field gel electrophoresis (pfge) analysis of m213 revealed the presence of three different sized replicons- a circ ...201627532207
folding analysis of the most complex stevedore's protein knot.dehi is a homodimeric haloacid dehalogenase from pseudomonas putida that contains the most complex 61 stevedore's protein knot within its folding topology. to examine how dehi attains such an intricate knotted topology we combined far-uv circular dichroism (cd), intrinsic fluorescence spectroscopy and small angle x-ray scattering (saxs) to investigate its folding mechanism. equilibrium unfolding of dehi by chemical denaturation indicated the presence of two highly populated folding intermediates ...201627527519
listeria monocytogenes dna glycosylase adlp affects flagellar motility, biofilm formation, virulence, and stress responses.the temperature-dependent alteration of flagellar motility gene expression is critical for the foodborne pathogen listeria monocytogenes to respond to a changing environment. in this study, a genetic determinant, l. monocytogenes f2365_0220 (lmof2365_0220), encoding a putative protein that is structurally similar to the bacillus cereus alkyl base dna glycosylase (alkd), was identified. this determinant was involved in the transcriptional repression of flagellar motility genes and was named adlp ...201627316964
comparative single-cell analysis of different e. coli expression systems during microfluidic cultivation.recombinant protein production is mostly realized with large-scale cultivations and monitored at the level of the entire population. detailed knowledge of cell-to-cell variations with respect to cellular growth and product formation is limited, even though phenotypic heterogeneity may distinctly hamper overall production yields, especially for toxic or difficult-to-express proteins. unraveling phenotypic heterogeneity is thus a key aspect in understanding and optimizing recombinant protein produ ...201627525986
replisome assembly at bacterial chromosomes and iteron plasmids.the proper initiation and occurrence of dna synthesis depends on the formation and rearrangements of nucleoprotein complexes within the origin of dna replication. in this review article, we present the current knowledge on the molecular mechanism of replication complex assembly at the origin of bacterial chromosome and plasmid replicon containing direct repeats (iterons) within the origin sequence. we describe recent findings on chromosomal and plasmid replication initiators, dnaa and rep protei ...201627563644
overexpression of transport proteins improves the production of 5-aminovalerate from l-lysine in escherichia coli.bacterial transporters mediate the exchanges between intracellular and extracellular environments. modification of transport route could be applied to speed up the metabolic reactions and promote the production of aimed compounds. herein, lysine 2-monooxygenase (davb) and δ-aminovaleramidase (dava) were co-expressed in escherichia coli bl21(de3) to produce nylon-5 monomer 5-aminovalerate from l-lysine. then, pp2911 (4-aminobutyrate transporter in pseudomonas putida) and lysp (the lysine specific ...201627510748
modeling central metabolism and energy biosynthesis across microbial life.automatically generated bacterial metabolic models, and even some curated models, lack accuracy in predicting energy yields due to poor representation of key pathways in energy biosynthesis and the electron transport chain (etc). further compounding the problem, complex interlinking pathways in genome-scale metabolic models, and the need for extensive gapfilling to support complex biomass reactions, often results in predicting unrealistic yields or unrealistic physiological flux profiles.201627502787
recent advances on multi-parameter flow cytometry to characterize antimicrobial treatments.the investigation on antimicrobial mechanisms is a challenging and crucial issue in the fields of food or clinical microbiology, as it constitutes a prerequisite to the development of new antimicrobial processes or compounds, as well as to anticipate phenomenon of microbial resistance. nowadays it is accepted that a cells population exposed to a stress can cause the appearance of different cell populations and in particular sub-lethally compromised cells which could be defined as viable but non- ...201627551279
insights into the genome sequences of an n-acyl homoserine lactone molecule producing two pseudomonas spp. isolated from the arctic.we report for the first time the draft genome sequence of two psychrotrophic pseudomonas species, pseudomonas simiae rgcb 73 and pseudomonas brenneri rgcb 108, from the arctic that produce more than one acyl homoserine lactone molecule of varied n-acyl length. the study confirms the presence of a luxr-luxi (type) mediated quorum-sensing system in both the pseudomonas species and enables us to understand the role of quorum sensing in their survival in extremely cold environments.201627491995
from the lab to the farm: an industrial perspective of plant beneficial microorganisms.any successful strategy aimed at enhancing crop productivity with microbial products ultimately relies on the ability to scale at regional to global levels. microorganisms that show promise in the lab may lack key characteristics for widespread adoption in sustainable and productive agricultural systems. this paper provides an overview of critical considerations involved with taking a strain from discovery to the farmer's field. in addition, we review some of the most effective microbial product ...201627540383
expression of a grapevine nac transcription factor gene is induced in response to powdery mildew colonization in salicylic acid-independent manner.tissue colonization by grape powdery mildew (pm) pathogen erysiphe necator (schw.) burr triggers a major remodeling of the transcriptome in the susceptible grapevine vitis vinifera l. while changes in the expression of many genes bear the signature of salicylic acid (sa) mediated regulation, the breadth of pm-induced changes suggests the involvement of additional regulatory networks. to explore pm-associated gene regulation mediated by other sa-independent systems, we designed a microarray exper ...201627488171
new family of biosensors for monitoring btx in aquatic and edaphic environments.benzene, toluene, ethylbenzene and xylenes (btex) contamination is a serious threat to public health and the environment, and therefore, there is an urgent need to detect its presence in nature. the use of whole-cell reporters is an efficient, easy-to-use and low-cost approach to detect and follow contaminants outside specialized laboratories; this is especially important in oil spills that are frequent in marine environments. the aim of this study is the construction of a bioreporter system and ...201627484951
flra, flrb and flrc regulate adhesion by controlling the expression of critical virulence genes in vibrio alginolyticus.adhesion is an important virulence trait of vibrio alginolyticus. bacterial adhesion is influenced by environmental conditions; however, the molecular mechanism underlying this effect remains unknown. the expression levels of flra, flrb and flrc were significantly downregulated in adhesion-deficient v. alginolyticus strains cultured under cu(2+), pb(2+), hg(2+) and low-ph stresses. silencing these genes led to deficiencies in adhesion, motility, flagellar assembly, biofilm formation and exopolys ...201627485498
mapping the patent landscape of synthetic biology for fine chemical production pathways.a goal of synthetic biology bio-foundries is to innovate through an iterative design/build/test/learn pipeline. in assessing the value of new chemical production routes, the intellectual property (ip) novelty of the pathway is important. exploratory studies can be carried using knowledge of the patent/ip landscape for synthetic biology and metabolic engineering. in this paper, we perform an assessment of pathways as potential targets for chemical production across the full catalogue of reachable ...201627489206
lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism-induced responses in the early exponential growth phase.lactobacillus oligofermentans has been mostly isolated from cold-stored packaged meat products in connection with their spoilage, but its precise role in meat spoilage is unknown. it belongs to the l. vaccinostercus group of obligate heterofermentative lactobacilli that generally ferment pentoses (e.g. xylose and ribose) more efficiently than hexoses (e.g. glucose). however, more efficient hexose utilization can be induced. the regulation mechanisms of the carbohydrate catabolism in such bacteri ...201627487841
bacterial dispersal promotes biodegradation in heterogeneous systems exposed to osmotic stress.contaminant biodegradation in soils is hampered by the heterogeneous distribution of degrading communities colonizing isolated microenvironments as a result of the soil architecture. over the last years, soil salinization was recognized as an additional problem especially in arid and semiarid ecosystems as it drastically reduces the activity and motility of bacteria. here, we studied the importance of different spatial processes for benzoate biodegradation at an environmentally relevant range of ...201627536297
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