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bio-statistical enhancement of acyl transfer activity of amidase for biotransformation of n-substituted aromatic amides.acyl transfer activity (ata) of amidase transfers an acyl group of different amides to hydroxylamine to form the corresponding hydroxamic acid. bacterial isolate br-1 was isolated from cyanogenic plant cirsium vulgare rhizosphere and identified as pseudomonas putida br-1 by 16s rdna sequencing. this organism exhibited high ata for the biotransformation of n-substituted aromatic amide to the corresponding hydroxamic acid. optimization of media, tryptone (0.6%), inducer, ph 8.5, and a growth tempe ...201627118077
in vivo model for microbial invasion of tooth root dentinal tubules.objective bacterial penetration of dentinal tubules via exposed dentine can lead to root caries and promote infections of the pulp and root canal system. the aim of this work was to develop a new experimental model for studying bacterial invasion of dentinal tubules within the human oral cavity. material and methods sections of human root dentine were mounted into lower oral appliances that were worn by four human subjects for 15 d. roots were then fixed, sectioned, stained and examined microsco ...201627119760
c-di-gmp regulates the expression of lapa and bcs operons via fleq in pseudomonas putida kt2440.cyclic diguanylate (c-di-gmp) positively modulates the production of biofilm matrix components from the transcriptional to the post-translational level in a variety of bacterial species. however, mechanisms by which it regulates these opponents in pseudomonas putida kt2440 remain unclear. here we show that c-di-gmp regulates the adhesin lapa, lapf and exopolysaccharides bcs, pea at transcriptional level. transcriptional regulator fleq is required for the modulation of lapa and bcs expression by ...201627120564
metabolic fingerprinting of pseudomonas putida dot-t1e strains: understanding the influence of divalent cations in adaptation mechanisms following exposure to toluene.pseudomonas putida strains can adapt and overcome the activity of toxic organic solvents by the employment of several resistant mechanisms including efflux pumps and modification to lipopolysaccharides (lps) in their membranes. divalent cations such as magnesium and calcium play a crucial role in the development of solvent tolerance in bacterial cells. here, we have used fourier transform infrared (ft-ir) spectroscopy directly on cells (metabolic fingerprinting) to monitor bacterial response to ...201627128955
preparation and biological activity of new collagen composites, part i: collagen/zinc titanate nanocomposites.the aim of this investigation was to develop new antimicrobial collagen/zinc titanate (zntio3) biomaterials using a sol-gel cryogenic draying technology in keeping the native collagen activity. broad-spectrum antimicrobial activity was demonstrated against firmicutes (staphylococcus epidermidis, bacillus cereus, and candida lusitaniae) and gracilicutes (escherichia coli, salmonella enterica, and pseudomonas putida) microorganisms. the antimicrobial activity as well as the cytotoxicity were speci ...201627138724
integrated analysis of gene expression and metabolic fluxes in pha-producing pseudomonas putida grown on glycerol.given its high surplus and low cost, glycerol has emerged as interesting carbon substrate for the synthesis of value-added chemicals. the soil bacterium pseudomonas putida kt2440 can use glycerol to synthesize medium-chain-length poly(3-hydroxyalkanoates) (mcl-pha), a class of biopolymers of industrial interest. here, glycerol metabolism in p. putida kt2440 was studied on the level of gene expression (transcriptome) and metabolic fluxes (fluxome), using precisely adjusted chemostat cultures, gro ...201627142075
bioprospecting sponge-associated microbes for antimicrobial compounds.sponges are the most prolific marine organisms with respect to their arsenal of bioactive compounds including antimicrobials. however, the majority of these substances are probably not produced by the sponge itself, but rather by bacteria or fungi that are associated with their host. this review for the first time provides a comprehensive overview of antimicrobial compounds that are known to be produced by sponge-associated microbes. we discuss the current state-of-the-art by grouping the bioact ...201627144573
community analysis and recovery of phenol-degrading bacteria from drinking water biofilters.phenol is a ubiquitous organic contaminant in drinking water. biodegradation plays an important role in the elimination of phenol pollution in the environment, but the information about phenol removal by drinking water biofilters is still lacking. herein, we study an acclimated bacterial community that can degrade over 80% of 300 mg/l phenol within 3 days. pcr detection of genotypes involved in bacterial phenol degradation revealed that the degradation pathways contained the initial oxidative at ...201627148185
phenylacetic acid is isr determinant produced by bacillus fortis iags162, which involves extensive re-modulation in metabolomics of tomato to protect against fusarium wilt.bacillus fortis iags162 has been previously shown to induce systemic resistance in tomato plants against fusarium wilt disease. in the first phase of current study, the isr determinant was isolated from extracellular metabolites of this bacterium. isr bioassays combined with solvent extraction, column chromatography and gc/ms analysis proved that phenylacetic acid (paa) was the potential isr determinant that significantly ameliorated fusarium wilt disease of tomato at concentrations of 0.1 and 1 ...201627148321
enhancing indigo production by over-expression of the styrene monooxygenase in pseudomonas putida.as an important traditional blue dye, indigo has been used in food and textile industry for centuries, which can be produced via the styrene oxygenation pathway in pseudomonas putida. hence, the styrene monooxygenase gene styab and oxide isomerase gene styc are over-expressed in p. putida to investigate their roles in indigo biosynthesis. rt-qpcr analysis indicated that transcriptions of stya and styb were increased by 2500- and 750-folds in the styab over-expressed strain b4-01, compared with t ...201627154464
the preprotein translocase yidc controls respiratory metabolism in mycobacterium tuberculosis.the yidc-oxa1-alb3 preprotein translocases play a vital role in membrane insertion of proteins in eukaryotes and bacteria. in a recent study we observed that rv3921c, which encodes putative yidc translocase in mycobacterium tuberculosis (mtb), is essential for in vitro growth of bacteria. however, the exact function of this particular protein remains to identify in mycobacterial pathogens. by performing a systematic study here we show that yidc of mtb is an envelope protein, which is required fo ...201627166092
dna sequence-selective c8-linked pyrrolobenzodiazepine-heterocyclic polyamide conjugates show anti-tubercular-specific activities.new chemotherapeutic agents with novel mechanisms of action are in urgent need to combat the tuberculosis pandemic. a library of 12 c8-linked pyrrolo[2,1-c][1,4]benzodiazepine (pbd)-heterocyclic polyamide conjugates (1-12) was evaluated for anti-tubercular activity and dna sequence selectivity. the pbd conjugates were screened against slow-growing mycobacterium bovis bacillus calmette-guérin and m. tuberculosis h37rv, and fast-growing escherichia coli, pseudomonas putida and rhodococcus sp. rha1 ...201627168314
different inocula produce distinctive microbial consortia with similar lignocellulose degradation capacity.despite multiple research efforts, the current strategies for exploitation of lignocellulosic plant matter are still far from optimal, being hampered mostly by the difficulty of degrading the recalcitrant parts. an interesting approach is to use lignocellulose-degrading microbial communities by using different environmental sources of microbial inocula. however, it remains unclear whether the inoculum source matters for the degradation process. here, we addressed this question by verifying the l ...201627170322
three-way interaction among plants, bacteria, and coleopteran insects.coleoptera, the largest and the most diverse insecta order, is characterized by multiple adaptations to plant feeding. insect-associated microorganisms can be important mediators and modulators of interactions between insects and plants. interactions between plants and insects are highly complex and involve multiple factors. there are various defense mechanisms initiated by plants upon attack by herbivorous insects, including the development of morphological structures and the synthesis of toxic ...201627170360
in vitro and in vivo antimicrobial activity of combined therapy of silver nanoparticles and visible blue light against pseudomonas aeruginosa.silver nanoparticles (agnps) have been used as potential antimicrobial agents against resistant pathogens. we investigated the possible therapeutic use of agnps in combination with visible blue light against a multidrug resistant clinical isolate of pseudomonas aeruginosa in vitro and in vivo. the antibacterial activity of agnps against p. aeruginosa (1×10(5) colony forming unit/ml) was investigated at its minimal inhibitory concentration (mic) and sub-mic, alone and in combination with blue lig ...201627175075
regulation of motility and phenazine pigment production by flia is cyclic-di-gmp dependent in pseudomonas aeruginosa pao1.the transcription factor flia, also called sigma 28, is a major regulator of bacterial flagellar biosynthesis genes. growing evidence suggest that in addition to motility, flia is involved in controlling numerous bacterial behaviors, even though the underlying regulatory mechanism remains unclear. by using a transcriptional fusion to gfp that responds to cyclic (c)-di-gmp, this study revealed a higher c-di-gmp concentration in the flia deletion mutant of pseudomonas aeruginosa than in its wild-t ...201627175902
sulfhydryl binding sites within bacterial extracellular polymeric substances.in this study, the concentration of sulfhydryl sites on bacterial biomass samples with and without extracellular polymeric substances (eps) was measured in order to determine the distribution of sulfhydryl sites on bacteria. three different approaches were employed for eps removal from pseudomonas putida, and the measured sulfhydryl concentrations on bacterial eps molecules are independent of the eps removal protocols used. prior to eps removal, the measured sulfhydryl sites within p. putida sam ...201627177017
a new mercury-accumulating mucor hiemalis strain eh8 from cold sulfidic spring water biofilms.here, we report about a unique aquatic fungus mucor hiemaliseh8 that can remove toxic ionic mercury from water by intracellular accumulation and reduction into elemental mercury (hg(0) ). eh8 was isolated from a microbial biofilm grown in sulfidic-reducing spring water sourced at a marching's site located downhill from hop cultivation areas with a history of mercury use. a thorough biodiversity survey and mercury-removal function analyses were undertaken in an area of about 200 km(2) in bavaria ...201627177603
deep sequencing approach for investigating infectious agents causing fever.acute undifferentiated fever (auf) poses a diagnostic challenge due to the variety of possible aetiologies. while the majority of aufs resolve spontaneously, some cases become prolonged and cause significant morbidity and mortality, necessitating improved diagnostic methods. this study evaluated the utility of deep sequencing in fever investigation. dna and rna were isolated from plasma/sera of auf cases being investigated at cairns hospital in northern australia, including eight control samples ...201627180244
u(vi) biosorption by bi-functionalized pseudomonas putida @ chitosan bead: modeling and optimization using rsm.in this work, pseudomonas putida cells immobilized into chitosan beads (picb) were synthesized to investigate the impact of microorganism entrapment on biosorption capacity of prepared biosorbent for u(vi) biosorption from aqueous solutions. response surface methodology (rsm) based on central composite design (ccd) was utilized to evaluate the performance of the picb in comparison with chitosan beads (cb) under batch mode. performing experiments under optimal condition sets viz. ph 5, initial u( ...201627180295
global changes in the proteome of cupriavidus necator h16 during poly-(3-hydroxybutyrate) synthesis from various biodiesel by-product substrates.synthesis of poly-[3-hydroxybutyrate] (phb) by cupriavidus necator h16 in batch cultures was evaluated using three biodiesel-derived by-products as the sole carbon sources: waste glycerol (reg-80, refined to 80 % purity with negligible free fatty acids); glycerol bottom (reg-gb, with up to 65 % glycerol and 35 % free fatty acids), and free fatty acids (reg-ffa, with up to 75 % ffa and no glycerol). all the three substrates supported growth and phb production by c. necator, with polymer accumulat ...201627184362
profiling expression of lipoxygenase in cucumber during compatible and incompatible plant-pathogen interactions.we compared lipoxygenase (lox) expression in cucumber in response to host and non-host pathogens. our results displayed significant difference in expression of lox between compatible and incompatible interaction at 12, 24 and 48 h after inoculation. moreover, lox expression at 72 h after inoculation was similar in both compatible and incompatible interaction. it seems that early induction of lox plays a crucial role in plant defense against pathogens.201527186031
profiling expression of lipoxygenase in cucumber during compatible and incompatible plant-pathogen interactions.we compared lipoxygenase (lox) expression in cucumber in response to host and non-host pathogens. our results displayed significant difference in expression of lox between compatible and incompatible interaction at 12, 24 and 48 h after inoculation. moreover, lox expression at 72 h after inoculation was similar in both compatible and incompatible interaction. it seems that early induction of lox plays a crucial role in plant defense against pathogens.201527186031
effects of bloom-forming cyanobacterial extracellular polymeric substances on the adsorption of cadmium onto kaolinite: behaviors and possible mechanisms.cyanobacterial blooms result in high level of cyanobacterial extracellular polymeric substances (eps) in water. the effects of bloom-forming cyanobacterial eps on the distribution of cd(ii) in the interface between sediment and water is unknown. clay is a main component in sediment. the effects of eps, originated from a typical bloom-forming cyanobacterium microcystis aeruginosa, on the adsorption and desorption characteristics of cd(ii) by kaolinite were investigated in this study. results of x ...201627186506
evaluation of heavy metal removal from wastewater in a modified packed bed biofilm reactor.for the effective application of a modified packed bed biofilm reactor (pbbr) in wastewater industrial practice, it is essential to distinguish the tolerance of the system for heavy metals removal. the industrial contamination of wastewater from various sources (e.g. zn, cu, cd and ni) was studied to assess the impacts on a pbbr. this biological system was examined by evaluating the tolerance of different strengths of composite heavy metals at the optimum hydraulic retention time (hrt) of 2 hour ...201627186636
microbial inoculation of seed for improved crop performance: issues and opportunities.there is increasing interest in the use of beneficial microorganisms as alternatives to chemical pesticides and synthetic fertilisers in agricultural production. application of beneficial microorganisms to seeds is an efficient mechanism for placement of microbial inocula into soil where they will be well positioned to colonise seedling roots and protect against soil-borne diseases and pests. however, despite the long history of inoculation of legume seeds with rhizobia spp. and clear laboratory ...201627188775
biofilm formation-defective mutants in pseudomonas putida.out of 8000 candidates from a genetic screening for pseudomonas putida kt2442 mutants showing defects in biofilm formation, 40 independent mutants with diminished levels of biofilm were analyzed. most of these mutants carried insertions in genes of the lap cluster, whose products are responsible for synthesis, export and degradation of the adhesin lapa. all mutants in this class were strongly defective in biofilm formation. mutants in the flagellar regulatory genes fleq and flhf showed similar d ...201627190143
impact of pnpr, a lysr-type regulator-encoding gene, on the cellular processes of pseudomonas putida dll-e4.lysr-type transcriptional regulators (lttrs) regulate various cellular processes in bacteria. pnpr is an lttr-encoding gene involved in the regulation of hydroquinone (hq) degradation, and its effects on the cellular processes of pseudomonas putida dll-e4 were investigated at the physiological, biochemical and molecular levels. reverse transcription polymerase chain reaction revealed that pnpr positively regulated its own expression and that of the pnpc1c2decx1x2 operon; additionally, pnpr parti ...201627190157
the regulation of para-nitrophenol degradation in pseudomonas putida dll-e4.pseudomonas putida dll-e4 can efficiently degrade para-nitrophenol and its intermediate metabolite hydroquinone. the regulation of para-nitrophenol degradation was studied, and pnp induced a global change in the transcriptome of p. putida dll-e4. when grown on pnp, the wild-type strain exhibited significant downregulation of 2912 genes and upregulation of 845 genes, whereas 2927 genes were downregulated and 891 genes upregulated in a pnpr-deleted strain. genes related to two non-coding rnas (ins ...201627191401
the oxygen dilemma: a severe challenge for the application of monooxygenases?monooxygenases are promising catalysts because they in principle enable the organic chemist to perform highly selective oxyfunctionalisation reactions that are otherwise difficult to achieve. for this, monooxygenases require reducing equivalents, to allow reductive activation of molecular oxygen at the enzymes' active sites. however, these reducing equivalents are often delivered to o2 either directly or via a reduced intermediate (uncoupling), yielding hazardous reactive oxygen species and wast ...201627194219
long-term ferrocyanide application via deicing salts promotes the establishment of actinomycetales assimilating ferrocyanide-derived carbon in soil.cyanides are highly toxic and produced by various microorganisms as defence strategy or to increase their competitiveness. as degradation is the most efficient way of detoxification, some microbes developed the capability to use cyanides as carbon and nitrogen source. however, it is not clear if this potential also helps to lower cyanide concentrations in roadside soils where deicing salt application leads to significant inputs of ferrocyanide. the question remains if biodegradation in soils can ...201627194597
control of fluxes in metabolic networks.understanding the control of large-scale metabolic networks is central to biology and medicine. however, existing approaches either require specifying a cellular objective or can only be used for small networks. we introduce new coupling types describing the relations between reaction activities, and develop an efficient computational framework, which does not require any cellular objective for systematic studies of large-scale metabolism. we identify the driver reactions facilitating control of ...201627197218
a wide spectrum of fastidious and ampicillin-susceptible bacteria dominate in animal-caused wounds.the main purpose of this study was to assess the actual occurrence of gram-negative oxidase-positive bacteria (gnop) in human wounds caused by animals, mostly cat and dog bites and scratches, and with signs of infection. we report a prospective series of 92 wound samples. routine culturing was combined with a procedure optimised for fastidious gnop. all gnop isolates were identified by 16s rdna sequencing to the species level. we observed a more prominent role of gnop, including at least 30 spec ...201627197725
industrial production of acetone and butanol by fermentation-100 years later.microbial production of acetone and butanol was one of the first large-scale industrial fermentation processes of global importance. during the first part of the 20th century, it was indeed the second largest fermentation process, superseded in importance only by the ethanol fermentation. after a rapid decline after the 1950s, acetone-butanol-ethanol (abe) fermentation has recently gained renewed interest in the context of biorefinery approaches for the production of fuels and chemicals from ren ...201627199350
biodegradation of mycotoxins: tales from known and unexplored worlds.exposure to mycotoxins, secondary metabolites produced by fungi, may infer serious risks for animal and human health and lead to economic losses. several approaches to reduce these mycotoxins have been investigated such as chemical removal, physical binding, or microbial degradation. this review focuses on the microbial degradation or transformation of mycotoxins, with specific attention to the actual detoxification mechanisms of the mother compound. furthermore, based on the similarities in che ...201627199907
antibiotic resistance patterns of pseudomonas spp. isolated from the river danube.spread and persistence of antibiotic resistance pose a severe threat to human health, yet there is still lack of knowledge about reservoirs of antibiotic resistant bacteria in the environment. we took the opportunity of the joint danube survey 3 (jds3), the world's biggest river research expedition of its kind in 2013, to analyse samples originating from different sampling points along the whole length of the river. due to its high clinical relevance, we concentrated on the characterization of p ...201627199920
mechanism of antiactivation at the pseudomonas sp. strain adp σn-dependent patzt promoter.patzt is an internal promoter of the atzrstuvw operon that directs the synthesis of atzt, atzu, atzv, and atzw, components of an abc-type cyanuric acid transport system. patzt is σ(n) dependent, activated by the general nitrogen control regulator ntrc with the assistance of protein integration host factor (ihf), and repressed by the lysr-type transcriptional regulator (lttr) atzr. we have used a variety of in vivo and in vitro gene expression and protein-dna interaction assays to assess the mech ...201627208099
influence of 3-chloroaniline on the biofilm lifestyle of comamonas testosteroni and its implications on bioaugmentation.bioaugmentation has been frequently proposed in wastewater and soil treatment to remove toxic aromatic compounds. the performance of bioaugmentation is affected by a number of biological and environmental factors, including the interaction between the target pollutant and the augmented bacterial cells. in this study, using comamonas testosteroni and 3-chloroaniline (3-ca) as the model organism and target pollutant, we explored the influence of toxic aromatic pollutants on the biofilm lifestyle o ...201627208104
metabolic pathway involved in 6-chloro-2-benzoxazolinone degradation by pigmentiphaga sp. strain dl-8 and identification of the novel metal-dependent hydrolase cbaa.6-chloro-2-benzoxazolinone (cdhb) is a precursor of herbicide, insecticide, and fungicide synthesis and has a broad spectrum of biological activity. pigmentiphaga sp. strain dl-8 can transform cdhb into 2-amino-5-chlorophenol (2a5cp), which it then utilizes as a carbon source for growth. the cdhb hydrolase (cbaa) was purified from strain dl-8, which can also hydrolyze 2-benzoxazolinone (boa), 5-chloro-2-boa, and benzamide. the specific activity of purified cbaa was 5,900 u · mg protein(-1) for c ...201627208123
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
paralogous regulators arsr1 and arsr2 of pseudomonas putida kt2440 as a basis for arsenic biosensor development.the remarkable metal resistance of many microorganisms is related to the presence of multiple metal resistance operons. pseudomonas putida kt2440 can be considered a model for these microorganisms since its arsenic resistance is due to the action of proteins encoded by the two paralogous arsenic resistance operons ars1 and ars2. both operons contain the genes encoding the transcriptional regulators arsr1 and arsr2 that control operon expression. we show here that purified arsr1 and arsr2 bind th ...201627208139
the bark-beetle-associated fungus, endoconidiophora polonica, utilizes the phenolic defense compounds of its host as a carbon source.norway spruce (picea abies) is periodically attacked by the bark beetle ips typographus and its fungal associate, endoconidiophora polonica, whose infection is thought to be required for successful beetle attack. norway spruce produces terpenoid resins and phenolics in response to fungal and bark beetle invasion. however, how the fungal associate copes with these chemical defenses is still unclear. in this study, we investigated changes in the phenolic content of norway spruce bark upon e. polon ...201627208235
interrupting peptidoglycan deacetylation during bdellovibrio predator-prey interaction prevents ultimate destruction of prey wall, liberating bacterial-ghosts.the peptidoglycan wall, located in the periplasm between the inner and outer membranes of the cell envelope in gram-negative bacteria, maintains cell shape and endows osmotic robustness. predatory bdellovibrio bacteria invade the periplasm of other bacterial prey cells, usually crossing the peptidoglycan layer, forming transient structures called bdelloplasts within which the predators replicate. prey peptidoglycan remains intact for several hours, but is modified and then degraded by escaping p ...201627211869
marine invertebrate metabolites with anticancer activities: solutions to the "supply problem".marine invertebrates provide a rich source of metabolites with anticancer activities and several marine-derived agents have been approved for the treatment of cancer. however, the limited supply of promising anticancer metabolites from their natural sources is a major hurdle to their preclinical and clinical development. thus, the lack of a sustainable large-scale supply has been an important challenge facing chemists and biologists involved in marine-based drug discovery. in the current review ...201627213412
identification, characterization and molecular adaptation of class i redox systems for the production of hydroxylated diterpenoids.de novo production of multi-hydroxylated diterpenoids is challenging due to the lack of efficient redox systems.201627216162
polyhydroxyalkanoate (pha) granules have no phospholipids.polyhydroxybutyrate (phb) granules, also designated as carbonosomes, are supra-molecular complexes in prokaryotes consisting of a phb polymer core and a surface layer of structural and functional proteins. the presence of suspected phospholipids in the surface layer is based on in vitro data of isolated phb granules and is often shown in cartoons of the phb granule structure in reviews on phb metabolism. however, the in vivo presence of a phospholipid layer has never been demonstrated. we addres ...201627222167
rapid classification and identification of microcystis aeruginosa strains using maldi-tof ms and polygenetic analysis.matrix-assisted laser desorption-ionization-time-of-flight mass spectrometry (maldi-tof ms) was used to establish a rapid, simple, and accurate method to differentiate among strains of microcystis aeruginosa, one of the most prevalent types of bloom-forming cyanobacteria. m. aeruginosa nies-843, for which a complete genome has been sequenced, was used to characterize ribosomal proteins as biomarkers and to optimize conditions for observing ribosomal proteins as major peaks in a given mass spectr ...201627227555
[microbial composition of various surfaces of skin during develop- ment of atopic dermatitis based on data from maldi-tof mass-spectrometry identification method].study transformation of skin microflora during development of atopic dermatitis.201627228668
regulation of hydroxylation and nitroreduction pathways during metabolism of the neonicotinoid insecticide imidacloprid by pseudomonas putida.imidacloprid (imi) is mainly metabolized via nitroreduction and hydroxylation pathways, which produce different metabolites that are toxic to mammals and insects. however, regulation of imi metabolic flux between nitroreduction and hydroxylation pathways is still unclear. in this study, pseudomonas putida was found to metabolize imi to 5-hydroxy and nitroso imi and was therefore used for investigating the regulation of imi metabolic flux. the cell growth time, cosubstrate, dissolved oxygen conce ...201627230024
high production of 3-hydroxypropionic acid in klebsiella pneumoniae by systematic optimization of glycerol metabolism.3-hydroxypropionic acid (3-hp) is an important platform chemical proposed by the united states department of energy. 3-hp can be converted to a series of bulk chemicals. biological production of 3-hp has made great progress in recent years. however, low yield of 3-hp restricts its commercialization. in this study, systematic optimization was conducted towards high-yield production of 3-hp in klebsiella pneumoniae. we first investigated appropriate promoters for the key enzyme (aldehyde dehydroge ...201627230116
complete biodegradation of chlorpyrifos by engineered pseudomonas putida cells expressing surface-immobilized laccases.the long-term abuse use of chlorpyrifos-like pesticides in agriculture and horticulture has resulted in significant soil or water contamination and a worldwide ecosystem threat. in this study, the ability of a solvent-tolerant bacterium, pseudomonas putida mb285, with surface-displayed bacterial laccase, to biodegrade chlorpyrifos was investigated. the results of compositional analyses of the degraded products demonstrate that the engineered mb285 was capable of completely eliminating chlorpyrif ...201627231878
crystal structure of cytochrome p450 (cyp105p2) from streptomyces peucetius and its conformational changes in response to substrate binding.cytochrome p450 monooxygenases (cyp, ec 1.14.14.1) belong to a large family of enzymes that catalyze the hydroxylation of various substrates. here, we present the crystal structure of cyp105p2 isolated from streptomyces peucetius atcc27952 at a 2.1 å resolution. the structure shows the presence of a pseudo-ligand molecule in the active site, which was co-purified fortuitously and is presumed to be a biphenyl derivative. comparison with previously determined substrate-bound cyp structures showed ...201627231902
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
effects of bacterial community members on the proteome of the ammonia-oxidizing bacterium nitrosomonas sp. strain is79.microorganisms in the environment do not exist as the often-studied pure cultures but as members of complex microbial communities. characterizing the interactions within microbial communities is essential to understand their function in both natural and engineered environments. in this study, we investigated how the presence of a nitrite-oxidizing bacterium (nob) and heterotrophic bacteria affect the growth and proteome of the chemolithoautotrophic ammonia-oxidizing bacterium (aob) nitrosomonas ...201627235442
from dirt to industrial applications: pseudomonas putida as a synthetic biology chassis for hosting harsh biochemical reactions.the soil bacterium pseudomonas putida is endowed with a central carbon metabolic network capable of fulfilling high demands of reducing power. this situation arises from a unique metabolic architecture that encompasses the partial recycling of triose phosphates to hexose phosphates-the so-called edemp cycle. in this article, the value of p. putida as a bacterial chassis of choice for contemporary, industrially-oriented metabolic engineering is addressed. the biochemical properties that make this ...201627239751
editorial: wired for life. 201627242692
degradation of polynuclear aromatic hydrocarbons by two strains of pseudomonas.the goal of this investigation was to isolate competent polynuclear aromatic hydrocarbons degraders that can utilize polynuclear aromatic hydrocarbons of former industrial sites at mcdoel switchyard in bloomington, indiana. using conventional enrichment method based on soil slurry, we isolated, screened and purified two bacterial species strains pb1 and pb2. applying the ribotyping technique using the 16s rrna gene analysis, the strains were assigned to the genus pseudomonas (pseudomonas plecogl ...201627245129
potential of pseudomonas putida pci2 for the protection of tomato plants against fungal pathogens.tomato is one of the most economically attractive vegetable crops due to its high yields. diseases cause significant losses in tomato production worldwide. we carried out polymerase chain reaction studies to detect the presence of genes encoding antifungal compounds in the dna of pseudomonas putida strain pci2. we also used liquid chromatography-electrospray tandem mass spectrometry to detect and quantify the production of compounds that increase the resistance of plants to diseases from culture ...201627246499
cultural, transcriptomic, and proteomic analyses of water-stressed cells of actinobacterial strains isolated from compost: ecological implications in the fed-batch composting process.this study was undertaken to examine the effects of water activity (aw) on the viability of actinobacterial isolates from a fed-batch composting (fbc) process by comparing culturability and stainability with 5-cyano-2,3-ditoryl tetrazolium chloride (ctc). the fbc reactor as the source of these bacteria was operated with the daily loading of household biowaste for 70 d. during this period of composting, aw in the reactor decreased linearly with time and reached approximately 0.95 at the end of op ...201627246805
highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element.horizontal gene transfer is an important evolutionary mechanism for bacterial adaptation. however, given the typical low transfer frequencies in a bacterial population, little is known about the fate and interplay of donor cells and the mobilized dna during transfer. here we study transfer of an integrative and conjugative element (ice) among individual live bacterial cells. ices are widely distributed mobile dna elements that are different than plasmids because they reside silent in the host ch ...201627247406
nitrile-synthesizing enzyme: screening, purification and characterization.cyanide is known as a toxic compound for almost all living organisms. we have searched for cyanide-resistant bacteria from the soil and stock culture collection of our laboratory, and have found the existence of a lot of microorganisms grown on culture media containing 10 mm potassium cyanide. almost all of these cyanide-resistant bacteria were found to show β-cyano-l-alanine (β-cnala) synthetic activity. β-cnala synthase is known to catalyze nitrile synthesis: the formation of β-cnala from pota ...201627250663
nitrile-synthesizing enzyme: gene cloning, overexpression and application for the production of useful compounds.one of the nitrile-synthesizing enzymes, β-cyano-l-alanine synthase, catalyzes β-cyano-l-alanine (β-cnala) from potassium cyanide and o-acetyl-l-serine or l-cysteine. we have identified this enzyme from pseudomonas ovalis no. 111. in this study, we cloned the β-cnala synthase gene and expressed it in escherichia coli and rhodococcus rhodochrous. furthermore, we carried out co-expression of β-cnala synthase with nitrilase or nitrile hydratases in order to synthesize aspartic acid and asparagine f ...201627250664
identification and characterization of a novel (+)-γ-lactamase from microbacterium hydrocarbonoxydans.2-azabicyclo[2.2.1]hept-5-en-3-one (γ-lactam) is an important precursor of many carbocyclic nucleoside analogs and pharmaceuticals. (-)-γ-lactam has attracted much attention because of its role as an intermediate of antiviral drugs such as abacavir and carbovir. (+)-γ-lactamase can be used for the kinetic resolution of γ-lactam to obtain (-)-γ-lactam. in this study, a novel (+)-γ-lactamase (mh33h4-5540) was discovered from the gene library of microbacterium hydrocarbonoxydans based on a colorime ...201627255489
thigh abscess and necrotizing fasciitis following an inside-out transobturator tape intervention: a case report.tension-free vaginal transobturator tapes are used worldwide in the treatment of urinary incontinence in women. very few severe complications have been described following this procedure, with no standard treatment yet established.201627256334
muts regulates access of the error-prone dna polymerase pol iv to replication sites: a novel mechanism for maintaining replication fidelity.translesion dna polymerases (pol) function in the bypass of template lesions to relieve stalled replication forks but also display potentially deleterious mutagenic phenotypes that contribute to antibiotic resistance in bacteria and lead to human disease. effective activity of these enzymes requires association with ring-shaped processivity factors, which dictate their access to sites of dna synthesis. here, we show for the first time that the mismatch repair protein muts plays a role in regulat ...201627257069
characterization of genome-reduced bacillus subtilis strains and their application for the production of guanosine and thymidine.genome streamlining has emerged as an effective strategy to boost the production efficiency of bio-based products. many efforts have been made to construct desirable chassis cells by reducing the genome size of microbes. it has been reported that the genome-reduced bacillus subtilis strain mbg874 showed clear advantages for the production of several heterologous enzymes including alkaline cellulase and protease. in addition to enzymes, b. subtilis is also used for the production of chemicals. to ...201627260256
recombinant ralstonia eutropha engineered to utilize xylose and its use for the production of poly(3-hydroxybutyrate) from sunflower stalk hydrolysate solution.lignocellulosic raw materials have extensively been examined for the production of bio-based fuels, chemicals, and polymers using microbial platforms. since xylose is one of the major components of the hydrolyzed lignocelluloses, it is being considered a promising substrate in lignocelluloses based fermentation process. ralstonia eutropha, one of the most powerful and natural producers of polyhydroxyalkanoates (phas), has extensively been examined for the production of bio-based chemicals, fuels ...201627260327
3-chloro-1,2-propanediol biodegradation by ca-alginate immobilized pseudomonas putida dsm 437 cells applying different processes: mass transfer effects.3-chloro-1,2-propanediol (3-cpd) biodegradation by ca-alginate immobilized pseudomonas putida cells was performed in batch system, continuous stirred tank reactor (cstr), and packed-bed reactor (pbr). batch system exhibited higher biodegradation rates and 3-cpd uptakes compared to cstr and pbr. the two continuous systems (cstr and pbr) when compared at 200 mg/l 3-cpd in the inlet exhibited the same removal of 3-cpd at steady state. external mass-transfer limitations are found negligible at all s ...201627262716
efficient hydroxylation of 1,8-cineole with monoterpenoid-resistant recombinant pseudomonas putida gs1.in this work, monoterpenoid hydroxylation with pseudomonas putida gs1 and kt2440 were investigated as host strains, and the cytochrome p450 monooxygenase cyp176a1 (p450cin) and its native redox partner cindoxin (cinc) from citrobacter braakii were introduced in p. putida to catalyze the stereoselective hydroxylation of 1,8-cineole to (1r)-6β-hydroxy-1,8-cineole. growth experiments in the presence of 1,8-cineole confirmed pseudomonads' superior resilience compared to e. coli. whole-cell p. putida ...201627263007
chalcone-based selective inhibitors of a c4 plant key enzyme as novel potential herbicides.weeds are a challenge for global food production due to their rapidly evolving resistance against herbicides. we have identified chalcones as selective inhibitors of phosphoenolpyruvate carboxylase (pepc), a key enzyme for carbon fixation and biomass increase in the c4 photosynthetic pathway of many of the world's most damaging weeds. in contrast, many of the most important crop plants use c3 photosynthesis. here, we show that 2',3',4',3,4-pentahydroxychalcone (ic50 = 600 nm) and 2',3',4'-trihyd ...201627263468
integrated acoustic separation, enrichment, and microchip polymerase chain reaction detection of bacteria from blood for rapid sepsis diagnostics.this paper describes an integrated microsystem for rapid separation, enrichment, and detection of bacteria from blood, addressing the unmet clinical need for rapid sepsis diagnostics. the blood sample is first processed in an acoustophoresis chip, where red blood cells are focused to the center of the channel by an acoustic standing wave and sequentially removed. the bacteria-containing plasma proceeds to a glass capillary with a localized acoustic standing wave field where the bacteria are trap ...201627264110
coexistence of two d-lactate-utilizing systems in pseudomonas putida kt2440.it is advantageous for rhizosphere-dwelling microorganisms to utilize organic acids such as lactate. pseudomonas putida kt2440 is one of the most widely studied rhizosphere-dwelling model organisms. the p. putida kt2440 genome contains an nad-dependent d-lactate dehydrogenase encoding gene, but mutation of this gene does not play a role in d-lactate utilization. instead, it was found that d-lactate utilization in p. putida kt2440 proceeds via a multidomain nad-independent d-lactate dehydrogenase ...201627264531
the effect of using blood culture bottle of bronchoalveolar larvage fluid in pneumonia.pneumonia is a primary cause of morbidity and mortality in infectious disease, and increasing antimicrobial resistance has raised concerns of treatment failure. therefore, we evaluated the value of a blood culture bottle for bronchoalveolar lavage (bal) samples on pathogen identification and on treatment modification in patients with pneumonia.201627266871
effect of plant growth-promoting bacteria on the growth and fructan production of agave americana l.the effect of plant growth-promoting bacteria inoculation on plant growth and the sugar content in agave americana was assessed. the bacterial strains aco-34a, aco-40, and aco-140, isolated from the a. americana rhizosphere, were selected for this study to evaluate their phenotypic and genotypic characteristics. the three bacterial strains were evaluated via plant inoculation assays, and azospirillum brasilense cd served as a control strain. phylogenetic analysis based on the 16s rrna gene showe ...201627268113
metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community.dna derived from environmental samples is a rich source of novel bioactive molecules. the choice of the habitat to be sampled predefines the properties of the biomolecules to be discovered due to the physiological adaptation of the microbial community to the prevailing environmental conditions. we have constructed a metagenomic library in escherichia coli dh10b with environmental dna (edna) isolated from the microbial community of a slaughterhouse drain biofilm consisting mainly of species from ...201627271534
stenosis triggers spread of helical pseudomonas biofilms in cylindrical flow systems.biofilms are multicellular bacterial structures that adhere to surfaces and often endow the bacterial population with tolerance to antibiotics and other environmental insults. biofilms frequently colonize the tubing of medical devices through mechanisms that are poorly understood. here we studied the helicoidal spread of pseudomonas putida biofilms through cylindrical conduits of varied diameters in slow laminar flow regimes. numerical simulations of such flows reveal vortical motion at stenoses ...201627272623
evaluation of bacterial diversity recovered from petroleum samples using different physical matrices.unraveling the microbial diversity and its complexity in petroleum reservoir environments has been a challenge throughout the years. despite the techniques developed in order to improve methodologies involving dna extraction from crude oil, microbial enrichments using different culture conditions can be applied as a way to increase the recovery of dna from environments with low cellular density for further microbiological analyses. this work aimed at the evaluation of different matrices (arenite ...201627282730
mobilization of pollutant-degrading bacteria by eukaryotic zoospores.the controlled mobilization of pollutant-degrading bacteria has been identified as a promising strategy for improving bioremediation performance. we tested the hypothesis whether the mobilization of bacterial degraders may be achieved by the action of eukaryotic zoospores. we evaluated zoospores that are produced by the soil oomycete pythium aphanidermatum as a biological vector, and, respectively, the polycyclic aromatic hydrocarbon (pah)-degrading bacteria mycobacterium gilvum vm552 and pseudo ...201627286642
proof of concept for the simplified breakdown of cellulose by combining pseudomonas putida strains with surface displayed thermophilic endocellulase, exocellulase and β-glucosidase.the production and employment of cellulases still represents an economic bottleneck in the conversion of lignocellulosic biomass to biofuels and other biocommodities. this process could be simplified by displaying the necessary enzymes on a microbial cell surface. such an approach, however, requires an appropriate host organism which on the one hand can withstand the rough environment coming along with lignocellulose hydrolysis, and on the other hand does not consume the generated glucose so tha ...201627287198
regulation of pyrroloquinoline quinone-dependent glucose dehydrogenase activity in the model rhizosphere-dwelling bacterium pseudomonas putida kt2440.soil-dwelling microbes solubilize mineral phosphates by secreting gluconic acid, which is produced from glucose by a periplasmic glucose dehydrogenase (gdh) that requires pyrroloquinoline quinone (pqq) as a redox coenzyme. while gdh-dependent phosphate solubilization has been observed in numerous bacteria, little is known concerning the mechanism by which this process is regulated. here we use the model rhizosphere-dwelling bacterium pseudomonas putida kt2440 to explore gdh activity and pqq synt ...201627287323
investigation of plasmid-induced growth defect in pseudomonas putida.genetic engineering in bacteria mainly relies on the use of plasmids. but despite their pervasive use for physiological studies as well as for the design and optimization of industrially used production strains, only limited information about plasmid induced growth defects is available for different replicons and organisms. here, we present the identification and characterization of such a phenomenon for pseudomonas putida transformants carrying the pbbr1-derived plasmid pmis1. we identified the ...201627287537
total growth and root-cluster production by legumes and proteas depends on rhizobacterial strain, host species and nitrogen level.root clusters are bunches of hairy rootlets produced by >1800 species in nine families. the possible involvement of micro-organisms in root-cluster formation has produced conflicting results over the last 40 years. in addition, any effect of rhizobacteria on overall plant growth of root-cluster-bearing species remains unknown.201627288511
μmore: a microfluidic magnetic oscillation reactor for accelerated parameter optimization in biocatalysis.enzymatic parameter determination is an essential step in biocatalytic process development. therefore higher throughput in miniaturized devices is urgently needed. an ideal microfluidic device should combine easy immobilization and retention of a minimal amount of biocatalyst with a well-mixed reaction volume. together, all criteria are hardly met by current tools. here we describe a microfluidic reactor (μmore) which employs magnetic particles for both enzyme immobilization and efficient mixing ...201627288595
rational design, synthesis, anti-hiv-1 rt and antimicrobial activity of novel 3-(6-methoxy-3,4-dihydroquinolin-1(2h)-yl)-1-(piperazin-1-yl)propan-1-one derivatives.in the present study, fifteen novel 3-(6-methoxy-3,4-dihydroquinolin-1(2h)-yl)-1-(piperazin-1-yl)propan-1-one (6a-o) derivatives were designed as inhibitor of hiv-1 rt using ligand based drug design approach and in-silico evaluated for drug-likeness properties. designed compounds were synthesized, characterized and in-vitro evaluated for rt inhibitory activity against wild hiv-1 rt strain. among the tested compounds, four compounds (6a, 6b, 6j and 6o) exhibited significant inhibition of hiv-1 rt ...201627288643
fusion proteins of an enoate reductase and a baeyer-villiger monooxygenase facilitate the synthesis of chiral lactones.nature uses the advantages of fusion proteins for multi-step reactions to facilitate the metabolism in cells as the conversion of substrates through intermediates to the final product can take place more rapidly and with less side-product formation. in a similar fashion, also for enzyme cascade reactions, the fusion of biocatalysts involved can be advantageous. in the present study, we investigated fusion of an alcohol dehydrogenase (adh), an enoate reductase (ered) and a baeyer-villiger monooxy ...201727289001
signaling states of a short blue-light photoreceptor protein ppsb1-lov revealed from crystal structures and solution nmr spectroscopy.light-oxygen-voltage (lov) domains represent the photo-responsive domains of various blue-light photoreceptor proteins and are widely distributed in plants, algae, fungi, and bacteria. here, we report the dark-state crystal structure of ppsb1-lov, a slow-reverting short lov protein from pseudomonas putida that is remarkably different from our previously published "fully light-adapted" structure [1]. a direct comparison of the two structures provides insight into the light-activated signaling mec ...201627291287
potential of biological agents in decontamination of agricultural soil.pesticides are widely used for the control of weeds, diseases, and pests of cultivated plants all over the world, mainly since the period after the second world war. the use of pesticides is very extensive to control harm of pests all over the globe. persistent nature of most of the synthetic pesticides causes serious environmental concerns. decontamination of these hazardous chemicals is very essential. this review paper elaborates the potential of various biological agents in decontamination o ...201627293964
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
highly regio- and enantioselective multiple oxy- and amino-functionalizations of alkenes by modular cascade biocatalysis.new types of asymmetric functionalizations of alkenes are highly desirable for chemical synthesis. here, we develop three novel types of regio- and enantioselective multiple oxy- and amino-functionalizations of terminal alkenes via cascade biocatalysis to produce chiral α-hydroxy acids, 1,2-amino alcohols and α-amino acids, respectively. basic enzyme modules 1-4 are developed to convert alkenes to (s)-1,2-diols, (s)-1,2-diols to (s)-α-hydroxyacids, (s)-1,2-diols to (s)-aminoalcohols and (s)-α-hy ...201627297777
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
biological control of rice bakanae by an endophytic bacillus oryzicola yc7007.in our previous study, we reported that a novel endophytic bacterium bacillus oryzicola yc7007 has suppressed bacterial diseases of rice via induced systemic resistance and antibiotic production. this endophytic strain, b. oryzicola yc7007 was used as a biological control agent against bakanae disease of rice caused by fusarium fujikuroi, and its mechanism of interaction with the pathogen and the rice was further elucidated. root drenching with b. oryzicola yc7007 suspension reduced the disease ...201627298598
when genome-based approach meets the "old but good": revealing genes involved in the antibacterial activity of pseudomonas sp. p482 against soft rot pathogens.dickeya solani and pectobacterium carotovorum subsp. brasiliense are recently established species of bacterial plant pathogens causing black leg and soft rot of many vegetables and ornamental plants. pseudomonas sp. strain p482 inhibits the growth of these pathogens, a desired trait considering the limited measures to combat these diseases. in this study, we determined the genetic background of the antibacterial activity of p482, and established the phylogenetic position of this strain. pseudomo ...201627303376
gcsr, a tyrr-like enhancer-binding protein, regulates expression of the glycine cleavage system in pseudomonas aeruginosa pao1.glycine serves as a major source of single carbon units for biochemical reactions within bacterial cells. utilization of glycine is tightly regulated and revolves around a key group of proteins known as the glycine cleavage system (gcs). our lab previously identified the transcriptional regulator gcsr (pa2449) as being required for catabolism of glycine in the opportunistic pathogen pseudomonas aeruginosa pao1. in an effort to clarify and have an overall better understanding of the role of gcsr ...201627303730
engineering of baeyer-villiger monooxygenase-based escherichia coli biocatalyst for large scale biotransformation of ricinoleic acid into (z)-11-(heptanoyloxy)undec-9-enoic acid.baeyer-villiger monooxygenases (bvmos) are able to catalyze regiospecific baeyer-villiger oxygenation of a variety of cyclic and linear ketones to generate the corresponding lactones and esters, respectively. however, the enzymes are usually difficult to express in a functional form in microbial cells and are rather unstable under process conditions hindering their large-scale applications. thereby, we investigated engineering of the bvmo from pseudomonas putida kt2440 and the gene expression sy ...201627311560
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
characterization of quinohemoprotein amine dehydrogenase from pseudomonas putida.quinohemoprotein amine dehydrogenase (amdh) was purified and crystallized from the soluble fraction of pseudomonas putida ifo 15366 grown on n-butylamine medium. amdh gave a single component in analytical ultracentrifugation showing an intrinsic sedimentation coefficient of 5.8s. amdh showed a typical absorption spectrum of cytochrome c showing maxima at 554, 522, 420, and 320 nm in the reduced form and one peak at 410 nm, a shoulder at 350 nm, and a broad hill around 530 nm in the oxidized form ...199827315927
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
in silico analysis for prediction of degradative capacity of pseudomonas putida sf1.the study employs draft genome sequence data to explore p-nitrophenol (pnp) degradation activity of pseudomonas putida strain sf-1 at a genomic scale. annotation analysis proposes that the strain sf1 not only possesses the gene cluster for pnp utilization but also for the utilization of benzoate, catechol, hydroxybenzoate, protocatechuate, and homogentisate. further, the analysis was carried out to understand more details of pnp 4-monooxygenase and its regulator. a comparative analysis of pnp 4- ...201627317892
genomics of high molecular weight plasmids isolated from an on-farm biopurification system.the use of biopurification systems (bps) constitutes an efficient strategy to eliminate pesticides from polluted wastewaters from farm activities. bps environments contain a high microbial density and diversity facilitating the exchange of information among bacteria, mediated by mobile genetic elements (mges), which play a key role in bacterial adaptation and evolution in such environments. here we sequenced and characterized high-molecular-weight plasmids from a bacterial collection of an on-fa ...201627321040
phosphorus mobilizing consortium mammoth p(™) enhances plant growth.phosphorus (p) is a critical nutrient used to maximize plant growth and yield. current agriculture management practices commonly experience low plant p use efficiency due to natural chemical sorption and transformations when p fertilizer is applied to soils. a perplexing challenge facing agriculture production is finding sustainable solutions to deliver p more efficiently to plants. using prescribed applications of specific soil microbial assemblages to mobilize soil bound-p to improve crop nutr ...201627326379
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