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bacterial selection for biological control of plant disease: criterion determination and validation.this study aimed to evaluate the biocontrol potential of bacteria isolated from different plant species and soils. the production of compounds related to phytopathogen biocontrol and/or promotion of plant growth in bacterial isolates was evaluated by measuring the production of antimicrobial compounds (ammonia and antibiosis) and hydrolytic enzymes (amylases, lipases, proteases, and chitinases) and phosphate solubilization. of the 1219 bacterial isolates, 92% produced one or more of the eight co ...201627765523
bacterial selection for biological control of plant disease: criterion determination and validation.this study aimed to evaluate the biocontrol potential of bacteria isolated from different plant species and soils. the production of compounds related to phytopathogen biocontrol and/or promotion of plant growth in bacterial isolates was evaluated by measuring the production of antimicrobial compounds (ammonia and antibiosis) and hydrolytic enzymes (amylases, lipases, proteases, and chitinases) and phosphate solubilization. of the 1219 bacterial isolates, 92% produced one or more of the eight co ...201627765523
pseudomonas fluorescens f113 can produce a second flagellar apparatus, which is important for plant root colonization.the genomic sequence of pseudomonas fluorescens f113 has shown the presence of a 41 kb cluster of genes that encode the production of a second flagellar apparatus. among 2,535 pseudomonads strains with sequenced genomes, these genes are only present in the genomes of f113 and other six strains, all but one belonging to the p. fluorescens cluster of species, in the form of a genetic island. the genes are homologous to the flagellar genes of the soil bacterium azotobacter vinelandii. regulation of ...201627713729
complex interplay between fleq, cyclic diguanylate and multiple σ factors coordinately regulates flagellar motility and biofilm development in pseudomonas putida.most bacteria alternate between a free living planktonic lifestyle and the formation of structured surface-associated communities named biofilms. the transition between these two lifestyles requires a precise and timely regulation of the factors involved in each of the stages that has been likened to a developmental process. here we characterize the involvement of the transcriptional regulator fleq and the second messenger cyclic diguanylate in the coordinate regulation of multiple functions rel ...201627636892
a highly efficient sorbitol dehydrogenase from gluconobacter oxydans g624 and improvement of its stability through immobilization.a sorbitol dehydrogenase (gosldh) from gluconobacter oxydans g624 (g. oxydans g624) was expressed in escherichia coli bl21(de3)-codonplus ril. the complete 1455-bp codon-optimized gene was amplified, expressed, and thoroughly characterized for the first time. gosldh exhibited km and kcat values of 38.9 mm and 3820 s(-1) toward l-sorbitol, respectively. the enzyme exhibited high preference for nadp(+) (vs. only 2.5% relative activity with nad(+)). gosldh sequencing, structure analyses, and bioche ...201627633501
involvement of type vi secretion system in secretion of iron chelator pyoverdine in pseudomonas taiwanensis.rice bacterial blight caused by xanthomonas oryzae pv. oryzae (xoo) is one of the most destructive rice diseases worldwide. therefore, in addition to breeding disease-resistant rice cultivars, it is desirable to develop effective biocontrol agents against xoo. here, we report that a soil bacterium pseudomonas taiwanensis displayed strong antagonistic activity against xoo. using matrix-assisted laser desorption/ionization imaging mass spectrometry, we identified an iron chelator, pyoverdine, secr ...201627605490
screen of non-annotated small secreted proteins of pseudomonas syringae reveals a virulence factor that inhibits tomato immune proteases.pseudomonas syringae pv. tomato dc3000 (ptodc3000) is an extracellular model plant pathogen, yet its potential to produce secreted effectors that manipulate the apoplast has been under investigated. here we identified 131 candidate small, secreted, non-annotated proteins from the ptodc3000 genome, most of which are common to pseudomonas species and potentially expressed during apoplastic colonization. we produced 43 of these proteins through a custom-made gateway-compatible expression system for ...201627603016
high quality draft genome sequences of pseudomonas fulva dsm 17717(t), pseudomonas parafulva dsm 17004(t) and pseudomonas cremoricolorata dsm 17059(t) type strains.pseudomonas has the highest number of species out of any genus of gram-negative bacteria and is phylogenetically divided into several groups. the pseudomonas putida phylogenetic branch includes at least 13 species of environmental and industrial interest, plant-associated bacteria, insect pathogens, and even some members that have been found in clinical specimens. in the context of the genomic encyclopedia of bacteria and archaea project, we present the permanent, high-quality draft genomes of t ...201627594974
expression, purification and characterization of an endoglucanase from serratia proteamaculans cdbb-1961, isolated from the gut of dendroctonus adjunctus (coleoptera: scolytinae).serratia proteamaculans cdbb-1961, a gut symbiont from the roundheaded pine beetle dendroctonus adjunctus, displayed strong cellulolytic activity on agar-plates with carboxymethyl cellulose (cmc) as carbon source. automatic genome annotation of s. proteamaculans made possible the identification of a single endoglucanase encoding gene, designated spr cel8a. the predicted protein, named spr cel8a shows high similarity (59-94 %) to endo-1,4-β-d-glucanases (ec 3.2.1.4) from the glycoside hydrolase f ...201627576896
fluorescent pseudomonas strains with only few plant-beneficial properties are favored in the maize rhizosphere.plant growth-promoting rhizobacteria (pgpr) enhance plant health and growth using a variety of traits. effective pgpr strains typically exhibit multiple plant-beneficial properties, but whether they are better adapted to the rhizosphere than pgpr strains with fewer plant-beneficial properties is unknown. here, we tested the hypothesis that strains with higher numbers of plant-beneficial properties would be preferentially selected by plant roots. to this end, the co-occurrence of 18 properties in ...201627610110
high quality draft genome sequence of the type strain of pseudomonas lutea ok2(t), a phosphate-solubilizing rhizospheric bacterium.pseudomonas lutea ok2(t) (=lmg 21974(t), cect 5822(t)) is the type strain of the species and was isolated from the rhizosphere of grass growing in spain in 2003 based on its phosphate-solubilizing capacity. in order to identify the functional significance of phosphate solubilization in pseudomonas plant growth promoting rhizobacteria, we describe here the phenotypic characteristics of strain ok2(t) along with its high-quality draft genome sequence, its annotation, and analysis. the genome is com ...201627555890
molecular cloning and functional expression of a δ9- fatty acid desaturase from an antarctic pseudomonas sp. a3.fatty acid desaturase enzymes play an essential role in the synthesis of unsaturated fatty acids. pseudomonas sp. a3 was found to produce a large amount of palmitoleic and oleic acids after incubation at low temperatures. using polymerase chain reaction (pcr), a novel δ9- fatty acid desaturase gene was isolated, cloned, and successfully expressed in escherichia coli. the gene was designated as pa3fad9 and has an open reading frame of 1,185 bp which codes for 394 amino acids with a predicted mole ...201627494717
a luxr homolog in a cottonwood tree endophyte that activates gene expression in response to a plant signal or specific peptides.homologs of the luxr acyl-homoserine lactone (ahl) quorum-sensing signal receptor are prevalent in proteobacteria isolated from roots of the eastern cottonwood tree, populus deltoides many of these isolates possess an orphan luxr homolog, closely related to oryr from the rice pathogen xanthomonas oryzae oryr does not respond to ahl signals but, instead, responds to an unknown plant compound. we discovered an oryr homolog, pipr, in the cottonwood endophyte pseudomonas sp. strain gm79. the genes a ...201627486195
effect of shear stress on pseudomonas aeruginosa isolated from the cystic fibrosis lung.chronic colonization of the lungs by pseudomonas aeruginosa is one of the major causes of morbidity and mortality in cystic fibrosis (cf) patients. to gain insights into the characteristic biofilm phenotype of p. aeruginosa in the cf lungs, mimicking the cf lung environment is critical. we previously showed that growth of the non-cf-adapted p. aeruginosa pao1 strain in a rotating wall vessel, a device that simulates the low fluid shear (ls) conditions present in the cf lung, leads to the formati ...201627486191
structural and catalytic characterization of a fungal baeyer-villiger monooxygenase.baeyer-villiger monooxygenases (bvmos) are biocatalysts that convert ketones to esters. due to their high regio-, stereo- and enantioselectivity and ability to catalyse these reactions under mild conditions, they have gained interest as alternatives to chemical baeyer-villiger catalysts. despite their widespread occurrence within the fungal kingdom, most of the currently characterized bvmos are from bacterial origin. here we report the catalytic and structural characterization of bvmoafl838 from ...201627472055
pcr-independent detection of bacterial species-specific 16s rrna at 10 fm by a pore-blockage sensor.a pcr-free, optics-free device is used for the detection of escherichia coli (e. coli) 16s rrna at 10 fm, which corresponds to ~100-1000 colony forming units/ml (cfu/ml) depending on cellular rrna levels. the development of a rapid, sensitive, and cost-effective nucleic acid detection platform is sought for the detection of pathogenic microbes in food, water and body fluids. since 16s rrna sequences are species specific and are present at high copy number in viable cells, these nucleic acids off ...201627455337
comparative genomic, proteomic and exoproteomic analyses of three pseudomonas strains reveals novel insights into the phosphorus scavenging capabilities of soil bacteria.bacteria that inhabit the rhizosphere of agricultural crops can have a beneficial effect on crop growth. one such mechanism is the microbial-driven solubilization and remineralization of complex forms of phosphorus (p). it is known that bacteria secrete various phosphatases in response to low p conditions. however, our understanding of their global proteomic response to p stress is limited. here, exoproteomic analysis of pseudomonas putida bird-1 (bird-1), pseudomonas fluorescens sbw25 and pseud ...201627233093
comparative genomic and functional analyses: unearthing the diversity and specificity of nematicidal factors in pseudomonas putida strain 1a00316.we isolated pseudomonas putida (p. putida) strain 1a00316 from antarctica. this bacterium has a high efficiency against meloidogyne incognita (m. incognita) in vitro and under greenhouse conditions. the complete genome of p. putida 1a00316 was sequenced using pacbio single molecule real-time (smrt) technology. a comparative genomic analysis of 16 pseudomonas strains revealed that although p. putida 1a00316 belonged to p. putida, it was phenotypically more similar to nematicidal pseudomonas fluor ...201627384076
source-sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities.horizontal gene transfer is a fundamental process in bacterial evolution that can accelerate adaptation via the sharing of genes between lineages. conjugative plasmids are the principal genetic elements mediating the horizontal transfer of genes, both within and between bacterial species. in some species, plasmids are unstable and likely to be lost through purifying selection, but when alternative hosts are available, interspecific plasmid transfer could counteract this and maintain access to pl ...201627385827
degradation pathways of 2- and 4-nitrobenzoates in cupriavidus sp. strain st-14 and construction of a recombinant strain, st-14::3nba, capable of degrading 3-nitrobenzoate.strain st-14, characterized as a member of the genus cupriavidus, was capable of utilizing 2- and 4-nitrobenzoates individually as sole sources of carbon and energy. biochemical studies revealed the assimilation of 2- and 4-nitrobenzoates via 3-hydroxyanthranilate and protocatechuate, respectively. screening of a genomic fosmid library of strain st-14 constructed in escherichia coli identified two gene clusters, onb and pob-pca, to be responsible for the complete degradation of 2-nitrobenzoate a ...201627208126
a de-novo genome analysis pipeline (denogap) for large-scale comparative prokaryotic genomics studies.comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. while there are number of excellent tools developed for performing this task, most scale poorly when faced with hundreds of genome sequences, and many require extensive manual curation.201627363390
integrated analysis of root microbiomes of soybean and wheat from agricultural fields.root associated bacteria are critical for plant growth and health. understanding the composition and role of root microbiota is crucial toward agricultural practices that are less dependent on chemical fertilization, which has known negative effects on the environment and human health. here we analyzed the root-associated microbiomes of soybean and wheat under agricultural field conditions. we took samples from 11 different production fields across a large geographic area. we used 16s rrna pyros ...201627312589
isolation of bdellovibrio sp. from soil samples in mexico and their potential applications in control of pathogens.in this study, two strains of bdellovibrio were isolated from soil samples using the culture-dependent technique and two members of the family enterobacteriaceae (klebsiella sp. and salmonella sp.) as prey. the bdellovibrio strains were bacteriolytic, plaque-forming, and highly motile gram-negative bacteria. we identified and confirmed the bdellovibrio strains using microscopy, pcr amplification, and sequencing of the 16s rrna gene. they were observed to be different strains based on hit locus a ...201627297185
meta-analysis reveals that the genus pseudomonas can be a better choice of biological control agent against bacterial wilt disease caused by ralstonia solanacearum.biological control agents (bcas) from different microbial taxa are increasingly used to control bacterial wilt caused by ralstonia solanacearum. however, a quantitative research synthesis has not been conducted on the role of bcas in disease suppression. therefore, the present study aimed to meta-analyze the impacts of bcas on both ralstonia wilt disease suppression and plant (host) growth promotion. the analysis showed that the extent of disease suppression by bcas varied widely among studies, ...201627298597
coordinated regulation of species-specific hydroxycinnamic acid degradation and siderophore biosynthesis pathways in agrobacterium fabrum.the rhizosphere-inhabiting species agrobacterium fabrum (genomospecies g8 of the agrobacterium tumefaciens species complex) is known to degrade hydroxycinnamic acids (hcas), especially ferulic acid and p-coumaric acid, via the novel a. fabrum hca degradation pathway. gene expression profiles of a. fabrum strain c58 were investigated in the presence of hcas, using a c58 whole-genome oligoarray. both ferulic acid and p-coumaric acid caused variations in the expression of more than 10% of the c58 g ...201627060117
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
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
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
relating carbon and nitrogen isotope effects to reaction mechanisms during aerobic or anaerobic degradation of rdx (hexahydro-1,3,5-trinitro-1,3,5-triazine) by pure bacterial cultures.kinetic isotopic fractionation of carbon and nitrogen during rdx (hexahydro-1,3,5-trinitro-1,3,5-triazine) biodegradation was investigated with pure bacterial cultures under aerobic and anaerobic conditions. relatively large bulk enrichments in (15)n were observed during biodegradation of rdx via anaerobic ring cleavage (ε(15)n = -12.7‰ ± 0.8‰) and anaerobic nitro reduction (ε(15)n = -9.9‰ ± 0.7‰), in comparison to smaller effects during biodegradation via aerobic denitration (ε(15)n = -2.4‰ ± 0 ...201627016566
whole genome sequence analysis of an alachlor and endosulfan degrading pseudomonas strain w15feb9b isolated from ochlockonee river, florida.we recently isolated a pseudomonas sp. strain w15feb9b from ochlockonee river, florida and demonstrated potent biodegradative activity against two commonly used pesticides - alachlor [(2-chloro-2',6'-diethylphenyl-n (methoxymethyl)acetanilide)] and endosulfan [(6,7,8,9,10,10-hexachloro-1,5,5a,6,9,9a-hexahydro-6,9methano-2,3,4-benzo(e)di-oxathiepin-3-oxide], respectively. to further identify the repertoire of metabolic functions possessed by strain w15feb9b, a draft genome sequence was obtained, ...201627330991
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
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
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
biological low-ph mn(ii) oxidation in a manganese deposit influenced by metal-rich groundwater.the mechanisms, key organisms, and geochemical significance of biological low-ph mn(ii) oxidation are largely unexplored. here, we investigated the structure of indigenous mn(ii)-oxidizing microbial communities in a secondary subsurface mn oxide deposit influenced by acidic (ph 4.8) metal-rich groundwater in a former uranium mining area. microbial diversity was highest in the mn deposit compared to the adjacent soil layers and included the majority of known mn(ii)-oxidizing bacteria (mob) and tw ...201626969702
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
in silico structure and sequence analysis of bacterial porins and specific diffusion channels for hydrophilic molecules: conservation, multimericity and multifunctionality.diffusion channels are involved in the selective uptake of nutrients and form the largest outer membrane protein (omp) family in gram-negative bacteria. differences in pore size and amino acid composition contribute to the specificity. structure-based multiple sequence alignments shed light on the structure-function relations for all eight subclasses. entropy-variability analysis results are correlated to known structural and functional aspects, such as structural integrity, multimericity, speci ...201627110766
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
multi-host environments select for host-generalist conjugative plasmids.conjugative plasmids play an important role in bacterial evolution by transferring ecologically important genes within and between species. a key limit on interspecific horizontal gene transfer is plasmid host range. here, we experimentally test the effect of single and multi-host environments on the host-range evolution of a large conjugative mercury resistance plasmid, pqbr57. specifically, pqbr57 was conjugated between strains of a single host species, either p. fluorescens or p. putida, or a ...201627039285
cytokinin production by pseudomonas fluorescens g20-18 determines biocontrol activity against pseudomonas syringae in arabidopsis.plant beneficial microbes mediate biocontrol of diseases by interfering with pathogens or via strengthening the host. although phytohormones, including cytokinins, are known to regulate plant development and physiology as well as plant immunity, their production by microorganisms has not been considered as a biocontrol mechanism. here we identify the ability of pseudomonas fluorescens g20-18 to efficiently control p. syringae infection in arabidopsis, allowing maintenance of tissue integrity and ...201626984671
the higb/higa toxin/antitoxin system of pseudomonas aeruginosa influences the virulence factors pyochelin, pyocyanin, and biofilm formation.toxin/antitoxin (ta) systems are prevalent in most bacterial and archaeal genomes, and one of the emerging physiological roles of ta systems is to help regulate pathogenicity. although ta systems have been studied in several model organisms, few studies have investigated the role of ta systems in pseudomonads. here, we demonstrate that the previously uncharacterized proteins higb (unannotated) and higa (pa4674) of pseudomonas aeruginosa pa14 form a type ii ta system in which antitoxin higa masks ...201626987441
phenotypic heterogeneity and the evolution of bacterial life cycles.most bacteria live in colonies, where they often express different cell types. the ecological significance of these cell types and their evolutionary origin are often unknown. here, we study the evolution of cell differentiation in the context of surface colonization. we particularly focus on the evolution of a 'sticky' cell type that is required for surface attachment, but is costly to express. the sticky cells not only facilitate their own attachment, but also that of non-sticky cells. using i ...201626894881
biodegradation of ddt by stenotrophomonas sp. ddt-1: characterization and genome functional analysis.a novel bacterium capable of utilizing 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (ddt) as the sole carbon and energy source was isolated from a contaminated soil which was identified as stenotrophomonas sp. ddt-1 based on morphological characteristics, biolog gn2 microplate profile, and 16s rdna phylogeny. genome sequencing and functional annotation of the isolate ddt-1 showed a 4,514,569 bp genome size, 66.92% gc content, 4,033 protein-coding genes, and 76 rna genes including 8 rrna genes. ...201626888254
anoxic metabolism and biochemical production in pseudomonas putida f1 driven by a bioelectrochemical system.pseudomonas putida is a promising host for the bioproduction of chemicals, but its industrial applications are significantly limited by its obligate aerobic character. the aim of this paper is to empower the anoxic metabolism of wild-type pseudomonas putida to enable bioproduction anaerobically, with the redox power from a bioelectrochemical system (bes).201626893611
biocontrol agents promote growth of potato pathogens, depending on environmental conditions.there is a pressing need to understand and optimize biological control so as to avoid over-reliance on the synthetic chemical pesticides that can damage environmental and human health. this study focused on interactions between a novel biocontrol-strain, bacillus sp. jc12gb43, and potato-pathogenic phytophthora and fusarium species. in assays carried out in vitro and on the potato tuber, the bacterium was capable of near-complete inhibition of pathogens. this bacillus was sufficiently xerotolera ...201626880001
integrated foam fractionation for heterologous rhamnolipid production with recombinant pseudomonas putida in a bioreactor.heterologeous production of rhamnolipids in pseudomonas putida is characterized by advantages of a non-pathogenic host and avoidance of the native quorum sensing regulation in pseudomonas aeruginosa. yet, downstream processing is a major problem in rhamnolipid production and increases in complexity at low rhamnolipid titers and when using chemical foam control. this leaves the necessity of a simple concentrating and purification method. foam fractionation is an elegant method for in situ product ...201626860613
use of substrate-induced gene expression in metagenomic analysis of an aromatic hydrocarbon-contaminated soil.metagenomics allows the study of genes related to xenobiotic degradation in a culture-independent manner, but many of these studies are limited by the lack of genomic context for metagenomic sequences. this study combined a phenotypic screen known as substrate-induced gene expression (sigex) with whole-metagenome shotgun sequencing. sigex is a high-throughput promoter-trap method that relies on transcriptional activation of a green fluorescent protein (gfp) reporter gene in response to an induci ...201626590287
constitutive expression of a nag-like dioxygenase gene through an internal promoter in the 2-chloronitrobenzene catabolism gene cluster of pseudomonas stutzeri zwlr2-1.the gene cluster encoding the 2-chloronitrobenzene (2cnb) catabolism pathway in pseudomonas stutzeri zwlr2-1 is a patchwork assembly of a nag-like dioxygenase (dioxygenase belonging to the naphthalene dioxygenase nagaaabacad family from ralstonia sp. strain u2) gene cluster and a chlorocatechol catabolism cluster. however, the transcriptional regulator gene usually present in the nag-like dioxygenase gene cluster is missing, leaving it unclear how this cluster is expressed. the pattern of expres ...201627037114
epoxyalkane:coenzyme m transferase gene diversity and distribution in groundwater samples from chlorinated-ethene-contaminated sites.epoxyalkane:coenzyme m transferase (eacomt) plays a critical role in the aerobic biodegradation and assimilation of alkenes, including ethene, propene, and the toxic chloroethene vinyl chloride (vc). to improve our understanding of the diversity and distribution of eacomt genes in the environment, novel eacomt-specific terminal-restriction fragment length polymorphism (t-rflp) and nested-pcr methods were developed and applied to groundwater samples from six different contaminated sites. t-rflp a ...201627016563
extremophiles in an antarctic marine ecosystem.recent attempts to explore marine microbial diversity and the global marine microbiome have indicated a large proportion of previously unknown diversity. however, sequencing alone does not tell the whole story, as it relies heavily upon information that is already contained within sequence databases. in addition, microorganisms have been shown to present small-to-large scale biogeographical patterns worldwide, potentially making regional combinations of selection pressures unique. here, we focus ...201627681902
a new physiological role for the dna molecule as a protector against drying stress in desiccation-tolerant microorganisms.the dna molecule is associated with the role of encoding information required to produce rna which is translated into proteins needed by the cell. this encoding involves information transmission to offspring or to other organisms by horizontal transfer. however, despite the abundance of this molecule in both the cell and the environment, its physiological role seems to be restricted mainly to that of a coding and inheritance molecule. in this paper, we report a new physiological role for the dna ...201628066383
biological treatment of cyanide by using
klebsiella pneumoniae species.in this study, optimization conditions for cyanide biodegradation by klebsiella pneumoniae strain were determined to be 25 °c, ph=7 and 150 rpm at the concentration of 0.5 mm potassium cyanide in the medium. additionally, it was found that k. pneumoniae strain is not only able to degrade potassium cyanide, but also to degrade potassium hexacyanoferrate(ii) trihydrate and sodium ferrocyanide decahydrate with the efficiencies of 85 and 87.5%, respectively. furthermore, this strain degraded potassi ...201628115902
clinical relevance of molecular identification of microorganisms and detection of antimicrobial resistance genes in bloodstream infections of paediatric cancer patients.bloodstream infections (bsis) are the major cause of mortality in cancer patients. molecular techniques are used for rapid diagnosis of bsi, allowing early therapy and improving survival. we aimed to establish whether real-time quantitative polymerase chain reaction (qpcr) could improve early diagnosis and therapy in paediatric cancer patients, and describe the predominant pathogens of bsi and their antimicrobial susceptibility.201627585633
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
carbon sources for polyhydroxyalkanoates and an integrated biorefinery.polyhydroxyalkanoates (phas) are a group of bioplastics that have a wide range of applications. extensive progress has been made in our understanding of phas' biosynthesis, and currently, it is possible to engineer bacterial strains to produce phas with desired properties. the substrates for the fermentative production of phas are primarily derived from food-based carbon sources, raising concerns over the sustainability of their production in terms of their impact on food prices. this paper give ...201627447619
antimicrobial activities of bacteria associated with the brown alga padina pavonica.macroalgae belonging to the genus padina are known to produce antibacterial compounds that may inhibit growth of human- and animal pathogens. hitherto, it was unclear whether this antibacterial activity is produced by the macroalga itself or by secondary metabolite producing epiphytic bacteria. here we report antibacterial activities of epiphytic bacteria isolated from padina pavonica (peacocks tail) located on northern coast of tunisia. eighteen isolates were obtained in pure culture and tested ...201627462308
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
variable effects of exposure to formulated microbicides on antibiotic susceptibility in firmicutes and proteobacteria.microbicides are broad-spectrum antimicrobial agents that generally interact with multiple pharmacological targets. while they are widely deployed in disinfectant, antiseptic, and preservative formulations, data relating to their potential to select for microbicide or antibiotic resistance have been generated mainly by testing the compounds in much simpler aqueous solutions. in the current investigation, antibiotic susceptibility was determined for bacteria that had previously exhibited decrease ...201627060123
characterization of integrons and novel cassette arrays in bacteria from clinical isloates in china, 2000-2014.rapid dissemination of antibiotic resistance genes among bacterial isolates is an increasing problem in china. integron, a conserved dna sequence, which is carried on episomal genetic structures, plays a very important role in development of antibiotic resistance. this systematic analysis was based on medline and embase databases. we summarized the distribution and proportion of different types of gene cassette arrays of integrons (including class 1, 2, 3 and atypical class 1 integron) from clin ...201627533938
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
burns infection profile of singapore: prevalence of multidrug-resistant acinetobacter baumannii and the role of blood cultures.with various changes implemented such as perioperative antibiotics for tangential excision, this retrospective study reviews the infection profile of burn patients at singapore's only centralized burns unit. worldwide, the appearance of multidrug-resistant (mdr) strains of acinetobacter baumannii (a. baumannii) continues to worsen patient outcomes. this study also surveys the role of blood cultures in burns at our unit.201627574683
evaluation of a fully automated research prototype for the immediate identification of microorganisms from positive blood cultures under clinical conditions.a clinical laboratory evaluation of an intrinsic fluorescence spectroscopy (ifs)-based identification system paired to a bact/alert virtuo microbial detection system (biomérieux, inc., durham, nc) was performed to assess the potential for fully automated identification of positive blood cultures. the prototype ifs system incorporates a novel method combining a simple microbial purification procedure with rapid in situ identification via spectroscopy. results were available within 15 min of a bot ...201627094332
functional metagenomics of a biostimulated petroleum-contaminated soil reveals an extraordinary diversity of extradiol dioxygenases.a metagenomic library of a petroleum-contaminated soil was constructed in a fosmid vector that allowed heterologous expression of metagenomic dna. the library, consisting of 6.5 gb of metagenomic dna, was screened for extradiol dioxygenase (edo) activity using catechol and 2,3-dihydroxybiphenyl as the substrates. fifty-eight independent clones encoding extradiol dioxygenase activity were identified. forty-one different edo-encoding genes were identified. the population of edo genes was not domin ...201626896130
linking microbial community and catabolic gene structures during the adaptation of three contaminated soils under continuous long-term pollutant stress.three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (btex) for a period of 3 months. different from the soil from brazil (bra) and switzerland (sui), the czech republic (cze) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. bra and sui soil samples showed a clear succession of phylotypes. a rapid response to ...201626850298
towards an enhanced understanding of plant-microbiome interactions to improve phytoremediation: engineering the metaorganism.phytoremediation is a promising technology to clean-up contaminated soils based on the synergistic actions of plants and microorganisms. however, to become a widely accepted, and predictable remediation alternative, a deeper understanding of the plant-microbe interactions is needed. a number of studies link the success of phytoremediation to the plant-associated microbiome functioning, though whether the microbiome can exist in alternative, functional states for soil remediation, is incompletely ...201627014254
volatile compounds emitted by pseudomonas aeruginosa stimulate growth of the fungal pathogen aspergillus fumigatus.chronic lung infections with opportunistic bacterial and fungal pathogens are a major cause of morbidity and mortality especially in patients with cystic fibrosis. pseudomonas aeruginosa is the most frequently colonizing bacterium in these patients, and it is often found in association with the filamentous fungus aspergillus fumigatus. p. aeruginosa is known to inhibit the growth of a. fumigatus in situations of direct contact, suggesting the existence of interspecies communication that may infl ...201626980832
rhizospheric bacteria of maize with potential for biocontrol of fusarium verticillioides.the stalk, ear and root rot (serr) of maize caused by fusarium verticillioides (fv) severely impacts crop production in tropical and subtropical regions. the aim of the present work was to screen bacterial isolates in order to find novel native biocontrol agents against fv. a culturable bacterial collection consisting of 11,520 isolates enriched in firmicutes and proteobacteria was created from rhizosphere samples taken from serr symptomatic or asymptomatic maize plants. the complete collection ...201627066355
bacterial-plant-interactions: approaches to unravel the biological function of bacterial volatiles in the rhizosphere.rhizobacteria produce an enormous amount of volatile compounds, however, the function of these metabolites is scarcely understood. investigations evaluating influences on plants performed in various laboratories using individually developed experimental setups revealed different and often contradictory results, e.g., ranging from a significant plant growth promotion to a dramatic suppression of plant development. in addition to these discrepancies, these test systems neglected properties and com ...201626903987
regulation of the alkane hydroxylase cyp153 gene in a gram-positive alkane-degrading bacterium, dietzia sp. strain dq12-45-1b.cyp153, one of the most common medium-chain n-alkane hydroxylases belonging to the cytochrome p450 superfamily, is widely expressed in n-alkane-degrading bacteria. cyp153 is also thought to cooperate with alkb in degrading various n-alkanes. however, the mechanisms regulating the expression of the protein remain largely unknown. in this paper, we studied cyp153 gene transcription regulation by the potential arac family regulator (cypr) located upstream of the cyp153 gene cluster in a broad-spect ...201626567302
a microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor.a whole-cell biosensor utilizing a transcription factor (tf) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires access to an expanded repertoire of tfs. using homology modeling and ligand docking for binding pocket identification, assisted by conservative mutations in the pocket, we engineered a novel specificity in an acinetobacter tf, pobr, to 'sense' a chemical p-nitrophenol (pnp) and measured the response via a fluoresce ...201627536006
optical sensing of microbial life on surfaces.the label-free detection of microbial cells attached to a surface is an active field of research. the field is driven by the need to understand and control the growth of biofilms in a number of applications, including basic research in natural environments, industrial facilities, and clinical devices, to name a few. despite significant progress in the ability to monitor the growth of biofilms and related living cells, the sensitivity and selectivity of such sensors are still a challenge. we beli ...201626637605
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
crystal structures of apo and liganded 4-oxalocrotonate decarboxylase uncover a structural basis for the metal-assisted decarboxylation of a vinylogous β-keto acid.the enzymes in the catechol meta-fission pathway have been studied for more than 50 years in several species of bacteria capable of degrading a number of aromatic compounds. in a related pathway, naphthalene, a toxic polycyclic aromatic hydrocarbon, is fully degraded to intermediates of the tricarboxylic acid cycle by the soil bacteria pseudomonas putida g7. in this organism, the 83 kb nah7 plasmid carries several genes involved in this biotransformation process. one enzyme in this route, nahk, ...201627082660
bioaugmentation: an emerging strategy of industrial wastewater treatment for reuse and discharge.a promising long-term and sustainable solution to the growing scarcity of water worldwide is to recycle and reuse wastewater. in wastewater treatment plants, the biodegradation of contaminants or pollutants by harnessing microorganisms present in activated sludge is one of the most important strategies to remove organic contaminants from wastewater. however, this approach has limitations because many pollutants are not efficiently eliminated. to counterbalance the limitations, bioaugmentation ha ...201627571089
sulfide consumption in sulfurimonas denitrificans and heterologous expression of its three sulfide-quinone reductase homologs.sulfurimonas denitrificans is a sulfur-oxidizing epsilonproteobacterium. it has been reported to grow with sulfide and to harbor genes that encode sulfide-quinone reductases (sqrs) (catalyze sulfide oxidation). however, the actual sulfide concentrations at which s. denitrificans grows and whether its sqrs are functional remain enigmatic. here, we illustrate the sulfide concentrations at which s. denitrificans exhibits good growth, namely, 0.18 mm to roughly 1.7 mm. around 2.23 mm, sulfide appear ...201626833414
formaldehyde stress responses in bacterial pathogens.formaldehyde is the simplest of all aldehydes and is highly cytotoxic. its use and associated dangers from environmental exposure have been well documented. detoxification systems for formaldehyde are found throughout the biological world and they are especially important in methylotrophic bacteria, which generate this compound as part of their metabolism of methanol. formaldehyde metabolizing systems can be divided into those dependent upon pterin cofactors, sugar phosphates and those dependent ...201626973631
carbon nanomaterials in agriculture: a critical review.there has been great interest in the use of carbon nano-materials (cnms) in agriculture. however, the existing literature reveals mixed effects from cnm exposure on plants, ranging from enhanced crop yield to acute cytotoxicity and genetic alteration. these seemingly inconsistent research-outcomes, taken with the current technological limitations for in situ cnm detection, present significant hurdles to the wide scale use of cnms in agriculture. the objective of this review is to evaluate the cu ...201626941751
biochemical properties of paracoccus denitrificans fnrp: reactions with molecular oxygen and nitric oxide.in paracoccus denitrificans, three crp/fnr family regulatory proteins, narr, nnrr and fnrp, control the switch between aerobic and anaerobic (denitrification) respiration. fnrp is a [4fe-4s] cluster-containing homologue of the archetypal o2 sensor fnr from e. coli and accordingly regulates genes encoding aerobic and anaerobic respiratory enzymes in response to o2, and also no, availability. here we show that fnrp undergoes o2-driven [4fe-4s] to [2fe-2s] cluster conversion that involves up to 2 o ...201626790880
current state of knowledge in microbial degradation of polycyclic aromatic hydrocarbons (pahs): a review.polycyclic aromatic hydrocarbons (pahs) include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. the increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed toward removing pahs from the environment. pahs may undergo adsorption, volatilization, photoly ...201627630626
human interleukin-2 and hen egg white lysozyme: screening for bacteriolytic activity against various bacterial cells.the bacteriolytic activity of interleukin-2 and hen egg white lysozyme against 34 different species of microorganisms has been studied. it was found that 6 species of microorganisms are lysed in the presence of interleukin-2. all interleukin-2-sensitive microorganisms belong either to the enterobacteriaceae, bacillaceae, or the lactobacillaceae family. it was also found that 12 species of microorganisms are lysed in the presence of lysozyme, and 16 species of microorganisms are lysed in the pres ...201627099789
applicability of an in-house saponin-based extraction method in bruker biotyper matrix-assisted laser desorption/ionization time-of-flight mass spectrometry system for identification of bacterial and fungal species in positively flagged blood cultures.we used an in-house saponin-based extraction method to evaluate the performance of the bruker biotyper matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (maldi-tof/ms) system for the identification of bacteria and fungi in 405 positively flagged blood culture bottles. results obtained from maldi-tof/ms were compared with those obtained using conventional phenotypic identification methods. of the 405 positively flagged blood culture bottles, 365 showed monomicrobal grow ...201627695442
use of maldi-tof ms and culturomics to identify mosquitoes and their midgut microbiota.mosquitoes transmit a wide range of human parasitic and viral diseases. in recent years, new techniques such as maldi-tof ms have been developed to identify mosquitoes at the species level, which is key for entomological surveys. additionally, there is increasing interest in the mosquito microbiota and its role in vector capacity.201627613238
b1-metallo-β-lactamases: where do we stand?metallo-β-lactamases (mbls) are class bβ-lactamases that hydrolyze almost all clinically-availableβ-lactam antibiotics. mbls feature the distinctive αβ/βα sandwich fold of the metallo-hydrolase/oxidoreductase superfamily and possess a shallow active-site groove containing one or two divalent zinc ions, flanked by flexible loops. according to sequence identity and zinc ion dependence, mbls are classified into three subclasses (b1, b2 and b3), of which the b1 subclass enzymes have emerged as the m ...201626424398
antibiotic resistance mechanisms of myroides sp.bacteria of the genus myroides (myroides spp.) are rare opportunistic pathogens. myroides sp. infections have been reported mainly in china. myroides sp. is highly resistant to most available antibiotics, but the resistance mechanisms are not fully elucidated. current strain identification methods based on biochemical traits are unable to identify strains accurately at the species level. while 16s ribosomal rna (rrna) gene sequencing can accurately achieve this, it fails to give information on t ...201626984839
impact of soil salinity on the structure of the bacterial endophytic community identified from the roots of caliph medic (medicago truncatula).in addition to being a forage crop, caliph medic (medicago truncatula) is also a model legume plant and is used for research focusing on the molecular characterization of the interaction between rhizobia and plants. however, the endophytic microbiome in this plant is poorly defined. endophytic bacteria play a role in supplying plants with the basic requirements necessary for growth and development. moreover, these bacteria also play a role in the mechanism of salinity stress adaptation in plants ...201627391592
zinc-induced transposition of insertion sequence elements contributes to increased adaptability of cupriavidus metallidurans.bacteria can respond to adverse environments by increasing their genomic variability and subsequently facilitating adaptive evolution. to demonstrate this, the contribution of insertion sequence (is) elements to the genetic adaptation of cupriavidus metallidurans ae126 to toxic zinc concentrations was determined. this derivative of type strain ch34, devoid of its main zinc resistance determinant, is still able to increase its zinc resistance level. specifically, upon plating on medium supplement ...201627047473
characterization of three novel sxt/r391 integrating conjugative elements icemfuind1a and icemfuind1b, and icemprchn1 identified in the genomes of marinomonas fungiae jcm 18476(t) and marinomonas profundimaris strain d104.the genus marinomonas comprises gram negative bacteria which are widespread in the marine environment and there is no report on the genomic analysis of sxt/r391 ices derived from this group of bacteria. this study describes the genomic features of three new sxt/r391 integrating conjugating elements (ices) identified in the genome of marinomonas fungiae jcm 18476(t) (icemfuind1a and icemfuind1b) and in marinomonas profundimaris strain d104 (icemprchn1). structural organizations of the three ices ...201627933056
biosynthesis of α-pyrones.the α-pyrone moiety is a structural feature found in a huge variety of biologically active metabolites. in recent times new insights into additional biosynthetic mechanisms, yielding in such six-membered unsaturated ester ring residues have been obtained. the purpose of this mini-review is to give a brief overview of α-pyrones and the mechanisms forming the basis of their natural synthesis. especially the chain interconnecting enzymes, showing homology to ketosynthases which catalyze claisen-lik ...201627340449
comparative genomics of an endophytic pseudomonas putida isolated from mango orchard.we analyzed the genome sequence of an endophytic bacterial strain pseudomonas putida tji51 isolated from mango bark tissues. next generation dna sequencing and short read de novo assembly generated the 5,805,096 bp draft genome of p. putida tji51. out of 6,036 protein coding genes in p. putida tji51 sequences, 4,367 (72%) were annotated with functional specifications, while the remaining encoded hypothetical proteins. comparative genome sequence analysis revealed that the p. putida tji51genome c ...201627560648
keeping the wolves at bay: antitoxins of prokaryotic type ii toxin-antitoxin systems.in their initial stages of discovery, prokaryotic toxin-antitoxin (ta) systems were confined to bacterial plasmids where they function to mediate the maintenance and stability of usually low- to medium-copy number plasmids through the post-segregational killing of any plasmid-free daughter cells that developed. their eventual discovery as nearly ubiquitous and repetitive elements in bacterial chromosomes led to a wealth of knowledge and scientific debate as to their diversity and functionality i ...201627047942
genetic engineering and heterologous expression of the disorazol biosynthetic gene cluster via red/et recombineering.disorazol, a macrocyclic polykitide produced by the myxobacterium sorangium cellulosum so ce12 and it is reported to have potential cytotoxic activity towards several cancer cell lines, including multi-drug resistant cells. the disorazol biosynthetic gene cluster (dis) from sorangium cellulosum (so ce12) was identified by transposon mutagenesis and cloned in a bacterial artificial chromosome (bac) library. the 58-kb dis core gene cluster was reconstituted from bacs via red/et recombineering and ...201626875499
carbonate precipitation through microbial activities in natural environment, and their potential in biotechnology: a review.calcium carbonate represents a large portion of carbon reservoir and is used commercially for a variety of applications. microbial carbonate precipitation, a by-product of microbial activities, plays an important metal coprecipitation and cementation role in natural systems. this natural process occurring in various geological settings can be mimicked and used for a number of biotechnologies, such as metal remediation, carbon sequestration, enhanced oil recovery, and construction restoration. in ...201626835451
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
genetic analysis reveals the essential role of nitrogen phosphotransferase system components in sinorhizobium fredii ccbau 45436 symbioses with soybean and pigeonpea plants.the nitrogen phosphotransferase system (pts(ntr)) consists of ei(ntr), npr, and eiia(ntr). the active phosphate moiety derived from phosphoenolpyruvate is transferred through ei(ntr) and npr to eiia(ntr). sinorhizobium fredii can establish a nitrogen-fixing symbiosis with the legume crops soybean (as determinate nodules) and pigeonpea (as indeterminate nodules). in this study, s. fredii strains with mutations in ptsp and ptso (encoding ei(ntr) and npr, respectively) formed ineffective nodules on ...201626682851
prefiltering model for homology detection algorithms on gpu.homology detection has evolved over the time from heavy algorithms based on dynamic programming approaches to lightweight alternatives based on different heuristic models. however, the main problem with these algorithms is that they use complex statistical models, which makes it difficult to achieve a relevant speedup and find exact matches with the original results. thus, their acceleration is essential. the aim of this article was to prefilter a sequence database. to make this work, we have im ...201628008220
protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics.a functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. we investigated the use of protein domain architectures ...201627703668
identification of comamonas testosteroni as an androgen degrader in sewage.numerous studies have reported the masculinization of freshwater wildlife exposed to androgens in polluted rivers. microbial degradation is a crucial mechanism for eliminating steroid hormones from contaminated ecosystems. the aerobic degradation of testosterone was observed in various bacterial isolates. however, the ecophysiological relevance of androgen-degrading microorganisms in the environment is unclear. here, we investigated the biochemical mechanisms and corresponding microorganisms of ...201627734937
antimicrobial compounds from eukaryotic microalgae against human pathogens and diseases in aquaculture.the search for novel compounds of marine origin has increased in the last decades for their application in various areas such as pharmaceutical, human or animal nutrition, cosmetics or bioenergy. in this context of blue technology development, microalgae are of particular interest due to their immense biodiversity and their relatively simple growth needs. in this review, we discuss about the promising use of microalgae and microalgal compounds as sources of natural antibiotics against human path ...201627598176
delineation of steroid-degrading microorganisms through comparative genomic analysis.steroids are ubiquitous in natural environments and are a significant growth substrate for microorganisms. microbial steroid metabolism is also important for some pathogens and for biotechnical applications. this study delineated the distribution of aerobic steroid catabolism pathways among over 8,000 microorganisms whose genomes are available in the ncbi refseq database. combined analysis of bacterial, archaeal, and fungal genomes with both hidden markov models and reciprocal blast identified 2 ...201626956583
phosphotransferase-dependent accumulation of (p)ppgpp in response to glutamine deprivation in caulobacter crescentus.the alarmone (p)ppgpp is commonly used by bacteria to quickly respond to nutrient starvation. although (p)ppgpp synthetases such as spot have been extensively studied, little is known about the molecular mechanisms stimulating alarmone synthesis upon starvation. here, we describe an essential role of the nitrogen-related phosphotransferase system (pts(ntr)) in controlling (p)ppgpp accumulation in caulobacter crescentus. we show that cells sense nitrogen starvation by way of detecting glutamine d ...201627109061
metal-containing and related polymers for biomedical applications.a survey of the most recent progress in the biomedical applications of metal-containing polymers is given. due to the unique optical, electrochemical, and magnetic properties, at least 30 different metal elements, most of them transition metals, are introduced into polymeric frameworks for interactions with biology-relevant substrates via various means. inspired by the advance of metal-containing small molecular drugs and promoted by the great progress in polymer chemistry, metal-containing poly ...201626910408
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