Publications

identification of pseudomonas fluorescens chemotaxis sensory proteins for malate, succinate, and fumarate, and their involvement in root colonization.	pseudomonas fluorescens pf0-1 exhibited chemotactic responses to l-malate, succinate, and fumarate. we constructed a plasmid library of 37 methyl-accepting chemotaxis protein (mcp) genes of p. fluorescens pf0-1. to identify a mcp for l-malate, the plasmid library was screened using the pa2652 mutant of pseudomonas aeruginosa pao1, a mutant defective in chemotaxis to l-malate. the introduction of pfl01_0728 and pfl01_3768 genes restored the ability of the pa2652 mutant to respond to l-malate. the ...	2014	25491753
molecular modeling and computational analyses suggests that the sinorhizobium meliloti periplasmic regulator protein exor adopts a superhelical fold and is controlled by a unique mechanism of proteolysis.	the sinorhizobium meliloti periplasmic exor protein and the exos/chvi two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. in the absence of crystal structures, understanding the molecular mechanism of interaction between exor and the exos sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. in this study, we present a theoretical structural model of the active f ...	2014	25492513
molecular modeling and computational analyses suggests that the sinorhizobium meliloti periplasmic regulator protein exor adopts a superhelical fold and is controlled by a unique mechanism of proteolysis.	the sinorhizobium meliloti periplasmic exor protein and the exos/chvi two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. in the absence of crystal structures, understanding the molecular mechanism of interaction between exor and the exos sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. in this study, we present a theoretical structural model of the active f ...	2014	25492513
global analysis of photosynthesis transcriptional regulatory networks.	photosynthesis is a crucial biological process that depends on the interplay of many components. this work analyzed the gene targets for 4 transcription factors: fnrl, prra, crpk and mppg (rsp_2888), which are known or predicted to control photosynthesis in rhodobacter sphaeroides. chromatin immunoprecipitation followed by high-throughput sequencing (chip-seq) identified 52 operons under direct control of fnrl, illustrating its regulatory role in photosynthesis, iron homeostasis, nitrogen metabo ...	2014	25503406
formylglycine, a post-translationally generated residue with unique catalytic capabilities and biotechnology applications.	formylglycine (fgly) is a catalytically essential residue found almost exclusively in the active sites of type i sulfatases. formed by post-translational oxidation of cysteine or serine side chains, this aldehyde-functionalized residue participates in a unique and highly efficient catalytic mechanism for sulfate ester hydrolysis. the enzymes that produce fgly, formylglycine-generating enzyme (fge) and anaerobic sulfatase-maturating enzyme (ansme), are as unique and specialized as fgly itself. fg ...	2015	25514000
population genomics analysis of legume host preference for specific rhizobial genotypes in the rhizobium leguminosarum bv. viciae symbioses.	rhizobium leguminosarum bv. viciae establishes root nodule symbioses with several legume genera. although most isolates are equally effective in establishing symbioses with all host genera, previous evidence suggests that hosts select specific rhizobial genotypes among those present in the soil. we have used population genomics to further investigate this observation. pisum sativum, lens culinaris, vicia sativa, and v. faba plants were used to trap rhizobia from a well-characterized soil, and po ...	2015	25514682
plant-agrobacterium interaction mediated by ethylene and super-agrobacterium conferring efficient gene transfer.	agrobacterium tumefaciens has a unique ability to transfer genes into plant genomes. this ability has been utilized for plant genetic engineering. however, the efficiency is not sufficient for all plant species. several studies have shown that ethylene decreased the agrobacterium-mediated transformation frequency. thus, a. tumefaciens with an ability to suppress ethylene evolution would increase the efficiency of agrobacterium-mediated transformation. some studies showed that plant growth-promot ...	2014	25520733
structure and biological roles of sinorhizobium fredii hh103 exopolysaccharide.	here we report that the structure of the sinorhizobium fredii hh103 exopolysaccharide (eps) is composed of glucose, galactose, glucuronic acid, pyruvic acid, in the ratios 5∶2∶2∶1 and is partially acetylated. a s. fredii hh103 exoa mutant (svq530), unable to produce eps, not only forms nitrogen fixing nodules with soybean but also shows increased competitive capacity for nodule occupancy. mutant svq530 is, however, less competitive to nodulate vigna unguiculata. biofilm formation was reduced in ...	2014	25521500
fundamental shift in vitamin b12 eco-physiology of a model alga demonstrated by experimental evolution.	a widespread and complex distribution of vitamin requirements exists over the entire tree of life, with many species having evolved vitamin dependence, both within and between different lineages. vitamin availability has been proposed to drive selection for vitamin dependence, in a process that links an organism's metabolism to the environment, but this has never been demonstrated directly. moreover, understanding the physiological processes and evolutionary dynamics that influence metabolic dem ...	2014	25526368
fundamental shift in vitamin b12 eco-physiology of a model alga demonstrated by experimental evolution.	a widespread and complex distribution of vitamin requirements exists over the entire tree of life, with many species having evolved vitamin dependence, both within and between different lineages. vitamin availability has been proposed to drive selection for vitamin dependence, in a process that links an organism's metabolism to the environment, but this has never been demonstrated directly. moreover, understanding the physiological processes and evolutionary dynamics that influence metabolic dem ...	2014	25526368
activation of gab cluster transcription in bacillus thuringiensis by γ-aminobutyric acid or succinic semialdehyde is mediated by the sigma 54-dependent transcriptional activator gabr.	bacillus thuringiensis gabr is a sigma 54-dependent transcriptional activator containing three typical domains, an n-terminal regulatory domain per-arnt-sim (pas), a central aaa(+) (atpases associated with different cellular activities) domain and a c-terminal helix-turn-helix (hth) dna binding domain. gabr positively regulates the expression of the gabt gene of the gab gene cluster, which is responsible for the γ-aminobutyric acid (gaba) shunt.	2014	25527261
phaeobacter sp. strain y4i utilizes two separate cell-to-cell communication systems to regulate production of the antimicrobial indigoidine.	the marine roseobacter phaeobacter sp. strain y4i synthesizes the blue antimicrobial secondary metabolite indigoidine when grown in a biofilm or on agar plates. prior studies suggested that indigoidine production may be, in part, regulated by cell-to-cell communication systems. phaeobacter sp. strain y4i possesses two luxr and luxi homologous n-acyl-l-homoserine lactone (ahl)-mediated cell-to-cell communication systems, designated pgari and phari. we show here that y4i produces two dominantahls, ...	2015	25527537
counter-transcribed rnas of rhizobium leguminosarum repabc plasmids exert incompatibility effects only when highly expressed.	the six plasmids of rhizobium leguminosarum vf39sm comprise nearly 35% of the bacterium's genome and are all repabc replicons. the repabc operons of the three largest plasmids of vf39sm were found to have strong incompatibility determinants in the non-protein coding regions. however, in all three repabc operons, the intergenic region between repb and repc was the strongest incompatibility factor; this intergenic region has been shown, for most repabc plasmids, to encode a counter-transcribed rna ...	2015	25530178
genetic diversity of rhizobium from nodulating beans grown in a variety of mediterranean climate soils of chile.	in spite of potentially being an important source of rhizobial diversity and a key determinant of common bean productivity, there is a paucity of data on rhizobium genetic variation and species composition in the important bean producing area of chile and only one species has been documented (rhizobium leguminosarum). in this study, 240 rhizobium isolates from torcaza bean (phaseolus vulgaris l.) nodules established in the highest bean producing area in chile (33°34's-70°38'w and 37°36's-71°47'w ...	2015	25533847
global transcriptome analysis of mesorhizobium alhagi ccnwxj12-2 under salt stress.	mesorhizobium alhagi ccnwxj12-2 is a α-proteobacterium which could be able to fix nitrogen in the nodules formed with alhagi sparsifolia in northwest of china. desiccation and high salinity are the two major environmental problems faced by m. alhagi ccnwxj12-2. in order to identify genes involved in salt-stress adaption, a global transcriptional analysis of m. alhagi ccnwxj12-2 growing under salt-free and high salt conditions was carried out. the next generation sequencing technology, rna-seq, w ...	2014	25539655
the mannitol utilization system of the marine bacterium zobellia galactanivorans.	mannitol is a polyol that occurs in a wide range of living organisms, where it fulfills different physiological roles. in particular, mannitol can account for as much as 20 to 30% of the dry weight of brown algae and is likely to be an important source of carbon for marine heterotrophic bacteria. zobellia galactanivorans (flavobacteriia) is a model for the study of pathways involved in the degradation of seaweed carbohydrates. annotation of its genome revealed the presence of genes potentially i ...	2015	25548051
human clostridium difficile infection: inhibition of nhe3 and microbiota profile.	clostridium difficile infection (cdi) is principally responsible for hospital acquired, antibiotic-induced diarrhea and colitis and represents a significant financial burden on our healthcare system. little is known about c. difficile proliferation requirements, and a better understanding of these parameters is critical for development of new therapeutic targets. in cell lines, c. difficile toxin b has been shown to inhibit na(+)/h(+) exchanger 3 (nhe3) and loss of nhe3 in mice results in an alt ...	2014	25552580
human clostridium difficile infection: inhibition of nhe3 and microbiota profile.	clostridium difficile infection (cdi) is principally responsible for hospital acquired, antibiotic-induced diarrhea and colitis and represents a significant financial burden on our healthcare system. little is known about c. difficile proliferation requirements, and a better understanding of these parameters is critical for development of new therapeutic targets. in cell lines, c. difficile toxin b has been shown to inhibit na(+)/h(+) exchanger 3 (nhe3) and loss of nhe3 in mice results in an alt ...	2014	25552580
human clostridium difficile infection: altered mucus production and composition.	the majority of antibiotic-induced diarrhea is caused by clostridium difficile (c. difficile). hospitalizations for c. difficile infection (cdi) have tripled in the last decade, emphasizing the need to better understand how the organism colonizes the intestine and maintain infection. the mucus provides an interface for bacterial-host interactions and changes in intestinal mucus have been linked host health. to assess mucus production and composition in healthy and cdi patients, the main mucins m ...	2014	25552581
human clostridium difficile infection: altered mucus production and composition.	the majority of antibiotic-induced diarrhea is caused by clostridium difficile (c. difficile). hospitalizations for c. difficile infection (cdi) have tripled in the last decade, emphasizing the need to better understand how the organism colonizes the intestine and maintain infection. the mucus provides an interface for bacterial-host interactions and changes in intestinal mucus have been linked host health. to assess mucus production and composition in healthy and cdi patients, the main mucins m ...	2014	25552581
polyphenol oxidase affects normal nodule development in red clover (trifolium pratense l.).	polyphenol oxidase (ppo) may have multiple functions in tissues depending on its cellular or tissue localization. here we use ppo rnai transformants of red clover (trifolium pratense) to determine the role ppo plays in normal development of plants, and especially in n2-fixing nodules. in red clover, ppo was not essential for either growth or nodule production, or for nodule function in plants grown under optimal, n-free conditions. however, absence of ppo resulted in a more reduced environment i ...	2014	25566275
bacterial genospecies that are not ecologically coherent: population genomics of rhizobium leguminosarum.	biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. to establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium rhizobium leguminosarum by genomic sequencing of 72 isolates. although all strains have 16s rrna typical of r. leguminosarum, they fall into five genospecies by the criterion of average nucleotide identity (ani). many ...	2015	25589577
association between chloroplast and mitochondrial dna sequences in chinese prunus genotypes (prunus persica, prunus domestica, and prunus avium).	the nuclear dna is conventionally used to assess the diversity and relatedness among different species, but variations at the dna genome level has also been used to study the relationship among different organisms. in most species, mitochondrial and chloroplast genomes are inherited maternally; therefore it is anticipated that organelle dna remains completely associated. many research studies were conducted simultaneously on organelle genome. the objectives of this study was to analyze the genet ...	2015	25592231
leghemoglobin is nitrated in functional legume nodules in a tyrosine residue within the heme cavity by a nitrite/peroxide-dependent mechanism.	protein tyrosine (tyr) nitration is a post-translational modification yielding 3-nitrotyrosine (no2 -tyr). formation of no2 -tyr is generally considered as a marker of nitro-oxidative stress and is involved in some human pathophysiological disorders, but has been poorly studied in plants. leghemoglobin (lb) is an abundant hemeprotein of legume nodules that plays an essential role as an o2 transporter. liquid chromatography coupled to tandem mass spectrometry was used for a targeted search and qu ...	2015	25603991
udp-sulfoquinovose formation by sulfolobus acidocaldarius.	the udp-sulfoquinovose synthase agl3 from sulfolobus acidocaldarius converts udp-d-glucose and sulfite to udp-sulfoquinovose, the activated form of sulfoquinovose required for its incorporation into glycoconjugates. based on the amino acid sequence, agl3 belongs to the short-chain dehydrogenase/reductase enzyme superfamily, together with sqd1 from arabidopsis thaliana, the only udp-sulfoquinovose synthase with known crystal structure. by comparison of sequence and structure of agl3 and sqd1, put ...	2015	25605538
agrobacterium: nature's genetic engineer.	agrobacterium was identified as the agent causing the plant tumor, crown gall over 100 years ago. since then, studies have resulted in many surprising observations. armin braun demonstrated that agrobacterium infected cells had unusual nutritional properties, and that the bacterium was necessary to start the infection but not for continued tumor development. he developed the concept of a tumor inducing principle (tip), the factor that actually caused the disease. thirty years later the tip was s ...	2014	25610442
agrobacterium: nature's genetic engineer.	agrobacterium was identified as the agent causing the plant tumor, crown gall over 100 years ago. since then, studies have resulted in many surprising observations. armin braun demonstrated that agrobacterium infected cells had unusual nutritional properties, and that the bacterium was necessary to start the infection but not for continued tumor development. he developed the concept of a tumor inducing principle (tip), the factor that actually caused the disease. thirty years later the tip was s ...	2014	25610442
heterologous production of curcuminoids.	curcuminoids, components of the rhizome of turmeric, show several beneficial biological activities, including anticarcinogenic, antioxidant, anti-inflammatory, and antitumor activities. despite their numerous pharmaceutically important properties, the low natural abundance of curcuminoids represents a major drawback for their use as therapeutic agents. therefore, they represent attractive targets for heterologous production and metabolic engineering. the understanding of biosynthesis of curcumin ...	2015	25631288
new alkaline lipase from rhizomucor variabilis: biochemical properties and stability in the presence of microbial eps.	a new strain of rhizomucor variabilis producing an active extracellular lipase was identified and characterized in the present studies. the culture conditions were optimized and the highest lipase production amounting to 136 u/ml was achieved after 4 days of cultivation. the optimum ph (5.5) and temperature (28 °c) were determined as the best conditions for r. variabilis lipase production. the isolated enzyme preparation exhibited maximum activity at 40 °c and ph 8.0. lipase from r. variabilis w ...	2016	25643732
the extent of grain yield and plant growth enhancement by plant growth-promoting broad-spectrum streptomyces sp. in chickpea.	the physiological and molecular responses of five strains of streptomyces sp. (cai-17, cai-68, cai-78, kai-26 and kai-27), with their proven potential for charcoal rot disease control in sorghum and plant growth-promotion (pgp) in sorghum and rice, were studied to understand the mechanisms causing the beneficial effects. in this investigation, those five strains were evaluated for their pgp capabilities in chickpea in the 2012-13 and 2013-14 post-rainy seasons. all of the streptomyces sp. strain ...	2015	25646153
identification of ferredoxin ii as a major calcium binding protein in the nitrogen-fixing symbiotic bacterium mesorhizobium loti.	legumes establish with rhizobial bacteria a nitrogen-fixing symbiosis which is of the utmost importance for both plant nutrition and a sustainable agriculture. calcium is known to act as a key intracellular messenger in the perception of symbiotic signals by both the host plant and the microbial partner. regulation of intracellular free ca(2+) concentration, which is a fundamental prerequisite for any ca(2+)-based signalling system, is accomplished by complex mechanisms including ca(2+) binding ...	2015	25648224
novel mixed-linkage β-glucan activated by c-di-gmp in sinorhizobium meliloti.	an artificial increase of cyclic diguanylate (c-di-gmp) levels in sinorhizobium meliloti 8530, a bacterium that does not carry known cellulose synthesis genes, leads to overproduction of a substance that binds the dyes congo red and calcofluor. sugar composition and methylation analyses and nmr studies identified this compound as a linear mixed-linkage (1 → 3)(1 → 4)-β-d-glucan (ml β-glucan), not previously described in bacteria but resembling ml β-glucans found in plants and lichens. this uniqu ...	2015	25650430
rhizobium leguminosarum hupe is a highly-specific diffusion facilitator for nickel uptake.	bacteria require nickel transporters for the synthesis of ni-containing metalloenzymes in natural, low nickel habitats. in this work we carry out functional and topological characterization of rhizobium leguminosarum hupe, a nickel permease required for the provision of this element for [nife] hydrogenase synthesis. expression studies in the escherichia coli nikabcde mutant strain hyd723 revealed that hupe is a medium-affinity permease (apparent km 227 ± 21 nm; vmax 49 ± 21 pmol ni(2+) min(-1) m ...	2015	25652141
remodeling of the infection chamber before infection thread formation reveals a two-step mechanism for rhizobial entry into the host legume root hair.	in many legumes, root entry of symbiotic nitrogen-fixing rhizobia occurs via host-constructed tubular tip-growing structures known as infection threads (its). here, we have used a confocal microscopy live-tissue imaging approach to investigate early stages of it formation in medicago truncatula root hairs (rhs) expressing fluorescent protein fusion reporters. this has revealed that its only initiate 10 to 20 h after the completion of rh curling, by which time major modifications have occurred wi ...	2015	25659382
phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils.	phosphorus is the second important key element after nitrogen as a mineral nutrient in terms of quantitative plant requirement. although abundant in soils, in both organic and inorganic forms, its availability is restricted as it occurs mostly in insoluble forms. the p content in average soil is about 0.05% (w/w) but only 0.1% of the total p is available to plant because of poor solubility and its fixation in soil (illmer and schinner, soil biol biochem 27:257-263, 1995). an adequate supply of p ...	2013	25674415
a genomic encyclopedia of the root nodule bacteria: assessing genetic diversity through a systematic biogeographic survey.	root nodule bacteria are free-living soil bacteria, belonging to diverse genera within the alphaproteobacteria and betaproteobacteria, that have the capacity to form nitrogen-fixing symbioses with legumes. the symbiosis is specific and is governed by signaling molecules produced from both host and bacteria. sequencing of several model rnb genomes has provided valuable insights into the genetic basis of symbiosis. however, the small number of sequenced rnb genomes available does not currently ref ...	2015	25685260
the absence of protein y4ys affects negatively the abundance of t3ss mesorhizobium loti secretin, rhcc2, in bacterial membranes.	mesorhizobium loti maff303099 has a functional type iii secretion system (t3ss) that is involved in the determination of nodulation competitiveness on lotus. the m. loti t3ss cluster contains gene y4ys (mlr8765) that codes for a protein of unknown function (y4ys). a mutation in the y4ys gene favors the m. loti symbiotic competitive ability on lotus tenuis cv. esmeralda and affects negatively the secretion of proteins through t3ss. here we localize y4ys in the bacterial membrane using a translati ...	2015	25688250
a single serine residue determines selectivity to monovalent metal ions in metalloregulators of the merr family.	merr metalloregulators alleviate toxicity caused by an excess of metal ions, such as copper, zinc, mercury, lead, cadmium, silver, or gold, by triggering the expression of specific efflux or detoxification systems upon metal detection. the sensor protein binds the inducer metal ion by using two conserved cysteine residues at the c-terminal metal-binding loop (mbl). divalent metal ion sensors, such as merr and zntr, require a third cysteine residue, located at the beginning of the dimerization (α ...	2015	25691529
molecular and biochemical characterization of entamoeba histolytica fructokinase.	entamoeba histolytica is the causative agent of amoebic dysentery and liver abscess. the medium for its axenic culture contains glucose as energy source, and we addressed the question whether e. histolytica can also use fructose instead. as the amoebic hexokinases do not phosphorylate fructose, a separate fructokinase is essential. the genome project revealed a single candidate gene encoding an e. histolytica homolog of bacterial fructokinases. this gene was cloned, and the recombinant enzyme ha ...	2015	25700717
dephosphorylated npr is involved in an envelope stress response of escherichia coli.	besides the canonical phosphoenolpyruvate-dependent phosphotransferase system (pts) for carbohydrate transport, most proteobacteria possess the so-called nitrogen pts (pts(ntr)) that transfers a phosphate group from phosphoenolpyruvate (pep) over enzyme i(ntr) (ei(ntr)) and npr to enzyme iia(ntr) (eiia(ntr)). the pts(ntr) lacks membrane-bound components and functions exclusively in a regulatory capacity. while eiia(ntr) has been implicated in a variety of cellular processes such as potassium hom ...	2015	25701731
genome analysis of a novel bradyrhizobium sp. doa9 carrying a symbiotic plasmid.	bradyrhizobium sp. doa9 isolated from the legume aeschynomene americana exhibited a broad host range and divergent nodulation (nod) genes compared with other members of the bradyrhizobiaceae. genome analysis of doa9 revealed that its genome comprised a single chromosome of 7.1 mbp and a plasmid of 0.7 mbp. the chromosome showed highest similarity with that of the nod gene-harboring soybean symbiont b. japonicum usda110, whereas the plasmid showed highest similarity with pbbta01 of the nod gene-l ...	2015	25710540
starter unit flexibility for engineered product synthesis by the nonreducing polyketide synthase pksa.	nonreducing polyketide synthases (nr-pkss) are unique among pkss in their domain structure, notably including a starter unit:acyl-carrier protein (acp) transacylase (sat) domain that selects an acyl group as the primer for biosynthesis, most commonly acetyl-coa from central metabolism. this clan of mega-enzymes resembles fatty acid synthases (fass) by sharing both their central chain elongation steps and their capacity for iterative catalysis. in this mode of synthesis, catalytic domains involve ...	2015	25714897
[influence of calcium and rhizobial infections (rhizobium leguminosarum) on the dynamics of nitric oxide (no) content in roots of etiolated pea (pisum sativum l.) seedlings].	the effect of exogenous calcium (ca2+) and rhizobial infections (rhizobium leguminosarum bv viceae) on the dynamics of the level of nitric oxide (no) was studied in cross cuts of roots of two-day-old etiolated pea seedlings (pisum sativum l.) using a daf-2da fluorescent probe. fluctuations of the no level, indicating the presence of a rhythm in the generation of no in roots, were observed during the incubation of seedlings in water, a cacl2 solution, and with rhizobial infections. exogenous fact ...	2015	25726667
enzymatic production of defined chitosan oligomers with a specific pattern of acetylation using a combination of chitin oligosaccharide deacetylases.	chitin and chitosan oligomers have diverse biological activities with potentially valuable applications in fields like medicine, cosmetics, or agriculture. these properties may depend not only on the degrees of polymerization and acetylation, but also on a specific pattern of acetylation (pa) that cannot be controlled when the oligomers are produced by chemical hydrolysis. to determine the influence of the pa on the biological activities, defined chitosan oligomers in sufficient amounts are need ...	2015	25732514
against friend and foe: type 6 effectors in plant-associated bacteria.	bacterial secretion systems play critical roles in communication with neighboring bacteria and in the modulation of host immune responses via the secretion of small proteins called effectors. several secretion systems have been identified and these are denoted types i-vii. of these, the type vi secretion system (t6ss) and its effectors were only recently elucidated. most studies on the role and significance of the t6ss and its effectors have focused on human pathogens. in this review, type 6 eff ...	2015	25732741
characterization and evaluation of an arbitrary primed polymerase chain reaction (pcr) product for the specific detection of brucella species.	laboratory detection of brucella is based largely on bacterial isolation and phenotypic characterization. these methods are lengthy and labor-intensive and have been associated with a heightened risk of laboratory-acquired infection. antibody based indirect detection methods also suffer from limitations in proper diagnosis of the organism. to overcome these problems, nucleic acid amplification has been explored for rapid detection and confirmation of the presence of brucella spp. pcr-based diagn ...	2014	25737656
characterization and evaluation of an arbitrary primed polymerase chain reaction (pcr) product for the specific detection of brucella species.	laboratory detection of brucella is based largely on bacterial isolation and phenotypic characterization. these methods are lengthy and labor-intensive and have been associated with a heightened risk of laboratory-acquired infection. antibody based indirect detection methods also suffer from limitations in proper diagnosis of the organism. to overcome these problems, nucleic acid amplification has been explored for rapid detection and confirmation of the presence of brucella spp. pcr-based diagn ...	2014	25737656
high-throughput, signature-tagged mutagenic approach to identify novel virulence factors of yersinia pestis co92 in a mouse model of infection.	the identification of new virulence factors in yersinia pestis and understanding their molecular mechanisms during an infection process are necessary in designing a better vaccine or to formulate an appropriate therapeutic intervention. by using a high-throughput, signature-tagged mutagenic approach, we created 5,088 mutants of y. pestis strain co92 and screened them in a mouse model of pneumonic plague at a dose equivalent to 5 50% lethal doses (ld50) of wild-type (wt) co92. from this screen, w ...	2015	25754198
comparative genomics of roseobacter clade bacteria isolated from the accessory nidamental gland of euprymna scolopes.	the accessory nidamental gland (ang) of the female hawaiian bobtail squid, euprymna scolopes, houses a consortium of bacteria including members of the flavobacteriales, rhizobiales, and verrucomicrobia but is dominated by members of the roseobacter clade (rhodobacterales) within the alphaproteobacteria. these bacteria are deposited into the jelly coat of the squid's eggs, however, the function of the ang and its bacterial symbionts has yet to be elucidated. in order to gain insight into this con ...	2015	25755651
a bioinformatic survey of distribution, conservation, and probable functions of luxr solo regulators in bacteria.	luxr solo transcriptional regulators contain both an autoinducer binding domain (abd; n-terminal) and a dna binding helix-turn-helix domain (hth; c-terminal), but are not associated with a cognate n-acyl homoserine lactone (ahl) synthase coding gene in the same genome. although a few luxr solos have been characterized, their distributions as well as their role in bacterial signal perception and other processes are poorly understood. in this study we have carried out a systematic survey of distri ...	2015	25759807
pgprs and nitrogen-fixing legumes: a perfect team for efficient cd phytoremediation?	cadmium (cd) is a toxic, biologically non-essential and highly mobile metal that has become an increasingly important environmental hazard to both wildlife and humans. in contrast to conventional remediation technologies, phytoremediation based on legume-rhizobia symbiosis has emerged as an inexpensive decontamination alternative which also revitalize contaminated soils due to the role of legumes in nitrogen cycling. in recent years, there is a growing interest in understanding symbiotic legume- ...	2015	25763004
organic amendments to avocado crops induce suppressiveness and influence the composition and activity of soil microbial communities.	one of the main avocado diseases in southern spain is white root rot caused by the fungus rosellinia necatrix prill. the use of organic soil amendments to enhance the suppressiveness of natural soil is an inviting approach that has successfully controlled other soilborne pathogens. this study tested the suppressive capacity of different organic amendments against r. necatrix and analyzed their effects on soil microbial communities and enzymatic activities. two-year-old avocado trees were grown i ...	2015	25769825
thermodynamic matchers for the construction of the cuckoo rna family.	rna family models describe classes of functionally related, non-coding rnas based on sequence and structure conservation. the most important method for modeling rna families is the use of covariance models, which are stochastic models that serve in the discovery of yet unknown, homologous rnas. however, the performance of covariance models in finding remote homologs is poor for rna families with high sequence conservation, while for families with high structure but low sequence conservation, the ...	2015	25779873
genome-guided analysis of physiological capacities of tepidanaerobacter acetatoxydans provides insights into environmental adaptations and syntrophic acetate oxidation.	this paper describes the genome-based analysis of tepidanaerobacter acetatoxydans strain re1, a syntrophic acetate-oxidising bacterium (saob). principal issues such as environmental adaptations, metabolic capacities, and energy conserving systems have been investigated and the potential consequences for syntrophic acetate oxidation discussed. briefly, in pure culture, t. acetatoxydans grows with different organic compounds and produces acetate as the main product. in a syntrophic consortium with ...	2015	25811859
[population structure of the clover rhizobia rhizobium leguminosarum bv. trifolii upon transition from soil into the nodular niche].	high-throughput sequencing of the amplicon gene library revealed variations in the population structure of clover rhizobia (rhizobium leguminosarum bv. trifolii) upon transition from soil into the root nodules of the host plant (trifolium-hybridum). analysis of rhizobial-diversity using the noda gene revealed 3258 and 1449 nucleotide sequences (allelic-variants) for the soil and root nodule population, respectively. they were combined into 29 operational taxonomic units (otu) according to the 97 ...	2015	25844461
structural elucidation of the outer core tetrasaccharide isolated from the lps of rhizobium leguminosarum bv. trifolii strain 24.	the outer core oligosaccharide (os) was isolated from the lipopolysaccharide (lps) of rhizobium leguminosarum bv. trifolii strain 24 after smith degradation and then studied by sugar and methylation analyses along with nmr and mass spectrometry methods. negative-ion electrospray (esi-ms) mass spectrum showed two molecular ions at m/z 686.3 and 728.3, which corresponded to the core os having the composition rha2quinackdh. the mass difference between both ions indicated that the higher molecule ma ...	2015	25880336
regulatory nodd1 and nodd2 genes of rhizobium tropici strain ciat 899 and their roles in the early stages of molecular signaling and host-legume nodulation.	nodulation and symbiotic nitrogen fixation are mediated by several genes, both of the host legume and of the bacterium. the rhizobial regulatory nodd gene plays a critical role, orchestrating the transcription of the other nodulation genes. rhizobium tropici strain ciat 899 is an effective symbiont of several legumes-with an emphasis on common bean (phaseolus vulgaris)-and is unusual in carrying multiple copies of nodd, the roles of which remain to be elucidated.	2015	25880529
distribution in microbial genomes of genes similar to loda and goxa which encode a novel family of quinoproteins with amino acid oxidase activity.	l-amino acid oxidases (laos) have been generally described as flavoproteins that oxidize amino acids releasing the corresponding ketoacid, ammonium and hydrogen peroxide. the generation of hydrogen peroxide gives to these enzymes antimicrobial characteristics. they are involved in processes such as biofilm development and microbial competition. laos are of great biotechnological interest in different applications such as the design of biosensors, biotransformations and biomedicine. the marine ba ...	2015	25886995
biochemical and phylogenetic analyses of phosphatidylinositol production in angomonas deanei, an endosymbiont-harboring trypanosomatid.	the endosymbiosis in trypanosomatids is characterized by co-evolution between one bacterium and its host protozoan in a mutualistic relationship, thus constituting an excellent model to study organelle origin in the eukaryotic cell. in this association, an intense metabolic exchange is observed between both partners: the host provides energetic molecules and a stable environment to a reduced wall symbiont, while the bacterium is able to interfere in host metabolism by enhancing phospholipid prod ...	2015	25903782
role of root microbiota in plant productivity.	the growing human population requires increasing amounts of food, but modern agriculture has limited possibilities for increasing yields. new crop varieties may be bred to have increased yields and be more resistant to environmental stress and pests. however, they still require fertilization to supplement essential nutrients that are normally limited in the soil. soil microorganisms present an opportunity to reduce the requirement for inorganic fertilization in agriculture. microorganisms, due t ...	2015	25908654
rhizobium leguminosarum bv. viciae 3841 adapts to 2,4-dichlorophenoxyacetic acid with "auxin-like" morphological changes, cell envelope remodeling and upregulation of central metabolic pathways.	there is a growing need to characterize the effects of environmental stressors at the molecular level on model organisms with the ever increasing number and variety of anthropogenic chemical pollutants. the herbicide 2,4-dichlorophenoxyacetic acid (2,4-d), as one of the most widely applied pesticides in the world, is one such example. this herbicide is known to have non-targeted undesirable effects on humans, animals and soil microbes, but specific molecular targets at sublethal levels are unkno ...	2015	25919284
genomic features separating ten strains of neorhizobium galegae with different symbiotic phenotypes.	the symbiotic phenotype of neorhizobium galegae, with strains specifically fixing nitrogen with either galega orientalis or g. officinalis, has made it a target in research on determinants of host specificity in nitrogen fixation. the genomic differences between representative strains of the two symbiovars are, however, relatively small. this introduced a need for a dataset representing a larger bacterial population in order to make better conclusions on characteristics typical for a subset of t ...	2015	25933608
extensive identification of bacterial riboflavin transporters and their distribution across bacterial species.	riboflavin, the precursor for the cofactors flavin mononucleotide (fmn) and flavin adenine dinucleotide, is an essential metabolite in all organisms. while the functions for de novo riboflavin biosynthesis and riboflavin import may coexist in bacteria, the extent of this co-occurrence is undetermined. the ribm, ribn, rfuabcd and the energy-coupling factor-ribu bacterial riboflavin transporters have been experimentally characterized. in addition, impx, rfnt and ribxy are proposed as riboflavin tr ...	2015	25938806
e151 (sym15), a pleiotropic mutant of pea (pisum sativum l.), displays low nodule number, enhanced mycorrhizae, delayed lateral root emergence, and high root cytokinin levels.	in legumes, the formation of rhizobial and mycorrhizal root symbioses is a highly regulated process which requires close communication between plant and microorganism. plant mutants that have difficulties establishing symbioses are valuable tools for unravelling the mechanisms by which these symbioses are formed and regulated. here e151, a mutant of pisum sativum cv. sparkle, was examined to characterize its root growth and symbiotic defects. the symbioses in terms of colonization intensity, fun ...	2015	25948707
autoantigen cross-reactive environmental antigen can trigger multiple sclerosis-like disease.	multiple sclerosis is generally considered an autoimmune disease resulting from interaction between predisposing genes and environmental factors, together allowing immunological self-tolerance to be compromised. the precise nature of the environmental inputs has been elusive, infectious agents having received considerable attention. a recent study generated an algorithm predicting naturally occurring t cell receptor (tcr) ligands from the proteome database. taking the example of a multiple scler ...	2015	25962509
enhancing growth performance and systemic acquired resistance of medicinal plant sesbania sesban (l.) merr using arbuscular mycorrhizal fungi under salt stress.	pot experiments were conducted to evaluate the damaging effects of salinity on sesbania sesban plants in the presence and absence of arbuscular mycorrhizal fungi (amf). the selected morphological, physiological and biochemical parameters of s. sesban were measured. salinity reduced growth and chlorophyll content drastically while as amf inoculated plants improved growth. a decrease in the number of nodules, nodule weight and nitrogenase activity was also evident due to salinity stress causing re ...	2015	25972748
assessment of genetic diversity among faba bean genotypes using agro-morphological and molecular markers.	forty faba bean (vicia faba l.) genotypes were evaluated for their agro-morphological performance and molecular diversity under central region of saudi arabia conditions during 2010-11 and 2011-12 seasons. field performance results showed that faba genotypes exhibited a significant amount of variation for their agro-morphological studied parameters. giza40 recorded the tallest genotype (139.5 cm), highest number of seeds per plants (100.8), and the highest seed yield per plant (70.8 g). the best ...	2015	25972757
the pho regulon: a huge regulatory network in bacteria.	one of the most important achievements of bacteria is its capability to adapt to the changing conditions of the environment. the competition for nutrients with other microorganisms, especially in the soil, where nutritional conditions are more variable, has led bacteria to evolve a plethora of mechanisms to rapidly fine-tune the requirements of the cell. one of the essential nutrients that are normally found in low concentrations in nature is inorganic phosphate (pi). bacteria, as well as other ...	2015	25983732
multiple chaperonins in bacteria--novel functions and non-canonical behaviors.	chaperonins are a class of molecular chaperones that assemble into a large double ring architecture with each ring constituting seven to nine subunits and enclosing a cavity for substrate encapsulation. the well-studied escherichia coli chaperonin groel binds non-native substrates and encapsulates them in the cavity thereby sequestering the substrates from unfavorable conditions and allowing the substrates to fold. using this mechanism, groel assists folding of about 10-15 % of cellular proteins ...	2015	25986150
an update on iron acquisition by legionella pneumophila: new pathways for siderophore uptake and ferric iron reduction.	iron acquisition is critical for the growth and pathogenesis of legionella pneumophila, the causative agent of legionnaires' disease. l. pneumophila utilizes two main modes of iron assimilation, namely ferrous iron uptake via the feob system and ferric iron acquisition through the action of the siderophore legiobactin. this review highlights recent studies concerning the mechanism of legiobactin assimilation, the impact of c-type cytochromes on siderophore production, the importance of legiobact ...	2015	26000653
molecular detection of bacteria in plant tissues, using universal 16s ribosomal dna degenerated primers.	highly specific, sensitive and rapid tests are required for the detection and identification of covert bacterial contaminations in plant tissue cultures. current methods available for this purpose are tedious, time consuming, highly error prone, expensive, require advanced technical expertise and are sometimes ineffective. we report here the development of a sensitive polymerase chain reaction (pcr) based method for the rapid detection and identification of bacteria occurring in plant tissue cul ...	2014	26019546
candidatus frankia datiscae dg1, the actinobacterial microsymbiont of datisca glomerata, expresses the canonical nod genes nodabc in symbiosis with its host plant.	frankia strains are nitrogen-fixing soil actinobacteria that can form root symbioses with actinorhizal plants. phylogenetically, symbiotic frankiae can be divided into three clusters, and this division also corresponds to host specificity groups. the strains of cluster ii which form symbioses with actinorhizal rosales and cucurbitales, thus displaying a broad host range, show suprisingly low genetic diversity and to date can not be cultured. the genome of the first representative of this cluster ...	2015	26020781
dna microarray-based identification of genes regulated by ntrc in bradyrhizobium japonicum.	the bradyrhizobium japonicum ntrbc two-component system is a critical regulator of cellular nitrogen metabolism, including the acquisition and catabolism of nitrogenous compounds. to better define the roles of this system, genome-wide transcriptional profiling was performed to identify the ntrc regulon during the response to nitrogen limitation. upon cells perceiving low intracellular nitrogen, they stimulate the phosphorylation of ntrc, which induces genes responsible for alteration of the core ...	2015	26025905
cicer canariense, an endemic legume to the canary islands, is nodulated in mainland spain by fast-growing strains from symbiovar trifolii phylogenetically related to rhizobium leguminosarum.	cicer canariense is a threatened endemic legume from the canary islands where it can be nodulated by mesorhizobial strains from the symbiovar ciceri, which is the common worldwide endosymbiont of cicer arietinum linked to the genus mesorhizobium. however, when c. canariense was cultivated in a soil from mainland spain, where the symbiovar ciceri is present, only fast-growing rhizobial strains were unexpectedly isolated from its nodules. these strains were classified into the genus rhizobium by a ...	2015	26032249
nodulation characterization and proteomic profiling of bradyrhizobium liaoningense ccbau05525 in response to water-soluble humic materials.	the lignite biodegradation procedure to produce water-soluble humic materials (wshm) with a penicillium stain was established by previous studies in our laboratory. this study researched the effects of wshm on the growth of bradyrhizobium liaoningense ccbau05525 and its nodulation on soybean. results showed that wshm enhanced the cell density of ccbau05525 in culture, and increased the nodule number, nodule fresh weight and nitrogenase activity of the inoculated soybean plants. then the chemical ...	2015	26054030
bacterial cellulose biosynthesis: diversity of operons, subunits, products, and functions.	recent studies of bacterial cellulose biosynthesis, including structural characterization of a functional cellulose synthase complex, provided the first mechanistic insight into this fascinating process. in most studied bacteria, just two subunits, bcsa and bcsb, are necessary and sufficient for the formation of the polysaccharide chain in vitro. other subunits - which differ among various taxa - affect the enzymatic activity and product yield in vivo by modulating (i) the expression of the bios ...	2015	26077867
pseudorhizobium pelagicum gen. nov., sp. nov. isolated from a pelagic mediterranean zone.	two novel alphaproteobacteria strains, r1-200b4(t) and r2-400b4, were isolated from the mediterranean sea off the coast of alicante in spain. the phylogenetic analysis of the 16s rrna gene showed that they are related to members of family rhizobiaceae. the 16s rrna gene sequence of strain r1-200b4(t) presents 97.0% and 95.6% similarity with respect to the type strains of the type species from genera neorhizobium and rhizobium, neorhizobium galegae hambi 540(t) and rhizobium leguminosarum usda 23 ...	2015	26078205
influence of seeding ratio, planting date, and termination date on rye-hairy vetch cover crop mixture performance under organic management.	cover crop benefits include nitrogen accumulation and retention, weed suppression, organic matter maintenance, and reduced erosion. organic farmers need region-specific information on winter cover crop performance to effectively integrate cover crops into their crop rotations. our research objective was to compare cover crop seeding mixtures, planting dates, and termination dates on performance of rye (secale cereale l.) and hairy vetch (vicia villosa roth) monocultures and mixtures in the marit ...	2015	26080008
cooperative electrostatic interactions drive functional evolution in the alkaline phosphatase superfamily.	it is becoming widely accepted that catalytic promiscuity, i.e., the ability of a single enzyme to catalyze the turnover of multiple, chemically distinct substrates, plays a key role in the evolution of new enzyme functions. in this context, the members of the alkaline phosphatase superfamily have been extensively studied as model systems in order to understand the phenomenon of enzyme multifunctionality. in the present work, we model the selectivity of two multiply promiscuous members of this s ...	2015	26091851
nitrite-oxidizing bacterium nitrobacter winogradskyi produces n-acyl-homoserine lactone autoinducers.	nitrobacter winogradskyi is a chemolithotrophic bacterium that plays a role in the nitrogen cycle by oxidizing nitrite to nitrate. here, we demonstrate a functional n-acyl-homoserine lactone (acyl-hsl) synthase in this bacterium. the n. winogradskyi genome contains genes encoding a putative acyl-hsl autoinducer synthase (nwi0626, nwii) and a putative acyl-hsl autoinducer receptor (nwi0627, nwir) with amino acid sequences 38 to 78% identical to those in rhodopseudomonas palustris and other rhizob ...	2015	26092466
sitona lineatus (coleoptera: curculionidae) larval feeding on pisum sativum l. affects soil and plant nitrogen.	adults of sitona lineatus (pea leaf weevil, plw) feed on foliage of several fabaceae species but larvae prefer to feed on nodules of pisum sativum l. and vicia faba l. indirectly, through their feeding on rhizobia, weevils can reduce soil and plant available nitrogen (n). however, initial soil n can reduce nodulation and damage by the weevil and reduce control requirements. understanding these interactions is necessary to make integrated pest management recommendations for plw. we conducted a gr ...	2015	26106086
pseudomonas aeruginosa mifs-mifr two-component system is specific for α-ketoglutarate utilization.	pseudomonas aeruginosa is a gram-negative, metabolically versatile opportunistic pathogen that elaborates a multitude of virulence factors, and is extraordinarily resistant to a gamut of clinically significant antibiotics. this ability, in part, is mediated by two-component regulatory systems (tcs) that play a crucial role in modulating virulence mechanisms and metabolism. mifs (pa5512) and mifr (pa5511) form one such tcs implicated in biofilm formation. mifs is a sensor kinase whereas mifr belo ...	2015	26114434
the hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes.	all plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. these microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. the increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. the nature of plant-endophyte interactions ranges from mutualism to pathogenicity. this depends on a set of abiotic and bi ...	2015	26136581
plasmid-encoded repa proteins specifically autorepress individual repabc operons in the multipartite rhizobium leguminosarum bv. trifolii genome.	rhizobia commonly have very complex genomes with a chromosome and several large plasmids that possess genes belonging to the repabc family. repa and repb are members of the para and parb families of partitioning proteins, respectively, whereas repc is crucial for plasmid replication. in the repabc replicons, partitioning and replication functions are transcriptionally linked resulting in complex regulation of rep gene expression. the genome of r. leguminosarum bv. trifolii ta1 (rtta1) consists o ...	2015	26147968
role of the transporter-like sensor kinase cbra in histidine uptake and signal transduction.	cbra is an atypical sensor kinase found in pseudomonas. the autokinase domain is connected to a putative transporter of the sodium/solute symporter family (sssf). cbra functions together with its cognate response regulator, cbrb, and plays an important role in nutrient acquisition, including regulation of hut genes for the utilization of histidine and its derivative, urocanate. here we report on the findings of a genetic and biochemical analysis of cbra with a focus on the function of the putati ...	2015	26148710
deep characterization of the microbiomes of calophya spp. (hemiptera: calophyidae) gall-inducing psyllids reveals the absence of plant pathogenic bacteria and three dominant endosymbionts.	bacteria associated with sap-feeding insect herbivores include not only symbionts that may increase their hosts' fitness but also harmful plant pathogens. calophya spp. gall-inducing psyllids (hemiptera: calophyidae) are being investigated for their potential as biological control agents of the noxious weed, brazilian peppertree (schinus terebinthifolia), in florida. although there are no examples of plant pathogen transmission by members of the family calophyidae, several insects in the superfa ...	2015	26161659
arabinose and protocatechuate catabolism genes are important for growth of rhizobium leguminosarum biovar viciae in the pea rhizosphere.	to form nitrogen-fixing nodules on pea roots, rhizobium leguminosarum biovar viciae must be competitive in the rhizosphere. our aim was to identify genes important for rhizosphere fitness.	2015	26166901
img-abc: a knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites.	in the discovery of secondary metabolites, analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of computational platforms that enable such a systematic approach on a large scale. in this work, we present img-abc (https://img.jgi.doe.gov/abc), an atlas of biosynthetic gene clusters within the integrated microbial genomes (img) system, which is aimed at harnessing the power of "big" genomic data for discovering small molecules. img-abc relie ...	2015	26173699
identification of bradyrhizobium elkanii genes involved in incompatibility with soybean plants carrying the rj4 allele.	symbioses between leguminous plants and soil bacteria known as rhizobia are of great importance to agricultural production and nitrogen cycling. while these mutualistic symbioses can involve a wide range of rhizobia, some legumes exhibit incompatibility with specific strains, resulting in ineffective nodulation. the formation of nodules in soybean plants (glycine max) is controlled by several host genes, which are referred to as rj genes. the soybean cultivar barc2 carries the rj4 gene, which re ...	2015	26187957
bacterial cyanuric acid hydrolase for water treatment.	di- and trichloroisocyanuric acids are widely used as water disinfection agents, but cyanuric acid accumulates with repeated additions and must be removed to maintain free hypochlorite for disinfection. this study describes the development of methods for using a cyanuric acid-degrading enzyme contained within nonliving cells that were encapsulated within a porous silica matrix. initially, three different bacterial cyanuric acid hydrolases were compared: trzd from acidovorax citrulli strain 12227 ...	2015	26187963
characterization of para-nitrophenol-degrading bacterial communities in river water by using functional markers and stable isotope probing.	microbial degradation is a major determinant of the fate of pollutants in the environment. para-nitrophenol (pnp) is an epa-listed priority pollutant with a wide environmental distribution, but little is known about the microorganisms that degrade it in the environment. we studied the diversity of active pnp-degrading bacterial populations in river water using a novel functional marker approach coupled with [(13)c6]pnp stable isotope probing (sip). culturing together with culture-independent ter ...	2015	26209677
high-quality permanent draft genome sequence of rhizobium leguminosarum bv. viciae strain gb30; an effective microsymbiont of pisum sativum growing in poland.	rhizobium leguminosarum bv. viciae gb30 is an aerobic, motile, gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of pisum sativum. gb30 was isolated in poland from a nodule recovered from the roots of pisum sativum growing at janow. gb30 is also an effective microsymbiont of the annual forage legumes vetch and pea. here we describe the features of r. leguminosarum bv. viciae strain gb30, together with sequence and annotation. the 7,468,464 bp h ...	2015	26221417
draft genome sequence of the bacteriocin-producing bradyrhizobium japonicum strain fn1.	bradyrhizobium japonicum strain fn1 was found to produce bacteriocin-like zones of clearing when tested against other strains of bradyrhizbia. the genome was sequenced, and several putative bacteriocin-producing genes, in addition to the expected genes involved in nodulation and nitrogen fixation, were identified.	2015	26227594
bacteria-zinc co-localization implicates enhanced synthesis of cysteine-rich peptides in zinc detoxification when brassica juncea is inoculated with rhizobium leguminosarum.	some plant growth promoting bacteria (pgpb) are enigmatic in enhancing plant growth in the face of increased metal accumulation in plants. since most pgpb colonize the plant root epidermis, we hypothesized that pgpb confer tolerance to metals through changes in speciation at the root epidermis. we employed a novel combination of fluorophore-based confocal laser scanning microscopic imaging and synchrotron based microscopic x-ray fluorescence mapping with x-ray absorption spectroscopy to characte ...	2015	26263508
bacteria-zinc co-localization implicates enhanced synthesis of cysteine-rich peptides in zinc detoxification when brassica juncea is inoculated with rhizobium leguminosarum.	some plant growth promoting bacteria (pgpb) are enigmatic in enhancing plant growth in the face of increased metal accumulation in plants. since most pgpb colonize the plant root epidermis, we hypothesized that pgpb confer tolerance to metals through changes in speciation at the root epidermis. we employed a novel combination of fluorophore-based confocal laser scanning microscopic imaging and synchrotron based microscopic x-ray fluorescence mapping with x-ray absorption spectroscopy to characte ...	2015	26263508
industrial wastewater as raw material for exopolysaccharide production by rhizobium leguminosarum.	the objective of this study was to evaluate the exopolysaccharide (eps) production by rhizobium leguminosarum cultivated in wastewater generated by oil companies (wwoc1 and wwoc2) and fish processing industry (wwfp). the results obtained in erlenmeyer flasks indicated that the rhizobial strain grew well in industrial wastewater. generally, wastewater composition affected the growth and the eps production. wwfp allowed good bacterial growth similar to that obtained with the standard medium (ymb). ...	2015	26273255
identification of the mcpa and mcpm genes, encoding methyl-accepting proteins involved in amino acid and l-malate chemotaxis, and involvement of mcpm-mediated chemotaxis in plant infection by ralstonia pseudosolanacearum (formerly ralstonia solanacearum phylotypes i and iii).	sequence analysis has revealed the presence of 22 putative methyl-accepting chemotaxis protein (mcp) genes in the ralstonia pseudosolanacearum gmi1000 genome. pcr analysis and dna sequencing showed that the highly motile r. pseudosolanacearum strain ps29 possesses homologs of all 22 r. pseudosolanacearum gmi1000 mcp genes. we constructed a complete collection of single mcp gene deletion mutants of r. pseudosolanacearum ps29 by unmarked gene deletion. screening of the mutant collection revealed t ...	2015	26276117
identification of iron and heme utilization genes in aeromonas and their role in the colonization of the leech digestive tract.	it is known that many pathogens produce high-affinity iron uptake systems like siderophores and/or proteins for utilizing iron bound to heme-containing molecules, which facilitate iron-acquisition inside a host. in mutualistic digestive-tract associations, iron uptake systems have not been as well studied. we investigated the importance of two iron utilization systems within the beneficial digestive-tract association aeromonas veronii and the medicinal leech, hirudo verbana. siderophores were de ...	2015	26284048
identification of a core set of rhizobial infection genes using data from single cell-types.	genome-wide expression studies on nodulation have varied in their scale from entire root systems to dissected nodules or root sections containing nodule primordia (np). more recently efforts have focused on developing methods for isolation of root hairs from infected plants and the application of laser-capture microdissection technology to nodules. here we analyze two published data sets to identify a core set of infection genes that are expressed in the nodule and in root hairs during infection ...	2015	26284091
physiological and molecular aspects of tolerance to environmental constraints in grain and forage legumes.	despite the agronomical and environmental advantages of the cultivation of legumes, their production is limited by various environmental constraints such as water or nutrient limitation, frost or heat stress and soil salinity, which may be the result of pedoclimatic conditions, intensive use of agricultural lands, decline in soil fertility and environmental degradation. the development of more sustainable agroecosystems that are resilient to environmental constraints will therefore require bette ...	2015	26287163