Publications

betaproteobacteria dominance and diversity shifts in the bacterial community of a pah-contaminated soil exposed to phenanthrene.	in this study, the pah-degrading bacteria of a constructed wetland collecting road runoff has been studied through dna stable isotope probing. microcosms were spiked with (13)c-phenanthrene at 34 or 337 ppm, and bacterial diversity was monitored over a 14-day period. at 337 ppm, pah degraders became dominated after 5 days by betaproteobacteria, including novel acidovorax, rhodoferax and hydrogenophaga members, and unknown bacteria related to rhodocyclaceae. the prevalence of betaproteobacteria w ...	2012	22243884
biodiversity characterization of cellulolytic bacteria present on native chaco soil by comparison of ribosomal rna genes.	sequence analysis of the 16s ribosomal rna gene was used to study bacterial diversity of a pristine forest soil and of two cultures of the same soil enriched with cellulolytic bacteria. our analysis revealed high bacterial diversity in the native soil sample, evidencing at least 10 phyla, in which actinobacteria, proteobacteria and acidobacteria accounted for more than 76% of all sequences. in both enriched samples, members of proteobacteria were the most frequently represented. the majority of ...	2011	22202170
Green rust formation during Fe(II) oxidation by the nitrate-reducing Acidovorax sp. strain BoFeN1.	Green rust (GR) as highly reactive iron mineral potentially plays a key role for the fate of (in)organic contaminants, such as chromium or arsenic and nitroaromatic compounds functioning both as sorbent and reductant. GR forms as corrosion product of steel but is also naturally present in hydromorphic soils and sediments forming as metastable intermediate during microbial Fe(III) reduction. Although already suggested to form during microbial Fe(II) oxidation, clear evidence for GR formation duri ...	2011	22201257
[relationship of histidine auxotrophy of acidovorax citrulli with pathogenicity].	acidovorax citrulli (ac) is an important bacterium that occurs in watermelon, melon and other cucurbits. it mainly damages watermelon and melon, and can cause leaf blight, fruit rot, and even mortality.	2011	22126073
phenotypic variation in acidovorax radicisn35 influences plant growth promotion.	acidovorax radicis n35, isolated from surface-sterilized wheat roots (triticum aestivum), showed irreversible phenotypic variation in nutrient broth, resulting in a differing colony morphology. in addition to the wild-type form (rough colony type), a phenotypic variant form (smooth colony type) appeared at a frequency of 3.2 × 10(-3) per cell per generation on nb agar plates. in contrast to the n35 wild type, the variant n35v showed almost no cell aggregation and had lost its flagella and swarm ...	2011	22107346
Detection of Acidovorax valerianellae, the causing agent of bacterial leaf spots in corn salad [Valerianella locusta (L.) Laterr.], in corn salad seeds.	Aim: The black leaf spot disease on corn salad caused by the bacterium Acidovorax valerianellae has been observed in Europe for several years and causes economic losses in corn salad cropping. Contaminated seeds or infested soil are considered as the major infection sources. The use of healthy seed material is the only way to prevent disease outbreaks. Therefore a sensitive diagnostic method for seed testing should be developed. Methods and Results: Using a triple antibody sandwich ELISA with ...	2011	22098338
culturable bacterial communities on leaf sheaths and panicles of rice plants in japan.	culturable bacterial communities on rice plants were investigated from 2001 to 2003. in total, 1,394 bacterial isolates were obtained from the uppermost leaf sheaths at 1 month before heading time and from leaf sheaths and panicles at heading time. the average culturable bacterial population on the leaf sheaths was larger at heading time than at 1 month previously. furthermore, the population was significantly larger on panicles than on leaf sheaths, suggesting that the bacterial population is i ...	2011	22081407
evaluation of microbial biofilm communities from an alberta oil sands tailings pond.	bitumen extraction from the oil sands of alberta has resulted in millions of cubic meters of waste stored on-site in tailings ponds. unique microbial ecology is expected in these ponds, which may be key to their bioremediation potential. we considered that direct culturing of microbes from a tailings sample as biofilms could lead to the recovery of microbial communities that provide good representation of the ecology of the tailings. culturing of mixed species biofilms in vitro using the calgary ...	2011	22029695
enhanced growth of acidovorax sp. strain 2an during nitrate-dependent fe(ii) oxidation in batch and continuous-flow systems.	microbial nitrate-dependent, fe(ii) oxidation (ndfo) is a ubiquitous biogeochemical process in anoxic sediments. since most microorganisms that can oxidize fe(ii) with nitrate require an additional organic substrate for growth or sustained fe(ii) oxidation, the energetic benefits of ndfo are unclear. the process may also be self-limiting in batch cultures due to formation of fe-oxide cell encrustations. we hypothesized that ndfo provides energetic benefits via a mixotrophic physiology in environ ...	2011	22003007
pyrosequencing-based analysis of the mucosal microbiota in healthy individuals reveals ubiquitous bacterial groups and micro-heterogeneity.	this study used 16s rrna-based pyrosequencing to examine the microbial community that is closely associated with the colonic mucosa of five healthy individuals. spatial heterogeneity in microbiota was measured at right colon, left colon and rectum, and between biopsy duplicates spaced 1 cm apart. the data demonstrate that mucosal-associated microbiota is comprised of firmicutes (50.9% ± 21.3%), bacteroidetes (40.2% ± 23.8%) and proteobacteria (8.6%± 4.7%), and that interindividual differences we ...	2011	21966408
degradation of a benzene-toluene mixture by hydrocarbon-adapted bacterial communities.	we examined the rate of degradation of a benzene-toluene mixture in aerobic microcosms prepared with samples of an aquifer that lies below a petrochemical plant (siren, uk). five samples exposed to different concentrations of benzene (from 0.6 to 317 mg l(-1)) were used. fast degradation (approx. 1-6 mg l(-1) day(-1)) of both contaminants was observed in all groundwater samples and complete degradation was recorded by the seventh day except for one sample. we also identified the microbial commun ...	2011	21949494
Dynamics of microbial community structure of and enhanced biological phosphorus removal by aerobic granules cultivated on propionate or acetate.	Aerobic granules are dense microbial aggregates with the potential to replace floccular sludge for the treatment of wastewaters. In bubble-column sequencing batch reactors, distinct microbial populations dominated propionate- and acetate-cultivated aerobic granules after 50 days of reactor operation when only carbon removal was detected. Propionate granules were dominated by Zoogloea (40%), Acidovorax, and Thiothrix, whereas acetate granules were mainly dominated by Thiothrix (60%). Thereafter, ...	2011	21926195
evolution of a new bacterial pathway for 4-nitrotoluene degradation.	bacteria that assimilate synthetic nitroarene compounds represent unique evolutionary models, as their metabolic pathways are in the process of adaptation and optimization for the consumption of these toxic chemicals. we used acidovorax sp. strain js42, which is capable of growth on nitrobenzene and 2-nitrotoluene, in experiments to examine how a nitroarene degradation pathway evolves when its host strain is challenged with direct selective pressure to assimilate non-native substrates. although ...	2011	21895789
genome sequence of the rice-pathogenic bacterium acidovorax avenae subsp. avenae rs-1.	acidovorax avenae subsp. avenae is a phytobacterium which is the causative agent of several plant diseases with economic significance. here, we present the draft genome sequence of strain rs-1, which was isolated from rice shoots in a rice field in china. this strain can cause bacterial stripe of rice.	2011	21742879
comparative analysis of the xopd type iii secretion (t3s) effector family in plant pathogenic bacteria.	xopd is a type iii effector protein that is required for xanthomonas campestris pathovar vesicatoria (xcv) growth in tomato. it is a modular protein consisting of an n-terminal dna-binding domain, two ethylene-responsive element binding factor-associated amphiphilic repression (ear) transcriptional repressor motifs and a c-terminal small ubiquitin-related modifier (sumo) protease. in tomato, xopd functions as a transcriptional repressor, resulting in the suppression of defence responses at late ...	2011	21726373
glycosylation regulates the specific induction of rice immune responses by acidovorax avenae flagellin.	plants have a sensitive system that detects various pathogen-derived molecules to protect against infection. flagellin, a main component of the bacterial flagellum, from the rice avirulent n1141 strain of gram-negative phytopathogenic bacterium, acidovorax avenae, induces plant immune responses including h(2)o(2) generation, while flagellin from the rice virulent k1 strain of a. avenae does not induce these immune responses. to clarify the molecular mechanism that leads to these differing respon ...	2011	21628471
the cucurbit pathogenic bacterium acidovorax citrulli requires a polar flagellum for full virulence before and after host tissue penetration.	acidovorax citrulli causes seedling blight and bacterial fruit blotch of cucurbits. previous reports demonstrated the contribution of type iv pili (tfp) to a. citrulli virulence and to systemic infection of melon seedlings. microfluidic flow chamber assays demonstrated the involvement of tfp in surface adhesion and biofilm formation, whereas polar flagella did not appear to contribute to either of these features. on the other hand, a transposon mutant impaired in the biosynthesis of polar flagel ...	2011	21554180
a diverse bacterial community in an anoxic quinoline-degrading bioreactor determined by using pyrosequencing and clone library analysis.	there is a concern of whether the structure and diversity of a microbial community can be effectively revealed by short-length pyrosequencing reads. in this study, we performed a microbial community analysis on a sample from a high-efficiency denitrifying quinoline-degrading bioreactor and compared the results generated by pyrosequencing with those generated by clone library technology. by both technologies, 16s rrna gene analysis indicated that the bacteria in the sample were closely related to ...	2011	21538111
rapid on-site detection of acidovorax avenae subsp. citrulli by gold-labeled dna strip sensor.	acidovorax avenae subsp. citrulli (aac) is one of the most harmful diseases in cucurbit production. a rapid and sensitive dna strip sensor was constructed based on gold nanoparticle-labeled oligonucleotide probes for the detection of aac. both the qualitative and semi-quantitative detections of target dna were successfully achieved using the developed dna strip sensor. the qualitative limit of detection (lod) of the strip sensor was determined as 4nm. the lod for the semi-quantitative detection ...	2011	21536424
contrasting effects of ultraviolet radiation on the growth efficiency of freshwater bacteria.	in this study, we tested the hypothesis that the growth efficiency of freshwater bacteria is differentially affected by ultraviolet radiation (uvr, 280-400 nm) as mediated through changes in their production and respiration rates. five bacterial strains affiliated to alphaproteobacteria, betaproteobacteria, gammaproteobacteria, and actinobacteria were isolated from different freshwater habitats and exposed in the laboratory to photosynthetically active radiation (par) and par + uvr, or kept in t ...	2011	21516253
interaction of legionella pneumophila and helicobacter pylori with bacterial species isolated from drinking water biofilms.	it is well established that legionella pneumophila is a waterborne pathogen; by contrast, the mode of helicobacter pylori transmission remains unknown but water seems to play an important role. this work aims to study the influence of five microorganisms isolated from drinking water biofilms on the survival and integration of both of these pathogens into biofilms.	2011	21418578
pyrosequence analysis of bacterial communities in aerobic bioreactors treating polycyclic aromatic hydrocarbon-contaminated soil.	two aerobic, lab-scale, slurry-phase bioreactors were used to examine the biodegradation of polycyclic aromatic hydrocarbons (pahs) in contaminated soil and the associated bacterial communities. the two bioreactors were operated under semi-continuous (draw-and-fill) conditions at a residence time of 35 days, but one was fed weekly and the other monthly. most of the quantified pahs, including high-molecular-weight compounds, were removed to a greater extent in the weekly-fed bioreactor, which ach ...	2011	21369833
microbial characterization of the biofilms developed for treating ampicillin-bearing wastewater.	in this study, biofilms were developed in three airlift reactors to treat wastewaters with ampicillin (amp) of 0, 4 and 8 mg l(-1), respectively. during 60 days of operation, amp was not found to inhibit the biofilm growth. denaturing gradient gel electrophoresis (dgge) and 16s rrna gene sequencing were used to characterize the bacterial community of these biofilms. it was found that the community diversity was lowered, whereas the community stability was enhanced in the biofilm supplemented wit ...	2011	21308603
new detection systems of bacteria using highly selective media designed by smart: selective medium-design algorithm restricted by two constraints.	culturing is an indispensable technique in microbiological research, and culturing with selective media has played a crucial role in the detection of pathogenic microorganisms and the isolation of commercially useful microorganisms from environmental samples. although numerous selective media have been developed in empirical studies, unintended microorganisms often grow on such media probably due to the enormous numbers of microorganisms in the environment. here, we present a novel strategy for ...	2011	21304596
an investigation of a potential confounder in ex vivo microbiological studies--the bulk flow of fluid through apical foramina during tooth extraction.	to investigate the factors affecting bulk flow of dye and bacterial suspensions into and out of apical foramina during simulated tooth extraction, using an ex vivo model.	2011	21272043
application of nitroarene dioxygenases in the design of novel strains that degrade chloronitrobenzenes.	widespread application of chloronitrobenzenes as feedstocks for the production of industrial chemicals and pharmaceuticals has resulted in extensive environmental contamination with these toxic compounds, where they pose significant risks to the health of humans and wildlife. while biotreatment in general is an attractive solution for remediation, its effectiveness is limited with chloronitrobenzenes due to the small number of strains that can effectively mineralize these compounds and their abi ...	2009	21261918
a molecular toolbox to estimate the number and diversity of variovorax in the environment: application in soils treated with the phenylurea herbicide linuron.	real-time pcr and pcr-denaturing gradient gel electrophoresis (dgge) approaches that specifically target the variovorax 16s rrna gene were developed to estimate the number and diversity of variovorax in environmental ecosystems. pcr primers suitable for both methods were selected as such that the enclosed sequence showed maximum polymorphism. pcr specificity was maximized by combining pcr with a targeted endonuclease treatment of template dna to eliminate 16s rrna genes of the closely related ac ...	2011	21204875
acidovorax radicis sp. nov., a wheat root-colonizing bacterium.	acidovorax radicis sp. nov. strain n35(t) was isolated from surface sterilized wheat roots and is a gram-negative, aerobic and motile straight rod. strain n35(t) was tested as an oxidase-positive and catalase-negative bacterium which grew optimally at ph 7.0 at 30 °c and 0 % nacl (w/v). the 16s rrna gene sequence analysis showed over 97 % sequence similarities to the environmental acidovorax species a. delafieldii, a. facilis, a. defluvii, a. temperans, a. caeni and a. soli as well as a. valeria ...	2010	21131505
development of surface plasmon resonance imaging for detection of acidovorax avenae subsp. citrulli (aac) using specific monoclonal antibody.	an immunosensor based on surface plasmon resonance imaging (spr imaging) using a specific monoclonal antibody 11e5 (mab 11e5) was developed for the detection of the seed-borne bacterium acidovorax avenae subsp. citrulli (aac), which causes fruit blotch in watermelons and cantaloupes, and compared to the conventional elisa technique. the 1:40 mixed self-assembled monolayer (mixed sam) surface was used for the immobilized mab 11e5 on sensor surface for the detection of aac. both whole cells and br ...	2010	21093249
evidence for equilibrium iron isotope fractionation by nitrate-reducing iron(ii)-oxidizing bacteria.	iron isotope fractionations produced during chemical and biological fe(ii) oxidation are sensitive to the proportions and nature of dissolved and solid-phase fe species present, as well as the extent of isotopic exchange between precipitates and aqueous fe. iron isotopes therefore potentially constrain the mechanisms and pathways of fe redox transformations in modern and ancient environments. in the present study, we followed in batch experiments fe isotope fractionations between fe(ii)(aq) and ...	2010	21076519
assessing adhesion, biofilm formation and motility of acidovorax citrulli using microfluidic flow chambers.	acidovorax citrulli is the causal agent of bacterial fruit blotch of cucurbits. we have shown previously that type iv pili (tfp) are required for wild-type levels of virulence of a. citrulli on melon and that this pathogen can colonize and move thorough the xylem vessels of host seedlings. here, comparative studies between wild-type and tfp mutant strains using microfluidic flow chambers demonstrated that tfp play a critical role in both the surface attachment and the biofilm formation of a. cit ...	2010	20807236
bacteria from drinking water supply and their fate in gastrointestinal tracts of germ-free mice: a phylogenetic comparison study.	microorganisms in drinking water sources may colonize in gastrointestinal (gi) tracts and this phenomenon may pose a potential health risk especially to immunocompromised population. the microbial community diversity of the drinking water was compared with the gi tracts of the mice using phylogenetic and statistical analyses of 16s rrna gene sequences. a group of germ-free mice were fed with drinking water from public water supply that passed through an automated watering system with documented ...	2010	20705313
insights into the dynamics of bacterial communities during chalcopyrite bioleaching.	the microbial ecology of the bioleaching of chalcopyrite ores is poorly understood and little effort has been made to handle the microbiological components of these processes. in this study, the composition and structure of microbial communities in acid mineral bioleaching systems have been studied using a pcr-based cloning approach. denaturing gradient gel electrophoresis (dgge) analysis of pcr-amplified 16s rrna gene fragments from bacteria was used to evaluate the changes in the bacterial com ...	2010	20698885
functional assembly of bacterial communities with activity for the biodegradation of an organophosphorus pesticide in the rape phyllosphere.	although most pesticides sprayed on terrestrial plants remain on their leaf surfaces, the relationship between leaf-associated microbial populations and pesticide degradation remains unclear. here we examined changes in the bacterial community composition in the rape phyllosphere after treatment with dichlorvos, an organophosphorus pesticide. results indicate that the bacterial community showed marked changes after treatment. we evaluated the rate of dichlorvos degradation by a natural microbial ...	2010	20529133
elucidating mtbe degradation in a mixed consortium using a multidisciplinary approach.	the structure and function of a microbial community capable of biodegrading methyl-tert-butyl ether (mtbe) was characterized using compound-specific stable isotope analysis (csia), clone libraries and stable isotope probing of proteins (protein-sip). the enrichment culture (us3-m), which originated from a gasoline-impacted site in the united states, has been enriched on mtbe as the sole carbon source. the slope of isotopic enrichment factors (epsilon(c) of -2.29+/-0.03 per thousand; epsilon(h) o ...	2010	20491917
biofilm bacterial communities and abundance in a full-scale drinking water distribution system in shanghai.	community diversity and abundance of biofilms from a full-scale drinking water distribution system in shanghai were characterized by denaturing gradient gel electrophoresis (dgge) analysis of 16s rrna sequences and heterotrophic plate count (hpc), respectively. bacteria affiliated to the beta- and gamma-proteobacteria were dominating in both in-situ and hpc-culturable bacterial communities. other bacteria present included members of alphaproteobacteria, bacteroides, actinobacteria, nitrospirae a ...	2010	20375488
characterization of phosphobacteria isolated from eutrophic aquatic ecosystems.	phosphobacteria are able to enhance phosphorus availability in soil and improve crop yields. to develop such biofertilizers, 14 predominant phosphobacteria were isolated from eutrophic aquatic ecosystems. molecular identification and phylogenetic analysis revealed three groups among the nine isolates of inorganic phosphate-solubilizing bacteria (ipsb): ipsb1 and ipsb2 belonged to the actinobacteria and flavobacteria, respectively, and the other seven belonged to the gamma-proteobacteria. among f ...	2009	20170019
pamdb, a multilocus sequence typing and analysis database and website for plant-associated microbes.	although there are adequate dna sequence differences among plant-associated and plant-pathogenic bacteria to facilitate molecular approaches for their identification, identification at a taxonomic level that is predictive of their phenotype is a challenge. the problem is the absence of a taxonomy that describes genetic variation at a biologically relevant resolution and of a database containing reference strains for comparison. moreover, molecular evolution, population genetics, ecology, and epi ...	2010	20128693
acidovorax soli sp. nov., isolated from landfill soil.	a gram-negative, aerobic, rod-shaped, non-motile strain, bl21(t), was isolated from landfill soil in pohang, korea. strain bl21(t) grew optimally at ph&emsp14;7.0, 30 °c and 0 % nacl (w/v). phylogenetic analysis based on 16s rrna gene sequence indicated that strain bl21(t) belonged to the class betaproteobacteria and was related to the genus acidovorax. the 16s rrna gene sequence of strain bl21(t) was less than 98.30 % similar to those of other species in the genus acidovorax. dna-dna hybridizat ...	2010	20061503
completed genome sequence of the anaerobic iron-oxidizing bacterium acidovorax ebreus strain tpsy.	acidovorax ebreus strain tpsy is the first anaerobic nitrate-dependent fe(ii) oxidizer for which there is a completed genome sequence. preliminary protein annotation revealed an organism optimized for survival in a complex environmental system. here, we briefly report the completed and annotated genome sequence of strain tpsy.	2010	20023012
novel tn4371-ice like element in ralstonia pickettii and genome mining for comparative elements.	integrative conjugative elements (ices) are important factors in the plasticity of microbial genomes. an element related to the ice tn4371 was discovered during a bioinformatic search of the ralstonia pickettii 12j genome. this element was analysed and further searches carried out for additional elements.a pcr method was designed to detect and characterise new elements of this type based on this scaffold and a culture collection of fifty-eight ralstonia pickettii and ralstonia insidiosa strains ...	2009	19941653
acrylic acid removal from synthetic wastewater and industrial wastewater using ralstonia solanacearum and acidovorax avenae isolated from a wastewater treatment system manufactured with polyacrylonitrile fiber.	ralstonia solanacearum and acidovorax avenae were isolated from a wastewater treatment system manufactured with polyacrylonitrile fiber. the investigation goal is to elucidate the effectiveness of ralstonia solanacearum and acidovorax avenae in treating acrylic acid from synthetic wastewater and industrial wastewater. the results reveal that ralstonia solanacearum and acidovorax avenae could utilize acrylic acid from synthetic wastewater for growth, when the initial acrylic acid concentration wa ...	2009	19934523
reconstructing the evolutionary history of nitrotoluene detection in the transcriptional regulator ntdr.	many toxic man-made compounds have been introduced into the environment, and bacterial strains that are able to grow on them are ideal model systems for studying the evolution of metabolic pathways and regulatory systems. acidovorax sp. strain js42 is unique in its ability to use 2-nitrotoluene as a sole carbon, nitrogen, and energy source for growth. the lysr-type transcriptional regulator ntdr activates expression of the 2-nitrotoluene degradation genes not only when nitroaromatic compounds ar ...	2009	19849778
degradation of nitroaromatic compounds: a model to study evolution of metabolic pathways.	although many nitroaromatic compounds have been in nature for only a few decades, bacteria have already evolved the ability to metabolize them. both horizontal transfer of genes and mutagenesis induced under stressful conditions might facilitate evolution of new catabolic pathways. nitrotoluene degradation pathways are supposedly derived from an ancestral naphthalene degradation pathway. the 2-nitrotoluene degradation genes in acidovorax sp. strain js42 are controlled by the transcriptional acti ...	2009	19818019
selection of indicator bacteria based on screening of 16s rdna metagenomic library from a two-stage anoxic-oxic bioreactor system degrading azo dyes.	dye degradation has gained attention of late due to indiscriminate disposal from user industries. enhancing efficiency of biological treatment provides a cheaper alternative vis-à-vis other advanced technologies. dye molecules are metabolized biologically via anoxic and oxic treatments. in this study, bacterial community surviving on dye effluent working in anoxic-oxic bioreactor was analyzed using 16s rdna approach. azo-dye decolorizing and degrading bacterial community was enriched in lab-scal ...	2010	19748265
ecophysiology and the energetic benefit of mixotrophic fe(ii) oxidation by various strains of nitrate-reducing bacteria.	in order to assess the importance of nitrate-dependent fe(ii) oxidation and its impact on the growth physiology of dominant fe oxidizers, we counted these bacteria in freshwater lake sediments and studied their growth physiology. most probable number counts of nitrate-reducing fe(ii)-oxidizing bacteria in the sediment of lake constance, a freshwater lake in southern germany, yielded about 10(5) cells ml(-1) of the total heterotrophic nitrate-reducing bacteria, with about 1% (10(3) cells ml(-1)) ...	2009	19732145
nitrite reductase genes in halobenzoate degrading denitrifying bacteria.	abstract diversity of the functional genes encoding dissimilatory nitrite reductase was investigated for the first time in denitrifying halobenzoate degrading bacteria and in two 4-chlorobenzoate degrading denitrifying consortia. nitrite reductase genes were pcr-amplified with degenerate primers (specific to the two different types of respiratory nitrite reductase, nirs and nirk), cloned and sequenced to determine which type of nitrite reductase was present in each isolate and consortium. halobe ...	2003	19719666
chlorobenzene biodegradation under consecutive aerobic-anaerobic conditions.	the biodegradation of monochlorobenzene, the main contaminant in a quaternary aquifer at bitterfeld, central germany, was studied in microcosm experiments employing either original groundwater or defined mineral media together with the indigenous microbial community from the polluted site. the impact of consecutive aerobic-anaerobic-aerobic incubations on monochlorobenzene biodegradation, microbial diversity, and ph development was examined. the related changes in microbial community composition ...	2004	19712388
implanted-port-catheter-related sepsis caused by acidovorax avenae and methicillin-sensitive staphylococcus aureus.	acidovorax avenae is a gram-negative rod in the family comamonadaceae and a phytopathogen found in the environment. human infections caused by members of the comamonadaceae are extremely rare. we report a case of implanted-port-catheter-related sepsis caused by acidovorax avenae and methicillin (meticillin)-sensitive staphylococcus aureus (mssa).	2009	19710279
effect of organic carbon on nitrification efficiency and community composition of nitrifying biofilms.	the effects of organic carbon/inorganic nitrogen (c/n) ratio on the nitrification processes and the community shifts of nitrifying biofilms were investigated by kinetic comparison and denaturing gradient gel electrophoresis (dgge) analysis. the results showed that the nitrification rate decreased with an increasing organic concentration. however, the effect became weak when the carbon concentration reached a sufficiently high level. denitrification was detected after organic carbon was added. th ...	2009	19634453
multilocus sequence typing reveals two evolutionary lineages of acidovorax avenae subsp. citrulli.	acidovorax avenae subsp. citrulli, causal agent of bacterial fruit blotch, has caused considerable damage to the watermelon and melon industry in china and the united states. understanding the emergence and spread of this pathogen is important for controlling the disease. to build a fingerprinting database for reliable identification and tracking of strains of a. avenae subsp. citrulli, a multilocus sequence typing (mlst) scheme was developed using seven conserved loci. the study included 8 orig ...	2009	19594310
type iv pili are required for virulence, twitching motility, and biofilm formation of acidovorax avenae subsp. citrulli.	acidovorax avenae subsp. citrulli is the causal agent of bacterial fruit blotch (bfb), a threatening disease of watermelon, melon, and other cucurbits. despite the economic importance of bfb, relatively little is known about basic aspects of the pathogen's biology and the molecular basis of its interaction with host plants. to identify a. avenae subsp. citrulli genes associated with pathogenicity, we generated a transposon (tn5) mutant library on the background of strain m6, a group i strain of ...	2009	19589067
phenotypic and genetic diversity of rice seed-associated bacteria and their role in pathogenicity and biological control.	to study the phenotypic and genetic diversity of culturable bacteria associated with rice seed and to asses the antagonistic and pathogenic potential of the isolated bacteria.	2009	19486410
simultaneous detection of acidovorax avenae subsp. citrulli and didymella bryoniae in cucurbit seedlots using magnetic capture hybridization and real-time polymerase chain reaction.	to improve the simultaneous detection of two pathogens in cucurbit seed, a combination of magnetic capture hybridization (mch) and multiplex real-time polymerase chain reaction (pcr) was developed. single-stranded dna hybridization capture probes targeting dna of acidovorax avenae subsp. citrulli, causal agent of bacterial fruit blotch, and didymella bryoniae, causal agent of gummy stem blight, were covalently attached to magnetic particles and used to selectively concentrate template dna from c ...	2009	19453225
high yield synthesis of 12-aminolauric acid by "enzymatic transcrystallization" of omega-laurolactam using omega-laurolactam hydrolase from acidovorax sp. t31.	the genes encoding omega-laurolactam hydrolases from cupriavidus sp. t7, acidovorax sp. t31, cupriavidus sp. u124, and sphingomonas sp. u238 were cloned and sequenced. nucleotide and amino acid sequence analysis of the four genes indicated that the primary structures of these omega-laurolactam hydrolases are significantly similar to the 6-aminohexanoate-cyclic-dimer hydrolase (ec 3.5.2.12). these genes were expressed in escherichia coli, and the omega-laurolactam hydrolysing activity of the reco ...	2009	19420719
bacterial communities in a crude oil gathering and transferring system (china).	bacterial communities in crude oil and oil field production water samples from an oil gathering and transferring system in changqing oil field in china were investigated by 16s rrna denaturing gradient gel electrophoresis (dgge) analysis followed by gene cloning and sequencing. dgge profiles showed that bacterial communities are far more rich in the water samples than that in the crude oil samples, and that bacteria related to ochrobactrum sp. and stenotrophomonas sp. were detected in all crude ...	2009	19351561
compared microbiology of granular sludge under autotrophic, mixotrophic and heterotrophic denitrification conditions.	water contamination by nitrate is a wideworld extended phenomena. biological autotrophic denitrification has a real potential to face this problem and presents less drawbacks than the most extended heterotrophic denitrification. three bench-scale uasb reactors were operated under autotrophic (r1, h2s as electron donor), mixotrophic (r2, h2s plus p-cresol as electron donors) and heterotrophic (r3, p-cresol as electron donor) conditions using nitrate as terminal electron acceptor. 16s rdna genetic ...	2009	19342820
use of a microchip electrophoresis system for estimation of bacterial phylogeny and analysis of no3- reducing bacterial flora in field soils.	phylogenetic estimation method without determination of dna sequence was developed. by this method, fragment length polymorphism separately digested with multiple restriction enzymes was measured using microchip electrophoresis and affiliated with those calculated from corresponding dna sequence in the theoretical database. the phylogenies of 129 no(3)(-) reducing bacteria newly isolated from field soils were estimated by this method, and were compared to those by carbon source utilization profi ...	2009	19270404
characterization of a polycyclic aromatic hydrocarbon degradation gene cluster in a phenanthrene-degrading acidovorax strain.	acidovorax sp. strain na3 was isolated from polycyclic aromatic hydrocarbon (pah)-contaminated soil that had been treated in a bioreactor and enriched with phenanthrene. the 16s rrna gene of the isolate possessed 99.8 to 99.9% similarity to the dominant sequences recovered during a previous stable-isotope probing experiment with [u-(13)c]phenanthrene on the same soil (d. r. singleton, s. n. powell, r. sangaiah, a. gold, l. m. ball, and m. d. aitken, appl. environ. microbiol. 71:1202-1209, 2005). ...	2009	19270134
extracellular dna and type iv pili mediate surface attachment by acidovorax temperans.	extracellular dna can play a structural role in the microbial environment. here evidence is presented that an environmental isolate of acidovorax temperans utilises extracellular dna for intercellular and cell-surface attachment and that type iv pili and electrostatic interactions play a role in this interaction. preliminary attempts to isolate and purify extracellular polysaccharides from a. temperans strain cb2 yielded significant amounts of dna raising the question of whether this molecule wa ...	2009	19263234
characterization of geochemical constituents and bacterial populations associated with as mobilization in deep and shallow tube wells in bangladesh.	while millions of people drink arsenic-contaminated tube well water across bangladesh, there is no recent scientific explanation which is able to either comprehensively explain arsenic mobilization or to predict the spatial distribution of affected wells. rather, mitigation strategies have focused on the sinking of deep tube wells into the currently arsenic-free pleistocene aquifer. in this study, bangladesh shallow tube wells identified as contaminated and uncontaminated, as well as deep tube w ...	2009	19215956
molecular characterization and in situ quantification of anoxic arsenite-oxidizing denitrifying enrichment cultures.	to explore the bacteria involved in the oxidation of arsenite (as(iii)) under denitrifying conditions, three enrichment cultures (ecs) and one mixed culture (mc) were characterized that originated from anaerobic environmental samples. the oxidation of as(iii) (0.5 mm) was dependent on no(3) (-) addition and n(2) formation was dependent on as(iii) addition. the ratio of n(2)-n formed to as(iii) fed approximated the expected stoichiometry of 2.5. a 16s rrna gene clone library analysis revealed thr ...	2009	19187211
dna-based stable isotope probing enables the identification of active bacterial endophytes in potatoes.	a (13)co2 (99 atom-%, 350 ppm) incubation experiment was performed to identify active bacterial endophytes in two cultivars of solanum tuberosum, cultivars desirée and merkur. we showed that after the assimilation and photosynthetic transformation of (13)co2 into (13)c-labeled metabolites by the plant, the most directly active, cultivar specific heterotrophic endophytic bacteria that consume these labeled metabolite scan be identified by dna stable isotope probing (dna-sip).density-resolved dna ...	2009	19140937
carbon utilization profiles of bacteria colonizing the headbox water of two paper machines in a canadian mill.	forty-one bacterial strains isolated from the headbox water of two machines in a canadian paper mill were associated with the genera asticcacaulis, acidovorax, bacillus, exiguobacterium, hydrogenophaga, pseudomonas, pseudoxanthomonas, staphylococcus, stenotrophomonas based on the sequence of their 16s rrna genes. the metabolic profile of these strains were determined using biolog ecoplate, and the bacteria were divided into four metabolic groups. metabolic profiles of the bacterial communities c ...	2009	19137341
mixed aerobic and anaerobic microbial communities in benzene-contaminated groundwater.	to investigate the factors affecting benzene biodegradation and microbial community composition in a contaminated aquifer.	2009	19120616
isolation and identification of atrazine-degrading bacteria from corn field soil in fars province of iran.	in this study several agricultural fields with a long history of atrazine application in fars province of iran have been explored for their potential of atrazine biodegradation. after several subculturing for a period of 300 days acclimation, leads to an enhancement of atrazine biodegradation rate. a successful enrichment culture with a high capability for atrazine degradation was obtained (88%). a combination of enrichment culture technique, in a basal salt medium containing atrazine and carbon ...	2007	19069990
bacterial community and biological nitrate removal: comparisons of autotrophic and heterotrophic reactors for denitrification with raw sewage.	an autotrophic denitrification reactor (adr-1) and a heterotrophic denitrification reactor (hdr-2) were operated to remove nitrate and nitrite in an anoxic environment in raw sewage. the no3-n removal rate of adr-1 was shown to range from 52.8% to 78.7%, which was higher than the no3-n removal rate of hdr-2. specific denitrification rates (sdnr) of adr-1 and hdr-2 were 3.0 to 4.0 and 1.1 to 1.2mgno3- n/gvss/h, respectively. from results of restriction fragment length polymorphism (rflp) of the 1 ...	2008	19047828
resolving genetic functions within microbial populations: in situ analyses using rrna and mrna stable isotope probing coupled with single-cell raman-fluorescence in situ hybridization.	prokaryotes represent one-half of the living biomass on earth, with the vast majority remaining elusive to culture and study within the laboratory. as a result, we lack a basic understanding of the functions that many species perform in the natural world. to address this issue, we developed complementary population and single-cell stable isotope ((13)c)-linked analyses to determine microbial identity and function in situ. we demonstrated that the use of rrna/mrna stable isotope probing (sip) rec ...	2009	18997025
reclassification of subspecies of acidovorax avenae as a. avenae (manns 1905) emend., a. cattleyae (pavarino, 1911) comb. nov., a. citrulli schaad et al., 1978) comb. nov., and proposal of a. oryzae sp. nov.	the bacterium acidovorax avenae causes disease in a wide range of economically important monocotyledonous and dicotyledonous plants, including corn, rice, watermelon, anthurium, and orchids. genotypic and phenotypic relatedness among strains of phytopathogenic a. avenae subsp. avenae, a. avenae subsp. citrulli, a. avenae subsp. cattleyae and a. konjaci, as well as all other acidovorax species, including a. facilis, the type strain of acidovorax, was determined. the 16s rdna sequencing confirmed ...	2008	18993005
analysis of flagellin perception mediated by flg22 receptor osfls2 in rice.	plants have sensitive perception systems that recognize various pathogen-derived molecules. we previously reported that rice detects flagellin from a rice-incompatible strain of gram-negative phytopathogenic bacterium, acidovorax avenae, which induces subsequent immune responses involving cell death. the mechanism of flagellin perception in rice, however, has remained obscure. in this study, we found that flg22, a peptide derived from the flagellin n-terminus, induced weak immune responses witho ...	2008	18986259
investigating intraspecific variation of acidovorax avenae subsp. citrulli using dna fingerprinting and whole cell fatty acid analysis.	abstract to assess the diversity of acidovorax avenae subsp. citrulli, 121 strains from watermelon, cantaloupe, and pumpkin were compared using pulse field gel electrophoresis of spei-digested dna and gas chromatographic analysis of fatty acid methyl esters. twenty-nine unique dna fragments resulted from dna digestion, and 14 distinct haplotypes were observed. based on cluster analysis, two subgroups, i and ii, were recognized, which accounted for 84.8% (eight haplotypes) and 15.2% (six haplotyp ...	2000	18944608
biological control to protect watermelon blossoms and seed from infection by acidovorax avenae subsp. citrulli.	abstract the efficacy of biological control seed treatments with pseudomonas fluorescens (a506), acidovorax avenae subsp. avenae (aaa 99-2), and an unidentified gram-positive bacterium recovered from watermelon seed (ws-1) was evaluated for the management of bacterial fruit blotch (bfb) of watermelon. in growth chamber and greenhouse experiments, seed treated with aaa 99-2 displayed superior disease suppression, reducing bfb transmission by 96.5%. aaa 99-2, p. fluorescens a506, and kocide also s ...	2005	18943044
role of blossoms in watermelon seed infestation by acidovorax avenae subsp. citrulli.	abstract the role of watermelon blossom inoculation in seed infestation by acidovorax avenae subsp. citrulli was investigated. approximately 98% (84/87) of fruit developed from blossoms inoculated with 1 x 10(7) or 1 x 10(9) cfu of a. avenae subsp. citrulli per blossom were asymptomatic. using immunomagnetic separation and the polymerase chain reaction, a. avenae subsp. citrulli was detected in 44% of the seed lots assayed, despite the lack of fruit symptoms. furthermore, viable colonies were re ...	2003	18942974
influence of pharmaceutical residues on the structure of activated sludge bacterial communities in wastewater treatment bioreactors.	concern is growing over contamination of the environment with pharmaceuticals because of their widespread use and incomplete removal during wastewater treatment, where microorganisms drive the key processes. the influence of pharmaceuticals on bacterial community structure in activated sludge was assessed in small-scale wastewater treatment bioreactors containing different concentrations (5, 50, 200 and 500microgl(-1)) of several commonly used pharmaceuticals (ibuprofen, naproxen, ketoprofen, di ...	2008	18786690
verminephrobacter eiseniae gen. nov., sp. nov., a nephridial symbiont of the earthworm eisenia foetida (savigny).	a gram-negative, flagellated, heterotrophic, catalase-negative, rod-shaped bacterium previously identified as an earthworm symbiont was isolated from nephridia of the earthworm eisenia foetida. comparisons of 16s rrna gene sequences indicated its relatedness to the betaproteobacterial genus acidovorax and the novel isolates shared 92-94% sequence similarity with recognized species of this genus. gene sequence phylogenies revealed that the group of earthworm symbionts formed a cohesive and indepe ...	2008	18768621
expression of a bacterial flagellin gene triggers plant immune responses and confers disease resistance in transgenic rice plants.	flagellin is a component of bacterial flagella and acts as a proteinaceous elicitor of defence responses in organisms. flagellin from a phytopathogenic bacterium, acidovorax avenae strain n1141, induces immune responses in suspension-cultured rice cells. to analyse the function of flagellin in rice, we fused the n1141 flagellin gene to the cauliflower mosaic virus 35s promoter and introduced it into rice. many of the resulting transgenic rice plants accumulated flagellin at various levels. the t ...	2008	18705865
enrichment and characterization of chlorinated organophosphate ester-degrading mixed bacterial cultures.	chlorinated organophosphate ester (ope)-degrading enrichment cultures were obtained using tris(2-chloroethyl) phosphate (tcep) or tris(1,3-dichloro-2-propyl) phosphate (tdcpp) as the sole phosphorus source. in cultures with 46 environmental samples, significant tcep and tdcpp degradation was observed in 10 and 3 cultures, respectively, and successive subcultivation markedly increased their degradation rates. 67e and 45d stable enrichment cultures obtained with tcep and tdcpp, respectively, compl ...	2008	18691527
the screening, characterization, and use of omega-laurolactam hydrolase: a new enzymatic synthesis of 12-aminolauric acid.	several omega-laurolactam degrading microorganisms were isolated from soil samples. these strains were capable of growing in a medium containing omega-laurolactam as sole source of carbon and nitrogen. among them, five strains (t7, t31, u124, u224, and u238) were identified as cupriavidus sp. t7, acidovorax sp. t31, cupriavidus sp. u124, rhodococcus sp. u224, and sphingomonas sp. u238, respectively. the omega-laurolactam hydrolyzing enzyme from rhodococcus sp. u224 was purified to homogeneity, a ...	2008	18685217
phylogenetic and metabolic bacterial diversity of phragmites australis periphyton communities in two hungarian soda ponds.	bacterial diversity of reed (phragmites australis) periphyton communities of kelemen-szék and nagy-vadas (two hungarian soda ponds) was investigated using molecular cloning and cultivation-based techniques. the majority of the 80 kelemen-szék and 72 nagy-vadas bacterial isolates proved to be moderately halophilic and alkaliphilic. a great proportion of the isolates showed phosphatase and urease activity, utilized aesculin, citrate and certain biopolymers (e.g., gelatine and tween 80). partial 16 ...	2008	18679563
emergence of cold water strawberry disease of rainbow trout oncorynchus mykiss in england and wales: outbreak investigations and transmission studies.	cold water strawberry disease (cwsd), or red mark syndrome (rms), is a severe dermatitis affecting the rainbow trout oncorynchus mykiss. the condition, which presents as multifocal, raised lesions on the flanks of affected fish, was first diagnosed in scotland in 2003 and has since spread to england and wales. results of field investigations indicated the condition had an infectious aetiology, with outbreaks in england linked to movements of live fish from affected sites in scotland. transmissio ...	2008	18589997
microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels.	microbial enumeration, 16s rrna gene clone libraries, and chemical analysis were used to evaluate the in situ biological reduction and immobilization of uranium(vi) in a long-term experiment (more than 2 years) conducted at a highly uranium-contaminated site (up to 60 mg/liter and 800 mg/kg solids) of the u.s. department of energy in oak ridge, tn. bioreduction was achieved by conditioning groundwater above ground and then stimulating growth of denitrifying, fe(iii)-reducing, and sulfate-reducin ...	2008	18456853
[study of ectoparasitism of ultramicrobacteria of the genus kaistia, strains nf1 and nf3 by electron and fluorescence microscopy].	transmission electron and fluorescence microscopy was used to study the character of the interaction of free-living ultramicrobacterial (umb) strains nf1 and nf3, affiliated with the genus kaistia, and seven species of gram-positive and gram-negative heterotrophic bacteria. strains nf1 and nf3 were found to exhibit parasitic activity against gram-positive bacillus subtilis and gram-negative acidovorax delafildii. umb cells are tightly attached to the envelopes of the victim cells and induce thei ...	2008	18365722
cathodic oxygen reduction catalyzed by bacteria in microbial fuel cells.	microbial fuel cells (mfcs) have the potential to combine wastewater treatment efficiency with energetic efficiency. one of the major impediments to mfc implementation is the operation of the cathode compartment, as it employs environmentally unfriendly catalysts such as platinum. as recently shown, bacteria can facilitate sustainable and cost-effective cathode catalysis for nitrate and also oxygen. here we describe a carbon cathode open to the air, on which attached bacteria catalyzed oxygen re ...	2008	18288216
comparative phylogenies of burkholderia, ralstonia, comamonas, brevundimonas and related organisms derived from rpob, gyrb and rrs gene sequences.	phylogenetic analysis of strains from burkholderia, ralstonia, cupriavidus, comamonas, delftia, acidovorax, brevundimonas, herbaspirillum huttiense and "pseudomonas butanovora" was performed based on the protein-coding genes rpob and gyrb and on the 16s rrna-coding gene rrs. overall, the phylogenies deduced from the three genes were concordant among themselves and with current taxonomy. however, a few differences among individual gene phylogenies were noted. for example, the separation of cupria ...	2008	18280706
selective recruitment of bacteria during embryogenesis of an earthworm.	earthworms of the family lumbricidae harbor specific and stable populations of acidovorax-like bacteria within their excretory organs, the nephridia. the symbionts of eisenia foetida are deposited into the egg capsules during mating and the nephridia of the juveniles are colonized before they hatch. the timing and mechanisms governing bacterial recruitment and colonization are unknown for the earthworm-acidovorax association. this study examined the process of colonization of the symbiotic organ ...	2008	18273064
biodegradation potential and bacterial diversity of a petrochemical wastewater treatment plant in iran.	an activated sludge treatment was evaluated for its effectiveness in cleaning up a petrochemical wastewater in iran. for assessing biodegradation potential of activated sludge, seven characteristics of wastewater (temperature, ph, dissolved oxygen, chemical oxygen demand, concentrations of ethylene dichloride, vinyl chloride, and total hydrocarbons) were monitored during six months. it was shown that dominant pollutants in order of magnitude were normal-alkanes (c(10)-c(21)), aromatics, and poly ...	2008	18255283
pseudacidovorax intermedius gen. nov., sp. nov., a novel nitrogen-fixing betaproteobacterium isolated from soil.	a gram-negative, short rod-shaped, nitrogen-fixing bacterium (cc-21(t)) was isolated from a soil sample collected from the regional agricultural research station in kaohsiung county (taiwan). using 16s rrna gene sequence analysis, it could be clearly demonstrated that this isolate was novel: it showed <97 % similarity to species of the genera acidovorax, alicycliphilus, giesbergeria, simplicispira and diaphorobacter. the organism used several organic acids, but only a few sugars as substrates. t ...	2008	18218955
bacterial diversity in synovial fluids of patients with tmd determined by cloning and sequencing analysis of the 16s ribosomal rna gene.	the purpose of this study was to examine the presence of bacteria in synovial fluids from patients with temporomandibular joint disorder (tmd) by polymerase chain reaction (pcr) targeting the 16s ribosomal rna (rrna) gene, followed by cloning and sequencing.	2008	18206402
acidovorax caeni sp. nov., a denitrifying species with genetically diverse isolates from activated sludge.	four gram-negative, rod-shaped, non-spore-forming, denitrifying isolates were obtained from the activated sludge of an aerobic-anaerobic wastewater treatment plant in belgium. analysis of repetitive sequence-based pcr showed that the four isolates were genetically different from each other. results of 16s rrna gene sequence analysis and dna-dna hybridization experiments indicated that these four isolates were affiliated to the genus acidovorax and could be differentiated from all recognized spec ...	2008	18175686
correlation of patterns of denitrification instability in replicated bioreactor communities with shifts in the relative abundance and the denitrification patterns of specific populations.	to assess the effects of community structure on the stability of denitrification, six chemostat cultures derived from the same denitrifying community were subjected to step increases in feed nitrate concentration and monitored for evidence that denitrification was either not occurring (indicated by the presence of nitrate) or was incomplete (indicated by the presence of nitrite or nitrous oxide). functional stability was defined and quantified from the pattern of effluent concentration trends of ...	2007	18059495
two bacterial entophytes eliciting both plant growth promotion and plant defense on pepper (capsicum annuum l.).	plant growth-promoting rhizobacteria (pgpr) have the potential to be used as microbial inoculants to reduce disease incidence and severity and to increase crop yield. some of the pgpr have been reported to be able to enter plant tissues and establish endophytic populations. here, we demonstrated an approach to screen bacterial endophytes that have the capacity to promote the growth of pepper seedlings and protect pepper plants against a bacterial pathogen. initially, out of 150 bacterial isolate ...	2007	18051359
implementation of artificial neural networks (anns) to analysis of inter-taxa communities of benthic microorganisms and macroinvertebrates in a polluted stream.	this study was performed to gain an understanding of the structural and functional relationships between inter-taxa communities (macroinvertebrates as consumers, and microbes as decomposers or preys for the invertebrates) in a polluted stream using artificial neural networks techniques. sediment samples, carrying microorganisms (eubacteria) and macroinvertebrates, were seasonally collected from similar habitats in streams with different levels of pollution. microbial community taxa and densities ...	2008	17964635
kinetics of chlorobenzene biodegradation under reduced oxygen levels.	focussing on the role of chlorocatechol 1,2-dioxygenase (cc12o), an oxygen-dependent key enzyme in the aerobic catabolism of chlorobenzene (cb), pseudomonas veronii strain ufz b549, acidovorax facilis strain ufz b530, and a community of indigenous groundwater bacteria were amended with cb degradation under either oxic or hypoxic conditions. all cultures readily degraded cb at high oxygen availability, but had differing abilities to completely degrade cb when exposed to oxygen limitation. for the ...	2008	17934786
microbial community shifts as a response to efficient degradation of chlorobenzene under hypoxic conditions.	limitations in the availability of oxygen restrict aerobic biodegradation of chloroaromatic compounds in groundwater ecosystems. in this context the activity of ring-cleaving chlorocatechol dioxygenases (cc12o) is crucial for effective mineralization. previously we demonstrated that oxygen-related enzyme characteristics of cc12o can vary widely among the proteobacteria (balcke et al. submitted). here, we investigated how strains with different ability to transform intermediary 3-chlorocatechol i ...	2008	17882513
molecular mechanism of the redox-dependent interaction between nadh-dependent ferredoxin reductase and rieske-type [2fe-2s] ferredoxin.	the electron transfer system of the biphenyl dioxygenase bpha, which is derived from acidovorax sp. (formally pseudomonas sp.) strain kks102, is composed of an fad-containing nadh-ferredoxin reductase (bpha4) and a rieske-type [2fe-2s] ferredoxin (bpha3). biochemical studies have suggested that the whole electron transfer process from nadh to bpha3 comprises three consecutive elementary electron-transfer reactions, in which bpha3 and bpha4 interact transiently in a redox-dependent manner. initia ...	2007	17850818
diversity analysis of antagonists from rice-associated bacteria and their application in biocontrol of rice diseases.	to understand the diversity, taxonomy and antagonistic potential of rice-associated bacteria, and to discover new bacteria for biocontrol of rice foliar pathogens.	2008	17850318
protein engineering of nitrilase for chemoenzymatic production of glycolic acid.	a key step in a chemoenzymatic process for the production of high-purity glycolic acid (gla) is the enzymatic conversion of glycolonitrile (gln) to ammonium glycolate using a nitrilase derived from acidovorax facilis 72w. protein engineering and over-expression of this nitrilase, combined with optimized fermentation of an e. coli transformant were used to increase the enzyme-specific activity up to 15-fold and the biocatalyst-specific activity up to 125-fold. these improvements enabled achieveme ...	2008	17787011
isolation and antifungal activity of lignans from myristica fragrans against various plant pathogenic fungi.	in a search for plant extracts with potent in vivo antifungal activity against various plant diseases, we found that treatment with a methanol extract of myristica fragrans houttyn (nutmeg) seeds reduced the development of various plant diseases. the objectives of the present study were to isolate and determine antifungal substances from my. fragrans and to evaluate their antifungal activities.	2007	17659535
crystallization and preliminary x-ray analysis of the electron-transfer complex of rieske-type [2fe-2s] ferredoxin and nadh-dependent ferredoxin reductase derived from acidovorax sp. strain kks102.	the electron-transfer complex of bpha3, a rieske-type [2fe-2s] ferredoxin, and bpha4, a nadh-dependent ferredoxin reductase, was crystallized using the sitting-drop vapour-diffusion method under anaerobic conditions. the obtained crystals were analyzed by sds-page, which showed that they contained both bpha3 and bpha4. the crystals belong to space group p2(1), with unit-cell parameters a = 60.60, b = 173.72, c = 60.98 a, beta = 115.8 degrees, and diffracted to a resolution of 1.9 a.	2007	17554177
metabolic activity and phylogenetic diversity of reed (phragmites australis) periphyton bacterial communities in a hungarian shallow soda lake.	in the present study, the species composition and potential metabolic activities of bacterial communities of reed phragmites australis (cav.) (trin. ex steudel) periphyton from lake velencei were studied by cultivation-based and metabolic fingerprinting methods. serially diluted spring biofilm samples were used to test the community-level physiological profiling (clpp) using biolog microplates, and for plating onto different media. on the basis of their morphological, biochemical, and physiologi ...	2007	17406774