Publications

biotransformation of monoterpenes, bile acids, and other isoprenoids in anaerobic ecosystems.	isoprenoic compounds play a major part in the global carbon cycle. biosynthesis and mineralization by aerobic bacteria have been intensively studied. this review describes our knowledge on the anaerobic metabolism of isoprenoids, mainly by denitrifying and fermentative bacteria. nitrate-reducing beta-proteobacteria were isolated on monoterpenes as sole carbon source and electron donor. thauera spp. were obtained on the oxygen-containing monoterpenes linalool, menthol, and eucalyptol. several str ...	1998	9990726
metabolism of acrylate to beta-hydroxypropionate and its role in dimethylsulfoniopropionate lyase induction by a salt marsh sediment bacterium, alcaligenes faecalis m3a.	dimethylsulfoniopropionate (dmsp) is degraded to dimethylsulfide (dms) and acrylate by the enzyme dmsp lyase. dms or acrylate can serve as a carbon source for both free-living and endophytic bacteria in the marine environment. in this study, we report on the mechanism of dmsp-acrylate metabolism by alcaligenes faecalis m3a. suspensions of citrate-grown cells expressed a low level of dmsp lyase activity that could be induced to much higher levels in the presence of dmsp, acrylate, and its metabol ...	1999	10543825
population dynamics of an introduced bacterium degrading chlorinated benzenes in a soil column and in sewage sludge.	the capacity of the beta-proteobacterium pseudomonas sp. strain p51, which degrades chlorinated benzenes, to metabolize 1,2,4-trichlorobenzene (tcb) under environmental conditions was tested by its release into two experimental systems. the first system consisted of laboratory scale microcosms which were operated with and without the addition of tcb and which were inoculated with sludge from a wastewater treatment plant. the second system consisted of a non sterile, water saturated soil column. ...	1999	10466200
glyceraldehyde-3-phosphate dehydrogenase gene diversity in eubacteria and eukaryotes: evidence for intra- and inter-kingdom gene transfer.	cyanobacteria contain up to three highly divergent glyceraldehyde-3-phosphate dehydrogenase (gapdh) genes: gap1, gap2, and gap3. genes gap1 and gap2 are closely related at the sequence level to the nuclear genes encoding cytosolic and chloroplast gapdh of higher plants and have recently been shown to play distinct key roles in catabolic and anabolic carbon flow, respectively, of the unicellular cyanobacterium synechocystis sp. pcc6803. in the present study, sequences of 10 gapdh genes distribute ...	1999	10331270
geranic acid formation, an initial reaction of anaerobic monoterpene metabolism in denitrifying alcaligenes defragrans.	monoterpenes with an unsaturated hydrocarbon structure are mineralized anaerobically by the denitrifying beta-proteobacterium alcaligenes defragrans. organic acids occurring in cells of a. defragrans and culture medium were characterized to identify potential products of the monoterpene activation reaction. geranic acid (e,e-3,7-dimethyl-2,6-octadienoic acid) accumulated to 0.5 mm in cells grown on alpha-phellandrene under nitrate limitation. cell suspensions of a. defragrans 65phen synthesized ...	2000	10877798
hydrogenophilus hirschii sp. nov., a novel thermophilic hydrogen-oxidizing beta-proteobacterium isolated from yellowstone national park.	a novel thermophilic hydrogen-oxidizing bacterium, hydrogenophilus hirschii yel5at (= dsm 11420t = jcm 10831t) has been isolated from the angel terrace spring, yellowstone national park. the isolate was rod-shaped (1.0-1.5 x 0.8 microm) with a polarly inserted flagellum. cells grew chemolithoautotrophically under an atmosphere of h2 and co2 (80:20) in the presence of low concentrations of o2 (optimum 2.5%). organotrophic growth occurred on complex organic substrates such as yeast extract and pep ...	2001	11321094
phylogenetic analysis of culturable dimethyl sulfide-producing bacteria from a spartina-dominated salt marsh and estuarine water.	dimethylsulfoniopropionate (dmsp), an abundant osmoprotectant found in marine algae and salt marsh cordgrass, can be metabolized to dimethyl sulfide (dms) and acrylate by microbes having the enzyme dmsp lyase. a suite of dms-producing bacteria isolated from a salt marsh and adjacent estuarine water on dmsp agar plates differed markedly from the pelagic strains currently in culture. while many of the salt marsh and estuarine isolates produced dms and methanethiol from methionine and dimethyl sulf ...	2001	11229912
two similar gene clusters coding for enzymes of a new type of aerobic 2-aminobenzoate (anthranilate) metabolism in the bacterium azoarcus evansii.	in the beta-proteobacterium azoarcus evansii, the aerobic metabolism of 2-aminobenzoate (anthranilate), phenylacetate, and benzoate proceeds via three unprecedented pathways. the pathways have in common that all three substrates are initially activated to coenzyme a (coa) thioesters and further processed in this form. the two initial steps of 2-aminobenzoate metabolism are catalyzed by a 2-aminobenzoate-coa ligase forming 2-aminobenzoyl-coa and by a 2-aminobenzoyl-coa monooxygenase/reductase (ac ...	2001	11514509
ralstonia taiwanensis sp. nov., isolated from root nodules of mimosa species and sputum of a cystic fibrosis patient.	a polyphasic taxonomic study, including 16s rdna sequence analysis, dna-dna hybridizations, dna base ratio determinations, amplified 165 rdna restriction analysis, whole-cell protein analyses and extensive biochemical characterization, was conducted to clarify the relationships of eight isolates from root nodules of mimosa species and one isolate from sputum of a cystic fibrosis patient. all nine isolates were classified as a novel ralstonia species, for which the name ralstonia taiwanensis sp. ...	2001	11594603
analysis of a microbial community oxidizing inorganic sulfide and mercaptans.	successful treatment of refinery spent-sulfidic caustic (which results from the addition of sodium hydroxide solutions to petroleum refinery waste streams) was achieved in a bioreactor containing an enrichment culture immobilized in organic polymer beads with embedded powdered activated carbon (bio-sep). the aerobic enrichment culture had previously been selected using a gas mixture of hydrogen sulfide and methyl mercaptan (mesh) as the sole carbon and energy sources. the starting cultures for t ...	2001	11485441
the hydrogen-sensing apparatus in ralstonia eutropha.	molecular hydrogen is widely used by microorganisms as a source of energy. one of the best studied aerobic hydrogen oxidizers, the beta-proteobacterium ralstonia eutropha (formerly alcaligenes eutrophus), harbors two distinct [nife]-hydrogenases which catalyze the heterolytic cleavage of h2 into 2h+ and 2e-. the genes encoding the hydrogenase subunits are arranged in two large operons together with accessory and regulatory genes involved in hydrogenase biosynthesis. both operons are transcribed ...	2002	11931556
photosynthetic apparatus in roseateles depolymerans 61a is transcriptionally induced by carbon limitation.	production of a photosynthetic apparatus in roseateles depolymerans 61a, a recently discovered freshwater beta-proteobacterium showing characteristics of aerobic phototrophic bacteria, was observed when the cells were subjected to a sudden decrease in carbon sources (e.g., when cells grown with 0.1 to 0.4% casamino acids were diluted or transferred into medium containing <or=0.04% casamino acids). accumulation of bacteriochlorophyll (bchl) a was observed in the presence of oxygen and was enhance ...	2002	11916683
linking of microorganisms to phenanthrene metabolism in soil by analysis of (13)c-labeled cell lipids.	phenanthrene-metabolizing soil microbial communities were characterized by examining mineralization of [(14)c]phenanthrene, by most-probable-number (mpn) counting, by 16s-23s spacer dna analysis of the numerically dominant, culturable phenanthrene-degrading isolates, and by examining incorporation of [(13)c]phenanthrene-derived carbon into sterols and polar lipid fatty acids (plfas). an unpolluted agricultural soil, a roadside soil diffusely polluted with polycyclic aromatic hydrocarbons (pahs), ...	2002	12450834
aerobic metabolism of phenylacetic acids in azoarcus evansii.	the aerobic metabolism of phenylacetic acid (pa) and 4-hydroxyphenylacetic acid (4-ohpa) was investigated in the beta-proteobacterium azoarcus evansii. evidence for the existence of two independent catabolic pathways for pa and 4-ohpa is presented. 4-ohpa metabolism involves the formation of 2,5-dihydroxyphenylacetate (homogentisate) and maleylacetoacetate catalyzed by specifically induced 4-ohpa 1-monooxygenase and homogentisate 1,2-dioxygenase. the metabolism of pa starts by its activation to ...	2002	12189419
biodegradation of cis-dichloroethene as the sole carbon source by a beta-proteobacterium.	an aerobic bacterium capable of growth on cis-dichloroethene (cdce) as a sole carbon and energy source was isolated by enrichment culture. the 16s ribosomal dna sequence of the isolate (strain js666) had 97.9% identity to the sequence from polaromonas vacuolata, indicating that the isolate was a beta-proteobacterium. at 20 degrees c, strain js666 grew on cdce with a minimum doubling time of 73 +/- 7 h and a growth yield of 6.1 g of protein/mol of cdce. chloride analysis indicated that complete d ...	2002	12039726
quadricoccus australiensis gen. nov., sp. nov., a beta-proteobacterium from activated sludge biomass.	a gram-negative coccus, designated strain ben 117t, was obtained in axenic culture by micromanipulation from an australian activated sludge biomass sample, which had been subjected to chlorination in order to alleviate problems associated with foaming and bulking. this isolate was a strict aerobe and grew in axenic culture, also appearing in biomass samples as cocci or clusters of cocci in tetrads, thus resembling the morphotype 'g-bacteria' seen commonly in activated sludge samples. strain ben ...	2002	11858148
density separation and molecular methods to characterize enhanced biological phosphorus removal system populations.	a novel approach to the identification of microorganisms that accumulate high density microbial storage products based on density separation, denaturing gradient gel electrophoresis (dgge), and dna sequencing was developed and applied to bench and pilot scale enhanced biological phosphorus removal (ebpr) systems. polyphosphate (pp), glycogen, and polyhydroxyalkanoates (phas), are all of higher density than a typical bacterial cell. pp-accumulating organisms (paos), the organisms responsible for ...	2002	12216624
various bacterial pathogens and symbionts infect the amoeba dictyostelium discoideum.	the haploid soil amoeba dictyostelium discoideum is a suitable model organism to study host-pathogen interactions with legionella pneumophila. in this study we show that d. discoideum ax2 is also susceptible to infection with other important human pathogens and obligate intracellular symbionts. infection assays demonstrated that legionella-like amoebal pathogens (llap k62), mycobacterium avium and the obligate intracellular endosymbionts of acanthamoeba sp. strains tume1, uwe25 and uwc6 were abl ...	2002	12008915
genes coding for a new pathway of aerobic benzoate metabolism in azoarcus evansii.	a new pathway for aerobic benzoate oxidation has been postulated for azoarcus evansii and for a bacillus stearothermophilus-like strain. benzoate is first transformed into benzoyl coenzyme a (benzoyl-coa), which subsequently is oxidized to 3-hydroxyadipyl-coa and then to 3-ketoadipyl-coa; all intermediates are coa thioesters. the genes coding for this benzoate-induced pathway were investigated in the beta-proteobacterium a. evansii. they were identified on the basis of n-terminal amino acid sequ ...	2002	12399500
the aerobic electron transport system of eikenella corrodens.	the respiratory system of the fastidious beta-proteobacterium eikenella corrodens grown with limited oxygen was studied. membranes showed the highest oxidase activity with ascorbate plus n,n,n',n'-tetramethyl-p-phenylenediamine (tmpd) or succinate and the lowest activity with nadh and formate. the presence of a bc1-type complex was suggested by the inhibition exerted by 2-heptyl-4-hydroxyquinoline-n-oxide (hoqno), myxothiazol, and antimycin a on respiration with succinate and by the effect of th ...	2002	12489779
isolation of brachymonas petroleovorans chx, a novel cyclohexane-degrading beta-proteobacterium.	a new bacterium that grows aerobically on cyclohexane was isolated from the wastewater plant of a petroleum refinery. this strain grows on a range of light hydrocarbons (c5-c10) as well as on some aromatic compounds such as toluene and m-cresol. growth on hydrocarbons requires the presence of yeast extract and other complex media components that are not substrates for growth themselves. strain chx is resistant to cyclohexane and grows at concentrations up to 2 g l(-1). strain chx branches deeply ...	2003	14568154
2-oxoglutarate:nadp(+) oxidoreductase in azoarcus evansii: properties and function in electron transfer reactions in aromatic ring reduction.	the conversion of [(14)c]benzoyl-coenzyme a (coa) to nonaromatic products in the denitrifying beta-proteobacterium azoarcus evansii grown anaerobically on benzoate was investigated. with cell extracts and 2-oxoglutarate as the electron donor, benzoyl-coa reduction occurred at a rate of 10 to 15 nmol min(-1) mg(-1). 2-oxoglutarate could be replaced by dithionite (200% rate) and by nadph ( approximately 10% rate); in contrast nadh did not serve as an electron donor. anaerobic growth on aromatic co ...	2003	14526024
ralstonia metallidurans, a bacterium specifically adapted to toxic metals: towards a catalogue of metal-responsive genes.	ralstonia metallidurans, formerly known as alcaligenes eutrophus and thereafter as ralstonia eutropha, is a beta-proteobacterium colonizing industrial sediments, soils or wastes with a high content of heavy metals. the type strain ch34 carries two large plasmids (pmol28 and pmol30) bearing a variety of genes for metal resistance. a chronological overview describes the progress made in the knowledge of the plasmid-borne metal resistance mechanisms, the genetics of r. metallidurans ch34 and its ta ...	2003	12829276
distribution and organization of auxotrophic genes on the multichromosomal genome of burkholderia multivorans atcc 17616.	the burkholderia multivorans strain atcc 17616 carries three circular chromosomes with sizes of 3.4, 2.5, and 0.9 mb. to determine the distribution and organization of the amino acid biosynthetic genes on the genome of this beta-proteobacterium, various auxotrophic mutations were isolated using a tn5 derivative that was convenient not only for the determination of its insertion site on the genome map but also for the structural analysis of the flanking regions. analysis by pulsed-field gel elect ...	2003	12754231
bacterioplankton community structure in a maritime antarctic oligotrophic lake during a period of holomixis, as determined by denaturing gradient gel electrophoresis (dgge) and fluorescence in situ hybridization (fish).	the bacterioplankton community structure in moss lake, a maritime antarctic oligotrophic lake, was determined with vertical depth in the water column, during the ice-free period on signy island in the south orkney islands. bacterioplankton community structure was determined using a combination of direct counting of 4',6-diamidino-2-phenylindole (dapi) stained cells, pcr amplification of 16s rrna gene fragments, denaturing gradient gel electrophoresis (dgge) and in situ hybridization with group-s ...	2003	12739078
alicycliphilus denitrificans gen. nov., sp. nov., a cyclohexanol-degrading, nitrate-reducing beta-proteobacterium.	a facultatively denitrifying bacterium, strain k601t, was isolated at 30 degrees c from a municipal sewage plant on cyclohexanol as sole carbon source and nitrate as electron acceptor. under aerobic conditions this strain used acetate, fumarate, lactate, pyruvate, crotonate, indole, glucose, vanillate, 4-hydroxybenzoate, m-cresol, o-cresol and p-cresol. under denitrifying conditions the strain used cyclohexanol, cyclohexanone, 1,3-cyclohexanedione, 2-cyclohexenone, 1,3-cyclohexanediol (cis and t ...	2003	12661531
arsenite oxidase aox genes from a metal-resistant beta-proteobacterium.	the beta-proteobacterial strain ulpas1, isolated from an arsenic-contaminated environment, is able to efficiently oxidize arsenite [as(iii)] to arsenate [as(v)]. mutagenesis with a lacz-based reporter transposon yielded two knockout derivatives deficient in arsenite oxidation. sequence analysis of the dna flanking the transposon insertions in the two mutants identified two adjacent open reading frames, named aoxa and aoxb, as well as a putative promoter upstream of the aoxa gene. reverse transcr ...	2003	12486049
direct detection of a hydrogen ligand in the [nife] center of the regulatory h2-sensing hydrogenase from ralstonia eutropha in its reduced state by hyscore and endor spectroscopy.	the regulatory h2-sensing [nife] hydrogenase of the beta-proteobacterium ralstonia eutropha displays an ni-c "active" state after reduction with h2 that is very similar to the reduced ni-c state of standard [nife] hydrogenases. pulse electron nuclear double resonance (endor) and four-pulse eseem (hyperfine sublevel correlation, hyscore) spectroscopy are applied to obtain structural information on this state via detection of the electron-nuclear hyperfine coupling constants. two proton hyperfine ...	2003	14570480
discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment.	microorganisms maintain the biosphere by catalyzing biogeochemical processes, including biodegradation of organic chemical pollutants. yet seldom have the responsible agents and their respective genes been identified. here we used field-based stable isotopic probing (sip) to discover a group of bacteria responsible for in situ metabolism of an environmental pollutant, naphthalene. we released 13c-labeled naphthalene in a contaminated study site to trace the flow of pollutant carbon into the natu ...	2003	14597712
nodulation of mimosa spp. by the beta-proteobacterium ralstonia taiwanensis.	several beta-proteobacteria have been isolated from legume root nodules and some of these are thought to be capable of nodulating and fixing n2. however, in no case has there been detailed studies confirming that they are the active symbionts. here, ralstonia taiwanensis lmg19424, which was originally isolated from mimosa pudica nodules, was transformed to carry the green fluorescent protein (gfp) reporter gene before being used to inoculate axenically-grown seedlings of m. pudica and m. diplotr ...	2003	14651338
tepidimonas aquatica sp. nov., a new slightly thermophilic beta-proteobacterium isolated from a hot water tank.	a bacterial isolate, with an optimum growth temperature of about 50 degrees c, was recovered from a domestic hot water tank in coimbra. phylogenetic analysis using 16s rrna gene sequence indicated that strain cln-1t is a member of the beta-proteobacteria and represents a new species of the genus tepidimonas. the major fatty acids of strain cln-1t are 16:0, 17:0 cyclo and 16:1 omega7c. ubiquinone 8 is the major respiratory quinone, the major polar lipids are phosphatidylethanolamine, and phosphat ...	2003	14529180
sterolibacterium denitrificans gen. nov., sp. nov., a novel cholesterol-oxidizing, denitrifying member of the beta-proteobacteria.	a bacterial strain (chol-1s(t)) that is able to oxidize cholesterol to co2 and reduce nitrate to dinitrogen was enriched and isolated from an upflow sludge bed (usb) anoxic reactor that treats sanitary landfill leachate from the city of montevideo, uruguay. cells of strain chol-1s(t) were gram-negative, rod-shaped to slightly curved, measured 0.5-0.6 x 1.0-1.3 microm and were motile by a single polar flagellum. strain chol-1s(t) grew optimally at 30-32 degrees c and ph 7.0, with a doubling time ...	2003	12892131
a novel approach for high throughput cultivation assays and the isolation of planktonic bacteria.	abstract using the microdrop((r)) microdispenser system, a novel approach for high throughput cultivation assays for the determination of numbers of culturable bacteria, and for the isolation of bacteria in liquid media was established. the microdrop device works similar to an ink jet printer. droplets of 150-200 pl are created at the nozzle of a glass micropipette by means of a computer-driven piezo transducer, and are dispensed automatically at predetermined positions with the aid of a xyz-pos ...	2003	19719627
the chromosomally encoded cation diffusion facilitator proteins dmef and fief from wautersia metallidurans ch34 are transporters of broad metal specificity.	genomic sequencing of the beta-proteobacterium wautersia (previously ralstonia) metallidurans ch34 revealed the presence of three genes encoding proteins of the cation diffusion facilitator (cdf) family. one, czcd, was previously found to be part of the high-level metal resistance system czc that mediates the efflux of co(ii), zn(ii), and cd(ii) ions catalyzed by the czccba cation-proton antiporter. the second cdf protein, fief, is probably mainly a ferrous iron detoxifying protein but also medi ...	2004	15547276
long-chain n-acyltyrosine synthases from environmental dna.	the heterologous expression of dna extracted directly from environmental samples (environmental dna [edna]) in easily cultured hosts provides access to natural products produced by previously inaccessible microorganisms. when edna cosmid libraries were screened in escherichia coli for antibacterially active clones, long-chain n-acyltyrosine-producing clones were found in every edna library. these apparently common natural products have not been previously described from screening extracts of cul ...	2004	15528554
urease-encoding genes in ammonia-oxidizing bacteria.	many but not all ammonia-oxidizing bacteria (aob) produce urease (urea amidohydrolase, ec 3.5.1.5) and are capable of using urea for chemolithotrophic growth. we sequenced the urease operons from two aob, the beta-proteobacterium nitrosospira sp. strain npav and the gamma-proteobacterium nitrosococcus oceani. in both organisms, all seven urease genes were contiguous: the three structural urease genes ureabc were preceded and succeeded by the accessory genes ured and ureefg, respectively. green f ...	2004	15066830
molybdenum-containing arsenite oxidase of the chemolithoautotrophic arsenite oxidizer nt-26.	the chemolithoautotroph nt-26 oxidizes arsenite to arsenate by using a periplasmic arsenite oxidase. purification and preliminary characterization of the enzyme revealed that it (i) contains two heterologous subunits, aroa (98 kda) and arob (14 kda); (ii) has a native molecular mass of 219 kda, suggesting an alpha2beta2 configuration; and (iii) contains two molybdenum and 9 or 10 iron atoms per alpha2beta2 unit. the genes that encode the enzyme have been cloned and sequenced. sequence analyses r ...	2004	14996791
molecular evidence for the evolution of metal homeostasis genes by lateral gene transfer in bacteria from the deep terrestrial subsurface.	lateral gene transfer (lgt) plays a vital role in increasing the genetic diversity of microorganisms and promoting the spread of fitness-enhancing phenotypes throughout microbial communities. to date, lgt has been investigated in surface soils, natural waters, and biofilm communities but not in the deep terrestrial subsurface. here we used a combination of molecular analyses to investigate the role of lgt in the evolution of metal homeostasis in lead-resistant subsurface bacteria. a nested pcr a ...	2004	15006795
biogeography, evolution, and diversity of epibionts in phototrophic consortia.	motile phototrophic consortia are highly regular associations in which numerous cells of green sulfur bacteria surround a flagellated colorless beta-proteobacterium in the center. to date, seven different morphological types of such consortia have been described. in addition, two immotile associations involving green sulfur bacteria are known. by employing a culture-independent approach, different types of phototrophic consortia were mechanically isolated by micromanipulation from 14 freshwater ...	2004	15294820
isolation, free-living capacities, and genome structure of "candidatus glomeribacter gigasporarum," the endocellular bacterium of the mycorrhizal fungus gigaspora margarita.	"candidatus glomeribacter gigasporarum" is an endocellular beta-proteobacterium present in the arbuscular mycorrhizal (am) fungus gigaspora margarita. we established a protocol to isolate "ca. glomeribacter gigasporarum" from its host which allowed us to carry out morphological, physiological, and genomic investigations on purified bacteria. they are rod shaped, with a cell wall typical of gram-negative bacteria and a cytoplasm rich in ribosomes, and they present no flagella or pili. isolated ba ...	2004	15466041
phenylphosphate synthase: a new phosphotransferase catalyzing the first step in anaerobic phenol metabolism in thauera aromatica.	the anaerobic metabolism of phenol in the beta-proteobacterium thauera aromatica proceeds via para-carboxylation of phenol (biological kolbe-schmitt carboxylation). in the first step, phenol is converted to phenylphosphate which is then carboxylated to 4-hydroxybenzoate in the second step. phenylphosphate formation is catalyzed by the novel enzyme phenylphosphate synthase, which was studied. phenylphosphate synthase consists of three proteins whose genes are located adjacent to each other on the ...	2004	15547277
phenylphosphate carboxylase: a new c-c lyase involved in anaerobic phenol metabolism in thauera aromatica.	the anaerobic metabolism of phenol in the beta-proteobacterium thauera aromatica proceeds via carboxylation to 4-hydroxybenzoate and is initiated by the atp-dependent conversion of phenol to phenylphosphate. the subsequent para carboxylation of phenylphosphate to 4-hydroxybenzoate is catalyzed by phenylphosphate carboxylase, which was purified and studied. this enzyme consists of four proteins with molecular masses of 54, 53, 18, and 10 kda, whose genes are located adjacent to each other in the ...	2004	15231788
incidence and function of sigma factors in ralstonia metallidurans and other bacteria.	bacterial sigma factors are essential for directing the bacterial rna polymerase to promoter regions during transcription initiation. genomic sequencing of the highly heavy-metal-resistant beta-proteobacterium ralstonia metallidurans strain ch34 revealed 17 candidate genes for sigma factors. this review compares the sigma factor machinery of r. metallidurans to that of other bacteria. the sigma factors of 105 bacterial genomes were assigned to sigma factor clusters and families formed around the ...	2004	15022036
chemotaxis and flagellar genes of chromobacterium violaceum.	the availability of the complete genome of the gram-negative beta-proteobacterium chromobacterium violaceum has increasingly impacted our understanding of this microorganism. this review focuses on the genomic organization and structural analysis of the deduced proteins of the chemosensory adaptation system of c. violaceum. c. violaceum has multiple homologues of most chemotaxis genes, organized mostly in clusters in the bacterial genome. we found at least 67 genes, distributed in 10 gene cluste ...	2004	15100991
dna repair in chromobacterium violaceum.	chromobacterium violaceum is a gram-negative beta-proteobacterium that inhabits a variety of ecosystems in tropical and subtropical regions, including the water and banks of the negro river in the brazilian amazon. this bacterium has been the subject of extensive study over the last three decades, due to its biotechnological properties, including the characteristic violacein pigment, which has antimicrobial and anti-tumoral activities. c. violaceum promotes the solubilization of gold in a mercur ...	2004	15100997
hydrogen sensing by enzyme-catalyzed electrochemical detection.	hydrogen (h2) is a possible future alternative to current fossil-based transportation fuels; however, its lower explosive limit in air requires a reliable sensor to detect leaks wherever h2 is produced, stored, or used. most current h2 sensors employ palladium or its alloy as the sensing element, featuring high operating temperature and limited selectivity. in this study, we report using soluble hydrogenase (sh) of aerobic beta-proteobacterium ralstonia eutropha strain h16 to accomplish ambient, ...	2005	16053311
electrocatalytic hydrogen oxidation by an enzyme at high carbon monoxide or oxygen levels.	use of hydrogen in fuel cells requires catalysts that are tolerant to oxygen and are able to function in the presence of poisons such as carbon monoxide. hydrogen-cycling catalysts are widespread in the bacterial world in the form of hydrogenases, enzymes with unusual active sites composed of iron, or nickel and iron, that are buried within the protein. we have established that the membrane-bound hydrogenase from the beta-proteobacterium ralstonia eutropha h16, when adsorbed at a graphite electr ...	2005	16260746
proposed involvement of a soluble methane monooxygenase homologue in the cyclohexane-dependent growth of a new brachymonas species.	high-throughput mrna differential display (dd) was used to identify genes induced by cyclohexane in brachymonas petroleovorans chx, a recently isolated beta-proteobacterium that grows on cyclohexane. two metabolic gene clusters were identified multiple times in independent reverse transcription polymerase chain reactions (rt-pcr) in the course of this dd experiment. these clusters encode genes believed to be required for cyclohexane metabolism. one gene cluster (8 kb) encodes the subunits of a m ...	2005	15658985
propylphenols are metabolites in the anaerobic biodegradation of propylbenzene under iron-reducing conditions.	the metabolism of monoaromatic hydrocarbons by an iron-reducing bacterial enrichment culture originating from diesel-contaminated groundwater was examined using d7-propylbenzene as a model hydrocarbon. sequence analysis of the 16s rdna gene showed that the dominant part (10 of 10 clones) of the enrichment culture consisted of a bacterium closely related to clones found in benzene-contaminated groundwater and to the iron-reducing beta-proteobacterium, rhodoferax ferrireducens (similarity values w ...	2005	15865149
arsenite oxidation in batch reactors with alginate-immobilized ulpas1 strain.	arsenic is one of the major groundwater contaminants worldwide. it was previously demonstrated that the beta-proteobacterium cenibacterium arsenoxidans has an efficient as[iii] oxidation ability. the present study was conducted to evaluate the performance of alginate-immobilized ulpas1 in the oxidation of as[iii] to as[v] in batch reactors. a two-level full factorial experimental design was applied to investigate the influence of main parameters involved in the oxidation process, i.e., ph (7-8), ...	2005	15981279
identification of genes and proteins involved in the pleiotropic response to arsenic stress in caenibacter arsenoxydans, a metalloresistant beta-proteobacterium with an unsequenced genome.	the effect of high concentrations of arsenic has been investigated in caenibacter arsenoxydans, a beta-proteobacterium isolated from an arsenic contaminated environment and able to oxidize arsenite to arsenate. as the genome of this bacterium has not yet been sequenced, the use of a specific proteomic approach based on nano-high performance liquid chromatography tandem mass spectrometry (nanolc-ms/ms) studies and de novo sequencing to perform cross-species protein identifications was necessary. ...	2006	16380199
light-driven hydrogen production by a hybrid complex of a [nife]-hydrogenase and the cyanobacterial photosystem i.	in order to generate renewable and clean fuels, increasing efforts are focused on the exploitation of photosynthetic microorganisms for the production of molecular hydrogen from water and light. in this study we engineered a 'hard-wired' protein complex consisting of a hydrogenase and photosystem i (hydrogenase-psi complex) as a direct light-to-hydrogen conversion system. the key component was an artificial fusion protein composed of the membrane-bound [nife] hydrogenase from the beta-proteobact ...	2006	16542111
aerobic benzoyl-coenzyme a (coa) catabolic pathway in azoarcus evansii: conversion of ring cleavage product by 3,4-dehydroadipyl-coa semialdehyde dehydrogenase.	benzoate, a strategic intermediate in aerobic aromatic metabolism, is metabolized in various bacteria via an unorthodox pathway. the intermediates of this pathway are coenzyme a (coa) thioesters throughout, and ring cleavage is nonoxygenolytic. the fate of the ring cleavage product 3,4-dehydroadipyl-coa semialdehyde was studied in the beta-proteobacterium azoarcus evansii. cell extracts contained a benzoate-induced, nadp(+)-specific aldehyde dehydrogenase, which oxidized this intermediate. a pos ...	2006	16585753
temporal analysis of french bordetella pertussis isolates by comparative whole-genome hybridization.	bordetella pertussis, a gram-negative beta-proteobacterium, is the agent of whooping cough in humans. whooping cough remains a public health problem worldwide, despite well-implemented infant/child vaccination programs. it continues to be endemic and is observed cyclically in vaccinated populations. classical molecular subtyping methods indicate that genome diversity among b. pertussis isolates is limited. although the whole bacterial genome has been studied by pulsed-field gel electrophoresis, ...	2006	16787756
a comparison of alternative 60-mer probe designs in an in-situ synthesized oligonucleotide microarray.	dna microarrays have proven powerful for functional genomics studies. several technologies exist for the generation of whole-genome arrays. it is well documented that 25mer probes directed against different regions of the same gene produce variable signal intensity values. however, the extent to which this is true for probes of greater length (60mers) is not well characterized. moreover, this information has not previously been reported for whole-genome arrays designed against bacteria, whose ge ...	2006	16595014
production and properties of the native chromobacterium violaceum fucose-binding lectin (cv-iil) compared to homologous lectins of pseudomonas aeruginosa (pa-iil) and ralstonia solanacearum (rs-iil).	chromobacterium violaceum is a versatile, violet pigment (violacein)-producing beta-proteobacterium, confined to tropical and subtropical regions, dwelling in soil and water, like pseudomonas aeruginosa and ralstonia solanacearum. these three bacteria are saprophytes that occasionally become aggressive opportunistic pathogens virulently attacking animals (the first two) and plants (the third). the recent availability of their genome sequences enabled identification in the c. violaceum genome of ...	2006	16436433
the genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium thiobacillus denitrificans.	the complete genome sequence of thiobacillus denitrificans atcc 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, beta-proteobacterium. analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of fe(ii) and u(iv), and to ...	2006	16452431
macroscopic streamer growths in acidic, metal-rich mine waters in north wales consist of novel and remarkably simple bacterial communities.	the microbial composition of acid streamers (macroscopic biofilms) in acidic, metal-rich waters in two locations (an abandoned copper mine and a chalybeate spa) in north wales was studied using cultivation-based and biomolecular techniques. known chemolithotrophic and heterotrophic acidophiles were readily isolated from disrupted streamers, but they accounted for only <1 to 7% of the total microorganisms present. fluorescent in situ hybridization (fish) revealed that 80 to 90% of the microbes in ...	2006	16517651
erythromycin resistance-conferring plasmid prsb105, isolated from a sewage treatment plant, harbors a new macrolide resistance determinant, an integron-containing tn402-like element, and a large region of unknown function.	the erythromycin resistance plasmid prsb105 was previously isolated from an activated sludge bacterial community of a municipal wastewater treatment plant. compilation of the complete prsb105 nucleotide sequence revealed that the plasmid is 57,137 bp in size and has a mean g+c content of 56.66 mol%. the prsb105 backbone is composed of two different replication and/or partitioning modules and a functional mobilization region encoding the mobilization genes mobcde and mobba. the first replicon (re ...	2007	17261525
genomic structure and phylogeny of the plant pathogen ralstonia solanacearum inferred from gene distribution analysis.	in the present study, we investigated the gene distribution among strains of the highly polymorphic plant pathogenic beta-proteobacterium ralstonia solanacearum, paying particular attention to the status of known or candidate pathogenicity genes. based on the use of comparative genomic hybridization on a pangenomic microarray for the gmi1000 reference strain, we have defined the conditions that allowed comparison of the repertoires of genes among a collection of 18 strains that are representativ ...	2007	17085551
whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium methylibium petroleiphilum pm1.	methylibium petroleiphilum pm1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (mtbe). strain pm1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (c(5) to c(12)) hydrocarbons present in petroleum products. whole-genome analysis of pm1 revealed an approximately 4-mb circular chromosome and an approximately 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. aromatic hydrocarbon and alkane deg ...	2007	17158667
cyclic amp directly activates nasp, an n-acyl amino acid antibiotic biosynthetic enzyme cloned from an uncultured beta-proteobacterium.	the cyclic amp (camp)-dependent biosynthesis of n-acylphenylalanine antibiotics by nasp, an environmental dna-derived n-acyl amino acid synthase, is controlled by an nasp-associated cyclic nucleotide-binding domain and is independent of the global camp signal transducer, camp receptor protein. a 16s rrna gene sequence found on the same environmental dna cosmid as nasp is most closely related to 16s sequences from beta-proteobacteria.	2007	17586635
investigation of microbial communities on reverse osmosis membranes used for process water production.	in the present study, the diversity and the phylogenetic affiliation of bacteria in a biofouling layer on reverse osmosis (ro) membranes were determined. fresh surface water was used as a feed in a membrane-based water purification process. total dna was extracted from attached cells from feed spacer, ro membrane and product spacer. universal primers were used to amplify the bacterial 16s rrna genes. the biofilm community was analysed by 16s rrna-gene-targeted denaturing gradient gel electrophor ...	2007	17546985
butane monooxygenase of 'pseudomonas butanovora': purification and biochemical characterization of a terminal-alkane hydroxylating diiron monooxygenase.	butane monooxygenase (sbmo) has been purified to homogeneity from the gram-negative beta-proteobacterium 'pseudomonas butanovora' and confirmed to be a three-component diiron monooxygenase system. the reconstituted enzyme complex oxidized c(3)-c(6) linear and branched aliphatic alkanes, which are growth substrates for 'p. butanovora'. the sbmo complex was composed of an iron-containing hydroxylase (bmoh), a flavo-iron sulfur-containing nadh-oxidoreductase (bmor) and a small regulatory component ...	2007	17526838
stenoxybacter acetivorans gen. nov., sp. nov., an acetate-oxidizing obligate microaerophile among diverse o2-consuming bacteria from termite guts.	in termite hindguts, fermentative production of acetate--a major carbon and energy source for the insect--depends on efficient removal of inwardly diffusing oxygen by microbes residing on and near the hindgut wall. however, little is known about the identity of these organisms or about the substrate(s) used to support their respiratory activity. a cultivation-based approach was used to isolate o(2)-consuming organisms from hindguts of reticulitermes flavipes. a consistently greater (albeit not s ...	2007	17827334
physiological ecology of stenoxybacter acetivorans, an obligate microaerophile in termite guts.	stenoxybacter acetivorans is a newly described, obligately microaerophilic beta-proteobacterium that is abundant in the acetate-rich hindgut of reticulitermes. here we tested the hypotheses that cells are located in the hypoxic, peripheral region of reticulitermes flavipes hindguts and use acetate to fuel their o(2)-consuming respiratory activity in situ. physical fractionation of r. flavipes guts, followed by limited-cycle pcr with s. acetivorans-specific 16s rrna gene primers, indicated that c ...	2007	17827335
isolation and characterization of a novel simazine-degrading beta-proteobacterium and detection of genes encoding s-triazine-degrading enzymes.	a moderately persistent herbicide, simazine, has been used globally and detected as a contaminant in soil and water. the authors have isolated a simazine-degrading bacterium from a simazine-degrading bacterial consortium that was enriched using charcoal as a microhabitat. the isolate, strain cdb21, was gram-negative, rod-shaped (0.5-0.6 microm x 1.0-1.2 microm) and motile by means of a single polar flagellum. based on 16s rrna sequence analysis, strain cdb21 was identified as a novel beta-proteo ...	2007	17304635
enigmatic dual symbiosis in the excretory organ of nautilus macromphalus (cephalopoda: nautiloidea).	symbiosis is an important driving force in metazoan evolution and the study of ancient lineages can provide an insight into the influence of symbiotic associations on morphological and physiological adaptations. in the 'living fossil' nautilus, bacterial associations are found in the highly specialized pericardial appendage. this organ is responsible for most of the excretory processes (ultrafiltration, reabsorption and secretion) and secretes an acidic ammonia-rich excretory fluid. in this stud ...	2007	17311780
a tale of two oxidation states: bacterial colonization of arsenic-rich environments.	microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. finding a means of preserving natural environments-including ground and surface waters-from arsenic constitutes a major challenge facing modern society. although this metalloid is ubiquitous on earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. in-depth exploration of the genome of the beta ...	2007	17432936
[microbial dynamics during the composting process].	microbial dynamics of microbial community during the composting process was investigated with the methods of denaturing gradient gel electrophoresis (dgge) and plating. the results showed that the most of microorganism count was bacterium, the second was actinomycete and the least was fungi. at the same time, the count of the thermophilic microorganism was always less than that of the mesophilic during the composting process. the count of mesophilic microorganism at later stage was less than tha ...	2007	18290488
variations in 13c/12c and d/h enrichment factors of aerobic bacterial fuel oxygenate degradation.	reliable compound-specific isotope enrichment factors are needed for a quantitative assessment of in situ biodegradation in contaminated groundwater. to obtain information on the variability on carbon and hydrogen enrichment factors (epsilonc, epsilonh) the isotope fractionation of methyl tertiary (tert-) butyl ether (mtbe) and ethyl tert-butyl ether (etbe) upon aerobic degradation was studied with different bacterial isolates. methylibium sp. r8 showed a carbon and hydrogen isotope enrichment u ...	2007	17410802
[microbial diversity analysis in rotating drum biofilter for nitric oxide denitrifying removal].	pcr-dgge was applied to analyze the microbial communities in rotating drum biofilter (rdb) for nitric oxide denitrifying removal under anaerobic conditions. the 16s rrna genes (v3 region) were amplified with two universal primers (338f-gc and 518r). these amplified dna fragments were separated by parallel dgge. the dgge profiles of biofilm samples from different sections of rdb are similar and about sixteen types of microorganisms are identified in the biofilm samples. these results show that mi ...	2008	18637367
[variation of diversity and activity of ammonia-oxidizing bacteria community in the integrated vertical-flow constructed wetlands].	the activity of ammonia-oxidizing bacteria (aob) in different layers of integrated vertical-flow constructed wetlands (ivcw) treating eutrophic scenic water was measured, and the diversity and spatial distribution of aob community structure in ivcw was investigated using pcr-dgge. the results indicated that because of the integrated influence of competition of plant rhizodeposition, heterotrophic bacteria, do and ammonia concentration, there were significant spatial differences in the activity a ...	2008	18839566
identification and analysis of a glutaryl-coa dehydrogenase-encoding gene and its cognate transcriptional regulator from azoarcus sp. cib.	in this work, the gcdh gene from the denitrifying beta-proteobacterium azoarcus sp. cib was shown to encode a glutaryl-coa dehydrogenase, which is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. the primary structure of the gcdh protein is highly conserved in many organisms. the divergently transcribed gcdr gene, encoding a lysr-type transcriptional regulator, accounts for the glutaconate/glutarate-specific activation of the pg promote ...	2008	18177371
control of bacterial biofilms with marine alkaloid derivatives.	bacterial biofilms are defined as a community of surface-attached bacteria that are protected by an extracellular matrix of biomolecules. we have recently reported the synthesis of a small molecule, denoted tage, based on the natural product bromoageliferin and demonstrated that tage has anti-biofilm activity against pseudomonas aeruginosa. herein we demonstrate that tage: (1) does not have selective toxicity against cells within the biofilm state, (2) will inhibit biofilm development under flow ...	2008	18493660
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
molecular diversity of bacterial production of the climate-changing gas, dimethyl sulphide, a molecule that impinges on local and global symbioses.	this paper describes the ddd genes that are involved in the production of the gas dimethyl sulphide from the substrate dimethylsulphoniopropionate (dmsp), an abundant molecule that is a stress protectant in many marine algae and a few genera of angiosperms. what is known of the arrangement of the ddd genes in different bacteria that can undertake this reaction is reviewed here, stressing the fact that these genes are probably subject to horizontal gene transfer and that the same functions (e.g. ...	2008	18281720
cellulose biosynthesis by the beta-proteobacterium, chromobacterium violaceum.	the chromobacterium violaceum atcc 12472 genome was sequenced by the brazilian national genome project consortium. previous annotation reported the presence of cellulose biosynthesis genes in that genome. analysis of these genes showed that, as observed in other bacteria, they are organized in two operons. in the present work, experimental evidences of the presence of cellulose in the extracellular matrix of the biofilm produced by c. violaceum in static cultures are shown. biofilm samples were ...	2008	18820969
crystal structures of cif from bacterial pathogens photorhabdus luminescens and burkholderia pseudomallei.	a pre-requisite for bacterial pathogenesis is the successful interaction of a pathogen with a host. one mechanism used by a broad range of gram negative bacterial pathogens is to deliver effector proteins directly into host cells through a dedicated type iii secretion system where they modulate host cell function. the cycle inhibiting factor (cif) family of effector proteins, identified in a growing number of pathogens that harbour functional type iii secretion systems and have a wide host range ...	2009	19440549
genomic view of energy metabolism in ralstonia eutropha h16.	ralstonia eutropha is a strictly respiratory facultative lithoautotrophic beta-proteobacterium. in the absence of organic substrates, h2 and co2 are used as sole sources of energy and carbon. in the absence of oxygen, the organism can respire by denitrification. the recent determination of the complete genome sequence of strain h16 provides the opportunity to reconcile the results of previous physiological and biochemical studies in light of the coding capacity. these analyses revealed genes for ...	2009	18957861
new mobile genetic elements in cupriavidus metallidurans ch34, their possible roles and occurrence in other bacteria.	cupriavidus metallidurans strain ch34 is a beta-proteobacterium that thrives in low concentrations of heavy metals. the genetic determinants of resistance to heavy metals are located on its two chromosomes, and are particularly abundant in the two megaplasmids, pmol28 and pmol30. we explored the involvement of mobile genetic elements in acquiring these and others traits that might be advantageous in this strain using genome comparison of cupriavidus/ralstonia strains and related beta-proteobacte ...	2009	19390985
cycle inhibiting factors (cifs) are a growing family of functional cyclomodulins present in invertebrate and mammal bacterial pathogens.	the cycle inhibiting factor (cif) produced by enteropathogenic and enterohemorrhagic escherichia coli was the first cyclomodulin to be identified that is injected into host cells via the type iii secretion machinery. cif provokes cytopathic effects characterized by g(1) and g(2) cell cycle arrests, accumulation of the cyclin-dependent kinase inhibitors (ckis) p21(waf1/cip1) and p27(kip1) and formation of actin stress fibres. the x-ray crystal structure of cif revealed it to be a divergent member ...	2009	19308257
mass spectrometric characterization of the covalent modification of the nitrogenase fe-protein in azoarcus sp. bh72.	nitrogenase fe-protein modification was analyzed in the endophytic beta-proteobacterium azoarcus sp. bh72. application of modern ms techniques localized the modification in the peptide sequence and revealed it to be an adp-ribosylation on arg102 of one subunit of nitrogenase fe-protein. a double digest with trypsin and endoproteinase asp-n was necessary to obtain an analyzable peptide because the modification blocked the trypsin cleavage site at this residue. furthermore, a peptide extraction pr ...	2009	19490119
coordinated surface activities in variovorax paradoxus eps.	variovorax paradoxus is an aerobic soil bacterium frequently associated with important biodegradative processes in nature. our group has cultivated a mucoid strain of variovorax paradoxus for study as a model of bacterial development and response to environmental conditions. colonies of this organism vary widely in appearance depending on agar plate type.	2009	19523213
concerted action of two novel auxiliary proteins in assembly of the active site in a membrane-bound [nife] hydrogenase.	[nife] hydrogenases catalyze the reversible conversion of h2 into protons and electrons. the reaction takes place at the active site, which is composed of a nickel and an iron atom and three diatomic ligands, two cyanides and one carbon monoxide, bound to the iron. the nife(cn-)2co cofactor is synthesized by an intricate posttranslational maturation process, which is mediated by a set of six conserved hyp proteins. depending on the cellular location and the physiological function, additional aux ...	2009	19017638
genetics of the glutamate-mediated methylamine utilization pathway in the facultative methylotrophic beta-proteobacterium methyloversatilis universalis fam5.	the ability of some microbial species to oxidize monomethylamine via glutamate-mediated pathways was proposed in the 1960s; however, genetic determinants of the pathways have never been described. in the present study we describe a gene cluster essential for operation of the n-methylglutamate pathway in the methylotrophic beta-proteobacterium methyloversatilis universalis fam5. four major polypeptides from protein fractions displaying high activities of n-methylglutamate synthetase, n-methylglut ...	2010	19943898
molecular diversity of katg genes in the soil bacteria comamonas.	three complete katg genes coding for bifunctional catalase-peroxidases (katgs) from the beta-proteobacterium comamonas terrigena and two related strains of comamonas testosteroni have been cloned and sequenced. catalase-peroxidases are unique bifunctional enzymes known to be expressed in these soil bacteria in response to environmental and/or oxidative stress. the evolutionary and structural diversity of these enzymes is investigated based on multiple sequence alignment and comprehensive phyloge ...	2010	20062977
insertion sequence elements in cupriavidus metallidurans ch34: distribution and role in adaptation.	cupriavidus metallidurans ch34 is a β-proteobacterium well equipped to cope with harsh environmental conditions such as heavy metal pollution. the strain carries two megaplasmids specialized in the response to heavy metals and a considerable number of genomic islands, transposons and insertion sequence (is) elements. the latter were characterized in detail in this study, which revealed nine new is elements totaling to 21 distinct is elements from 10 different is families and reaching a total of ...	2010	21185859
characterization of cycp gene expression in achromobacter xylosoxidans ncimb 11015 and high-level heterologous synthesis of cytochrome c' in escherichia coli.	the cycp gene encoding a periplasmic cytochrome c' from the denitrifying beta-proteobacterium achromobacter xylosoxidans was characterized. the genes flanking cycp encode components of a mobile genetic element characteristic of the beta-proteobacteria, suggesting that cycp has inserted within a transposon or insertion element. the gene therefore does not form part of a denitrification operon or gene cluster. the level of expression of the cycp gene and the level of synthesis of its corresponding ...	2010	20185933
the involvement of the nif-associated ferredoxin-like genes fdxa and fdxn of herbaspirillum seropedicae in nitrogen fixation.	the pathway of electron transport to nitrogenase in the endophytic beta-proteobacterium herbaspirillum seropedicae has not been characterized. we have generated mutants in two nif-associated genes encoding putative ferredoxins, fdxa and fdxn. the fdxa gene is part of the operon nifhdkenxorf1orf2fdxanifqmodabc and is transcribed from the nifh promoter, as revealed by lacz gene fusion. the fdxn gene is probably cotranscribed with the nifb gene. mutational analysis suggests that the fdxa protein is ...	2010	20221733
arsenite oxidase from ralstonia sp. 22: characterization of the enzyme and its interaction with soluble cytochromes.	we characterized the aro arsenite oxidation system in the novel strain ralstonia sp. 22, a beta-proteobacterium isolated from soil samples of the salsigne mine in southern france. the inducible aro system consists of a heterodimeric membrane-associated enzyme reacting with a dedicated soluble cytochrome c(554). our biochemical results suggest that the weak association of the enzyme to the membrane probably arises from a still unknown interaction partner. analysis of the phylogeny of the aro gene ...	2010	20421652
comparison of ca2+ and mg2+ enhancing aerobic granulation in sbr.	two sequencing batch reactors (sbrs) were operated to investigate the effect of ca(2+) and mg(2+) augmentation on aerobic granulation. reactor r1 was augmented with ca(2+) at 40 mg/l, while mg(2+) was added to the reactor r2 with 40 mg/l. results showed that the reactor r1 had a faster granulation process compared with r2, and the mature granules in r1 showed better physical characteristics. however, the mature granules in r2 had the higher production yield of polysaccharides and proteins, and a ...	2010	20537460
electrokinetic remediation and microbial community shift of β-cyclodextrin-dissolved petroleum hydrocarbon-contaminated soil.	electrokinetic (ek) migration of β-cyclodextrin (β-cd), which is inclusive of total petroleum hydrocarbon (tph), is an economically beneficial and environmentally friendly remediation process for oil-contaminated soils. remediation studies of oil-contaminated soils generally prepared samples using particular tphs. this study investigates the removal of tphs from, and electromigration of microbial cells in field samples via ek remediation. both tph content and soil respiration declined after the ...	2010	21052991
chromosome translocation and its consequence in the genome of burkholderia cenocepacia au-1054.	most bacterial genomes have one single chromosome. the species burkholderia cenocepacia, a gram-negative β-proteobacterium, is one of the exceptions. genomes of four strains of the species have been sequenced and each has three circular chromosomes. in the genus burkholderia, there are another seven sequenced strains that have three chromosomes. in this paper, the numbers of essential genes and trna genes among the 11 strains of the genus burkholderia are compared. interestingly, it is found tha ...	2010	21078295
the complete multipartite genome sequence of cupriavidus necator jmp134, a versatile pollutant degrader.	cupriavidus necator jmp134 is a gram-negative beta-proteobacterium able to grow on a variety of aromatic and chloroaromatic compounds as its sole carbon and energy source.	2010	20339589
establishment of an alternative phosphoketolase-dependent pathway for fructose catabolism in ralstonia eutropha h16.	the β-proteobacterium ralstonia eutropha h16 utilizes fructose and gluconate as carbon sources for heterotrophic growth exclusively via the entner-doudoroff pathway with its key enzyme 2-keto-3-deoxy-6-phosphogluconate (kdpg) aldolase. by deletion of the responsible gene eda, we constructed a kdpg aldolase-negative strain, which is disabled to supply pyruvate for energy metabolism from fructose or gluconate as sole carbon sources. to restore growth on fructose, an alternative pathway, similar to ...	2011	21519932
independent evolutionary origins of functional polyamine biosynthetic enzyme fusions catalysing de novo diamine to triamine formation.	we have identified gene fusions of polyamine biosynthetic enzymes s-adenosylmethionine decarboxylase (adometdc, sped) and aminopropyltransferase (spee) orthologues in diverse bacterial phyla. both domains are functionally active and we demonstrate the novel de novo synthesis of the triamine spermidine from the diamine putrescine by fusion enzymes from ß-proteobacterium delftia acidovorans and d-proteobacterium syntrophus aciditrophicus, in a ?spede gene deletion strain of salmonella enterica sv. ...	2011	21762220
Structural and functional insight into the mechanism of an alkaline exonuclease from Laribacter hongkongensis.	Alkaline exonuclease and single-strand DNA (ssDNA) annealing proteins (SSAPs) are key components of DNA recombination and repair systems within many prokaryotes, bacteriophages and virus-like genetic elements. The recently sequenced ß-proteobacterium Laribacter hongkongensis (strain HLHK9) encodes putative homologs of alkaline exonuclease (LHK-Exo) and SSAP (LHK-Bet) proteins on its 3.17 Mb genome. Here, we report the biophysical, biochemical and structural characterization of recombinant LHK-Ex ...	2011	21893587
assimilation of 17a-ethinylestradiol by sludge and its stress on microbial communities under aerobic and anaerobic conditions.	the efficiency of 2 common types sludge, activated sludge and digesting sludge, to biodegrade ethinylestradiol (ee2) under aerobic and anaerobic conditions, and the impacts of ee2 on microbial community structure were investigated. the results showed that 75%-88% ee2 were removed under aerobic conditions and the values were 75%-84% under anaerobic conditions. the diversity of microbial species in the tested sludge decreased when exposed to ee2 and the shift of microbial community structures was ...	2011	21279894
characterization of a microbial consortium capable of degrading lignocellulose.	a microbial consortium, designated wcs-6, was established by successive subcultivation in the presence of rice straw under static conditions. the degradation efficiencies of wsc-6 for 0.5g filter paper, cotton and rice straw after 3days of cultivation were 99.0-¦0.7%, 76.9-¦1.5% and 81.3-¦0.8%, respectively as determined by gravimetrical methods. nine bacterial isolates were obtained from wcs-6 plated under aerobic conditions, and sequencing of their 16s rdna indicated that these bacteria were r ...	2011	21831630