| sequence and structural organization of a nif a-like gene and part of a nifb-like gene of herbaspirillum seropedicae strain z78. | the deduced amino acid sequence derived from the sequence of a fragment of dna from the free-living diazotroph herbaspirillum seropedicae was aligned to the homologous protein sequences encoded by the nifa genes from azorhizobium caulinodans, rhizobium leguminosarum, rhizobium meliloti and klebsiella pneumoniae. high similarity was found in the central domain and in the c-terminal region. the h. seropedicae putative nifa sequence was also found to contain an interdomain linker similar to that co ... | 1991 | 1840608 |
| cloning and characterization of the nifa gene from herbaspirillum seropedicae strain z78. | a genomic library of herbaspirillum seropedicae was constructed and screened for the nifa gene by complementation of a nifa mutant of azospirillum brasilense (fp10). a recombinant plasmid, pems1, capable of restoring acetylene reduction activity in the mutant fp10, was isolated and found to hybridize to the nifa gene of klebsiella pneumoniae. the results suggest that nifa is involved in the regulation of nif genes in h. seropedicae. | 1991 | 1913346 |
| ammonium inhibition of nitrogenase activity in herbaspirillum seropedicae. | the effect of oxygen, ammonium ion, and amino acids on nitrogenase activity in the root-associated n2-fixing bacterium herbaspirillum seropedicae was investigated in comparison with azospirillum spp. and rhodospirillum rubrum. h. seropedicae is microaerophilic, and its optimal dissolved oxygen level is from 0.04 to 0.2 kpa for dinitrogen fixation but higher when it is supplied with fixed nitrogen. no nitrogenase activity was detected when the dissolved o2 level corresponded to 4.0 kpa. ammonium, ... | 1989 | 2498287 |
| specific flavonoids promote intercellular root colonization of arabidopsis thaliana by azorhizobium caulinodans ors571. | the ability of azorhizobium caulinodans ors571 and other diazotrophic bacteria to internally colonize roots of arabidopsis thaliana has been studied. strains tagged with lacz or gusa reporter genes were used, and the principal colonization sites were found to be the points of emergence of lateral roots, lateral root cracks (lrcs). high frequencies of colonization were found; 63 to 100% of plants were colonized by ors571, and 100% of plants were colonized by herbaspirillum seropedicae. after lrcs ... | 1997 | 9204562 |
| evidence for two possible glnb-type genes in herbaspirillum seropedicae. | two glnb-like genes have been isolated from herbaspirillum seropedicae by complementation of the klebsiella pneumoniae glnb502 mutant for growth on nitrate. one of these glnb-like genes has been sequenced and shows strong identity with glnb proteins derived from other organisms. a tn5-20 mutation of this glnb was nif negative. | 1997 | 9226275 |
| control of herbaspirillum seropedicae nifa activity by ammonium ions and oxygen. | the activity of a truncated form of herbaspirillum seropedicae nifa in different genetic backgrounds showed that its regulatory domain is involved in nitrogen control but not in o2 sensitivity or fe dependence. the model for nitrogen control involving pii could thus apply to the proteobacteria at large. nifa may have a role in controlling adp-ribosylation of nitrogenase in azospirillum brasilense. | 1999 | 9882688 |
| expression and functional analysis of an n-truncated nifa protein of herbaspirillum seropedicae. | in herbaspirillum seropedicae, an endophytic diazotroph, nif gene expression is under the control of the transcriptional activator nifa. we have over-expressed and purified a protein containing the central and c-terminal domains of the h. seropedicae nifa protein, n-truncated nifa, fused to a his-tag sequence. this fusion protein was found to be partially soluble and was purified by affinity chromatography. band shift and footprinting assays showed that the n-truncated nifa protein was able to b ... | 1999 | 10214962 |
| in-trans regulation of the n-truncated-nifa protein of herbaspirillum seropedicae by the n-terminal domain. | the nifa protein is responsible for transcription activation of nif genes in the endophytic diazotroph herbaspirillum seropedicae. when expressed in escherichia coli this nifa protein is unable to activate the transcription of a klebsiella pneumoniae nifh::lacz fusion. however, a form of nifa lacking the n-terminal domain did activate transcription and its activity was not inhibited by ammonium. in this work we show that when expressed separately, the n-terminal domain of h. seropedicae nifa pro ... | 1999 | 10556706 |
| 16s ribosomal dna characterization of nitrogen-fixing bacteria isolated from banana (musa spp.) and pineapple (ananas comosus (l.) merril). | nitrogen-fixing bacteria isolated from banana (musa spp.) and pineapple (ananas comosus (l.) merril) were characterized by amplified 16s ribosomal dna restriction analysis and 16s rrna sequence analysis. herbaspirillum seropedicae, herbaspirillum rubrisubalbicans, burkholderia brasilensis, and burkholderia tropicalis were identified. eight other types were placed in close proximity to these genera and other alpha and beta proteobacteria. | 2001 | 11319127 |
| cloning of a reca-like gene from the diazotroph herbaspirillum seropedicae strain z78. | a recombinant plasmid, pbmr5, carrying a reca-like gene of herbaspirillum seropedicae, was isolated from a h. seropedicae genomic library by intergeneric complementation of escherichia coli reca mutant strain hb101. quantitative survival experiments showed that pbmr5 restored the ultraviolet radiation and methyl methanesulfonate resistances and recombinational proficiency of this strain. hybridization studies showed that there is dna sequence homology between the reca gene of e. coli k12 and tha ... | 1993 | 8131107 |
| recent developments in the structural organization and regulation of nitrogen fixation genes in herbaspirillum seropedicae. | herbaspirillum seropedicae is a nitrogen-fixing bacterium found in association with economically important gramineae. regulation of nitrogen fixation involves the transcriptional activator nifa protein. the regulation of nifa protein and its truncated mutant proteins is described and compared with that of other nitrogen fixation bacteria. nitrogen fixation control in h. seropedicae, of the beta-subgroup of proteobacteria, has regulatory features in common with klebsiella pneumoniae, of the gamma ... | 2001 | 11566390 |
| membrane protein patterns of three azospirillum species and herbaspirillum seropedicae. | membrane protein patterns in sds-page clearly characterized azospirillum amazonense, a. brasilense, a. lipoferum, and herbaspirillum seropedicae. each species showed also a typical major band with approximate molecular weights (amws) of 44, 39.5, 35.5, and 37.5 kdaltons for the four species respectively. characteristic lighter bands with amws of 63.5 and 19 kdaltons were shown by a. amazonense. similar bands of 54, 24 and 24.5 kdaltons were typical of a. brazilense, a. lipoferum and h. seropedic ... | 1989 | 2629550 |
| azospirillum irakense sp. nov., a nitrogen-fixing bacterium associated with rice roots and rhizosphere soil. | a new species of nitrogen-fixing bacteria, azospirillum irakense, was found associated with roots and the rhizosphere of rice in the region of diwaniyah (qadisya), iraq. the seven isolates, on which the species description is based, have vibrioid to s-shaped cells with one polar flagellum in liquid medium. additional lateral flagella are seen on cells grown on nutrient agar. poly-beta-hydroxybutyrate granules are present in cells. nitrogen fixation occurs in microaerobic conditions. the phenotyp ... | 1989 | 2626596 |
| survival of and wheat-root colonization by alginate encapsulated herbaspirillum spp. | the survival of herbaspirillum spp. cells added directly or encapsulated in alginate beads and colonization of wheat roots was evaluated in soil microcosms. cells entrapped in alginate in the presence of jnfb-broth and introduced into unplanted non-sterile clay loamy and sandy soils survived better than cells added directly to the same soils after 50 d incubation. on amendment by jnfb broth and/or skim milk the entrapped cells survived better than those prepared in water. encapsulated cells surv ... | 2001 | 11501470 |
| the diversity of archaea and bacteria in association with the roots of zea mays l. | the diversity of bacteria and archaea associating on the surface and interior of maize roots (zea mays l.) was investigated. a bacterial 16s rdna primer was designed to amplify bacterial sequences directly from maize roots by pcr to the exclusion of eukaryotic and chloroplast dna. the mitochondrial sequence from maize was easily separated from the pcr-amplified bacterial sequences by size fractionation. the culturable component of the bacterial community was also assessed, reflecting a community ... | 2001 | 11391463 |
| characterization of unusual bacteria isolated from respiratory secretions of cystic fibrosis patients and description of inquilinus limosus gen. nov., sp. nov. | using a polyphasic approach (including cellular protein and fatty acid analysis, biochemical characterization, 16s ribosomal dna sequencing, and dna-dna hybridizations), we characterized 51 bacterial isolates recovered from respiratory secretions of cystic fibrosis (cf) patients. our analyses showed that 24 isolates belong to taxa that have so far not (or only rarely) been reported from cf patients. these taxa include acinetobacter sp., bordetella hinzii, burkholderia fungorum, comamonas testost ... | 2002 | 12037065 |
| uridylylation of the pii protein from herbaspirillum seropedicae. | the pii protein is apparently involved in the control of nifa activity in herbaspirillum seropedicae. to evaluate the probable role of pii in signal transduction, uridylylation assays were conducted with purified h. seropedicae pii and escherichia coli glnd, or a cell-free extract of h. seropedicae as sources of uridylylating activity. the results showed that alpha-ketoglutarate and atp stimulate uridylylation whereas glutamine inhibits uridylylation. deuridylylation of pii-ump was dependent on ... | 2001 | 11358170 |
| herbaspirillum frisingense sp. nov., a new nitrogen-fixing bacterial species that occurs in c4-fibre plants. | the enrichment of nitrogen-fixing bacteria from the c4-fibre plants, spartina pectinata, miscanthus sinensis, miscanthus sacchariflorus and pennisetum purpureum, with nitrogen-free semi-solid media led to the isolation of herbaspirillum-like strains among other diazotrophic bacteria. on the basis of physiological properties, phylogenetic analysis comparing 16s rdna sequences and dna-dna hybridization experiments of chromosomal dna the new isolates could be grouped together in a new species with ... | 2001 | 11211253 |
| use of lactose to induce expression of soluble nifa protein domains of herbaspirillum seropedicae in escherichia coli. | overexpression and purification are procedures used to allow functional and structural characterization of proteins. many overexpressed proteins are partially or completely insoluble, and can not be easily purified. the nifa protein is an enhancer-binding protein involved in activating the expression of nif and some fix genes. the nifa protein from many organisms is usually insoluble when over-expressed, and therefore difficult to work with in vitro. in this work we have overexpressed the centra ... | 2000 | 11109500 |
| expression, purification, and functional analysis of the c-terminal domain of herbaspirillum seropedicae nifa protein. | the herbaspirillum seropedicae nifa protein is responsible for nif gene expression. the c-terminal domain of the h. seropedicae nifa protein, fused to a his-tag sequence (his-tag-c-terminal), was over-expressed and purified by metal-affinity chromatography to yield a highly purified and active protein. band-shift assays showed that the nifa his-tag-c-terminal bound specifically to the h. seropedicae nifb promoter region in vitro. in vivo analysis showed that this protein inhibited the central + ... | 2003 | 12597891 |
| fnr is involved in oxygen control of herbaspirillum seropedicae n-truncated nifa protein activity in escherichia coli. | herbaspirillum seropedicae is an endophytic diazotroph belonging to the beta-subclass of the class proteobacteria, which colonizes many members of the gramineae. the activity of the nifa protein, a transcriptional activator of nif genes in h. seropedicae, is controlled by ammonium ions through its n-terminal domain and by oxygen through mechanisms that are not well understood. here we report that the nifa protein of h. seropedicae is inactive and more susceptible to degradation in an fnr escheri ... | 2003 | 12620839 |
| anaerobic mineralization of quaternary carbon atoms: isolation of denitrifying bacteria on pivalic acid (2,2-dimethylpropionic acid). | the degradability of pivalic acid was established by the isolation of several facultative denitrifying strains belonging to zoogloea resiniphila, to thauera and herbaspirillum, and to comamonadaceae, related to [aquaspirillum] and acidovorax, and of a nitrate-reducing bacterium affiliated with moraxella osloensis. pivalic acid was completely mineralized to carbon dioxide. the catabolic pathways may involve an oxidation to dimethylmalonate or a carbon skeleton rearrangement, a putative 2,2-dimeth ... | 2003 | 12620885 |
| the transcriptional activator ntrc controls the expression and activity of glutamine synthetase in herbaspirillum seropedicae. | the role of the ntr system in herbaspirillum seropedicae was determined via ntrb and ntrc mutants. three phenotypes were identified in these mutants: nif(-), deficiency in growth using nitrate, and low glutamine synthetase (gs) activity. all phenotypes were restored by the plasmid pkrt1 containing the intact glna, ntrb and ntrc genes of h. seropedicae. the promoter region of glna was subcloned into a beta-galactosidase fusion vector and the results suggested that ntrc positively regulates the gl ... | 2000 | 11064198 |
| azospirillum, a free-living nitrogen-fixing bacterium closely associated with grasses: genetic, biochemical and ecological aspects. | azospirillum represents the best characterized genus of plant growth-promoting rhizobacteria. other free-living diazotrophs repeatedly detected in association with plant roots, include acetobacter diazotrophicus, herbaspirillum seropedicae, azoarcus spp. and azotobacter. four aspects of the azospirillum-plant root interaction are highlighted: natural habitat, plant root interaction, nitrogen fixation and biosynthesis of plant growth hormones. each of these aspects is dealt with in a comparative ... | 2000 | 10978548 |
| biocontrol of the sugarcane borer eldana saccharina by expression of the bacillus thuringiensis cry1ac7 and serratia marcescens chia genes in sugarcane-associated bacteria. | the cry1ac7 gene of bacillus thuringiensis strain 234, showing activity against the sugarcane borer eldana saccharina, was cloned under the control of the tac promoter. the fusion was introduced into the broad-host-range plasmid pkt240 and the integration vector pjff350 and without the tac promoter into the broad-host-range plasmids pml122 and pkmm0. these plasmids were introduced into a pseudomonas fluorescens strain isolated from the phylloplane of sugarcane and the endophytic bacterium herbas ... | 2000 | 10877771 |
| expression of the nifa gene of herbaspirillum seropedicae: role of the ntrc and nifa binding sites and of the -24/-12 promoter element. | the nifa promoter of herbaspirillum seropedicae contains potential ntrc, nifa and ihf binding sites together with a -12/-24 sigma(n)-dependent promoter. this region has now been investigated by deletion mutagenesis for the effect of ntrc and nifa on the expression of a nifa::lacz fusion. a 5' end to the rna was identified at position 641, 12 bp downstream from the -12/-24 promoter. footprinting experiments showed that the g residues at positions -26 and -9 are hypermethylated, and that the regio ... | 2000 | 10846219 |
| two roles for integration host factor at an enhancer-dependent nifa promoter. | control of transcription in prokaryotes often involves direct contact of regulatory proteins with rna polymerase. for the sigma54 rna polymerase, regulatory proteins bound to distally located enhancers engage the polymerase via dna looping. the sigma54-dependent nifa promoter of herbaspirillum seropedicae (hs) is activated under nitrogen-limiting growth conditions. potential enhancers for the nitrogen control activators ntrc and nifa and binding sites for integration host factor (ihf) and sigma5 ... | 2000 | 10692153 |
| sequencing and functional analysis of the nifenxorf1orf2 gene cluster of herbaspirillum seropedicae. | a 5.1-kb dna fragment from the nifhdk region of h. seropedicae was isolated and sequenced. sequence analysis showed the presence of nifenxorf1orf2 but nifty were not present. no nif or consensus promoter was identified. furthermore, orf1 expression occurred only under nitrogen-fixing conditions and no promoter activity was detected between nifk and nife, suggesting that these genes are expressed from the upstream nifh promoter and are parts of a unique nif operon. mutagenesis studies indicate th ... | 1999 | 10564803 |
| janthinobacterium agaricidamnosum sp. nov., a soft rot pathogen of agaricus bisporus. | a novel bacterium has been found that causes a soft rot disease of agaricus bisporus, the cultivated mushroom. it has been characterized using nutritional, physiological, chemical and molecular techniques. based on these data, it was shown to have many characteristics in common with members of the genus janthinobacterium. despite similarities to the only described species within this genus, janthinobacterium lividum, there were a number of differences between the mushroom pathogen isolated and t ... | 1999 | 10555339 |
| anaerobic mineralization of quaternary carbon atoms: isolation of denitrifying bacteria on dimethylmalonate. | the microbial capacity to degrade simple organic compounds with quaternary carbon atoms was demonstrated by enrichment and isolation of five denitrifying strains on dimethylmalonate as the sole electron donor and carbon source. quantitative growth experiments showed a complete mineralization of dimethylmalonate. according to phylogenetic analysis of the complete 16s rrna genes, two strains isolated from activated sewage sludge were related to the genus paracoccus within the alpha-proteobacteria ... | 1999 | 10427013 |
| genes similar to naphthalene dioxygenase genes in trifluralin-degrading bacteria. | trifluralin (alpha,alpha,alpha-trifluoro-2,6-dinitro-n,n-dipropyl-p-toluidine) is a dinitroaniline compound which was first produced in the 1960s and has been used extensively as an agricultural herbicide. there are a few publications on the biodegradation of this xenobiotic compound, but to our knowledge nothing has been documented on the genetic aspects of its catabolism. in this article, we report the analysis of dna isolated from bacteria previously shown to degrade trifluralin, using as pro ... | 2004 | 15154514 |
| analysis of nifh gene pool complexity in soil and litter at a douglas fir forest site in the oregon cascade mountain range. | nitrogen-fixing microbial populations in a douglas fir forest on the western slope of the oregon cascade mountain range were analyzed. the complexity of the nifh gene pool (nifh is the marker gene which encodes nitrogenase reductase) was assessed by performing nested pcr with bulk dna extracted from plant litter and soil. the restriction fragment length polymorphisms (rflps) of pcr products obtained from litter were reproducibly different than the rflps of pcr products obtained from the underlyi ... | 1999 | 9925556 |
| bacterial community composition determined by culture-independent and -dependent methods during propane-stimulated bioremediation in trichloroethene-contaminated groundwater. | an in situ co-metabolic air sparging (cas) study was carried out at mcclellan air force base (mafb), sacramento, ca, usa, in a trichloroethene- (tce) and cis-dichloroethene (cis-dce)-contaminated aquifer where one test zone received 2% propane in air and the other served as a control and received only air. as part of that study, bacterial population shifts were evaluated by length heterogeneity polymerase chain reaction (lh-pcr). the results showed that an organism(s) that had a fragment size of ... | 2005 | 15658984 |
| effect of t- and c-loop mutations on the herbaspirillum seropedicae glnb protein in nitrogen signalling. | proteins of the pii family are found in species of all kingdoms. although these proteins usually share high identity, their functions are specific to the different organisms. comparison of structural data from escherichia coli glnb and glnk and herbaspirillum seropedicae glnb showed that the t-loop and c-terminus were variable regions. to evaluate the role of these regions in signal transduction by the h. seropedicae glnb protein, four mutants were constructed: y51f, g108a/p109a, g108w and q3r/t ... | 2005 | 15950123 |
| history on the biological nitrogen fixation research in graminaceous plants: special emphasis on the brazilian experience. | this review covers the history on biological nitrogen fixation (bnf) in graminaceous plants grown in brazil, and describes research progress made over the last 40 years, most of which was coordinated by johanna döbereiner. one notable accomplishment during this period was the discovery of several nitrogen-fixing bacteria such as the rhizospheric (beijerinckia fluminensis and azotobacter paspali), associative (azospirillum lipoferum, a. brasilense, a. amazonense) and the endophytic (herbaspirillu ... | 2005 | 16127558 |
| phylogenetic identification of two major nitrogen-fixing bacteria associated with sugarcane. | acetobacter diazotrophicus and herbaspirillum seropedicae were identified by genetic methods based on 16s rrna sequences. a specific pcr method in combination with probing was developed for a. diazotrophicus. the pcr system includes four primers, of which the primers named ac (ctgtttcccgcaagggac) and di (gcgccccattgctgggtt) generated an 445 bp amplicon in all of the 11 a. diazotrophicus strains tested. the phylogenetic position of h. seropedicae was determined. h. seropedicae forms with oxalobac ... | 1998 | 9924818 |
| three stages of a biofilm community developing at the liquid-liquid interface between polychlorinated biphenyls and water. | soil contaminated with polychlorinated biphenyls (pcb) was used as an inoculum to grow a complex biofilm community on pcb oil (aroclor 1242) on a substratum (permanox). the biofilm was monitored for 31 days by confocal laser scanning microscopy, community fingerprinting using single-strand conformational polymorphism (sscp), amplicons of the 16s rrna genes, and chemical analyses of the pcb congeners. sscp analysis of the young biofilm revealed a rather diverse microbial community with species of ... | 2005 | 16269772 |
| specific ribosomal dna sequences from diverse environmental settings correlate with experimental contaminants. | phylogenetic analysis of 16s ribosomal dna (rdna) clones obtained by pcr from uncultured bacteria inhabiting a wide range of environments has increased our knowledge of bacterial diversity. one possible problem in the assessment of bacterial diversity based on sequence information is that pcr is exquisitely sensitive to contaminating 16s rdna. this raises the possibility that some putative environmental rrna sequences in fact correspond to contaminant sequences. to document potential contaminant ... | 1998 | 9687486 |
| biocidal activity in plant pathogenic acidovorax, burkholderia, herbaspirillum, ralstonia and xanthomonas spp. | antibacterial and antifungal activity was investigated for strains of acidovorax spp., burkholderia spp., herbaspirillum rubrisubalbicans and ralstonia solanacearum; strains representing 118 species and pathovars of xanthomonas were also tested for phytotoxic capacity. antibacterial activity was present in all burkholderia spp. except b. andropogonis, in biovars ii and iii of r. solanacearum but not in biovars i and iv, and in two strains of xanthomonas. little antibacterial activity was recorde ... | 1998 | 9633641 |
| isolation and characterization of polymeric galloyl-ester-degrading bacteria from a tannery discharge place. | the culturable bacteria colonizing the rhizosphere of plants growing in the area of discharge of a tannery effluent were characterized. relative proportions of aerobic, denitrifying, and sulfate-reducing bacteria were determined in the rhizosphere of typha latifolia, canna indica, and phragmites australis. aerobic bacteria were observed to be the most abundant group in the rhizosphere, and plant type did not seem to influence the abundance of the bacterial types analyzed. to isolate bacteria abl ... | 2005 | 16341641 |
| colonization of barley (hordeum vulgare) with salmonella enterica and listeria spp. | colonization of barley plants by the food-borne pathogens salmonella enterica serovar typhimurium and three listeria spp. (l. monocytogenes, l. ivanovii, l. innocua) was investigated in a monoxenic system. herbaspirillum sp. n3 was used as a positive control and escherichia coli hb101 as a negative control for endophytic root colonization. colonization of the plants was tested 1-4 weeks after inoculation by determination of cfu, specific pcr assays and fluorescence in situ hybridization (fish) w ... | 2006 | 16629755 |
| iron depletion affects nitrogenase activity and expression of nifh and nifa genes in herbaspirillum seropedicae. | herbaspirillum seropedicae z67 is a nitrogen-fixing bacterium able to colonize the rhizosphere and the interior of several plants. as iron is a key element for nitrogen fixation, we examined the response of this microorganism to iron deficiency under nitrogen fixing conditions. we identified a h. seropedicae exbd gene that was induced in response to iron limitation and is involved in iron homeostasis. we found that an exbd mutant grown in iron-chelated medium is unable to fix nitrogen. moreover, ... | 2006 | 16640576 |
| cloning and sequencing of the nitrogenase structural genes nifhdk of herbaspirillum seropedicae. | the nitrogenase structural genes (nifhdk) of the endophytic diazotroph herbaspirillum seropedicae were isolated from a genomic bank by plate hybridization. sequence analysis of the dna showed a consensus promoter region upstream for the nifh gene containing a -24/-12 type promoter together with nifa- and integration host factor (ihf)- binding sites. the derived protein sequences of nifh, nifd and nifk contained conserved cysteine residues for binding iron-sulfur clusters and the iron-molybdenum ... | 1996 | 9222418 |
| emended description of herbaspirillum; inclusion of [pseudomonas] rubrisubalbicans, a milk plant pathogen, as herbaspirillum rubrisubalbicans comb. nov.; and classification of a group of clinical isolates (ef group 1) as herbaspirillum species 3. | [pseudomonas] rubrisubalbicans, a mild plant pathogen. herbaspirillum seropedicae, and ef group 1 strains (clustered by an immunological method) were investigated by a polyphasic approach with dna-rrna and dna-dna hybridizations and auxanography on 147 substrates. our results show that they all belong to the genus herbaspirillum. in addition to h. seropedicae, two other species are described: herbaspirillum rubrisubalbicans and a new unnamed species, herbaspirillum species 3, containing mainly s ... | 1996 | 8782693 |
| l-arabinose metabolism in herbaspirillum seropedicae. | the pathway for l-arabinose metabolism in herbaspirillum seropedicae was shown to involve nonphosphorylated intermediates and to produce alpha-ketoglutarate. the activities of the enzymes and the natures of several intermediates were determined. the pathway was inducible by l-arabinose, and two key enzymes, l-arabinose dehydrogenase and 2-keto-glutarate semialdehyde dehydrogenase, were present in all strains of h. seropedicae tested. | 1989 | 2768202 |
| degradation of 2,3,4,6-tetrachlorophenol at low temperature and low dioxygen concentrations by phylogenetically different groundwater and bioreactor bacteria. | effects of low temperature and low oxygen partial pressure on the occurrence and activity of 2,3,4,6-tetrachlorophenol degrading bacteria in a boreal chlorophenol contaminated groundwater and a full-scale fluidized-bed bioreactor were studied using four polychlorophenol degrading bacterial isolates of different phylogenetic backgrounds. these included an alpha-proteobacterial sphingomonas sp. strain mt1 isolated from the full-scale bioreactor and three isolates from the contaminated groundwater ... | 2001 | 11995822 |
| nodulation of legumes by members of the beta-subclass of proteobacteria. | members of the leguminosae form the largest plant family on earth, with around 18,000 species. the success of legumes can largely be attributed to their ability to form a nitrogen-fixing symbiosis with specific bacteria known as rhizobia, manifested by the development of nodules on the plant roots in which the bacteria fix atmospheric nitrogen, a major contributor to the global nitrogen cycle. rhizobia described so far belong exclusively to the alpha-subclass of proteobacteria, where they are di ... | 2001 | 11418858 |
| bacterial diversity in aortic aneurysms determined by 16s ribosomal rna gene analysis. | aortic aneurysms are common vascular conditions that cause considerable morbidity and mortality. understanding of the mechanisms involved in the pathogenesis of the condition remains limited. recently, infection has been suggested as possible contributor in the development of the disease. the aim of the present study was to examine aortic aneurysms for the presence of bacterial dna using polymerase chain reaction (pcr) targeting the 16s ribosomal rna (rrna) gene, followed by cloning and sequenci ... | 2006 | 17098542 |
| herbaspirillum seropedicae signal transduction protein pii is structurally similar to the enteric glnk. | pii-like proteins are signal transduction proteins found in bacteria, archaea and eukaryotes. they mediate a variety of cellular responses. a second pii-like protein, called glnk, has been found in several organisms. in the diazotroph herbaspirillum seropedicae, pii protein is involved in sensing nitrogen levels and controlling nitrogen fixation genes. in this work, the crystal structure of the unliganded h. seropedicae pii was solved by x-ray diffraction. h. seropedicae pii has a gly residue, g ... | 2002 | 12084071 |
| expression, purification and biochemical characterization of a single-stranded dna binding protein from herbaspirillum seropedicae. | an open reading frame encoding a protein similar in size and sequence to the escherichia coli single-stranded dna binding protein (ssb protein) was identified in the herbaspirillum seropedicae genome. this open reading frame was cloned into the expression plasmid pet14b. the ssb protein from h. seropedicae, named hs_ssb, was overexpressed in e. coli strain bl21(de3) and purified to homogeneity. mass spectrometry data confirmed the identity of this protein. the apparent molecular mass of the nati ... | 2007 | 17223357 |
| control of autogenous activation of herbaspirillum seropedicae nifa promoter by the ihf protein. | analysis of the expression of the herbaspirillum seropedicae nifa promoter in escherichia coli and herbaspirillum seropedicae, showed that nifa expression is primarily dependent on ntrc but also required nifa for maximal expression under nitrogen-fixing conditions. deletion of the ihf (integration host factor)-binding site produced a promoter with two-fold higher activity than the native promoter in the h. seropedicae wild-type strain but not in a nifa strain, indicating that ihf controls nifa a ... | 2002 | 12113931 |
| signal transduction-related responses to phytohormones and environmental challenges in sugarcane. | sugarcane is an increasingly economically and environmentally important c4 grass, used for the production of sugar and bioethanol, a low-carbon emission fuel. sugarcane originated from crosses of saccharum species and is noted for its unique capacity to accumulate high amounts of sucrose in its stems. environmental stresses limit enormously sugarcane productivity worldwide. to investigate transcriptome changes in response to environmental inputs that alter yield we used cdna microarrays to profi ... | 2007 | 17355627 |
| enumeration, isolation and identification of diazotrophs from korean wetland rice varieties grown with long-term application of n and compost and their short-term inoculation effect on rice plants. | this study has been aimed (i) to isolate and identify diazotrophs from korean rice varieties; (ii) to examine the long-term effect of n and compost on the population dynamics of diazotrophs and (iii) to realize the shot-term inoculation effect of these diazotrophs on rice seedlings. | 2007 | 17381741 |
| infection and colonization of rice seedlings by the plant growth-promoting bacterium herbaspirillum seropedicae z67. | a beta-glucoronidase (gus)-marked strain of herbaspirillum seropedicae z67 was inoculated onto rice seedling cvs. ir42 and ir72. internal populations peaked at over 10(6) log cfu per gram of fresh weight by 5 to 7 days after inoculation (dai) but declined to 10(3) to 10(4) log cfu per gram of fresh weight by 28 dai. gus staining was most intense on coleoptiles, lateral roots, and at the junctions of some of the main and lateral roots. bacteria entered the roots via cracks at the points of latera ... | 2002 | 12236596 |
| the recx gene product is involved in the sos response in herbaspirillum seropedicae. | the reca and the recx genes of herbaspirillum seropedicae were sequenced. the recx is located 359 bp downstream from reca. sequence analysis indicated the presence of a putative operator site overlapping a probable sigma70-dependent promoter upstream of reca and a transcription terminator downstream from recx, with no apparent promoter sequence in the intergenic region. transcriptional analysis using lacz promoter fusions indicated that reca expression increased three- to fourfold in the presenc ... | 2003 | 12718403 |
| the expression of nifb gene from herbaspirillum seropedicae is dependent upon the nifa and rpon proteins. | the putative nifb promoter region of herbaspirillum seropedicae contained two sequences homologous to nifa-binding site and a -24/-12 type promoter. a nifb::lacz fusion was assayed in the backgrounds of both escherichia coli and h. seropedicae. in e. coli, the expression of nifb::lacz occurred only in the presence of functional rpon and klebsiella pneumoniae nifa genes. in addition, the integration host factor (ihf) stimulated the expression of the nifb::lacz fusion in this background. in h. ser ... | 2006 | 17473889 |
| expression, purification, and dna-binding activity of the solubilized ntrc protein of herbaspirillum seropedicae. | ntrc is a bacterial enhancer-binding protein (ebp) that activates transcription by the sigma54 rna polymerase holoenzyme. ntrc has a three domain structure typical of ebp family. in herbaspirillum seropedicae, an endophytic diazotroph, ntrc regulates several operons involved in nitrogen assimilation, including glnantrbc. in order to over-express and purify the ntrc protein, dna fragments containing the complete structural gene for the whole protein, and for the n-terminal+central and central+c-t ... | 2003 | 12821329 |
| nitrogenase activity of herbaspirillum seropedicae grown under low iron levels requires the products of nifxorf1 genes. | herbaspirillum seropedicae strains mutated in the nifx or orf1 genes showed 90% or 50% reduction in nitrogenase activity under low levels of iron or molybdenum respectively. mutations in nifx or orf1 genes did not affect nif gene expression since a nifh::lacz fusion was fully active in both mutants. nifx and the contiguous gene orf1 are essential for maximum nitrogen fixation under iron limitation and are probably involved in synthesis of nitrogenase iron or iron-molybdenum clusters. | 2003 | 12892890 |
| herbaspirillum lusitanum sp. nov., a novel nitrogen-fixing bacterium associated with root nodules of phaseolus vulgaris. | several bacterial strains were isolated from root nodules of phaseolus vulgaris plants grown in a soil from portugal. the strains were gram-negative, aerobic, curved rod-shaped and motile. the isolates were catalase- and oxidase-positive. the tp-rapd (two-primer randomly amplified polymorphic dna) patterns of all strains were identical, suggesting that they belong to the same species. the complete 16s rdna sequence of a representative strain was obtained and phylogenetic analysis based on the ne ... | 2003 | 14657133 |
| significance of herbaspirillum seropedicae inoculation and/or straw amendment on growth and dinitrogen fixation of wheat using 15n-dilution method. | the effect of herbaspirillum seropedicae inoculation and/or maize straw (0, 5 and 10 mg/hm2) amendment on the growth and n2 fixation of wheat was determined in pot experiments using 15n-dilution method. inoculation resulted in accumulation of fixed nitrogen, and % n from atmosphere being 24.6 and 26.5% in wheat shoot and grain, respectively. straw amendment reduced % natm to 16.1 and 20.2% at high straw level (10 mg/hm2). rational nitrogen fertilization (180 kg n/hm2) completely inhibited n2 fix ... | 2003 | 15058193 |
| expression, purification, and dna-binding activity of the herbaspirillum seropedicae recx protein. | the herbaspirillum seropedicae recx protein participates in the sos response: a process in which the reca protein plays a central role. the recx protein of the h. seropedicae, fused to a his-tag sequence (recx his-tagged), was over-expressed in escherichia coli and purified by metal-affinity chromatography to yield a highly purified and active protein. dna band-shift assays showed that the recx his-tagged protein bound to both circular and linear double-stranded dna and also to circular single-s ... | 2004 | 15135406 |
| herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium. | a 4-chlorophenol-degrading bacterial strain, formerly designated as a strain of comamonas testosteroni, was reclassified as a member of the genus herbaspirillum based on its phenotypic and chemotaxonomic characteristics, as well as phylogenetic analysis using 16s rdna sequences. phylogenetic inference based on 16s rdna sequences showed that strain cpw301(t) clusters in a phylogenetic branch that contains herbaspirillum species. 16s rdna sequence similarity of strain cpw301(t) to species of the g ... | 2004 | 15143035 |
| herbaspirillum rhizosphaerae sp. nov., isolated from rhizosphere soil of allium victorialis var. platyphyllum. | two gram-negative, milky-white-pigmented, motile, slightly curved rod-shaped bacterial isolates, ums-37(t) and ums-40, were isolated from rhizosphere soil of wild edible greens cultivated on ulleung island, korea, and their taxonomic positions were investigated by a polyphasic approach. they grew optimally at 25-30 degrees c and contained q-8 as the predominant ubiquinone. the major cellular fatty acids (>10 % of total fatty acids) were c(16 : 0), cyclo c(17 : 0) and c(16 : 1)omega7c and/oriso-c ... | 2007 | 17911298 |
| collimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on living fungal hyphae. | a polyphasic approach was used to describe the phylogenetic position of 22 chitinolytic bacterial isolates that were able to grow at the expense of intact, living hyphae of several soil fungi. these isolates, which were found in slightly acidic dune soils in the netherlands, were strictly aerobic, gram-negative rods. cells grown in liquid cultures were flagellated and possessed pili. a wide range of sugars, alcohols, organic acids and amino acids could be metabolized, whereas several di- and tri ... | 2004 | 15143036 |
| proposals of curvibacter gracilis gen. nov., sp. nov. and herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [pseudomonas] huttiensis, [pseudomonas] lanceolata, [aquaspirillum] delicatum and [aquaspirillum] autotrophicum as herbaspirillum huttiense comb. nov., curvibacter lanceolatus comb. nov., curvibacter delicatus comb. nov. and herbaspirillum autotrophicum comb. nov. | two strains of curved bacteria, 7-1(t) and 7-2(t), isolated from well water, were phylogenetically examined to determine their taxonomic position. strain 7-1(t) is a gram-negative, slightly curved rod. analysis of the 16s rrna gene sequence showed that strain 7-1(t) formed a cluster with [aquaspirillum] delicatum and [pseudomonas] lanceolata. it has some similar characteristics to [a.] delicatum and [p.] lanceolata, but has sufficient distance to separate it from other genera. dna-dna hybridizat ... | 2004 | 15545462 |
| the rhizosphere as a reservoir for opportunistic human pathogenic bacteria. | during the last years, the number of human infections caused by opportunistic pathogens has increased dramatically. one natural reservoir of opportunistic pathogens is the rhizosphere, the zone around roots that is influenced by the plant. due to a high content of nutrients, this habitat is a 'microbial hot-spot', where bacterial abundances including those with strong antagonistic traits are enhanced. various bacterial genera, including burkholderia, enterobacter, herbaspirillum, ochrobactrum, p ... | 2005 | 16232283 |
| characterization of the orf1glnkamtb operon of herbaspirillum seropedicae. | herbaspirillum seropedicae is an endophytic nitrogen-fixing bacterium that colonizes economically important grasses. in this organism, the amtb gene is co-transcribed with two other genes: glnk that codes for a pii-like protein and orf1 that codes for a probable periplasmatic protein of unknown function. the expression of the orf1glnkamtb operon is increased under nitrogen-limiting conditions and is dependent on ntrc. an amtb mutant failed to transport methylammonium. post-translational control ... | 2006 | 16331441 |
| expression of the nifh gene of a herbaspirillum endophyte in wild rice species: daily rhythm during the light-dark cycle. | the expression of nitrogenase genes of herbaspirillum sp. b501 associated in shoot (leaf and stem) of wild rice, oryza officinalis, was studied by means of reverse transcription-pcr (rt-pcr) targeted at the nifh gene. rt-pcr analyses indicate that nifh transcript was detected exclusively from nitrogen-fixing cells of gfp-tagged strain b501gfp1 in both free-living and endophytic states by using a constitutive gfp gene transcript as a positive control. transcription of nifh and nitrogen fixation i ... | 2005 | 16332801 |
| adsorption of protein glnb of herbaspirillum seropedicae on si(111) investigated by afm and xps. | the protein glnb-hs (glnb of herbaspirillum seropedicae) in diazotroph micro-organisms signalizes levels of nitrogen, carbon, and energy for a series of proteins involved in the regulation of expression and control of the activity of nitrogenase complex that converts atmospheric nitrogen in ammonia, resulting in biological nitrogen fixation. its structure has already been determined by x-ray diffraction, revealing a trimer of (36 kda) with lateral cavities having hydrophilic boundaries. the inte ... | 2006 | 16679538 |
| life in grasses: diazotrophic endophytes. | n2-fixing bacteria such as azoarcus spp., herbaspirillum spp, and acetobacter diazotrophicus can infect the interior of gramineous plants without causing symptoms of plant disease but do not survive in soil. like phytopathogens, they can penetrate into central tissues and spread systemically. there is no evidence for an endosymbiosis in living plant cells; however, the bacteria are physiologically active in the plant apoplast. | 1998 | 9587190 |
| herbaspirillum hiltneri sp. nov., isolated from surface-sterilized wheat roots. | the genus herbaspirillum of the betaproteobacteria mainly comprises diazotrophic bacteria with a potential for endophytic and systemic colonization of a variety of plants. the plant-associated bacterial isolates n3(t), n5 and n9 were derived from surface-sterilized wheat roots. after phylogenetic analysis of 16s rrna gene sequence data the isolates could be allocated to the genus herbaspirillum, and 99.9 % similarity to the sequence of herbaspirillum lusitanum p6-12(t) was found. a set of 16s rr ... | 2006 | 16738112 |
| n-fertilizer saving by the inoculation of gluconacetobacter diazotrophicus and herbaspirillum sp. in micropropagated sugarcane plants. | colonization of micropropagated sugarcane plants by gluconacetobacter diazotrophicus and herbaspirillum sp. was confirmed by a dot-immunoblot assay. in all, a 45-day short-term and 180-day long-term experiments conducted on micropropagated sugarcane plants of co 86032, a sugar rich popular variety in south india, indicated the usefulness of these diazotrophs as plant growth promoting bacteria. co-inoculation of these two bacteria enhanced the biomass considerably under n-limited condition in the ... | 2006 | 16765840 |
| endophytic colonization and in planta nitrogen fixation by a herbaspirillum sp. isolated from wild rice species. | nitrogen-fixing bacteria were isolated from the stems of wild and cultivated rice on a modified rennie medium. based on 16s ribosomal dna (rdna) sequences, the diazotrophic isolates were phylogenetically close to four genera: herbaspirillum, ideonella, enterobacter, and azospirillum. phenotypic properties and signature sequences of 16s rdna indicated that three isolates (b65, b501, and b512) belong to the herbaspirillum genus. to examine whether herbaspirillum sp. strain b501 isolated from wild ... | 2001 | 11679357 |
| composition of bacterial communities associated with natural and laboratory populations of asobara tabida infected with wolbachia. | asobara tabida wasps are fly endoparasitoids that naturally harbor three wolbachia strains, which induce cytoplasmic incompatibility and control oogenesis. to investigate whether other bacteria play a role in wasp biology, we surveyed the bacterial communities of wild a. tabida populations originating from different regions of france and of laboratory colonies using pcr-denaturing gradient gel electrophoresis and culture methods. proteobacteria and firmicutes were found to be the main phyla repr ... | 2009 | 19376923 |
| inter-domain cross-talk controls the nifa protein activity of herbaspirillum seropedicae. | herbaspirillum seropedicae is an endophytic diazotroph, which colonizes sugar cane, wheat, rice and maize. the activity of nifa, a transcriptional activator of nif genes in h. seropedicae, is controlled by ammonium ions through a mechanism involving its n-terminal domain. here we show that this domain interacts specifically in vitro with the n-truncated nifa protein, as revealed by protection against proteolysis, and this interaction caused an inhibitory effect on both the atpase and dna-binding ... | 2001 | 11707257 |
| relationships within the proteobacteria of plant pathogenic acidovorax species and subspecies, burkholderia species, and herbaspirillum rubrisubalbicans by sequence analysis of 16s rdna, numerical analysis and determinative tests. | sequence data for 16s rdna of the type strains of acidovorax avenae subsp. avenae, a. avenae subsp. cattleyae, a. avenae subsp. citrulli, a. konjaci and herbaspirillum rubrisubalbicans were compared with genbank library accessions of burkholderia spp., comamonas sp., ralstonia solanacearum and variovorax sp. maximum parsimony analysis produced two clusters: 1. acidovorax spp., comamonas sp., and variovorax sp. (all in the comamonadaceae), and 2. burkholderia spp., ralstonia solanacearum, and her ... | 2001 | 11827206 |
| removal of cyanobacteria, cyanotoxins, heterotrophic bacteria and endotoxins at an operating surface water treatment plant. | the removal of cyanobacteria, hepatotoxins produced by them (microcystins), phytoplankton, heterotrophic bacteria and endotoxins were monitored at a surface water treatment plant with coagulation, clarification, sand filtration, ozonation, slow sand filtration and chlorination as the treatment process. coagulation-sand filtration reduced microcystins by 1.2-2.4, and endotoxins by 0.72-2.01 log10 units. ozonation effectively removed the residual microcystins. the treatment process reduced phytopl ... | 2006 | 17037128 |
| members of the ethylene signalling pathway are regulated in sugarcane during the association with nitrogen-fixing endophytic bacteria. | nitrogen-fixing bacteria have been isolated from sugarcane in an endophytic and beneficial interaction that promotes plant growth. in this work, for the first time, the involvement of ethylene signalling in this interaction was investigated by molecular characterizing members of this pathway in sugarcane. the expression pattern of a putative ethylene receptor (scer1) and two putative erf transcription factors (scerf1 and scerf2) show exclusive modulation in plants inoculated with the diazotrophi ... | 2007 | 17210990 |
| effects of the inoculation of burkholderia vietnamensis and related endophytic diazotrophic bacteria on grain yield of rice. | during a survey of endophytic diazotrophic bacteria associated with different rice varieties in tamilnadu, some "endophytes" were obtained. thirteen bacterial isolates from surface-sterilized roots and shoots were obtained in pure culture, which produced indole acetic acid (iaa) and reduced acetylene to ethylene. polymerase chain reaction (pcr) amplification confirmed the presence of nif-h gene in all the isolates. morphological, biochemical, and molecular characteristics indicated that all of t ... | 2008 | 17406771 |
| [mobilization of simazine degradation genes by the plasmid psa]. | the plasmid psa was found to mobilize the genes for simazine degradation (smz) of the rhizosphere bacterium herbaspirillum sp.b601 by forming hybrid psa-smz plasmids. independent migration of smz genes into various loci of genome during transfer and elimination of the hybrid plasmids indicated that the genes were parts of a "catabolic island" which could be unstable under certain conditions. | 2007 | 17427413 |
| biodegradation of the herbicide trifluralin by bacteria isolated from soil. | trifluralin (alpha,alpha,alpha-trifluoro-2,6-dinitro-n,n-dipropyl-p-toluidine; tfl) is a pre-emergence, soil-incorporated herbicide that has been in agricultural use since the early 1960s and is moderately persistent in soil. the purpose of this study was to isolate and characterise tfl-resistant bacteria from a soil in which this pesticide has been used for the last four decades and to determine their ability to degrade tfl using hplc. eight bacteria were isolated by repeated subculture in liqu ... | 2003 | 19719679 |
| the glnantrbc operon of herbaspirillum seropedicae is transcribed by two oppositely regulated promoters upstream of glna. | herbaspirillum seropedicae is an endophytic bacterium that fixes nitrogen under microaerophilic conditions. the putative promoter sequences glnap1 (sigma70-dependent) and glnap2 (sigma54), and two ntrc-binding sites were identified upstream from the glna, ntrb and ntrc genes of this microorganism. to study their transcriptional regulation, we used lacz fusions to the h. seropedicae glna gene, and the glna-ntrb and ntrb-ntrc intergenic regions. expression of glna was up-regulated under low ammoni ... | 2007 | 17496955 |
| purification and characterization of the bifunctional uridylyltransferase and the signal transducing proteins glnb and glnk from herbaspirillum seropedicae. | glnd is a bifunctional uridylyltransferase/uridylyl-removing enzyme that has a central role in the general nitrogen regulatory system ntr. in enterobacteria, glnd uridylylates the pii proteins glnb and glnk under low levels of fixed nitrogen or ammonium. under high ammonium levels, glnd removes ump from these proteins (deuridylylation). the pii proteins are signal transduction elements that integrate the signals of nitrogen, carbon and energy, and transduce this information to proteins involved ... | 2007 | 17553696 |
| [diversity of associated nitrogen-fixing bacteria isolated from the pioneer plants-vetiver zizanioides]. | vetiver zizanioides is a perennial grass of the poaceae family, known of its silage, soil and water conservation role. the aim of the study was to collect and identify the resources of the nitrogen-fixing bacteria associated with vetiver zizanioides. | 2009 | 20112669 |
| undibacterium pigrum gen. nov., sp. nov., isolated from drinking water. | two gram-negative, rod-shaped, oxidase-positive, non-spore-forming, non-motile bacteria (strains ccug 49009(t) and ccug 49012), both isolated from drinking water, were characterized. on the basis of chemotaxonomic data [major ubiquinone, q-8; predominant polyamines, putrescine and 2-hydroxyputrescine; major polar lipids, phosphatidylethanolamine, moderate amounts of diphosphatidylglycerol and phosphatidylglycerol and minor amounts of three aminolipids and phosphatidylserine; major fatty acids, c ... | 2007 | 17625185 |
| characterization of efficient aerobic denitrifiers isolated from two different sequencing batch reactors by 16s-rrna analysis. | by adopting two sequencing batch reactors (sbrs) a and b, nitrate as the substrate, and the intermittent aeration mode, activated sludge was domesticated to enrich aerobic denitrifiers. the phs of reactor a were approximately 6.3 at dos 2.2-6.1 mg/l for a carbon source of 720 mg/l cod; the phs of reactor b were 6.8-7.8 at dos 2.2-3.0 mg/l for a carbon source of 1500 mg/l cod. both reactors maintained an influent nitrate concentration of 80 mg/l no3- -n. when the total inorganic nitrogen (tin) re ... | 2007 | 17630129 |
| a two-dimensional proteome reference map of herbaspirillum seropedicae proteins. | herbaspirillum seropedicae is an endophytic diazotroph associated with economically important crops such as rice, sugarcane, and wheat. here, we present a 2-d reference map for h. seropedicae. using maldi-tof-ms we identified 205 spots representing 173 different proteins with a calculated average of 1.18 proteins/gene. seventeen hypothetical or conserved hypothetical orfs were shown to code for true gene products. these data will support the genome annotation process and provide a basis on which ... | 2007 | 17853511 |
| isolation of the acrylamide denitrifying bacteria from a wastewater treatment system manufactured with polyacrylonitrile fiber. | acrylamide has carcinogenicity and toxicity, so its discharge to natural water and soil systems might have an adverse impact on water quality, endangering public health and welfare. the investigation attempts to isolate acrylamide denitrifying bacteria from a wastewater treatment system manufactured with polyacrylonitrile (pan) fiber. the goal is to elucidate the effectiveness of isolated pure strain and pan mixed strains in treating acrylamide from synthetic wastewater. the results reveal that ... | 2007 | 17882504 |
| 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 |
| recent advances in nitrogen-fixing acetic acid bacteria. | nitrogen is an essential plant nutrient, widely applied as n-fertilizer to improve yield of agriculturally important crops. an interesting alternative to avoid or reduce the use of n-fertilizers could be the exploitation of plant growth-promoting bacteria (pgpb), capable of enhancing growth and yield of many plant species, several of agronomic and ecological significance. pgpb belong to diverse genera, including azospirillum, azotobacter, herbaspirillum, bacillus, burkholderia, pseudomonas, rhiz ... | 2008 | 18177965 |
| 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 |
| effect of an ntrc mutation on amino acid or urea utilization and on nitrogenase switch-off in herbaspirillum seropedicae. | herbaspirillum seropedicae is a nitrogen-fixing bacterium that grows well with ammonium chloride or sodium nitrate as alternative single nitrogen sources but that grows more slowly with l-alanine, l-serine, l-proline, or urea. the ntrc mutant strain dcp286a was able to utilize only ammonium or urea of these nitrogen sources. the addition of 1 mmol.l-1 ammonium chloride to the nitrogen-fixing wild-type strain inhibited nitrogenase activity rapidly and completely. urea was a less effective inhibit ... | 2008 | 18388995 |
| herbaspirillum species bacteremia in a pediatric oncology patient. | herbaspirillum species, an organism commonly found in soil, has only recently been linked to disease in humans. we report herbaspirillum bacteremia in a 2-year-old female patient following a hematopoietic stem cell transplant for relapsed acute lymphoblastic leukemia. | 2010 | 20739483 |
| a molecular microbial ecology approach to studying hemodialysis water and fluid. | bacteria, or bacteria-derived products, might be responsible for deleterious effects in hemodialysis patients. most microorganisms in hemodialysis water, including potential pathogens, are difficult to isolate and might subsist in a 'viable but not culturable' state or may need specific culture media. a molecular culture-independent approach based on the analysis of the 16s rdna obtained from total dna has been used to better know the diversity of bacteria inhabiting hemodialysis water and fluid ... | 2006 | 16900091 |
| a two-dimensional electrophoretic profile of the proteins secreted by herbaspirillum seropedicae strain z78. | herbaspirillum seropedicae is an endophytic bacterium that associates with rice, sugarcane and other economically important crops. secreted proteins play a key role in the plant-bacterial interaction. using 2d electrophoresis and peptide mass fingerprint mass spectrometry, 63 protein spots representing 41 different secreted proteins were identified during growth of h. seropedicae under nitrogen-sufficient conditions. in silico analysis showed that 25.4% of the proteins had signal peptides and 15 ... | 2009 | 19664734 |
| reclassification of herbaspirillum putei as a later heterotypic synonym of herbaspirillum huttiense, with the description of h. huttiense subsp. huttiense subsp. nov. and h. huttiense subsp. putei subsp. nov., comb. nov., and description of herbaspirillum aquaticum sp. nov. | resequencing of the 16s rrna gene of the type strain of herbaspirillum putei ding and yokota 2004 revealed 99.9 % sequence similarity to that of the type strain of herbaspirillum huttiense (leifson 1962) ding and yokota 2004. this high phylogenetic relatedness of h. putei and h. huttiense was confirmed by the results of dna-dna hybridization between h. huttiense dsm 10281(t) and h. putei atcc baa-806(t) (reassociation value 96 %). therefore, it is proposed to reclassify the type strain of h. put ... | 2010 | 19671717 |
| identification of nh4+-regulated genes of herbaspirillum seropedicae by random insertional mutagenesis. | random mutagenesis using transposons with promoterless reporter genes has been widely used to examine differential gene expression patterns in bacteria. using this approach, we have identified 26 genes of the endophytic nitrogen-fixing bacterium herbaspirillum seropedicae regulated in response to ammonium content in the growth medium. these include nine genes involved in the transport of nitrogen compounds, such as the high-affinity ammonium transporter amtb, and uptake systems for alternative n ... | 2007 | 17323064 |
| endophytic herbaspirillum seropedicae expresses nif genes in gramineous plants. | abstract the interactions between maize, sorghum, wheat and rice plants and herbaspirillum seropedicae were examined microscopically following inoculation with the h. seropedicae lr15 strain, a nif(+) (pnif::gusa) mutant obtained by the insertion of a gusa-kanamycin cassette into the nifh gene of the h. seropedicae wild-type strain. the expression of the pnif::gusa fusion was followed during the association of the diazotroph with the gramineous species. histochemical analysis of seedlings of mai ... | 2003 | 19719605 |
| characterization of herbaspirillum- and limnobacter-related strains isolated from young volcanic deposits in miyake-jima island, japan. | the role of microbes in the early development of ecosystems on new volcanic materials seems to be crucial to primary plant succession but is not well characterized. here we analyzed the bacterial community colonizing 22-year-old volcanic deposits of the miyake-jima island (japan) using culture-based and 16s rrna gene clone library methods. the majority of 91 bacterial isolates were placed phylogenetically in two clusters (a and b) of the betaproteobacteria. cluster a (82% of isolates) was relate ... | 2008 | 21558690 |
| microbial populations responsive to denitrification-inducing conditions in rice paddy soil, as revealed by comparative 16s rrna gene analysis. | rice paddy soil has been shown to have strong denitrifying activity. however, the microbial populations responsible for nitrate respiration and denitrification have not been well characterized. in this study, we performed a clone library analysis of >1,000 clones of the nearly full-length 16s rrna gene to characterize bacterial community structure in rice paddy soil. we also identified potential key players in nitrate respiration and denitrification by comparing the community structures of soils ... | 2009 | 19767468 |