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detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoa, mmox, mxaf, and 16s rrna and ribosomal dna, including pmoa-based terminal restriction fragment length polymorphism profiling.the diversity of methanotrophic bacteria associated with roots of submerged rice plants was assessed using cultivation-independent techniques. the research focused mainly on the retrieval of pmoa, which encodes the alpha subunit of the particulate methane monooxygenase. a novel methanotroph-specific community-profiling method was established using the terminal restriction fragment length polymorphism (t-rflp) technique. the t-rflp profiles clearly revealed a more complex root-associated methanot ...200111526021
genetic characterization of the klebsiella pneumoniae waa gene cluster, involved in core lipopolysaccharide biosynthesis.a recombinant cosmid containing genes involved in klebsiella pneumoniae c3 core lipopolysaccharide biosynthesis was identified by its ability to confer bacteriocin 28b resistance to escherichia coli k-12. the recombinant cosmid contains 12 genes, the whole waa gene cluster, flanked by kbl and coad genes, as was found in e. coli k-12. pcr amplification analysis showed that this cluster is conserved in representative k. pneumoniae strains. partial nucleotide sequence determination showed that the ...200111371519
halomethane:bisulfide/halide ion methyltransferase, an unusual corrinoid enzyme of environmental significance isolated from an aerobic methylotroph using chloromethane as the sole carbon source.a novel dehalogenating/transhalogenating enzyme, halomethane:bisulfide/halide ion methyltransferase, has been isolated from the facultatively methylotrophic bacterium strain cc495, which uses chloromethane (ch(3)cl) as the sole carbon source. purification of the enzyme to homogeneity was achieved in high yield by anion-exchange chromatography and gel filtration. the methyltransferase was composed of a 67-kda protein with a corrinoid-bound cobalt atom. the purified enzyme was inactive but was act ...199910508052
distribution of tetrahydromethanopterin-dependent enzymes in methylotrophic bacteria and phylogeny of methenyl tetrahydromethanopterin cyclohydrolases.the methylotrophic proteobacterium methylobacterium extorquens am1 possesses tetrahydromethanopterin (h(4)mpt)-dependent enzymes, which are otherwise specific to methanogenic and sulfate-reducing archaea and which have been suggested to be involved in formaldehyde oxidation to co(2) in m. extorquens am1. the distribution of h(4)mpt-dependent enzyme activities in cell extracts of methylotrophic bacteria from 13 different genera are reported. h(4)mpt-dependent activities were detected in all of th ...199910482517
cloning, sequencing, and role in virulence of two phospholipases (a1 and c) from mesophilic aeromonas sp. serogroup o:34.two different representative recombinant clones encoding aeromonas hydrophila lipases were found upon screening on tributyrin (phospholipase a1) and egg yolk agar (lecithinase-phospholipase c) plates of a cosmid-based genomic library of aeromonas hydrophila ah-3 (serogroup o34) introduced into escherichia coli dh5alpha. subcloning, nucleotide sequencing, and in vitro-coupled transcription-translation experiments showed that the phospholipase a1 (pla) and c (plc) genes code for an 83-kda putative ...199910417167
methylotrophic methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes.rhizobia described so far belong to three distinct phylogenetic branches within the alpha-2 subclass of proteobacteria. here we report the discovery of a fourth rhizobial branch involving bacteria of the methylobacterium genus. rhizobia isolated from crotalaria legumes were assigned to a new species, "methylobacterium nodulans," within the methylobacterium genus on the basis of 16s ribosomal dna analyses. we demonstrated that these rhizobia facultatively grow on methanol, which is a characterist ...200111114919
chloromethane-induced genes define a third c1 utilization pathway in methylobacterium chloromethanicum cm4.methylobacterium chloromethanicum cm4 is an aerobic alpha-proteobacterium capable of growth with chloromethane as the sole carbon and energy source. two proteins, cmua and cmub, were previously purified and shown to catalyze the dehalogenation of chloromethane and the vitamin b12-mediated transfer of the methyl group of chloromethane to tetrahydrofolate. three genes located near cmua and cmub, designated metf, fold and puru and encoding homologs of methylene tetrahydrofolate (methylene-h4folate) ...200212057941
expression of individual copies of methylococcus capsulatus bath particulate methane monooxygenase genes.the expression of the two gene clusters encoding the particulate methane monooxygenase (pmmo) in methylococcus capsulatus bath was assessed by analysis of transcripts and by use of chromosomal gene fusions. the results suggest that the two clusters are functionally redundant but that relative expression alters depending on the copper levels available for growth.200111160118
two-component system that regulates methanol and formaldehyde oxidation in paracoccus denitrificans.a chromosomal region encoding a two-component regulatory system, flhrs, has been isolated from paracoccus denitrificans. flhrs-deficient mutants were unable to grow on methanol, methylamine, or choline as the carbon and energy source. expression of the gene encoding glutathione-dependent formaldehyde dehydrogenase (fhla) was undetectable in the mutant, and expression of the s-formylglutathione hydrolase gene (fgha) was reduced in the mutant background. in addition, methanol dehydrogenase was imm ...200111133961
cloning and sequencing of the klebsiella pneumoniae o5 wb gene cluster and its role in pathogenesis.one representative recombinant clone encoding klebsiella pneumoniae o5-antigen lipopolysaccharide (lps) was found upon screening for serum resistance in a cosmid-based genomic library of k. pneumoniae kt769 (o5:k57) introduced into escherichia coli dh5alpha. a total of eight open reading frames (wb(o5) gene cluster) were necessary to produce k. pneumoniae o5-antigen lps in e. coli k-12. the enzymatic activities proposed for the wb(o5) gene cluster are in agreement with the activities proposed fo ...200010768928
cloning, sequencing, and role in serum susceptibility of porin ii from mesophilic aeromonas hydrophila.we cloned and sequenced the structural gene for aeromonas hydrophila porin ii from strain ah-3 (serogroup o:34). the genetic position of this gene, like that of ompf in escherichia coli, is adjacent to aspc and transcribed in the same direction. however, upstream of the porin ii gene no similarities with e. coli were found. we obtained defined insertion mutants in porin ii gene either in a. hydrophila (o:34) or a. veronii sobria (serogroup o:11) serum-resistant or -sensitive strains. furthermore ...200010722573
location and survival of leaf-associated bacteria in relation to pathogenicity and potential for growth within the leafthe growth and survival of pathogenic and nonpathogenic pseudomonas syringae strains and of the nonpathogenic species pantoea agglomerans, stenotrophomonas maltophilia, and methylobacterium organophilum were compared in the phyllosphere of bean. in general, the plant pathogens survived better than the nonpathogens on leaves under environmental stress. the sizes of the total leaf-associated populations of the pathogenic p. syringae strains were greater than the sizes of the total leaf-associated ...199910103233
molecular cloning, sequencing, purification, and characterization of pseudomonas aeruginosa ribosome recycling factor.ribosome recycling factor (rrf) is required for release of 70s ribosomes from mrna on reaching the termination codon for the next cycle of protein synthesis. the rrf-encoding gene (frr) of pseudomonas aeruginosa pao1 was functionally cloned by using a temperature-sensitive frr mutant of escherichia coli and sequenced. the p. aeruginosa frr was mapped at 30 to 32 min of the p. aeruginosa chromosome. the deduced amino acid sequence of rrf showed a 64% identity to that of e. coli rrf. in an assay i ...19999973356
cloning and molecular analysis of the poly(3-hydroxybutyrate) and poly(3-hydroxybutyrate-co-3-hydroxyalkanoate) biosynthesis genes in pseudomonas sp. strain 61-3.two types of polyhydroxyalkanoate (pha) biosynthesis gene loci (phb and pha) of pseudomonas sp. strain 61-3, which produces a blend of poly(3-hydroxybutyrate) [p(3hb)] homopolymer and a random copolymer (poly(3-hydroxybutyrate-co-3-hydroxyalkanoate) [p(3hb-co-3ha]) consisting of 3ha units of 4 to 12 carbon atoms, were cloned and analyzed at the molecular level. in the phb locus, three open reading frames encoding polyhydroxybutyrate (phb) synthase (phbcps), beta-ketothiolase (phbaps), and nadph- ...19989851987
molecular genetics of the genus paracoccus: metabolically versatile bacteria with bioenergetic flexibility.paracoccus denitrificans and its near relative paracoccus versutus (formerly known as thiobacilllus versutus) have been attracting increasing attention because the aerobic respiratory system of p. denitrificans has long been regarded as a model for that of the mitochondrion, with which there are many components (e.g., cytochrome aa3 oxidase) in common. members of the genus exhibit a great range of metabolic flexibility, particularly with respect to processes involving respiration. prominent exam ...19989841665
linkage map of escherichia coli k-12, edition 10: the traditional map.this map is an update of the edition 9 map by berlyn et al. (m. k. b. berlyn, k. b. low, and k. e. rudd, p. 1715-1902, in f. c. neidhardt et al., ed., escherichia coli and salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). it uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. the latter are included as ...19989729611
genetic analysis of comamonas acidovorans polyhydroxyalkanoate synthase and factors affecting the incorporation of 4-hydroxybutyrate monomer.the polyhydroxyalkanoate (pha) synthase gene of comamonas acidovorans ds-17 (phacca) was cloned by using the synthase gene of alcaligenes eutrophus as a heterologous hybridization probe. complete sequencing of a 4.0-kbp smai-hindiii (sh40) subfragment revealed the presence of a 1,893-bp pha synthase coding region which was followed by a 1,182-bp beta-ketothiolase gene (phaaca). both the translated products of these genes showed significant identity, 51.1 and 74.2%, respectively, to the primary s ...19989726894
bacterial community dynamics during start-up of a trickle-bed bioreactor degrading aromatic compounds.this study was performed with a laboratory-scale fixed-bed bioreactor degrading a mixture of aromatic compounds (solvesso100). the starter culture for the bioreactor was prepared in a fermentor with a wastewater sample of a care painting facility as the inoculum and solvesso100 as the sole carbon source. the bacterial community dynamics in the fermentor and the bioreactor were examined by a conventional isolation procedure and in situ hybridization with fluorescently labeled rrna-targeted oligon ...19989501433
isolation, phenotypic characterization, and complementation analysis of mutants of methylobacterium extorquens am1 unable to synthesize pyrroloquinoline quinone and sequences of pqqd, pqqg, and pqqc.aerobic gram-negative methylotrophs oxidize methanol to formaldehyde by using a methanol dehydrogenase that has pyrroloquinoline quinone (pqq) as a prosthetic group. seventy-two mutants which are unable to grow on methanol unless the growth medium is supplemented with pqq have been isolated in the facultative methanol utilizer methylobacterium extorquens am1. in addition, 12 previously isolated methanol oxidation mutants of m. extorquens am1 were shown to be able to grow on methanol in the prese ...19948132470
extension of the model concerning linkage of genes coding for c-1 related functions in methylobacterium organophilum.evidence is presented which suggests that methylobacterium organophilum contains isoenzymes of phosphoenolpyruvate carboxylase activity. methanol-grown cells contained an acetyl coenzyme a (coa)-insensitive activity which precipitated in a 65 to 75% of saturation ammonium sulfate fraction. succinate-grown cells contained an acetyl-coa-stimulated activity which precipitated in a 55 to 65% of saturation ammonium sulfate fraction. mutants unable to grow on methanol appeared to lack acetyl-coa-insen ...19816786218
isolation and nucleotide sequence of the methanol dehydrogenase structural gene from paracoccus denitrificans.a genomic clone bank of paracoccus denitrificans dna has been constructed in the expression vector set pex1, pex2, and pex3. screening of this clone bank with antibodies raised against p. denitrificans methanol dehydrogenase resulted in the isolation of a clone, pnh3, that synthesized methanol dehydrogenase cross-reactive proteins. the nucleotide sequence of the p. denitrificans dna fragment inserted in this clone has been determined and shown to contain the full methanol dehydrogenase structura ...19873114231
construction of broad-host-range cosmid cloning vectors: identification of genes necessary for growth of methylobacterium organophilum on methanol.four new cloning vectors have been constructed from the broad-host-range cloning vector prk290. these vectors, pla2901, pla2905, pla2910, and pla2917, confer resistance to kanamycin and tetracycline. the latter two are cosmid derivatives of pla2901. the new vectors can be mobilized into, and are stably maintained in, a variety of gram-negative bacteria. a sau3a genomic bank of methylobacterium organophilum strain xx dna has been constructed in pla2917, and complementation analysis, with a variet ...19852982796
detection and isolation of ultrasmall microorganisms from a 120,000-year-old greenland glacier ice core.the abundant microbial population in a 3,043-m-deep greenland glacier ice core was dominated by ultrasmall cells (<0.1 microm3) that may represent intrinsically small organisms or starved, minute forms of normal-sized microbes. in order to examine their diversity and obtain isolates, we enriched for ultrasmall psychrophiles by filtering melted ice through filters with different pore sizes, inoculating anaerobic low-nutrient liquid media, and performing successive rounds of filtrations and recult ...200516332755
genetic and physical analyses of methylobacterium organophilum xx genes encoding methanol oxidation.when allyl alcohol was used as a suicide substrate, spontaneous mutants and uv light- and nitrous acid-generated mutants of methylobacterium organophilum xx were selected which grew on methylamine but not on methanol. there was no detectable methanol dehydrogenase (mdh) activity in crude extracts of these mutants, yet western blots revealed that some mutants still produced mdh protein. complementation of 50 mutants by a cosmid gene bank of m. organophilum xx demonstrated that three major regions ...19882826390
cloning and sequencing of the gene encoding the 72-kilodalton dehydrogenase subunit of alcohol dehydrogenase from acetobacter aceti.a genomic library of acetobacter aceti dna was constructed by using a broad-host-range cosmid vector. complementation of a spontaneous alcohol dehydrogenase-deficient mutant resulted in the isolation of a plasmid designated paa701. subcloning and deletion analysis of paa701 limited the region that complemented the deficiency in alcohol dehydrogenase activity of the mutant. the nucleotide sequence of this region was determined and showed that this region contained the full structural gene for the ...19892722742
coexistence among epiphytic bacterial populations mediated through nutritional resource partitioning.the levels of coexistence between pseudomonas syringae and various nonpathogenic epiphytic species in the phyllosphere of beans (phaseolus vulgaris) were assessed by using replacement series. the epiphytic species pseudomonas fluorescens, pantoea agglomerans, stenotrophomonas maltophilia, and methylobacterium organophilum were all capable of exhibiting higher levels of coexistence with p. syringae than was observed with a near-isogenic p. syringae strain pair. the ecological similarity of the ep ...199416349462
nucleotide sequence and transcriptional start site of the methylobacterium organophilum xx methanol dehydrogenase structural gene.the nucleotide sequence of a cloned 2.5-kilobase-pair smai fragment containing the methanol dehydrogenase (mdh) structural gene from methylobacterium organophilum xx was determined. a single open reading frame with a coding capacity of 626 amino acids (molecular weight, 66,000) was identified on one strand, and n-terminal sequencing of purified mdh revealed that 27 of these residues constituted a putative signal peptide. primer extension mapping of in vivo transcripts indicated that the start of ...19882459109
methanol promotes atmospheric methane oxidation by methanotrophic cultures and soils.two methanotrophic bacteria, methylobacter albus bg8 and methylosinus trichosporium ob3b, oxidized atmospheric methane during batch growth on methanol. methane consumption was rapidly and substantially diminished (95% over 9 days) when washed cell suspensions were incubated without methanol in the presence of atmospheric methane (1.7 ppm). methanotrophic activity was stimulated after methanol (10 mm) but not methane (1,000 ppm) addition. m. albus bg8 grown in continuous culture for 80 days with ...199816349514
organization of genes required for the oxidation of methanol to formaldehyde in three type ii methylotrophs.restriction maps of genes required for the synthesis of active methanol dehydrogenase in methylobacterium organophilum xx and methylobacterium sp. strain am1 have been completed and compared. in these two species of pink-pigmented, type ii methylotrophs, 15 genes were identified that were required for the expression of methanol dehydrogenase activity. none of these genes were required for the synthesis of the prosthetic group of methanol dehydrogenase, pyrroloquinoline quinone. the structural ge ...198916348074
phylogenetic study of methanol oxidizers from chilika-lake sediments using genomic and metagenomic approaches.group-wise diversity of sediment methylotrophs of chilika lake (lat. 19°28'-19°54'n; long. 85°06'-85°35'e) odisha, india at various identified sites was studied. both the culturable and unculturable (metagenome) methylotrophs were investigated in the lake sediments employing both mxaf and 16s rrna genes as markers. ardra profiling, 16s rrna gene sequencing, page profiling of haeiii, ecori restricted mxaf gene and the mxaf gene sequences using culture-dependent approach revealed the relatedness o ...201525805901
methylocella species are facultatively methanotrophic.all aerobic methanotrophic bacteria described to date are unable to grow on substrates containing carbon-carbon bonds. here we demonstrate that members of the recently discovered genus methylocella are an exception to this. these bacteria are able to use as their sole energy source the one-carbon compounds methane and methanol, as well as the multicarbon compounds acetate, pyruvate, succinate, malate, and ethanol. to conclusively verify facultative growth, acetate and methane were used as model ...200515968078
kinetic isotope effects and ligand binding in pqq-dependent methanol dehydrogenase.the reaction of pqq (2,7,9-tricarboxypyrroloquinoline quinone)-dependent mdh (methanol dehydrogenase) from methylophilus methylotrophus has been studied under steady-state conditions in the presence of an alternative activator [gee (glycine ethyl ester)] and compared with similar reactions performed with ammonium (used more generally as an activator in steady-state analysis of mdh). studies of initial velocity with methanol (protiated methanol, c1h3o1h) and [2h]methanol (deuteriated methanol, c2 ...200515617516
plasmid donor affects host range of promiscuous incp-1beta plasmid pb10 in an activated-sludge microbial community.horizontal transfer of multiresistance plasmids in the environment contributes to the growing problem of drug-resistant pathogens. even though the plasmid host cell is the primary environment in which the plasmid functions, possible effects of the plasmid donor on the range of bacteria to which plasmids spread in microbial communities have not been investigated. in this study we show that the host range of a broad-host-range plasmid within an activated-sludge microbial community was influenced b ...200516151119
identification of candidate periodontal pathogens and beneficial species by quantitative 16s clonal analysis.most studies of the bacterial etiology of periodontitis have used either culture-based or targeted dna approaches, and so it is likely that pathogens remain undiscovered. the purpose of this study was to use culture-independent, quantitative analysis of biofilms associated with chronic periodontitis and periodontal health to identify pathogens and beneficial species. samples from subjects with periodontitis and controls were analyzed using ribosomal 16s cloning and sequencing. several genera, ma ...200516081935
microbial diversity in ultra-high-pressure rocks and fluids from the chinese continental scientific drilling project in china.microbial communities in ultra-high-pressure (uhp) rocks and drilling fluids from the chinese continental scientific drilling project were characterized. the rocks had a porosity of 1 to 3.5% and a permeability of approximately 0.5 mdarcy. abundant fluid and gas inclusions were present in the minerals. the rocks contained significant amounts of fe2o3, feo, p2o5, and nitrate (3 to 16 ppm). acridine orange direct counting and phospholipid fatty acid analysis indicated that the total counts in the ...200515933024
methylotrophic autotrophy in beijerinckia mobilis.representatives of the genus beijerinckia are known as heterotrophic, dinitrogen-fixing bacteria which utilize a wide range of multicarbon compounds. here we show that at least one of the currently known species of this genus, i.e., beijerinckia mobilis, is also capable of methylotrophic metabolism coupled with the ribulose bisphosphate (rubp) pathway of c1 assimilation. a complete suite of dehydrogenases commonly involved in the sequential oxidation of methanol via formaldehyde and formate to c ...200515901717
the paleoproterozoic snowball earth: a climate disaster triggered by the evolution of oxygenic photosynthesis.although biomarker, trace element, and isotopic evidence have been used to claim that oxygenic photosynthesis evolved by 2.8 giga-annum before present (ga) and perhaps as early as 3.7 ga, a skeptical examination raises considerable doubt about the presence of oxygen producers at these times. geological features suggestive of oxygen, such as red beds, lateritic paleosols, and the return of sedimentary sulfate deposits after a approximately 900-million year hiatus, occur shortly before the approxi ...200516061801
the methanol dehydrogenase gene, mxaf, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments.the mxaf gene, coding for the large (α) subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the alpha-, beta- and gammaproteobacteria. it is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoa and mmox genes, which are absent in some methanotrophic proteobacterial genera. this study examined the potential for using the mxaf gene as a functional and phylogenetic marker for methanotrophs. mxaf and 16s r ...201323451130
metaproteomic identification of diazotrophic methanotrophs and their localization in root tissues of field-grown rice plants.in a previous study by our group, ch4 oxidation and n2 fixation were simultaneously activated in the roots of wild-type rice plants in a paddy field with no n input; both processes are likely controlled by a rice gene for microbial symbiosis. the present study examined which microorganisms in rice roots were responsible for ch4 oxidation and n2 fixation under the field conditions. metaproteomic analysis of root-associated bacteria from field-grown rice (oryza sativa nipponbare) revealed that nit ...201424928870
a census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial iq, extroverts and introverts.analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction.200515955239
the opportunity for high-performance biomaterials from methane.polyhydroxyalkanoate (pha) biopolymers are widely recognised as outstanding candidates to replace conventional petroleum-derived polymers. their mechanical properties are good and can be tailored through copolymer composition, they are biodegradable, and unlike many alternatives, they do not rely on oil-based feedstocks. further, they are the only commodity polymer that can be synthesised intracellularly, ensuring stereoregularity and high molecular weight. however, despite offering enormous pot ...201627681905
inter individual variations of the fish skin microbiota: host genetics basis of mutualism?the commensal microbiota of fish skin is suspected to provide a protection against opportunist infections. the skin of fish harbors a complex and diverse microbiota that closely interacts with the surrounding water microbial communities. up to now there is no clear evidence as to whether the host regulates the recruitment of environmental bacteria to build a specific skin microbiota. to address this question, we detected quantitative trait loci (qtl) associated with the abundance of specific ski ...201425068850
intrigues and intricacies of the biosynthetic pathways for the enzymatic quinocofactors: pqq, ttq, ctq, tpq, and ltq. 201324350630
intrigues and intricacies of the biosynthetic pathways for the enzymatic quinocofactors: pqq, ttq, ctq, tpq, and ltq. 201324350630
hopanoids as functional analogues of cholesterol in bacterial membranes.the functionality of cellular membranes relies on the molecular order imparted by lipids. in eukaryotes, sterols such as cholesterol modulate membrane order, yet they are not typically found in prokaryotes. the structurally similar bacterial hopanoids exhibit similar ordering properties as sterols in vitro, but their exact physiological role in living bacteria is relatively uncharted. we present evidence that hopanoids interact with glycolipids in bacterial outer membranes to form a highly order ...201526351677
fatty acid biosynthesis pathways in methylomicrobium buryatense 5g(b1).methane utilization by methanotrophic bacteria is an attractive application for biotechnological conversion of natural or biogas into high-added-value products. haloalcaliphilic methanotrophic bacteria belonging to the genus methylomicrobium are among the most promising strains for methane-based biotechnology, providing easy and inexpensive cultivation, rapid growth, and the availability of established genetic tools. a number of methane bioconversions using these microbial cultures have been dis ...201628119683
facultative methanotrophs revisited. 200515968038
genome-wide detection of fitness genes in uropathogenic escherichia coli during systemic infection.uropathogenic escherichia coli (upec) is a leading etiological agent of bacteremia in humans. virulence mechanisms of upec in the context of urinary tract infections have been subjected to extensive research. however, understanding of the fitness mechanisms used by upec during bacteremia and systemic infection is limited. a forward genetic screen was utilized to detect transposon insertion mutants with fitness defects during colonization of mouse spleens. an inoculum comprised of 360,000 transpo ...201324339777
methylobacteria isolated from bryophytes and the 2-fold description of the same microbial species.on the surface of healthy land plants (embryophytes), numerous non-pathogenic bacteria have been discovered and described. among these epiphytic microbes, pink-pigmented facultative methylotrophic microbes of the genus methylobacterium are of special significance, because these microorganisms consume methanol emitted via the stomatal pores and secrete growth-promoting phytohormones. methylobacterium funariae, schauer and kutschera 2011, a species isolated in our lab from the common cord moss, de ...201323299423
fatty acid biosynthesis pathways in methylomicrobium buryatense 5g(b1).methane utilization by methanotrophic bacteria is an attractive application for biotechnological conversion of natural or biogas into high-added-value products. haloalcaliphilic methanotrophic bacteria belonging to the genus methylomicrobium are among the most promising strains for methane-based biotechnology, providing easy and inexpensive cultivation, rapid growth, and the availability of established genetic tools. a number of methane bioconversions using these microbial cultures have been dis ...201628119683
resource recovery from wastewater by biological technologies: opportunities, challenges, and prospects.limits in resource availability are driving a change in current societal production systems, changing the focus from residues treatment, such as wastewater treatment, toward resource recovery. biotechnological processes offer an economic and versatile way to concentrate and transform resources from waste/wastewater into valuable products, which is a prerequisite for the technological development of a cradle-to-cradle bio-based economy. this review identifies emerging technologies that enable res ...201628111567
smoking, pregnancy and the subgingival microbiome.the periodontal microbiome is known to be altered during pregnancy as well as by smoking. however, despite the fact that 2.1 million women in the united states smoke during their pregnancy, the potentially synergistic effects of smoking and pregnancy on the subgingival microbiome have never been studied. subgingival plaque was collected from 44 systemically and periodontally healthy non-pregnant nonsmokers (control), non-pregnant smokers, pregnant nonsmokers and pregnant smokers and sequenced us ...201627461975
resource recovery from wastewater by biological technologies: opportunities, challenges, and prospects.limits in resource availability are driving a change in current societal production systems, changing the focus from residues treatment, such as wastewater treatment, toward resource recovery. biotechnological processes offer an economic and versatile way to concentrate and transform resources from waste/wastewater into valuable products, which is a prerequisite for the technological development of a cradle-to-cradle bio-based economy. this review identifies emerging technologies that enable res ...201628111567
development of a novel genus-specific real-time pcr assay for detection and differentiation of bartonella species and genotypes.the genus bartonella includes numerous species with varied host associations, including several that infect humans. development of a molecular diagnostic method capable of detecting the diverse repertoire of bartonella species while maintaining genus specificity has been a challenge. we developed a novel real-time pcr assay targeting a 301-bp region of the ssra gene of bartonella and demonstrated specific amplification in over 30 bartonella species, subspecies, and strains. subsequent analysis o ...201222378904
pqqe from methylobacterium extorquens am1: a radical s-adenosyl-l-methionine enzyme with an unusual tolerance to oxygen.methylobacterium extorquens am1 is an aerobic facultative methylotroph known to secrete pyrroloquinoline quinone (pqq), a cofactor of a number of bacterial dehydrogenases, into the culture medium. to elucidate the molecular mechanism of pqq biosynthesis, we are focusing on pqqe which is believed to be the enzyme catalysing the first reaction of the pathway. pqqe belongs to the radical s-adenosyl-l-methionine (sam) superfamily, in which most, if not all, enzymes are very sensitive to dissolved ox ...201526188050
pqqe from methylobacterium extorquens am1: a radical s-adenosyl-l-methionine enzyme with an unusual tolerance to oxygen.methylobacterium extorquens am1 is an aerobic facultative methylotroph known to secrete pyrroloquinoline quinone (pqq), a cofactor of a number of bacterial dehydrogenases, into the culture medium. to elucidate the molecular mechanism of pqq biosynthesis, we are focusing on pqqe which is believed to be the enzyme catalysing the first reaction of the pathway. pqqe belongs to the radical s-adenosyl-l-methionine (sam) superfamily, in which most, if not all, enzymes are very sensitive to dissolved ox ...201526188050
molecular ecology techniques for the study of aerobic methanotrophs. 200718165358
ribosylhopane, a novel bacterial hopanoid, as precursor of c35 bacteriohopanepolyols in streptomyces coelicolor a3(2).wild-type streptomyces coelicolor a3(2) produces aminobacteriohopanetriol as the only elongated c35 hopanoid. the hopanoid phenotype of two mutants bearing a deletion of genes from a previously identified hopanoid biosynthesis gene cluster provides clues to the formation of c35 bacteriohopanepolyols. orf14 encodes a putative nucleosidase; its deletion induces the accumulation of adenosylhopane as it cannot be converted into ribosylhopane. orf18 encodes a putative transaminase; its deletion resul ...201425155017
mutations derived from the thermophilic polyhydroxyalkanoate synthase phac enhance the thermostability and activity of phac from cupriavidus necator h16.the thermophile cupriavidus sp. strain s-6 accumulated polyhydroxybutyrate (phb) from glucose at 50°c. a 9.0-kbp ecori fragment cloned from the genomic dna of cupriavidus sp. s-6 enabled escherichia coli xl1-blue to synthesize phb at 45°c. nucleotide sequence analysis showed a pha locus in the clone. the thermophilic polyhydroxyalkanoate (pha) synthase (phac(csp)) shared 81% identity with mesophilic phac of cupriavidus necator h16. the diversity between these two strains was found dominantly on ...201222408158
steroids, triterpenoids and molecular oxygen.there is a close connection between modern-day biosynthesis of particular triterpenoid biomarkers and presence of molecular oxygen in the environment. thus, the detection of steroid and triterpenoid hydrocarbons far back in earth history has been used to infer the antiquity of oxygenic photosynthesis. this prompts the question: were these compounds produced similarly in the past? in this paper, we address this question with a review of the current state of knowledge surrounding the oxygen requir ...200616754609
molecular ecology techniques for the study of aerobic methanotrophs. 200718165358
detection of antibiotic-resistant bacteria endowed with antimicrobial activity from a freshwater lake and their phylogenetic affiliation.antimicrobial resistance poses a serious challenge to global public health. in this study, fifty bacterial strains were isolated from the sediments of a freshwater lake and were screened for antibiotic resistance. out of fifty isolates, thirty-three isolates showed resistance against at least two of the selected antibiotics. analysis of 16s rdna sequencing revealed that the isolates belonged to ten different genera, namely staphylococcus(n = 8), bacillus(n = 7), lysinibacillus(n = 4), achromobac ...201627330861
carbon sources for polyhydroxyalkanoates and an integrated biorefinery.polyhydroxyalkanoates (phas) are a group of bioplastics that have a wide range of applications. extensive progress has been made in our understanding of phas' biosynthesis, and currently, it is possible to engineer bacterial strains to produce phas with desired properties. the substrates for the fermentative production of phas are primarily derived from food-based carbon sources, raising concerns over the sustainability of their production in terms of their impact on food prices. this paper give ...201627447619
knockout and overexpression of pyrroloquinoline quinone biosynthetic genes in gluconobacter oxydans 621h.in gluconobacter oxydans, pyrroloquinoline quinone (pqq) serves as the cofactor for various membrane-bound dehydrogenases that oxidize sugars and alcohols in the periplasm. proteins for the biosynthesis of pqq are encoded by the pqqabcde gene cluster. our reverse transcription-pcr and promoter analysis data indicated that the pqqa promoter represents the only promoter within the pqqabcde cluster of g. oxydans 621h. pqq overproduction in g. oxydans was achieved by transformation with the plasmid- ...200616936032
2-methylhopanoids are maximally produced in akinetes of nostoc punctiforme: geobiological implications.2-methylhopanes, molecular fossils of 2-methylbacteriohopanepolyol (2-mebhp) lipids, have been proposed as biomarkers for cyanobacteria, and by extension, oxygenic photosynthesis. however, the robustness of this interpretation is unclear, as 2-methylhopanoids occur in organisms besides cyanobacteria and their physiological functions are unknown. as a first step toward understanding the role of 2-mebhp in cyanobacteria, we examined the expression and intercellular localization of hopanoids in the ...200919811542
identification of proteins involved in formaldehyde metabolism by rhodobacter sphaeroides.formaldehyde is an intermediate formed during the metabolism of methanol or other methylated compounds. many gram-negative bacteria generate formaldehyde from methanol via a periplasmic pyrroloquinoline quinone (pqq)-dependent dehydrogenase in which the alpha subunit of an alpha(2)beta(2) tetramer has catalytic activity. the genome of the facultative formaldehyde-oxidizing bacterium rhodobacter sphaeroides encodes xoxf, a homologue of the catalytic subunit of a proposed pqq-containing dehydrogen ...200818174148
cultivation-independent characterization of methylobacterium populations in the plant phyllosphere by automated ribosomal intergenic spacer analysis.bacteria of the genus methylobacterium are widespread in the environment, but their ecological role in ecosystems, such as the plant phyllosphere, is not very well understood. to gain better insight into the distribution of different methylobacterium species in diverse ecosystems, a rapid and specific cultivation-independent method for detection of these organisms and analysis of their community structure is needed. therefore, 16s rrna gene-targeted primers specific for this genus were designed ...200818263752
diversity and seasonal dynamics of bacterial community in indoor environment.we spend most of our lives in indoor environments and are exposed to microbes present in these environments. hence, knowledge about this exposure is important for understanding how it impacts on human health. however, the bacterial flora in indoor environments has been only fragmentarily explored and mostly using culture methods. the application of molecular methods previously utilised in other environments has resulted in a substantial increase in our awareness of microbial diversity.200818397514
occurrence and phylogenetic diversity of sphingomonas strains in soils contaminated with polycyclic aromatic hydrocarbons.bacterial strains of the genus sphingomonas are often isolated from contaminated soils for their ability to use polycyclic aromatic hydrocarbons (pah) as the sole source of carbon and energy. the direct detection of sphingomonas strains in contaminated soils, either indigenous or inoculated, is, as such, of interest for bioremediation purposes. in this study, a culture-independent pcr-based detection method using specific primers targeting the sphingomonas 16s rrna gene combined with denaturing ...200415066784
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