| phylogenetic analysis of particle-attached and free-living bacterial communities in the columbia river, its estuary, and the adjacent coastal ocean. | the columbia river estuary is a dynamic system in which estuarine turbidity maxima trap and extend the residence time of particles and particle-attached bacteria over those of the water and free-living bacteria. particle-attached bacteria dominate bacterial activity in the estuary and are an important part of the estuarine food web. pcr-amplified 16s rrna genes from particle-attached and free-living bacteria in the columbia river, its estuary, and the adjacent coastal ocean were cloned, and 239 ... | 1999 | 10388721 |
| enzymatic manganese(ii) oxidation by a marine alpha-proteobacterium. | a yellow-pigmented marine bacterium, designated strain sd-21, was isolated from surface sediments of san diego bay, san diego, calif., based on its ability to oxidize soluble mn(ii) to insoluble mn(iii, iv) oxides. 16s rrna analysis revealed that this organism was most closely related to members of the genus erythrobacter, aerobic anoxygenic phototrophic bacteria within the alpha-4 subgroup of the proteobacteria (alpha-4 proteobacteria). sd-21, however, has a number of distinguishing phenotypic ... | 2001 | 11526000 |
| the tep1 gene of sinorhizobium meliloti coding for a putative transmembrane efflux protein and n-acetyl glucosamine affect nod gene expression and nodulation of alfalfa plants. | soil bacteria collectively known as rhizobium, characterized by their ability to establish beneficial symbiosis with legumes, share several common characteristics with pathogenic bacteria when infecting the host plant. recently, it was demonstrated that a fadd mutant of sinorhizobium meliloti is altered in the control of swarming, a type of co-ordinated movement previously associated with pathogenicity, and is also impaired in nodulation efficiency on alfalfa roots. in the phytopathogen xanthomo ... | 2009 | 19173735 |
| comparative phylogenetic assignment of environmental sequences of genes encoding 16s rrna and numerically abundant culturable bacteria from an anoxic rice paddy soil. | we used both cultivation and direct recovery of bacterial 16s rrna gene (rdna) sequences to investigate the structure of the bacterial community in anoxic rice paddy soil. isolation and phenotypic characterization of 19 saccharolytic and cellulolytic strains are described in the accompanying paper (k.-j. chin, d. hahn, u. hengstmann, w. liesack, and p. h. janssen, appl. environ. microbiol. 65:5042-5049, 1999). here we describe the phylogenetic positions of these strains in relation to 57 environ ... | 1999 | 10543822 |
| molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16s rrna, particulate methane monooxygenase, and methanol dehydrogenase | rice field soil with a nonsaturated water content induced ch4 consumption activity when it was supplemented with 5% ch4. after a lag phase of 3 days, ch4 was consumed rapidly until the concentration was less than 1.8 parts per million by volume (ppmv). however, the soil was not able to maintain the oxidation activity at near-atmospheric ch4 mixing ratios (i.e., 5 ppmv). the soil microbial community was monitored by performing denaturing gradient gel electrophoresis (dgge) during the oxidation pr ... | 1999 | 10223989 |
| molecular characterization of epiphytic bacterial communities on charophycean green algae | epiphytic bacterial communities within the sheath material of three filamentous green algae, desmidium grevillii, hyalotheca dissiliens, and spondylosium pulchrum (class charophyceae, order zygnematales), collected from a sphagnum bog were characterized by pcr amplification, cloning, and sequencing of 16s ribosomal dna. a total of 20 partial sequences and nine different sequence types were obtained, and one sequence type was recovered from the bacterial communities on all three algae. by phyloge ... | 1998 | 9797295 |
| type ivb secretion systems of legionella and other gram-negative bacteria. | type iv secretion systems (t4sss) play a central role in the pathogenicity of many important pathogens, including agrobacterium tumefaciens, helicobacter pylori, and legionella pneumophila. the t4sss are related to bacterial conjugation systems, and are classified into two subgroups, type iva (t4ass) and type ivb (t4bss). the t4bss, which is closely related to conjugation systems of inci plasmids, was originally found in human pathogen l. pneumophila; pathogenesis by l. pneumophila infection req ... | 2011 | 21743810 |
| identification and characterization of a bacterial glutamic peptidase. | glutamic peptidases, from the merops family g1, are a distinct group of peptidases characterized by a catalytic dyad consisting of a glutamate and a glutamine residue, optimal activity at acidic ph and insensitivity towards the microbial derived protease inhibitor, pepstatin. previously, only glutamic peptidases derived from filamentous fungi have been characterized. | 2010 | 21122090 |
| symbiotic legume nodules employ both rhizobial exo- and endo-hydrogenases to recycle hydrogen produced by nitrogen fixation. | in symbiotic legume nodules, endosymbiotic rhizobia (bacteroids) fix atmospheric n(2), an atp-dependent catalytic process yielding stoichiometric ammonium and hydrogen gas (h(2)). while in most legume nodules this h(2) is quantitatively evolved, which loss drains metabolic energy, certain bacteroid strains employ uptake hydrogenase activity and thus evolve little or no h(2). rather, endogenous h(2) is efficiently respired at the expense of o(2), driving oxidative phosphorylation, recouping atp u ... | 2010 | 20838423 |
| complete genome sequence of beijerinckia indica subsp. indica. | beijerinckia indica subsp. indica is an aerobic, acidophilic, exopolysaccharide-producing, n(2)-fixing soil bacterium. it is a generalist chemoorganotroph that is phylogenetically closely related to facultative and obligate methanotrophs of the genera methylocella and methylocapsa. here we report the full genome sequence of this bacterium. | 2010 | 20601475 |
| genome sequence of azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes. | azotobacter vinelandii is a soil bacterium related to the pseudomonas genus that fixes nitrogen under aerobic conditions while simultaneously protecting nitrogenase from oxygen damage. in response to carbon availability, this organism undergoes a simple differentiation process to form cysts that are resistant to drought and other physical and chemical agents. here we report the complete genome sequence of a. vinelandii dj, which has a single circular genome of 5,365,318 bp. in order to reconcile ... | 2009 | 19429624 |
| high rate of n2 fixation by east siberian cryophilic soil bacteria as determined by measuring acetylene reduction in nitrogen-poor medium solidified with gellan gum. | for evaluating n(2) fixation of diazotrophic bacteria, nitrogen-poor liquid media supplemented with at least 0.5% sugar and 0.2% agar are widely used for acetylene reduction assays. in such a soft gel medium, however, many n(2)-fixing soil bacteria generally show only trace acetylene reduction activity. here, we report that use of a n(2) fixation medium solidified with gellan gum instead of agar promoted growth of some gellan-preferring soil bacteria. in a soft gel medium solidified with 0.3% ge ... | 2009 | 19286791 |
| poly(3-hydroxybutyrate) granules at the early stages of formation are localized close to the cytoplasmic membrane in caryophanon latum. | localization of newly synthesized poly(3hydroxybutyrate) (phb) granules was determined by confocal laser scanning fluorescence microscopy of nile red-stained cells and by transmission electron microscopy (tem). phb granules of nile red-stained living cells of caryophanon latum at the early stages of phb accumulation were frequently found at or close to the cytoplasmic membrane. tem analysis of the same culture revealed electron-translucent globular structures resembling phb granules that were no ... | 2007 | 17085698 |
| poly(3-hydroxybutyrate) granules at the early stages of formation are localized close to the cytoplasmic membrane in caryophanon latum. | localization of newly synthesized poly(3hydroxybutyrate) (phb) granules was determined by confocal laser scanning fluorescence microscopy of nile red-stained cells and by transmission electron microscopy (tem). phb granules of nile red-stained living cells of caryophanon latum at the early stages of phb accumulation were frequently found at or close to the cytoplasmic membrane. tem analysis of the same culture revealed electron-translucent globular structures resembling phb granules that were no ... | 2007 | 17085698 |
| biodiversity of amoebae and amoeba-resisting bacteria in a hospital water network. | free-living amoebae (fla) are ubiquitous organisms that have been isolated from various domestic water systems, such as cooling towers and hospital water networks. in addition to their own pathogenicity, fla can also act as trojan horses and be naturally infected with amoeba-resisting bacteria (arb) that may be involved in human infections, such as pneumonia. we investigated the biodiversity of bacteria and their amoebal hosts in a hospital water network. using amoebal enrichment on nonnutrient ... | 2006 | 16597941 |
| comparative cytochrome oxidase and superoxide dismutase analyses on strains of azotobacter vinelandii and other related free-living nitrogen-fixing bacteria. | quantitative n,n,n',n'-tetramethyl-p-phenylenediamine (tmpd) oxidase and superoxide dismutase (sod) analyses were performed on representative organisms of the family azotobacteraceae. azotobacter vinelandii, azotobacter chroococcum, azotobacter paspali, and derxia gummosa exhibited high quantitative tmpd oxidase activities, and their extracts possessed very active and electrophoretically homogeneous (single gel band) fe-type sods. azomonas macrocytogenes extracts had similar single fe-type sods, ... | 1984 | 16346548 |
| first genome data from uncultured upland soil cluster alpha methanotrophs provide further evidence for a close phylogenetic relationship to methylocapsa acidiphila b2 and for high-affinity methanotrophy involving particulate methane monooxygenase. | members of upland soil cluster alpha (usc alpha) are assumed to be methanotrophic bacteria (mb) adapted to the trace level of atmospheric methane. so far, these mb have eluded all cultivation attempts. while the 16s rrna phylogeny of usc alpha members is still not known, phylogenies constructed for the active-site polypeptide (encoded by pmoa) of particulate methane monooxygenase (pmmo) placed usc alpha next to the alphaproteobacterial methylocapsa acidiphila b2. to assess whether the pmoa tree ... | 2005 | 16269789 |
| 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 ... | 2005 | 15901717 |
| quantitative molecular assay for fingerprinting microbial communities of wastewater and estrogen-degrading consortia. | a quantitative fingerprinting method, called the real-time terminal restriction fragment length polymorphism (real-time-t-rflp) assay, was developed for simultaneous determination of microbial diversity and abundance within a complex community. the real-time-t-rflp assay was developed by incorporating the quantitative feature of real-time pcr and the fingerprinting feature of t-rflp analysis. the assay was validated by using a model microbial community containing three pure strains, an escherich ... | 2005 | 15746346 |
| quantitative detection of methanotrophs in soil by novel pmoa-targeted real-time pcr assays. | methane oxidation in soils is mostly accomplished by methanotrophic bacteria. little is known about the abundance of methanotrophs in soils, since quantification by cultivation and microscopic techniques is cumbersome. comparison of 16s ribosomal dna and pmoa (alpha subunit of the particulate methane monooxygenase) phylogenetic trees showed good correlation and revealed five distinct groups of methanotrophs within the alpha and gamma subclasses of proteobacteria: the methylococcus group, the met ... | 2003 | 12732507 |
| biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil. | isolated soil dna from an oak-hornbeam forest close to cologne, germany, was suitable for pcr amplification of gene segments coding for the 16s rrna and nitrogenase reductase (nifh), nitrous oxide reductase (nosz), cytochrome cd(1)-containing nitrite reductase (nirs), and cu-containing nitrite reductase (nirk) of denitrification. for each gene segment, diverse pcr products were characterized by cloning and sequencing. none of the 16s rrna gene sequences was identical to any deposited in the data ... | 2002 | 12147477 |
| detection and enumeration of methanotrophs in acidic sphagnum peat by 16s rrna fluorescence in situ hybridization, including the use of newly developed oligonucleotide probes for methylocella palustris. | two 16s rrna-targeted oligonucleotide probes, mcell-1026 and mcell-181, were developed for specific detection of the acidophilic methanotroph methylocella palustris using fluorescence in situ hybridization (fish). the fluorescence signal of probe mcell-181 was enhanced by its combined application with the oligonucleotide helper probe h158. mcell-1026 and mcell-181, as well as 16s rrna oligonucleotide probes with reported group specificity for either type i methanotrophs (probes m-84 and m-705) o ... | 2001 | 11571193 |
| comparative 16s rrna analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. | in a search for cosmopolitan phylogenetic clusters of freshwater bacteria, we recovered a total of 190 full and partial 16s ribosomal dna (rdna) sequences from three different lakes (lake gossenköllesee, austria; lake fuchskuhle, germany; and lake baikal, russia). the phylogenetic comparison with the currently available rdna data set showed that our sequences fall into 16 clusters, which otherwise include bacterial rdna sequences of primarily freshwater and soil, but not marine, origin. six of t ... | 2000 | 11055963 |
| bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rrna gene restriction analysis and sequence analysis of 16s rrna genes. | the nearly universal colonization of surfaces in marine waters by bacteria and the formation of biofilms and biofouling communities have important implications for ecological function and industrial processes. however, the dynamics of surface attachment and colonization in situ, particularly during the early stages of biofilm establishment, are not well understood. experimental surfaces that differed in their degrees of hydrophilicity or hydrophobicity were incubated in a salt marsh estuary tida ... | 2000 | 10653705 |
| biosynthesis of novel exopolymers by aureobasidium pullulans. | aureobasidium pullulans atcc 42023 was cultured under aerobic conditions with glucose, mannose, and glucose analogs as energy sources. the exopolymer extracts produced under these conditions were composed of glucose and mannose. the molar ratio of glucose to mannose in the exopolymer extract and the molecular weight of the exopolymer varied depending on the energy source and culture time. the glucose content of exopolymer extracts formed with glucose and mannose as the carbon sources was between ... | 1999 | 10583975 |
| molecular modeling and computational analyses suggests that the sinorhizobium meliloti periplasmic regulator protein exor adopts a superhelical fold and is controlled by a unique mechanism of proteolysis. | the sinorhizobium meliloti periplasmic exor protein and the exos/chvi two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. in the absence of crystal structures, understanding the molecular mechanism of interaction between exor and the exos sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. in this study, we present a theoretical structural model of the active f ... | 2014 | 25492513 |
| soluble methane monooxygenase gene clusters from trichloroethylene-degrading methylomonas sp. strains and detection of methanotrophs during in situ bioremediation. | the soluble mmo (smmo) gene clusters from group i methanotrophs were characterized. an 8.1-kb kpni fragment from methylomonas sp. strain kswiii and a 7.5-kb sali fragment from methylomonas sp. strain kspiii which contained the smmo gene clusters were cloned and sequenced. the sequences of these two fragments were almost identical. the smmo gene clusters in the fragment consisted of six open reading frames which were 52 to 79% similar to the corresponding genes of previously described smmo gene c ... | 1999 | 10583965 |
| mycobacterium tuberculosis rv0899 defines a family of membrane proteins widespread in nitrogen-fixing bacteria. | the mycobacterium tuberculosis membrane protein rv0899 confers adaptation of the bacterium to acidic environments. due to strong sequence homology of its c-terminus to bacterial ompa-like domains, rv0899 has been proposed to constitute an outer membrane porin of m. tuberculosis. however, ompa-like domains are widespread in a wide variety of bacterial proteins with different functions. furthermore, the three-dimensional structure of rv0899 does not contain a transmembrane β-barrel, and recent evi ... | 2011 | 21905117 |
| widespread occurrence of secondary lipid biosynthesis potential in microbial lineages. | bacterial production of long-chain omega-3 polyunsaturated fatty acids (pufas), such as eicosapentaenoic acid (epa, 20:5n-3) and docosahexaenoic acid (dha, 22:6n-3), is constrained to a narrow subset of marine γ-proteobacteria. the genes responsible for de novo bacterial pufa biosynthesis, designated pfaeabcd, encode large, multi-domain protein complexes akin to type i iterative fatty acid and polyketide synthases, herein referred to as "pfa synthases". in addition to the archetypal pfa synthase ... | 2011 | 21629834 |
| 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 ... | 2014 | 24928870 |
| evolution of mitochondria reconstructed from the energy metabolism of living bacteria. | the ancestors of mitochondria, or proto-mitochondria, played a crucial role in the evolution of eukaryotic cells and derived from symbiotic α-proteobacteria which merged with other microorganisms - the basis of the widely accepted endosymbiotic theory. however, the identity and relatives of proto-mitochondria remain elusive. here we show that methylotrophic α-proteobacteria could be the closest living models for mitochondrial ancestors. we reached this conclusion after reconstructing the possibl ... | 2014 | 24804722 |
| distribution of genes encoding nucleoid-associated protein homologs in plasmids. | bacterial nucleoid-associated proteins (naps) form nucleoprotein complexes and influence the expression of genes. recent studies have shown that some plasmids carry genes encoding nap homologs, which play important roles in transcriptional regulation networks between plasmids and host chromosomes. in this study, we determined the distributions of the well-known naps fis, h-ns, hu, ihf, and lrp and the newly found naps mvat and ndpa among the whole-sequenced 1382 plasmids found in gram-negative b ... | 2011 | 21350637 |
| bioenergetic evolution in proteobacteria and mitochondria. | mitochondria are the energy-producing organelles of our cells and derive from bacterial ancestors that became endosymbionts of microorganisms from a different lineage, together with which they formed eukaryotic cells. for a long time it has remained unclear from which bacteria mitochondria actually evolved, even if these organisms in all likelihood originated from the α lineage of proteobacteria. a recent article (degli esposti m, et al. 2014. evolution of mitochondria reconstructed from the ene ... | 2014 | 25432941 |
| the (d)evolution of methanotrophy in the beijerinckiaceae--a comparative genomics analysis. | the alphaproteobacterial family beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. we investigated the evolution of this family by comparing the genomes of the generalist organotroph beijerinckia indica, the facultative methanotroph methylocella silvestris and the obligate methanotroph methylocapsa acidiphila. highly resolved phylogenetic construction based on universally conserved genes demonstrated that the bei ... | 2013 | 23985741 |
| phylogenetic co-occurrence of exor, exos, and chvi, components of the rsi bacterial invasion switch, suggests a key adaptive mechanism regulating the transition between free-living and host-invading phases in rhizobiales. | both bacterial symbionts and pathogens rely on their host-sensing mechanisms to activate the biosynthetic pathways necessary for their invasion into host cells. the gram-negative bacterium sinorhizobium meliloti relies on its rsi (exor-exos-chvi) invasion switch to turn on the production of succinoglycan, an exopolysaccharide required for its host invasion. recent whole-genome sequencing efforts have uncovered putative components of rsi-like invasion switches in many other symbiotic and pathogen ... | 2015 | 26309130 |
| 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 ... | 2005 | 15968078 |
| regen: ancestral genome reconstruction for bacteria. | ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. we present a new computational system called regen for ancestral bacterial genome reconstruction at both the gene and replicon levels. regen reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. along each branch of the phylogenetic tree, regen infers evolutionary events, including gene creation and deletion ... | 2012 | 24704978 |
| a survey of srna families in α-proteobacteria. | we have performed a computational comparative analysis of six small non-coding rna (srna) families in α-proteobacteria. members of these families were first identified in the intergenic regions of the nitrogen-fixing endosymbiont s. meliloti by a combined bioinformatics screen followed by experimental verification. consensus secondary structures inferred from covariance models for each srna family evidenced in some cases conserved motifs putatively relevant to the function of trans-encoded base- ... | 2012 | 22418845 |
| riboregulation in plant-associated α-proteobacteria. | the symbiotic α-rhizobia sinorhizobium meliloti, bradyrhizobium japonicum, rhizobium etli and the related plant pathogen agrobacterium tumefaciens are important model organisms for studying plant-microbe interactions. these metabolically versatile soil bacteria are characterized by complex lifestyles and large genomes. here we summarize the recent knowledge on their small non-coding rnas (srnas) including conservation, function, and interaction of the srnas with the rna chaperone hfq. in each of ... | 2014 | 25003187 |
| whole-proteome analysis of twelve species of alphaproteobacteria links four pathogens. | thousands of whole-genome and whole-proteome sequences have been made available through advances in sequencing technology, and sequences of millions more organisms will become available in the coming years. this wealth of genetic information will provide numerous opportunities to enhance our understanding of these organisms including a greater understanding of relationships among species. researchers have used 16s rrna and other gene sequences to study the evolutionary origins of bacteria, but t ... | 2013 | 25437336 |
| molecular modeling and computational analyses suggests that the sinorhizobium meliloti periplasmic regulator protein exor adopts a superhelical fold and is controlled by a unique mechanism of proteolysis. | the sinorhizobium meliloti periplasmic exor protein and the exos/chvi two-component system form a regulatory mechanism that directly controls the transformation of free-living to host-invading cells. in the absence of crystal structures, understanding the molecular mechanism of interaction between exor and the exos sensor, which is believed to drive the key regulatory step in the invasion process, remains a major challenge. in this study, we present a theoretical structural model of the active f ... | 2014 | 25492513 |
| extent and variation of phage-borne bacterial 16s rrna gene sequences in wastewater environments. | phage metagenomes isolated from wastewater over a 12-month period were analyzed. the results suggested that various strains of proteobacteria, bacteroidetes, and other phyla are likely to participate in transduction. the patterns of 16s rrna sequences found in phage metagenomes did not follow changes in the total bacterial community. | 2011 | 21666016 |
| the preterm placental microbiome varies in association with excess maternal gestational weight gain. | although a higher maternal body mass index is associated with preterm birth, it is unclear whether excess gestational weight gain (gwg) or obesity drives increased risk. we and others have shown that the placenta harbors microbiota, which is significantly different among preterm births. our aim in this study was to investigate whether the preterm placental microbiome varies by virtue of obesity or alternately by excess gwg. | 2014 | 25557210 |
| the preterm placental microbiome varies in association with excess maternal gestational weight gain. | although a higher maternal body mass index is associated with preterm birth, it is unclear whether excess gestational weight gain (gwg) or obesity drives increased risk. we and others have shown that the placenta harbors microbiota, which is significantly different among preterm births. our aim in this study was to investigate whether the preterm placental microbiome varies by virtue of obesity or alternately by excess gwg. | 2014 | 25557210 |
| production of a chaetomium globosum enolase monoclonal antibody. | chaetomium globosum is a hydrophilic fungal species and a contaminant of water-damaged building materials in north america. methods to detect chaetomium species include subjective identification of ascospores, viable culture, or molecular-based detection methods. in this study, we describe the production and initial characterization of a monoclonal antibody (mab) for c. globosum enolase. mab 1c7, a murine igg1 isotype mab, was produced and reacted with recombinant c. globosum enolase (rcgeno) in ... | 2014 | 25495488 |
| Evolutionary and functional insights into Leishmania META1: evidence for lateral gene transfer and a role for META1 in secretion. | ABSTRACT: BACKGROUND: Leishmania META1 has for long been a candidate molecule for involvement in virulence: META1 transcript and protein are up-regulated in metacyclic Leishmania. Yet, how META1 contributes to virulence remains unclear. We sought insights into the possible functions of META1 by studying its evolutionary origins. RESULTS: Using multiple criteria including sequence similarity, nucleotide composition, phylogenetic analysis and selection pressure on gene sequence, we present evide ... | 2011 | 22093578 |
| annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. | the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ... | 2011 | 24710297 |
| structure/function analysis of a type iii polyketide synthase in the brown alga ectocarpus siliculosus reveals a biochemical pathway in phlorotannin monomer biosynthesis. | brown algal phlorotannins are structural analogs of condensed tannins in terrestrial plants and, like plant phenols, they have numerous biological functions. despite their importance in brown algae, phlorotannin biosynthetic pathways have been poorly characterized at the molecular level. we found that a predicted type iii polyketide synthase in the genome of the brown alga ectocarpus siliculosus, pks1, catalyzes a major step in the biosynthetic pathway of phlorotannins (i.e., the synthesis of ph ... | 2013 | 23983220 |
| phb granules are attached to the nucleoid via pham in ralstonia eutropha. | poly(3-hydroxybutyrate) (phb) granules are important storage compounds of carbon and energy in many prokaryotes which allow survival of the cells in the absence of suitable carbon sources. formation and subcellular localization of phb granules was previously assumed to occur randomly in the cytoplasm of phb accumulating bacteria. however, contradictionary results on subcellular localization of phb granules in ralstonia eutropha were published, recently. | 2012 | 23157596 |
| new feel for new phyla. | | 2008 | 18665943 |
| a persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations. | acute exacerbations of chronic obstructive pulmonary disease (copd) are a major source of morbidity and contribute significantly to healthcare costs. although bacterial infections are implicated in nearly 50% of exacerbations, only a handful of pathogens have been consistently identified in copd airways, primarily by culture-based methods, and the bacterial microbiota in acute exacerbations remains largely uncharacterized. the aim of this study was to comprehensively profile airway bacterial com ... | 2010 | 20141328 |
| the (d)evolution of methanotrophy in the beijerinckiaceae--a comparative genomics analysis. | the alphaproteobacterial family beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. we investigated the evolution of this family by comparing the genomes of the generalist organotroph beijerinckia indica, the facultative methanotroph methylocella silvestris and the obligate methanotroph methylocapsa acidiphila. highly resolved phylogenetic construction based on universally conserved genes demonstrated that the bei ... | 2013 | 23985741 |
| 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 ... | 2014 | 25155017 |
| methanotrophic bacteria in oilsands tailings ponds of northern alberta. | we investigated methanotrophic bacteria in slightly alkaline surface water (ph 7.4-8.7) of oilsands tailings ponds in fort mcmurray, canada. these large lakes (up to 10 km(2)) contain water, silt, clay and residual hydrocarbons that are not recovered in oilsands mining. they are primarily anoxic and produce methane but have an aerobic surface layer. aerobic methane oxidation was measured in the surface water at rates up to 152 nmol ch4 ml(-1) water d(-1). microbial diversity was investigated via ... | 2012 | 23254511 |
| respiratory membrane endo-hydrogenase activity in the microaerophile azorhizobium caulinodans is bidirectional. | the microaerophilic bacterium azorhizobium caulinodans, when fixing n(2) both in pure cultures held at 20 µm dissolved o(2) tension and as endosymbiont of sesbania rostrata legume nodules, employs a novel, respiratory-membrane endo-hydrogenase to oxidize and recycle endogenous h(2) produced by soluble mo-dinitrogenase activity at the expense of o(2). | 2012 | 22662125 |
| fingerprinting diazotroph communities in the chesapeake bay by using a dna macroarray. | investigations of the distribution and diversity of nitrogen-fixing microorganisms in natural environments have often relied on pcr amplification and sequence analysis of a portion of one of the key enzymes in nitrogen fixation, dinitrogenase reductase, encoded by nifh. recent work has suggested that dna macroarrays provide semiquantitative fingerprints of diversity within mixtures of nifh amplicons (g. f. steward, b. d. jenkins, b. b. ward, and j. p. zehr, appl. environ. microbiol. 70:1455-1465 ... | 2004 | 15006803 |
| methanotrophic bacteria in oilsands tailings ponds of northern alberta. | we investigated methanotrophic bacteria in slightly alkaline surface water (ph 7.4-8.7) of oilsands tailings ponds in fort mcmurray, canada. these large lakes (up to 10 km(2)) contain water, silt, clay and residual hydrocarbons that are not recovered in oilsands mining. they are primarily anoxic and produce methane but have an aerobic surface layer. aerobic methane oxidation was measured in the surface water at rates up to 152 nmol ch4 ml(-1) water d(-1). microbial diversity was investigated via ... | 2012 | 23254511 |
| the rhizome of reclinomonas americana, homo sapiens, pediculus humanus and saccharomyces cerevisiae mitochondria. | mitochondria are thought to have evolved from eubacteria-like endosymbionts; however, the origin of the mitochondrion remains a subject of debate. in this study, we investigated the phenomenon of chimerism in mitochondria to shed light on the origin of these organelles by determining which species played a role in their formation. we used the mitochondria of four distinct organisms, reclinomonas americana, homo sapiens, saccharomyces cerevisiae and multichromosome pediculus humanus, and attempte ... | 2011 | 22014084 |
| coordinated expression of fdxd and molybdenum nitrogenase genes promotes nitrogen fixation by rhodobacter capsulatus in the presence of oxygen. | rhodobacter capsulatus is able to grow with n2 as the sole nitrogen source using either a molybdenum-dependent or a molybdenum-free iron-only nitrogenase whose expression is strictly inhibited by ammonium. disruption of the fdxd gene, which is located directly upstream of the mo-nitrogenase genes, nifhdk, abolished diazotrophic growth via mo-nitrogenase at oxygen concentrations still tolerated by the wild type, thus demonstrating the importance of fdxd under semiaerobic conditions. in contrast, ... | 2014 | 24272776 |
| an evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin. | to test the predictions of competing and mutually exclusive hypotheses for the origin of eukaryotes, we identified from a sample of 27 sequenced eukaryotic and 994 sequenced prokaryotic genomes 571 genes that were present in the eukaryote common ancestor and that have homologues among eubacterial and archaebacterial genomes. maximum-likelihood trees identified the prokaryotic genomes that most frequently contained genes branching as the sister to the eukaryotic nuclear homologues. among the arch ... | 2012 | 22355196 |
| dual role of hupf in the biosynthesis of [nife] hydrogenase in rhizobium leguminosarum. | [nife] hydrogenases are enzymes that catalyze the oxidation of hydrogen into protons and electrons, to use h₂ as energy source, or the production of hydrogen through proton reduction, as an escape valve for the excess of reduction equivalents in anaerobic metabolism. biosynthesis of [nife] hydrogenases is a complex process that occurs in the cytoplasm, where a number of auxiliary proteins are required to synthesize and insert the metal cofactors into the enzyme structural units. the endosymbioti ... | 2012 | 23136881 |
| spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. | molecular ecology techniques were applied to assess changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. microsensor measurements showed that oxygen was depleted from 140 microm at the floodwater/soil interface to nondetectable amounts at a depth of approximately 2.0 mm and below. bacterial 16s rrna gene (rdna)-based community fingerprint patterns were obtained from 200-microm-thick soil slices of both the oxic and anoxic zones by using the t ... | 2000 | 10653747 |
| structure and functional characterization of pyruvate decarboxylase from gluconacetobacter diazotrophicus. | bacterial pyruvate decarboxylases (pdc) are rare. their role in ethanol production and in bacterially mediated ethanologenic processes has, however, ensured a continued and growing interest. pdcs from zymomonas mobilis (zmpdc), zymobacter palmae (zppdc) and sarcina ventriculi (svpdc) have been characterized and zmpdc has been produced successfully in a range of heterologous hosts. pdcs from the acetobacteraceae and their role in metabolism have not been characterized to the same extent. examples ... | 2014 | 25369873 |
| identification of nitrogen-fixing genes and gene clusters from metagenomic library of acid mine drainage. | biological nitrogen fixation is an essential function of acid mine drainage (amd) microbial communities. however, most acidophiles in amd environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in amd microbial communities. in this study, we used metagenomic sequencing to isolate nif genes in the amd microbial community from dexing copper mine, china. meanwhile, a metagenome microarray containing 7,776 large-in ... | 2014 | 24498417 |
| the effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly. | the influence of resource availability on planktonic and biofilm microbial community membership is poorly understood. heterotrophic bacteria derive some to all of their organic carbon (c) from photoautotrophs while simultaneously competing with photoautotrophs for inorganic nutrients such as phosphorus (p) or nitrogen (n). therefore, c inputs have the potential to shift the competitive balance of aquatic microbial communities by increasing the resource space available to heterotrophs (more c) wh ... | 2015 | 26236289 |
| structure of the legionella effector, lpg1496, suggests a role in nucleotide metabolism. | pathogenic gram-negative bacteria use specialized secretion systems that translocate bacterial proteins, termed effectors, directly into host cells where they interact with host proteins and biochemical processes for the benefit of the pathogen. lpg1496 is a previously uncharacterized effector of legionella pneumophila, the causative agent of legionnaires disease. here, we crystallized three nucleotide binding domains from lpg1496. the c-terminal domain, which is conserved among the side family ... | 2015 | 26294765 |
| door: a database for prokaryotic operons. | we present a database door (database for prokaryotic operons) containing computationally predicted operons of all the sequenced prokaryotic genomes. all the operons in door are predicted using our own prediction program, which was ranked to be the best among 14 operon prediction programs by a recent independent review. currently, the door database contains operons for 675 prokaryotic genomes, and supports a number of search capabilities to facilitate easy access and utilization of the informatio ... | 2008 | 18988623 |
| door: a database for prokaryotic operons. | we present a database door (database for prokaryotic operons) containing computationally predicted operons of all the sequenced prokaryotic genomes. all the operons in door are predicted using our own prediction program, which was ranked to be the best among 14 operon prediction programs by a recent independent review. currently, the door database contains operons for 675 prokaryotic genomes, and supports a number of search capabilities to facilitate easy access and utilization of the informatio ... | 2008 | 18988623 |
| improvement of penicillin g acylase expression in escherichia coli through uv induced mutations. | we used ultraviolet (uv) radiation to induce mutation in three locally isolated strains of escherichia coli. different dilutions of bacterial cultures were exposed to uv lamp of 254 nm wavelength for different time intervals at varied distances ranging from 5 to 210 sec and 5 to 100 cm. viable colonies were screened for mutants with an increased production of penicillin g acylase (pga) and a reduced production of β-lactamase, which are the desired properties of pga producing industrial strains. ... | 2010 | 24031596 |
| stable-isotope probing identifies uncultured planctomycetes as primary degraders of a complex heteropolysaccharide in soil. | the exopolysaccharides (epss) produced by some bacteria are potential growth substrates for other bacteria in soil. we used stable-isotope probing (sip) to identify aerobic soil bacteria that assimilated the cellulose produced by gluconacetobacter xylinus or the eps produced by beijerinckia indica. the latter is a heteropolysaccharide comprised primarily of l-guluronic acid, d-glucose, and d-glycero-d-mannoheptose. (13)c-labeled eps and (13)c-labeled cellulose were purified from bacterial cultur ... | 2015 | 25934620 |
| high throughput sequencing to detect differences in methanotrophic methylococcaceae and methylocystaceae in surface peat, forest soil, and sphagnum moss in cranesville swamp preserve, west virginia, usa. | northern temperate forest soils and sphagnum-dominated peatlands are a major source and sink of methane. in these ecosystems, methane is mainly oxidized by aerobic methanotrophic bacteria, which are typically found in aerated forest soils, surface peat, and sphagnum moss. we contrasted methanotrophic bacterial diversity and abundances from the (i) organic horizon of forest soil; (ii) surface peat; and (iii) submerged sphagnum moss from cranesville swamp preserve, west virginia, using multiplex s ... | 2015 | 27682082 |
| draft genome sequence of methyloferula stellata ar4, an obligate methanotroph possessing only a soluble methane monooxygenase. | methyloferula stellata ar4 is an aerobic acidophilic methanotroph, which, in contrast to most known methanotrophs but similar to methylocella spp., possesses only a soluble methane monooxygenase. however, it differs from methylocella spp. by its inability to grow on multicarbon substrates. here, we report the draft genome sequence of this bacterium. | 2015 | 25745010 |
| footprint area analysis of binary imaged cupriavidus necator cells to study phb production at balanced, transient, and limited growth conditions in a cascade process. | statistical distribution of cell and poly[3-(r)-hydroxybutyrate] (phb) granule size and number of granules per cell are investigated for phb production in a five-stage cascade (5cstr). electron microscopic pictures of cells from individual cascade stages (r1-r5) were converted to binary pictures to visualize footprint areas for polyhydroxyalkanoate (pha) and non-pha biomass. results for each stage were correlated to the corresponding experimentally determined kinetics (specific growth rate μ and ... | 2016 | 27695913 |