a phylogenetic study of rubrobacter radiotolerans by sequence analysis of the 16s ribosomal rna gene.partial sequence of the 16s ribosomal rna gene of an extremely high radiotolerant bacterium, rubrobacter radiotolerans (reclassified from arthrobacter radiotolerans by chemical characteristics) was determined by pcr-amplification from a small amount of heat-lysed biomass, followed by direct sequencing of the pcr product. the sequence was aligned with seven species of arthrobacter and also with representatives of various other bacterial groups. r. radiotolerans was confirmed to be out of the arth ...19968843337
molecular biological evidence for the occurrence of uncultured members of the actinomycete line of descent in different environments and geographical locations.a 16s rdna based molecular ecological study was performed on a sample taken from a peat bog in germany. total dna was extracted by directly lysing micro-organisms in the peat matrix. the 5' 1400 nucleotides of the bacterial 16s rdna were amplified using conserved bacterial pcr primers. a clone library was generated by blunt-end cloning and 262 16s rdna clones were analysed. of these, 37 were located in the gram-positive phylum, as determined by hybridization to an oligonucleotide probe specific ...19968885402
purification and characterization of a novel dna repair enzyme from the extremely radioresistant bacterium rubrobacter radiotolerans.rubrobacter radiotolerans is an extremely radioresistant bacterium. it exhibits higher resistance than the well-known radioresistant bacterium deinococcus radiodurans, but the molecular mechanisms responsible for the radio-resistance of r. radiotolerans remain unknown. in the present study, we have demonstrated the presence of a novel dna repair enzyme in r. radiotolerans cells that recognizes radiation-induced dna damages such as thymine glycol, urea residues, and abasic sites. the enzyme was p ...200010838807
[unique properties of highly radioresistant bacteria].in connection with the chernobyl nuclear power plant (chnpp) accident and the negative ecological after-effects for biota in this zone the interest has arisen to radioresistant bacteria, as to the most dynamic model of the given ecosystem, and to mechanisms which provide resistance of bacteria to ionizing radiation. the analysis of published data has shown that the radioresistant bacteria are not interrelated taxonomically and phylogenetically. the extreme radioresistant bacteria are represented ...200011300085
rubrobacter-related bacteria associated with rosy discolouration of masonry and lime wall paintings.a molecular approach was chosen to analyse the correlation between bacterial colonisation and rosy discolouration of masonry and lime wall paintings of two historically important buildings in austria and germany. the applied molecular method included pcr amplification of genes encoding the small subunit rrna of bacteria (16s rdna), genetic fingerprinting by denaturing gradient gel electrophoresis (dgge), construction of 16s rdna clone libraries, and comparative phylogenetic sequence analyses. th ...200111702076
thermoleophilum album and thermoleophilum minutum are culturable representatives of group 2 of the rubrobacteridae (actinobacteria).analysis of the morphological and genotypic properties of three obligately thermophilic strains of thermoleophilum album and thermoleophilum minutum, originally described as green non-sulfur bacteria, indicates that these taxa belong to the rubrobacter subdivision of the actinobacteria. em of the cell wall clearly showed morphology typical of gram-positive bacteria. a comparison of 16s rrna gene sequences, including signature nucleotide pairs and secondary structural features considered diagnost ...200312710601
new primers for the class actinobacteria: application to marine and terrestrial this study, we redesigned and evaluated primers for the class actinobacteria. in silico testing showed that the primers had a perfect match with 82% of genera in the class actinobacteria, representing a 26-213% improvement over previously reported primers. only 4% of genera that displayed mismatches did so in the terminal three bases of the 3' end, which is most critical for polymerase chain reaction success. the primers, designated s-c-act-0235-a-s-20 and s-c-act-0878-a-a-19, amplified an ap ...200314510836
rubrobacter taiwanensis sp. nov., a novel thermophilic, radiation-resistant species isolated from hot springs.two novel bacteria, with an optimum growth temperature of approximately 60 degrees c, were isolated from lu-shan hot springs in the central region of taiwan. these isolates were aerobic, thermophilic, halotolerant, pink-pigmented, heterotrophic and resistant to gamma-radiation. both pleomorphic, short, rod-shaped cells and coccoid cells were observed. strains ls-286 (= atcc baa-452 = bcrc 17198) and ls-293t (= atcc baa-406t = bcrc 17173t) represented a novel species of the genus rubrobacter, acc ...200415388754
a ring-like nucleoid is not necessary for radioresistance in the deinococcaceae.transmission electron microscopy images of deinococcus radiodurans r1 suggest that the nucleoid of this species exists as a "ring-like" body, and have led to speculation that this structure contributes to the radioresistance of the species. since extreme radioresistance is characteristic of six other species of deinococcus, we have attempted to correlate nucleoid morphology and radioresistance by determining whether the genomic dna of each of these species exhibit similar structures.200515799787
molecular microbial diversity of a soil sample and detection of ammonia oxidizers from cape evans, mcmurdo dry valley, antarctica.the aim of our study was to estimate the uncultured eubacterial diversity of a soil sample collected below a dead seal, cape evans, mcmurdo, antarctica by an ssu rdna gene library approach. our study by sequencing of clones from ssu rdna gene library approach revealed high diversity in the soil sample from antarctica. more than 50% of clones showed homology to cytophaga-flavobacterium-bacteroides group; sequences also belonged to alpha, beta, gamma proteobacteria, thermus-deinococcus and high gc ...200716517136
alignment-independent bilinear multivariate modelling (aibimm) for global analyses of 16s rrna gene phylogeny.alignment-independent phylogenetic methods have interesting properties for global phylogenetic reconstructions, particularly with respect to speed and accuracy. here, we present a novel multimer-based alignment-independent bilinear mathematical modelling (aibimm) approach for global 16s rrna gene phylogenetic analyses. in aibimm, jackknife cross-validated principal component analyses (pca) are used to explain the variance in nucleotide n-mer frequency data. we compared aibimm with alignment-base ...200616825631
organic solutes in rubrobacter xylanophilus: the first example of di-myo-inositol-phosphate in a thermophile.the thermophilic and halotolerant nature of rubrobacter xylanophilus led us to investigate the accumulation of compatible solutes in this member of the deepest lineage of the phylum actinobacteria. trehalose and mannosylglycerate (mg) were the major compounds accumulated under all conditions examined, including those for optimal growth. the addition of nacl to a complex medium and a defined medium had a slight or negligible effect on the accumulation of these compatible solutes. glycine betaine, ...200717510735
thermophilic biofiltration of benzene and the current studies, we characterized the degradation of a hot mixture of benzene and toluene (bt) gases by a thermophilic biofilter using polyurethane as packing material and high-temperature compost as a microbial source. we also examined the effect of supplementing the biofilter with yeast extract (ye). we found that ye substantially enhanced microbial activity in the thermophilic biofilter. the degrading activity of the biofilter supplied with ye was stable during long-term operation (app ...200718167445
basal dna repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria.ionizing-radiation-resistant bacteria (irrb) show a surprising capacity for adaptation to ionizing radiation and desiccation. positive darwinian selection is expected to play an important role in this trait, but no data are currently available regarding the role of positive adaptive selection in resistance to ionizing-radiation and tolerance of desiccation. we analyzed the four known genome sequences of irrb (deinococcus geothermalis, deinococcus radiodurans, kineococcus radiotolerans, and rubro ...200818570673
crystallization and preliminary crystallographic analysis of mannosyl-3-phosphoglycerate synthase from rubrobacter xylanophilus.rubrobacter xylanophilus is the only gram-positive bacterium known to synthesize the compatible solute mannosylglycerate (mg), which is commonly found in hyperthermophilic archaea and some thermophilic bacteria. unlike the salt-dependent pattern of accumulation observed in (hyper)thermophiles, in r. xylanophilus mg accumulates constitutively. the synthesis of mg in r. xylanophilus was tracked from gdp-mannose and 3-phosphoglycerate, but the genome sequence of the organism failed to reveal any of ...200818678952
a unique combination of genetic systems for the synthesis of trehalose in rubrobacter xylanophilus: properties of a rare actinobacterial tret.trehalose is the primary organic solute in rubrobacter xylanophilus under all conditions tested, including those for optimal growth. we detected genes of four different pathways for trehalose synthesis in the genome of this organism, namely, the trehalose-6-phosphate synthase (tps)/trehalose-6-phosphate phosphatase (tpp), tres, trey/trez, and tret pathways. moreover, r. xylanophilus is the only known member of the phylum actinobacteria to harbor tret. the tps sequence is typically bacterial, but ...200818835983
macroamphiphilic components of thermophilic actinomycetes: identification of lipoteichoic acid in thermobifida fusca.the cell envelopes of gram-positive bacteria contain structurally diverse membrane-anchored macroamphiphiles (lipoteichoic acids and lipoglycans) whose functions are poorly understood. since regulation of membrane composition is an important feature of adaptation to life at higher temperatures, we have examined the nature of the macroamphiphiles present in the thermophilic actinomycetes thermobifida fusca and rubrobacter xylanophilus. following hot-phenol-water extraction and purification by hyd ...200918931132
isolation of five rubrobacter strains from biodeteriorated the last few years, the microbial colonisation of mural paintings in ancient monuments has been attracting the attention of microbiologists and conservators. the genus rubrobacter is commonly found in biodeteriorated monuments, where it has been reported to cause rosy discolouration. however, to date, only three species of this genus have been isolated, all from thermophilic environments. in this paper, we studied three monuments: the servilia and postumio tombs in the roman necropolis of car ...200918953520
zinc contamination decreases the bacterial diversity of agricultural soil.abstract around half a million tonnes of biosolids (sewage sludge dry solids) are applied to agricultural land in the united kingdom each year, and this may increase to 732 000 t by 2005/6. the heavy metals contained in biosolids may permanently degrade the microbial decomposer communities of agricultural soils. we used amplified ribosomal dna restriction analysis of the extractable bacterial fraction to compare the diversity of a zinc-contaminated soil (400 mg kg(-1) zn; ph 5.7 and 1.36% c(org) ...200319719692
isolation, phylogenetic analysis and anti-infective activity screening of marine sponge-associated actinomycetes.terrestrial actinomycetes are noteworthy producers of a multitude of antibiotics, however the marine representatives are much less studied in this regard. in this study, 90 actinomycetes were isolated from 11 different species of marine sponges that had been collected from offshore ras mohamed (egypt) and from rovinj (croatia). phylogenetic characterization of the isolates based on 16s rrna gene sequencing supported their assignment to 18 different actinomycete genera representing seven differen ...201020411105
low temperature s(0) biomineralization at a supraglacial spring system in the canadian high arctic.elemental sulfur (s(0) ) is deposited each summer onto surface ice at borup fiord pass on ellesmere island, canada, when high concentrations of aqueous h(2) s are discharged from a supraglacial spring system. 16s rrna gene clone libraries generated from sulfur deposits were dominated by β-proteobacteria, particularly ralstonia sp. sulfur-cycling micro-organisms such as thiomicrospira sp., and ε-proteobacteria such as sulfuricurvales and sulfurovumales spp. were also abundant. concurrent cultivat ...201121592302
functional and structural characterization of a novel mannosyl-3-phosphoglycerate synthase from rubrobacter xylanophilus reveals its dual substrate specificity.rubrobacter xylanophilus is the only actinobacterium known to accumulate the organic solute mannosylglycerate (mg); moreover, the accumulation of mg is constitutive. the key enzyme for mg synthesis, catalysing the conversion of gdp-mannose (gdp-man) and d-3-phosphoglycerate (3-pga) into the phosphorylated intermediate mannosyl-3-phosphoglycerate and gdp, was purified from r. xylanophilus cell extracts and the corresponding gene was expressed in e. coli. despite the related solute glucosylglycera ...201021166895
microbial diversity in endostromatolites (cf. fissure calcretes) and in the surrounding permafrost landscape, haughton impact structure region, devon island, recent years, endostromatolites, which consist of finely laminated calcite columns that grow orthogonally within millimeter- to centimeter-thick fissures in limestone bedrock outcrops, have been discovered in dolomitic outcrops in the haughton impact structure region, devon island, canada. the growth mechanism of the endostromatolites is believed to be very slow and possibly intertwined with biotic and abiotic processes. therefore, to discern how endostromatolites form in this polar desert en ...200919968459
unusual production of glutathione in actinobacteria.most actinobacteria produce mycothiol as the major thiol. in addition to mycothiol rhodococcus ad45 generates a substantial level of glutathione possibly using genes acquired in a lateral transfer. instead of mycothiol, rubrobacter radiotolerans and rubrobacter xylanophilus produce glutathione, whose synthesis appears to involve enzymes substantially different from those in other organisms.200918719892
the bacterial aetiology of rosy discoloration of ancient wall paintings.the inventory of microorganisms responsible for biological deterioration of ancient paintings has become an integral part of restoration activities. here, the microbial agent of rosy discoloration on medieval frescoes in the crypt of the original sin (matera, italy) was investigated by a combination of microscopic, molecular and spectroscopic approaches. the bacterial community from three rosy-discoloured painting sites was characterized by 16s rrna gene-based techniques. the eubacterial populat ...200717922771
gene arrangements characteristic of the phylum actinobacteria.the availability of genomic sequence data allows new challenges to various biological problems. one of such attempts is the extraction of phylogenetic information from gene order data of genomes. phylogenetic inferences are most commonly carried out on the basis of 16s rrna trees, which sometimes produce unresolved or unreliable branching orders. one example for such a low resolution is recognized in the branching pattern among the phylum actinobacteria. here, gene arrangements characteristic of ...200717558547
bifunctional ctp:inositol-1-phosphate cytidylyltransferase/cdp-inositol:inositol-1-phosphate transferase, the key enzyme for di-myo-inositol-phosphate synthesis in several (hyper)thermophiles.the pathway for the synthesis of di-myo-inositol-phosphate (dip) was recently elucidated on the basis of the detection of the relevant activities in cell extracts of archaeoglobus fulgidus and structural characterization of products by nuclear magnetic resonance (nmr) (n. borges, l. g. gonçalves, m. v. rodrigues, f. siopa, r. ventura, c. maycock, p. lamosa, and h. santos, j. bacteriol. 188:8128-8135, 2006). here, a genomic approach was used to identify the genes involved in the synthesis of dip. ...200717526717
solirubrobacter pauli gen. nov., sp. nov., a mesophilic bacterium within the rubrobacteridae related to common soil clones.a novel bacterium, strain b33d1t, isolated from agricultural soil, was characterized taxonomically and phylogenetically. strain b33d1t was a gram-positive, aerobic rod of medium length that formed long chains on a common laboratory medium. however, b33d1t grew poorly on the surface of agar plates and was sensitive to desiccation. the optimal growth temperature was 30 degrees c (range 19-38 degrees c). the organism grew well on a variety of sugars and was capable of utilizing a few amino acids as ...200312710617
diverse, yet-to-be-cultured members of the rubrobacter subdivision of the actinobacteria are widespread in australian arid soils.phylogenetic analyses of ribosomal rna gene sequences (rdnas) retrieved from an australian desert soil sample (sturt national park) revealed the presence of a number of clones which branched deeply from the high gc gram-positive division line of descent. the most abundant group of these clones were related to rubrobacter. an oligonucleotide probe was designed to have broad specificity to rubrobacter and relatives. this probe was used to interrogate eight rdna libraries representing four distinct ...200010967210
characterization and radiation resistance of new isolates of rubrobacter radiotolerans and rubrobacter this study we characterized new strains of the slightly thermophilic species rubrobacter radiotolerans and the thermophilic species rubrobacter xylanophilus, both of which were previously represented only by the type strains isolated, respectively, from japan and the united kingdom. the new isolates were recovered from two hot springs in central portugal after gamma irradiation of water and biofilm samples. we assessed biochemical characteristics, performed dna-dna hybridization, and carried ...199910591012
16s rrna gene sequence of rubrobacter radiotolerans and its phylogenetic alignment with members of the genus arthrobacter, gram-positive bacteria, and members of the family deinococcaceae.the nearly complete sequence of the 16s rrna gene of an extremely highly radiotolerant bacterium, rubrobacter radiotolerans (reclassified from arthrobacter radiotolerans based on chemical characteristics), was determined by pcr amplification of the genomic dna followed by cloning of the amplified gene and sequencing by the dideoxynucleotide method. the sequence was aligned with the sequences of members of the genus arthrobacter and also with the sequences of representatives of the gram-positive ...19979226900
characterization and radio-resistant function of manganese superoxide dismutase of rubrobacter radiotolerans.rubrobacter radiotolerans is the most radio-resistant eubacterium without spore-formation in the life cycle, and its d(37) is 16,000 gy against gamma-rays. to understand the molecular mechanism of the high radio-resistance, we purified and characterized superoxide dismutase (sod) of this organism as enzymatic radical scavenger, and then analyzed its genetic information. the purified sod protein formed homo-tetramerization of 24,000 da-monomer, while maintaining its enzymatic activity against pot ...201121971036
sunlight-exposed biofilm microbial communities are naturally resistant to chernobyl ionizing-radiation levels.the chernobyl accident represents a long-term experiment on the effects of exposure to ionizing radiation at the ecosystem level. though studies of these effects on plants and animals are abundant, the study of how chernobyl radiation levels affect prokaryotic and eukaryotic microbial communities is practically non-existent, except for a few reports on human pathogens or soil microorganisms. environments enduring extreme desiccation and uv radiation, such as sunlight exposed biofilms could in pr ...201121765911
pyrosequence analysis of unamplified and whole genome amplified dna from hydrocarbon-contaminated groundwater.pyrosequence data was used to analyze the composition and metabolic potential of a metagenome from a hydrocarbon-contaminated site. unamplified and whole genome amplified (wga) sequence data was compared from this source. according to mg-rast, an additional 2,742,252 bp of dna was obtained with the wga, indicating that wga has the ability to generate a large amount of dna from a small amount of starting sample. however, it was observed that wga introduced a bias with respect to the distribution ...201121656086
diversity, biological roles and biosynthetic pathways for sugar-glycerate containing compatible solutes in bacteria and archaea.a decade ago the compatible solutes mannosylglycerate (mg) and glucosylglycerate (gg) were considered to be rare in nature. apart from two species of thermophilic bacteria, thermus thermophilus and rhodothermus marinus, and a restricted group of hyperthermophilic archaea, the thermococcales, mg had only been identified in a few red algae. glucosylglycerate was considered to be even rarer and had only been detected as an insignificant solute in two halophilic microorganisms, a cyanobacterium, as ...201021176052
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