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1.  Analysis of Anoxybacillus Genomes from the Aspects of Lifestyle Adaptations, Prophage Diversity, and Carbohydrate Metabolism 
PLoS ONE  2014;9(3):e90549.
Species of Anoxybacillus are widespread in geothermal springs, manure, and milk-processing plants. The genus is composed of 22 species and two subspecies, but the relationship between its lifestyle and genome is little understood. In this study, two high-quality draft genomes were generated from Anoxybacillus spp. SK3-4 and DT3-1, isolated from Malaysian hot springs. De novo assembly and annotation were performed, followed by comparative genome analysis with the complete genome of Anoxybacillus flavithermus WK1 and two additional draft genomes, of A. flavithermus TNO-09.006 and A. kamchatkensis G10. The genomes of Anoxybacillus spp. are among the smaller of the family Bacillaceae. Despite having smaller genomes, their essential genes related to lifestyle adaptations at elevated temperature, extreme pH, and protection against ultraviolet are complete. Due to the presence of various competence proteins, Anoxybacillus spp. SK3-4 and DT3-1 are able to take up foreign DNA fragments, and some of these transferred genes are important for the survival of the cells. The analysis of intact putative prophage genomes shows that they are highly diversified. Based on the genome analysis using SEED, many of the annotated sequences are involved in carbohydrate metabolism. The presence of glycosyl hydrolases among the Anoxybacillus spp. was compared, and the potential applications of these unexplored enzymes are suggested here. This is the first study that compares Anoxybacillus genomes from the aspect of lifestyle adaptations, the capacity for horizontal gene transfer, and carbohydrate metabolism.
PMCID: PMC3948429  PMID: 24603481
2.  Thermostable and Alkalistable Xylanases Produced by the Thermophilic Bacterium Anoxybacillus flavithermus TWXYL3 
ISRN Microbiology  2012;2012:517524.
With the rising cost and finite supply of fossil energy, there is an increasing economic incentive for the development of clean, efficient, and renewable domestic energy. The activities of microorganisms offer the potential conversion of lignocellulosic materials into fermentable sugars, usable for downstream fermentation processes. Strain TWXYL3, a thermophilic facultative anaerobe, was discovered in the Alvord Basin hydrothermal system in Oregon, USA. Phylogenetic analysis of strain TWXYL3 showed it to be 99% similar to the 16S rRNA gene of Anoxybacillus flavithermus WL (FJ950739). A. flavithermus TWXYL3 was shown to secrete a large multisubunit thermostable xylanase complex into the growth medium. Xylanase induction was achieved by resuspending the isolate in a selective xylan-containing medium. Extracellular xylanase activity showed a temperature optimum of 65°C and retained thermostability up to 85°C. Extracellular xylanase activity showed a bimodal pH optimum, with maxima at pH 6 and pH 8. Electrophoretic analysis of the extracellular xylanase shows 5 distinct proteins with xylanase activity. Strain TWXYL3 is the first xylanolytic isolate obtained from the Alvord Basin hydrothermal system and represents a new model system for development of processes where lignocellulosics are converted to biofuel precursors.
PMCID: PMC3671716  PMID: 23762752
3.  Complete Genome Sequence of Anoxybacillus flavithermus TNO-09.006, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment 
Genome Announcements  2013;1(1):e00010-13.
Spores of thermophilic spore-forming bacteria are a common cause of contamination in dairy products. We isolated the thermophilic strain Anoxybacillus flavithermus TNO-09.006 from a milk-processing plant, and we report the complete genome of this isolate consisting of a single chromosome of 2.65 Mb.
PMCID: PMC3587922  PMID: 23469333
4.  Influence of Cations on Growth of Thermophilic Geobacillus spp. and Anoxybacillus flavithermus in Planktonic Culture 
Free ions of Na+, K+, Ca2+, and Mg2+ influenced the optical density of planktonic cultures of thermophilic bacilli. Anoxybacillus flavithermus E16 and Geobacillus sp. strain F75 (milk powder manufacturing plant isolates) and A. flavithermus DSM 2641 and G. thermoleovorans DSM 5366 were studied. Ca2+ and Mg2+ were associated with increases in optical density more so than Na+ and K+. Overall, it appeared that Ca2+ and/or Mg2+ was required for the production of protein in thermophilic bacilli, as shown by results obtained with A. flavithermus E16, which was selected for further study.
PMCID: PMC3302610  PMID: 22287005
5.  Experimental Simulation of Evaporation-Driven Silica Sinter Formation and Microbial Silicification in Hot Spring Systems 
Astrobiology  2013;13(2):163-176.
Evaporation of silica-rich geothermal waters is one of the main abiotic drivers of the formation of silica sinters around hot springs. An important role in sinter structural development is also played by the indigenous microbial communities, which are fossilized and eventually encased in the silica matrix. The combination of these two factors results in a wide variety of sinter structures and fabrics. Despite this, no previous experimental fossilization studies have focused on evaporative-driven silica precipitation. We present here the results of several experiments aimed at simulating the formation of sinters through evaporation. Silica solutions at different concentrations were repeatedly allowed to evaporate in both the presence and absence of the cyanobacterium Synechococcus elongatus. Without microorganisms, consecutive silica additions led to the formation of well-laminated deposits. By contrast, when microorganisms were present, they acted as reactive surfaces for heterogeneous silica particle nucleation; depending on the initial silica concentration, the deposits were then either porous with a mixture of silicified and unmineralized cells, or they formed a denser structure with a complete entombment of the cells by a thick silica crust. The deposits obtained experimentally showed numerous similarities in terms of their fabric to those previously reported for natural hot springs, demonstrating the complex interplay between abiotic and biotic processes during silica sinter growth. Key Words: Silica—Cyanobacteria—Fossilization—Hot springs—Stromatolites. Astrobiology 13, 163–176.
PMCID: PMC3582282  PMID: 23384170
6.  Draft Genome Sequence of a Thermophilic Member of the Bacillaceae, Anoxybacillus flavithermus Strain Kn10, Isolated from the Kan-nawa Hot Spring in Japan 
Genome Announcements  2013;1(3):e00311-13.
Here, we report the draft genome sequence of the Anoxybacillus flavithermus Kn10 strain (NBRC 109594), isolated from a water drain of the Kan-nawa Hot Spring in Japan. The draft genome sequence is composed of 90 contigs for 2,772,624 bp with 41.6% G+C content and contains 2,883 protein-coding genes and 80 tRNA genes.
PMCID: PMC3668014  PMID: 23723406
7.  Preconditioning with Cations Increases the Attachment of Anoxybacillus flavithermus and Geobacillus Species to Stainless Steel 
Applied and Environmental Microbiology  2013;79(13):4186-4190.
Preconditioning of Anoxybacillus flavithermus E16 and Geobacillus sp. strain F75 with cations prior to attachment often significantly increased (P ≤ 0.05) the number of viable cells that attached to stainless steel (by up to 1.5 log CFU/cm2) compared with unconditioned bacteria. It is proposed that the transition of A. flavithermus and Geobacillus spp. from milk formulations to stainless steel product contact surfaces in milk powder manufacturing plants is mediated predominantly by bacterial physiological factors (e.g., surface-exposed adhesins) rather than the concentrations of cations in milk formulations surrounding bacteria.
PMCID: PMC3697576  PMID: 23645192
8.  Draft Genome Sequence of the Thermophilic Bacterium Anoxybacillus kamchatkensis G10 
Journal of Bacteriology  2012;194(23):6684-6685.
Anoxybacillus kamchatkensis G10 is a spore-forming thermophilic bacterium isolated from a hot spring in Indonesia. Here, we report the draft genome sequence of A. kamchatkensis G10 that may reveal insights into aerobic/anaerobic metabolisms and carbon utilization in moderate thermophiles.
PMCID: PMC3497483  PMID: 23144421
9.  The Use of Amino Sugars by Bacillus subtilis: Presence of a Unique Operon for the Catabolism of Glucosamine 
PLoS ONE  2013;8(5):e63025.
B. subtilis grows more rapidly using the amino sugar glucosamine as carbon source, than with N-acetylglucosamine. Genes for the transport and metabolism of N-acetylglucosamine (nagP and nagAB) are found in all the sequenced Bacilli (except Anoxybacillus flavithermus). In B. subtilis there is an additional operon (gamAP) encoding second copies of genes for the transport and catabolism of glucosamine. We have developed a method to make multiple deletion mutations in B. subtilis employing an excisable spectinomycin resistance cassette. Using this method we have analysed the contribution of the different genes of the nag and gam operons for their role in utilization of glucosamine and N-acetylglucosamine. Faster growth on glucosamine is due to the presence of the gamAP operon, which is strongly induced by glucosamine. Although the gamA and nagB genes encode isozymes of GlcN6P deaminase, catabolism of N-acetylglucosamine relies mostly upon the gamA gene product. The genes for use of N-acetylglucosamine, nagAB and nagP, are repressed by YvoA (NagR), a GntR family regulator, whose gene is part of the nagAB yvoA(nagR) operon. The gamAP operon is repressed by YbgA, another GntR family repressor, whose gene is expressed divergently from gamAP. The nagAB yvoA synton is found throughout the Bacilli and most firmicutes. On the other hand the ybgA-gamAP synton, which includes the ybgB gene for a small protein of unknown provenance, is only found in B. subtilis (and a few very close relatives). The origin of ybgBA-gamAP grouping is unknown but synteny analysis suggests lateral transfer from an unidentified donor. The presence of gamAP has enabled B. subtilis to efficiently use glucosamine as carbon source.
PMCID: PMC3648570  PMID: 23667565
10.  The genetic diversity of genus Bacillus and the related genera revealed by 16s rRNA gene sequences and ardra analyses isolated from geothermal regions of turkey 
Brazilian Journal of Microbiology  2012;43(1):309-324.
Previously isolated 115 endospore-forming bacilli were basically grouped according to their temperature requirements for growth: the thermophiles (74%), the facultative thermophiles (14%) and the mesophiles (12%). These isolates were taken into 16S rRNA gene sequence analyses, and they were clustered among the 7 genera: Anoxybacillus, Aeribacillus, Bacillus, Brevibacillus, Geobacillus, Paenibacillus, and Thermoactinomycetes. Of these bacilli, only the thirty two isolates belonging to genera Bacillus (16), Brevibacillus (13), Paenibacillus (1) and Thermoactinomycetes (2) were selected and presented in this paper. The comparative sequence analyses revealed that the similarity values were ranged as 91.4–100 %, 91.8- 99.2 %, 92.6- 99.8 % and 90.7 - 99.8 % between the isolates and the related type strains from these four genera, respectively. Twenty nine of them were found to be related with the validly published type strains. The most abundant species was B. thermoruber with 9 isolates followed by B. pumilus (6), B. lichenformis (3), B. subtilis (3), B. agri (3), B. smithii (2), T. vulgaris (2) and finally P. barengoltzii (1). In addition, isolates of A391a, B51a and D295 were proposed as novel species as their 16S rRNA gene sequences displayed similarities ≤ 97% to their closely related type strains. The AluI-, HaeIII- and TaqI-ARDRA results were in congruence with the 16S rRNA gene sequence analyses. The ARDRA results allowed us to differentiate these isolates, and their discriminative restriction fragments were able to be determined. Some of their phenotypic characters and their amylase, chitinase and protease production were also studied and biotechnologically valuable enzyme producing isolates were introduced in order to use in further studies.
PMCID: PMC3768990  PMID: 24031834
isolation; temperature requirement; endospore-forming bacilli; 16S rRNA gene; ARDRA
11.  Multiparticle Sintering Dynamics: From Fractal-Like Aggregates to Compact Structures 
Multiparticle sintering is encountered in almost all high temperature processes for material synthesis (titania, silica, and nickel) and energy generation (e.g., fly ash formation) resulting in aggregates of primary particles (hard- or sinter-bonded agglomerates). This mechanism of particle growth is investigated quantitatively by mass and energy balances during viscous sintering of amorphous aerosol materials (e.g., SiO2 and polymers) that typically have a distribution of sizes and complex morphology. This model is validated at limited cases of sintering between two (equally or unequally sized) particles, and chains of particles. The evolution of morphology, surface area and radii of gyration of multiparticle aggregates are elucidated for various sizes and initial fractal dimension. For each of these structures that had been generated by diffusion limited (DLA), cluster–cluster (DLCA), and ballistic particle–cluster agglomeration (BPCA) the surface area evolution is monitored and found to scale differently than that of the radius of gyration (moment of inertia). Expressions are proposed for the evolution of fractal dimension and the surface area of aggregates undergoing viscous sintering. These expressions are important in design of aerosol processes with population balance equations (PBE) and/or fluid dynamic simulations for material synthesis or minimization and even suppression of particle formation.
PMCID: PMC3569621  PMID: 21488641
12.  Anoxybacillus suryakundensis sp. nov, a Moderately Thermophilic, Alkalitolerant Bacterium Isolated from Hot Spring at Jharkhand, India 
PLoS ONE  2013;8(12):e85493.
Four closely related facultative anaerobe, moderately thermophilic, Gram positive rods (JS1T, JS5, JS11, and JS15) were isolated from sediment samples from a hot spring at Suryakund, Jharkhand, India. Colonies were pale yellow, rough surface with uneven edges on TSA after 72 h incubation. Heterotrophic growth was observed at 40-60°C and pH 5.5-11.5; optimum growth occurred at 55°C and pH 7.5. 16S rRNA gene sequence analysis revealed the strains belong to genus Anoxybacillus. DNA-DNA homology values among strains were above 70% and showed distinct ERIC and REP PCR profile. On the basis of morphology and biochemical characteristics, strain JS1T was studied further. Strain JS1T showed 99.30% sequence similarity with A. flavithermus subsp. yunnanensis, 99.23% with A. mongoliensis, 99.16% with A. eryuanensis, 98.74% with A. flavithermus subsp. flavithermus, 98.54% with A. tengchongensis, 98.51% with A. pushchinoensis, 97.91% with A. thermarum, 97.82% with A. kaynarcensis, 97.77% with A. ayderensis and A. kamchatkensis, 97.63% with A. salavatliensis, 97.55% with A. kestanbolensis, 97.48% with A. contaminans, 97.27% with A. gonensis and 97.17% with A. voinovskiensis. In 16S rRNA secondary structure based phylogenetic comparison, strain JS1T was clustered with Anoxybacillus eryuanensis, A. mongoliensis, and A. flavithermus subsp. yunnanensis and showed 15 species specific base substitutions with maximum variability in helix 6. Moreover, DNA-DNA relatedness between JS1T and the closely related type strains were well below 70%. The DNA G+C content was 42.1 mol%. The major fatty acids were C15:0 iso, C16:0 iso and C17:0iso. The polar lipids were a phosphatidylgylycerol, a diphosphatidylglycerol, a phosphatidylethnolamine, a phosphatidylcholine, a phosphatidyl monomethylethanolamine and four unknown lipids. Based on polyphasic approach, strain JS1T represent a novel species of the genus Anoxybacillus for which Anoxybacillus suryakundensis sp. nov. is proposed. The type strain is JS1T (= DSM 27374T = LMG 27616T =JCM19211T).
PMCID: PMC3869905  PMID: 24376881
13.  Stimulation of Expression of a Silica-Induced Protein (Sip) in Thermus thermophilus by Supersaturated Silicic Acid▿  
The effects of silicic acid on the growth of Thermus thermophilus TMY, an extreme thermophile isolated from a siliceous deposit formed from geothermal water at a geothermal power plant in Japan, were examined at 75°C. At concentrations higher than the solubility of amorphous silica (400 to 700 ppm SiO2), a silica-induced protein (Sip) was isolated from the cell envelope fraction of log-phase TMY cells grown in the presence of supersaturated silicic acid. Two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed the molecular mass and pI of Sip to be about 35 kDa and 9.5, respectively. Induction of Sip expression occurred within 1 h after the addition of a supersaturating concentration of silicic acid to TM broth. Expression of Sip-like proteins was also observed in other thermophiles, including T. thermophilus HB8 and Thermus aquaticus YT-1. The amino acid sequence of Sip was similar to that of the predicted solute-binding protein of the Fe3+ ABC transporter in T. thermophilus HB8 (locus tag, TTHA1628; GenBank accession no. NC_006461; GeneID, 3169376). The sip gene (987-bp) product showed 87% identity with the TTHA1628 product and the presumed Fe3+-binding protein of T. thermophilus HB27 (locus tag TTC1264; GenBank accession no. NC_005835; GeneID, 2774619). Within the genome, sip is situated as a component of the Fbp-type ABC transporter operon, which contains a palindromic structure immediately downstream of sip. This structure is conserved in other T. thermophilus genomes and may function as a terminator that causes definitive Sip expression in response to silica stress.
PMCID: PMC2675196  PMID: 19233950
14.  Abiotic and Microbiotic Factors Controlling Biofilm Formation by Thermophilic Sporeformers 
Applied and Environmental Microbiology  2013;79(18):5652-5660.
One of the major concerns in the production of dairy concentrates is the risk of contamination by heat-resistant spores from thermophilic bacteria. In order to acquire more insight in the composition of microbial communities occurring in the dairy concentrate industry, a bar-coded 16S amplicon sequencing analysis was carried out on milk, final products, and fouling samples taken from dairy concentrate production lines. The analysis of these samples revealed the presence of DNA from a broad range of bacterial taxa, including a majority of mesophiles and a minority of (thermophilic) spore-forming bacteria. Enrichments of fouling samples at 55°C showed the accumulation of predominantly Brevibacillus and Bacillus, whereas enrichments at 65°C led to the accumulation of Anoxybacillus and Geobacillus species. Bacterial population analysis of biofilms grown using fouling samples as an inoculum indicated that both Anoxybacillus and Geobacillus preferentially form biofilms on surfaces at air-liquid interfaces rather than on submerged surfaces. Three of the most potent biofilm-forming strains isolated from the dairy factory industrial samples, including Geobacillus thermoglucosidans, Geobacillus stearothermophilus, and Anoxybacillus flavithermus, have been characterized in detail with respect to their growth conditions and spore resistance. Strikingly, Geobacillus thermoglucosidans, which forms the most thermostable spores of these three species, is not able to grow in dairy intermediates as a pure culture but appears to be dependent for growth on other spoilage organisms present, probably as a result of their proteolytic activity. These results underscore the importance of abiotic and microbiotic factors in niche colonization in dairy factories, where the presence of thermophilic sporeformers can affect the quality of end products.
PMCID: PMC3754176  PMID: 23851093
15.  Nanosilica coating for bonding improvements to zirconia 
Resin bonding to zirconia cannot be established from standard methods that are currently utilized in conventional silica-based dental ceramics. The solution–gelatin (sol–gel) process is a well developed silica-coating technique used to modify the surface of nonsilica-based ceramics. Here, we use this technique to improve resin bonding to zirconia, which we compared to zirconia surfaces treated with alumina sandblasting and tribochemical silica coating. We used the shear bond strength test to examine the effect of the various coatings on the short-term resin bonding of zirconia. Furthermore, we employed field emission scanning electron microscopy, energy-dispersive X-ray spectroscopy, atomic force microscopy, and Fourier transform infrared spectroscopy to characterize the zirconia surfaces. Water–mist spraying was used to evaluate the durability of the coatings. To evaluate the biological safety of the experimental sol–gel silica coating, we conducted an in vitro Salmonella typhimurium reverse mutation assay (Ames mutagenicity test), cytotoxicity tests, and in vivo oral mucous membrane irritation tests. When compared to the conventional tribochemical silica coating, the experimental sol–gel silica coating provided the same shear bond strength, higher silicon contents, and better durability. Moreover, we observed no apparent mutagenicity, cytotoxicity, or irritation in this study. Therefore, the sol–gel technique represents a promising method for producing silica coatings on zirconia.
PMCID: PMC3810896  PMID: 24179333
zirconia; bond; silica coating; tribochemical silica coating; biocompatibility
16.  Draft Genome Sequence of an Anaerobic and Extremophilic Bacterium, Caldanaerobacter yonseiensis, Isolated from a Geothermal Hot Stream 
Genome Announcements  2013;1(6):e00923-13.
Caldanaerobacter yonseiensis is a strictly anaerobic, thermophilic, spore-forming bacterium, which was isolated from a geothermal hot stream in Indonesia. This bacterium utilizes xylose and produces a variety of proteases. Here, we report the draft genome sequence of C. yonseiensis, which reveals insights into the pentose phosphate pathway and protein degradation metabolism in thermophilic microorganisms.
PMCID: PMC3820782  PMID: 24201201
17.  Design of Controlled Release Non-erodible Polymeric Matrix Tablet Using Microwave Oven-assisted Sintering Technique 
The objective of the present study was to evaluate the effect of sintering condition on matrix formation and subsequent drug release from polymer matrix tablet for controlled release. The present study highlights the use of a microwave oven for the sintering process in order to achieve more uniform heat distribution with reduction in time required for sintering. We could achieve effective sintering within 8 min which is very less compared to conventional hot air oven sintering. The tablets containing the drug (propranolol hydrochloride) and sintering polymer (eudragit S-100) were prepared and kept in a microwave oven at 540 watt, 720 watt and 900 watt power for different time periods for sintering. The sintered tablets were evaluated for various tablet characteristics including dissolution study. Tablets sintered at 900 watt power for 8 min gave better dissolution profile compared to others. We conclude that microwave oven sintering is better than conventional hot air oven sintering process in preparation of controlled release tablets.
PMCID: PMC3159269  PMID: 21897655
Controlled release; eudragit S100; sintering
18.  Quantitative determination of minerals and anthropogenic particles in some Polish peat occurrences using a novel SEM point-counting method 
A method is proposed for determining the mineral composition of peat using scanning electron microscope. In an illustrative example, five groups of particles occurring in amounts of >0.05 % are distinguished in peat from Puścizna Mała bog in the Carpathian foreland, Poland. These are spheroidal aluminosilicate particles (SAP), feldspars, nondescript aluminosilicates (mainly clays), silica (quartz and opaline silica), and Fe(hydro)oxides. Two more site-specific groups (barite and ZnS) are distinguished in highly polluted fens (Bagno Bruch and Bagno Mikołeska) near a zinc smelter in Upper Silesia. At Bagno Bruch, peat contents of predominantly authigenic ZnS microspheroids range up to 1.1 %. SAP originating from coal-burning power stations account for maximum concentrations of <21–39 % of the inorganic fraction in the studied mires. SAP concentrations vary with depth, and mean spheroid diameters with distance from emission sources. A distinct feature of SAP is their common enrichment in Ti what questions the use of Ti as a proxy for soil dust in fly ash polluted bogs. As amounts of anthropogenic magnetic spherules, less abundant than SAP in all mires, relate to water table level position, they are unsuitable as tracers of air pollution. The proposed method is recommended for application with peats having ash contents > ~4 %.
PMCID: PMC3939010  PMID: 24442577
Peat; Dust deposition; SEM; Fly ash particles; Minerals
19.  Chemically Etched Open Tubular and Monolithic Emitters for Nanoelectrospray Ionization Mass Spectrometry 
Analytical chemistry  2006;78(22):7796-7801.
We have developed a new procedure for fabricating fused silica emitters for electrospray ionization-mass spectrometry (ESI-MS) in which the end of a bare fused silica capillary is immersed into aqueous hydrofluoric acid, and water is pumped through the capillary to prevent etching of the interior. Surface tension causes the etchant to climb the capillary exterior, and the etch rate in the resulting meniscus decreases as a function of distance from the bulk solution. Etching continues until the silica touching the hydrofluoric acid reservoir is completely removed, essentially stopping the etch process. The resulting emitters have no internal taper, making them much less prone to clogging compared to e.g. pulled emitters. The high aspect ratios and extremely thin walls at the orifice facilitate very low flow rate operation; stable ESI-MS signals were obtained for model analytes from 5-μm-diameter emitters at a flow rate of 5 nL/min with a high degree of inter-emitter reproducibility. In extensive evaluation, the etched emitters were found to enable approximately four times as many LC-MS analyses of proteomic samples before failing compared with conventional pulled emitters. The fabrication procedure was also employed to taper the ends of polymer monolith-containing silica capillaries for use as ESI emitters. In contrast to previous work, the monolithic material protrudes beyond the fused silica capillaries, improving the monolith-assisted electrospray process.
PMCID: PMC1769309  PMID: 17105173
20.  Draft genome sequence of Caminibacter mediatlanticus strain TB-2T, an epsilonproteobacterium isolated from a deep-sea hydrothermal vent 
Standards in Genomic Sciences  2011;5(1):135-143.
Caminibacter mediatlanticus strain TB-2T [1], is a thermophilic, anaerobic, chemolithoautotrophic bacterium, isolated from the walls of an active deep-sea hydrothermal vent chimney on the Mid-Atlantic Ridge and the type strain of the species. C. mediatlanticus is a Gram-negative member of the Epsilonproteobacteria (order Nautiliales) that grows chemolithoautotrophically with H2 as the energy source and CO2 as the carbon source. Nitrate or sulfur is used as the terminal electron acceptor, with resulting production of ammonium and hydrogen sulfide, respectively. In view of the widespread distribution, importance and physiological characteristics of thermophilic Epsilonproteobacteria in deep-sea geothermal environments, it is likely that these organisms provide a relevant contribution to both primary productivity and the biogeochemical cycling of carbon, nitrogen and sulfur at hydrothermal vents. Here we report the main features of the genome of C. mediatlanticus strain TB-2T.
PMCID: PMC3236049  PMID: 22180817
Epsilonproteobacteria; thermophiles; free-living; anaerobes; chemolithoautotrophy; Nautiliales; deep-sea hydrothermal vent
21.  Controlled synthesis and tunable properties of ultrathin silica nanotubes through spontaneous polycondensation on polyamine fibrils 
This paper describes a facile approach to a biomimetic rapid fabrication of ultrathin silica nanotubes with a highly uniform diameter of 10 nm and inner hollow of around 3 nm. The synthesis is carried out through a spontaneous polycondensation of alkoxysilane on polyamine crystalline fibrils that were conveniently produced from the neutralization of a solution of protonated linear polyethyleneimine (LPEI–H+) by alkali compounds. A simple mixing the fibrils with alkoxysilane in aqueous solution allowed for the rapid formation of silica to produce LPEI@silica hybrid nanotubes. These 10-nm nanotubes were hierarchically organized in a mat-like morphology with a typical size of 1–2 micrometers. The subsequent removal of organic LPEI via calcination resulted in silica nanotubes that keep this morphology. The morphology, the structure, the pore properties and the formation mechanism of the silica nanotubes were carefully investigated with scanning electron microscopy (SEM), transmission electron microscopy (TEM), Brunauer–Emmett–Teller measurements (BET), and X-ray diffraction (XRD). Detailed studies demonstrated that the formation of the nanotubes depends on the molar ratio of [OH]/[CH2CH2NH] during the neutralization as well as on the basicity of the alkali compound and on the concentration of the silica source. The synthesis of silica nanotubes established here could be easily applied to a fabrication on the kilogram scale. Silica nanotubes that were obtained from the calcination of hybrid nanotubes of LPEI@silica in an N2 atmosphere showed a distinct photoluminescence centered at 540 nm with a maximum excitation wavelength of 320 nm. Furthermore, LPEI@silica hybrid nanotubes were applied to create silica–carbon composite nanotubes by alternative adsorption of ionic polymers and subsequent carbonization.
PMCID: PMC3869340  PMID: 24367748
biomimetic silicification; polyethyleneimine; silica–carbon nanocomposite; silica nanotubes; template synthesis
22.  Effect of mesoporous silica under Neisseria meningitidis transformation process: environmental effects under meningococci transformation 
This study aimed the use of mesoporous silica under the naturally transformable Neisseria meningitidis, an important pathogen implicated in the genetic horizontal transfer of DNA causing a escape of the principal vaccination measures worldwide by the capsular switching process. This study verified the effects of mesoporous silica under N. meningitidis transformation specifically under the capsular replacement.
we used three different mesoporous silica particles to verify their action in N. meningitis transformation frequency.
we verified the increase in the capsular gene replacement of this bacterium with the three mesoporous silica nanoparticles.
the mesouporous silica particles were capable of increasing the capsule replacement frequency in N. meningitidis.
PMCID: PMC3152511  PMID: 21787408
23.  S-layer templated bioinspired synthesis of silica 
The current understanding of the molecular mechanisms involved in the bioinspired formation of silica structures laid foundation for investigating the potential of the S-layer protein SbpA from Lysinibacillus sphaericus CCM 2177 as catalyst, template and scaffold for the generation of novel silica architectures. SbpA reassembles into monomolecular lattices with square (p4) lattice symmetry and a lattice constant of 13.1 nm. Silica layers on the S-layer lattice were formed using tetramethoxysilane (TMOS) and visualized by transmission electron microscopy. In situ quartz crystal microbalance with dissipation monitoring (QCM-D) measurements showed the adsorption of silica in dependence on the presence of phosphate in the silicate solution and on the preceding chemical modification of the S-layer. An increased amount of precipitated silica could be observed when K2HPO4/KH2PO4 was present in the solution (pH 7.2). Further on, independent of the presence of phosphate the silica deposition was higher on S-layer lattices upon activation of their carboxyl groups with 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC) compared to native S-layers or EDC treated S-layers when the activated carboxyl groups were blocked with ethylene diamine (EDA). Fourier transform infrared attenuated total reflectance (FTIR-ATR) spectroscopy revealed the formation of an amorphous silica gel (SiO2)x·yH2O on the S-layer. The silica surface concentrations on the S-layer was 4 × 10−9 to 2 × 10−8 mol cm−2 depending on the modification of the protein layer and corresponded to 4–21 monolayers of SiO2.
PMCID: PMC2930811  PMID: 19853422
S-layer; Silica; Precipitation; Nanostructure; QCM-D; FTIR-ATR
24.  Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia 
Biology Direct  2008;3:26.
The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the Verrucomicrobia, strain V4, isolated from the Hell's Gate geothermal area in New Zealand. Similar organisms were independently isolated from geothermal systems in Italy and Russia.
We report the complete genome sequence of strain V4, the first one from a representative of the Verrucomicrobia. Isolate V4, initially named "Methylokorus infernorum" (and recently renamed Methylacidiphilum infernorum) is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of M. infernorum was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C1-utilization pathways compared to other known methylotrophs. The M. infernorum genome does not encode tubulin, which was previously discovered in bacteria of the genus Prosthecobacter, or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the M. infernorum lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of M. infernorum shows apparent adaptations for existence under extremely acidic conditions including a major upward shift in the isoelectric points of proteins.
The results of genome analysis of M. infernorum support the monophyly of the PVC superphylum. M. infernorum possesses a streamlined genome but seems to have acquired numerous genes including those for enzymes of methylotrophic pathways via horizontal gene transfer, in particular, from Proteobacteria.
This article was reviewed by John A. Fuerst, Ludmila Chistoserdova, and Radhey S. Gupta.
PMCID: PMC2474590  PMID: 18593465
25.  H2-induced copper and silver nanoparticle precipitation inside sol-gel silica optical fiber preforms 
Nanoscale Research Letters  2012;7(1):487.
Ionic copper- or silver-doped dense silica rods have been prepared by sintering sol-gel porous silica xerogels doped with ionic precursors. The precipitation of Cu or Ag nanoparticles was achieved by heat treatment under hydrogen followed by annealing under air atmosphere. The surface plasmon resonance bands of copper and silver nanoparticles have been clearly observed in the absorption spectra. The spectral positions of these bands were found to depend slightly on the particle size, which could be tuned by varying the annealing conditions. Hence, transmission electron microscopy showed the formation of spherical copper nanoparticles with diameters in the range of 3.3 to 5.6 nm. On the other hand, in the case of silver, both spherical nanoparticles with diameters in the range of 3 to 6 nm and nano-rods were obtained.
PMCID: PMC3462116  PMID: 22937818
copper nanoparticles; silver nanoparticles; surface plasmon resonance; sol-gel process; dense silica preforms.

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