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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.
doi:10.1371/journal.pone.0090549
PMCID: PMC3948429  PMID: 24603481
2.  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.
doi:10.1128/AEM.00949-13
PMCID: PMC3754176  PMID: 23851093
3.  Changes in Sodium, Calcium, and Magnesium Ion Concentrations That Inhibit Geobacillus Biofilms Have No Effect on Anoxybacillus flavithermus Biofilms 
Applied and Environmental Microbiology  2015;81(15):5115-5122.
This study investigated the effects of varied sodium, calcium, and magnesium concentrations in specialty milk formulations on biofilm formation by Geobacillus spp. and Anoxybacillus flavithermus. The numbers of attached viable cells (log CFU per square centimeter) after 6 to 18 h of biofilm formation by three dairy-derived strains of Geobacillus and three dairy-derived strains of A. flavithermus were compared in two commercial milk formulations. Milk formulation B had relatively high sodium and low calcium and magnesium concentrations compared with those of milk formulation A, but the two formulations had comparable fat, protein, and lactose concentrations. Biofilm formation by the three Geobacillus isolates was up to 4 log CFU cm−2 lower in milk formulation B than in milk formulation A after 6 to 18 h, and the difference was often significant (P ≤ 0.05). However, no significant differences (P ≤ 0.05) were found when biofilm formations by the three A. flavithermus isolates were compared in milk formulations A and B. Supplementation of milk formulation A with 100 mM NaCl significantly decreased (P ≤ 0.05) Geobacillus biofilm formation after 6 to 10 h. Furthermore, supplementation of milk formulation B with 2 mM CaCl2 or 2 mM MgCl2 significantly increased (P ≤ 0.05) Geobacillus biofilm formation after 10 to 18 h. It was concluded that relatively high free Na+ and low free Ca2+ and Mg2+ concentrations in milk formulations are collectively required to inhibit biofilm formation by Geobacillus spp., whereas biofilm formation by A. flavithermus is not impacted by typical cation concentration differences of milk formulations.
doi:10.1128/AEM.01037-15
PMCID: PMC4495209  PMID: 26002898
4.  Non-contiguous finished genome sequence of Anoxybacillus flavithermus subsp. yunnanensis type strain (E13T), a strictly thermophilic and organic solvent-tolerant bacterium 
Standards in Genomic Sciences  2014;9(3):735-743.
Anoxybacillus flavithermus subsp. yunnanensis is the only strictly thermophilic bacterium that is able to tolerate a broad range of toxic solvents at its optimal temperature of 55-60°C. The type strain E13T was isolated from water-sediment slurries collected from a hot spring. This study presents the draft genome sequence of A. flavithermus subsp. yunnanensis E13T and its annotation. The 2,838,393bp long genome (67 contigs) contains 3,035 protein-coding genes and 85 RNA genes, including 10 rRNA genes, and no plasmids. The genome information has been used to compare with the genomes from A. flavithermus subsp. flavithermus strains.
doi:10.4056/sigs.4968750
PMCID: PMC4148970  PMID: 25197458
Anoxybacillus flavithermus subsp. yunnanensis; genome; solvent tolerance; thermophile
5.  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).
doi:10.1371/journal.pone.0085493
PMCID: PMC3869905  PMID: 24376881
6.  Experimental Simulation of Evaporation-Driven Silica Sinter Formation and Microbial Silicification in Hot Spring Systems 
Astrobiology  2013;13(2):163-176.
Abstract
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.
doi:10.1089/ast.2012.0887
PMCID: PMC3582282  PMID: 23384170
7.  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.
doi:10.5402/2012/517524
PMCID: PMC3671716  PMID: 23762752
8.  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.
doi:10.1128/AEM.06951-11
PMCID: PMC3302610  PMID: 22287005
9.  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.
doi:10.1128/genomeA.00010-13
PMCID: PMC3587922  PMID: 23469333
10.  Chemolithoautotrophic arsenite oxidation by a thermophilic Anoxybacillus flavithermus strain TCC9-4 from a hot spring in Tengchong of Yunnan, China 
A new facultative chemolithoautotrophic arsenite (AsIII)-oxidizing bacterium TCC9-4 was isolated from a hot spring microbial mat in Tengchong of Yunnan, China. This strain could grow with AsIII as an energy source, CO2–HCO3- as a carbon source and oxygen as the electron acceptor in a minimal salts medium. Under chemolithoautotrophic conditions, more than 90% of 100 mg/L AsIII could be oxidized by the strain TCC9-4 in 36 h. Temperature was an important environmental factor that strongly influenced the AsIII oxidation rate and AsIII oxidase (Aio) activity; the highest Aio activity was found at the temperature of 40∘C. Addition of 0.01% yeast extract enhanced the growth significantly, but delayed the AsIII oxidation. On the basis of 16S rRNA phylogenetic sequence analysis, strain TCC9-4 was identified as Anoxybacillus flavithermus. To our best knowledge, this is the first report of arsenic (As) oxidation by A. flavithermus. The Aio gene in TCC9-4 might be quite novel relative to currently known gene sequences. The results of this study expand our current understanding of microbially mediated As oxidation in hot springs.
doi:10.3389/fmicb.2015.00360
PMCID: PMC4422093  PMID: 25999920
arsenite oxidation; Anoxybacillus; temperature; hot springs; Tengchong
11.  Isolation, Characterization, and Identification of Bacterial Contaminants in Semifinal Gelatin Extracts 
Bacterial contamination of gelatin is of great concern. Indeed, this animal colloid has many industrial applications, mainly in food and pharmaceutical products. In a previous study (E. De Clerck and P. De Vos, Syst. Appl. Microbiol. 25:611-618), contamination of a gelatin production process with a variety of gram-positive and gram-negative bacteria was demonstrated. In this study, bacterial contamination of semifinal gelatin extracts from several production plants was examined. Since these extracts are subjected to harsh conditions during production and a final ultrahigh-temperature treatment, the bacterial load at this stage is expected to be greatly reduced. In total, 1,129 isolates were obtained from a total of 73 gelatin batches originating from six different production plants. Each of these batches was suspected of having bacterial contamination based on quality control testing at the production plant from which it originated. For characterization and identification of the 1,129 bacterial isolates, repetitive-element PCR was used to obtain manageable groups. Representative strains were identified by means of 16S rRNA genesequencing, species-specific gyrB PCR, and gyrA and rpoB sequencing and were tested for gelatinase activity. The majority of isolates belonged to members of Bacillus or related endospore-forming genera. Representative strains were identified as Bacillus cereus, Bacillus coagulans, Bacillus fumarioli, Bacillus amyloliquefaciens, Bacillus licheniformis, Bacillus pumilus, Bacillus sonorensis, Bacillus subtilis, Bacillus gelatini, Bacillus thermoamylovorans, Anoxybacillus contaminans, Anoxybacillus flavithermus, Brevibacillus agri, Brevibacillus borstelensis, and Geobacillus stearothermophilus. The majority of these species include strains exhibiting gelatinase activity. Moreover, some of these species have known pathogenic properties. These findings are of great concern with regard to the safety and quality of gelatin and its applications.
doi:10.1128/AEM.70.6.3664-3672.2004
PMCID: PMC427776  PMID: 15184171
12.  Genome Sequence of Anoxybacillus geothermalis Strain GSsed3, a Novel Thermophilic Endospore-Forming Species 
Genome Announcements  2015;3(3):e00575-15.
Anoxybacillus geothermalis strain GSsed3 is an endospore-forming thermophilic bacterium isolated from filter deposits in a geothermal site. This novel species has a larger genome size (7.2 Mb) than that of any other Anoxybacillus species, and it possesses genes that support its phenotypic metabolic characterization and suggest an intriguing link to metals.
doi:10.1128/genomeA.00575-15
PMCID: PMC4463517  PMID: 26067952
13.  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.
doi:10.1128/AEM.00462-13
PMCID: PMC3697576  PMID: 23645192
14.  Genome sequence of Anoxybacillus ayderensis AB04T isolated from the Ayder hot spring in Turkey 
Species of Anoxybacillus are thermophiles and, therefore, their enzymes are suitable for many biotechnological applications. Anoxybacillus ayderensis AB04T (= NCIMB 13972T = NCCB 100050T) was isolated from the Ayder hot spring in Rize, Turkey, and is one of the earliest described Anoxybacillus type strains. The present work reports the cellular features of A. ayderensis AB04T, together with a high-quality draft genome sequence and its annotation. The genome is 2,832,347 bp long (74 contigs) and contains 2,895 protein-coding sequences and 103 RNA genes including 14 rRNAs, 88 tRNAs, and 1 tmRNA. Based on the genome annotation of strain AB04T, we identified genes encoding various glycoside hydrolases that are important for carbohydrate-related industries, which we compared with those of other, sequenced Anoxybacillus spp. Insights into under-explored industrially applicable enzymes and the possible applications of strain AB04T were also described.
doi:10.1186/s40793-015-0065-2
PMCID: PMC4584021  PMID: 26413199
Anoxybacillus; Bacillaceae; Bacillus; Geobacillus; Glycoside hydrolase; Thermophile
15.  Control of silicification by genetically engineered fusion proteins: Silk–silica binding peptides 
Acta biomaterialia  2014;15:173-180.
In the present study, an artificial spider silk gene, 6mer, derived from the consensus sequence of Nephila clavipes dragline silk gene, was fused with different silica-binding peptides (SiBPs), A1, A3 and R5, to study the impact of the fusion protein sequence chemistry on silica formation and the ability to generate a silk–silica composite in two different bioinspired silicification systems: solution–solution and solution– solid. Condensed silica nanoscale particles (600–800 nm) were formed in the presence of the recombinant silk and chimeras, which were smaller than those formed by 15mer-SiBP chimeras [1], revealing that the molecular weight of the silk domain correlated to the sizes of the condensed silica particles in the solution system. In addition, the chimeras (6mer-A1/A3/R5) produced smaller condensed silica particles than the control (6mer), revealing that the silica particle size formed in the solution system is controlled by the size of protein assemblies in solution. In the solution–solid interface system, silicification reactions were performed on the surface of films fabricated from the recombinant silk proteins and chimeras and then treated to induce β-sheet formation. A higher density of condensed silica formed on the films containing the lowest β-sheet content while the films with the highest β-sheet content precipitated the lowest density of silica, revealing an inverse correlation between the β-sheet secondary structure and the silica content formed on the films. Intriguingly, the 6mer-A3 showed the highest rate of silica condensation but the lowest density of silica deposition on the films, compared with 6mer-A1 and -R5, revealing antagonistic crosstalk between the silk and the SiBP domains in terms of protein assembly. These findings offer a path forward in the tailoring of biopolymer–silica composites for biomaterial related needs.
doi:10.1016/j.actbio.2014.10.040
PMCID: PMC4331239  PMID: 25462851
Spider silk; Silica; Silicification; Fusion proteins
16.  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.
doi:10.1128/genomeA.00311-13
PMCID: PMC3668014  PMID: 23723406
17.  Draft Genome Sequence of Anoxybacillus flavithermus Strain 25, Isolated from the Garga Hot Spring in the Barguzin Valley, Baikal Region, Russian Federation 
Genome Announcements  2014;2(6):e01258-14.
Anoxybacillus flavithermus strain 25 was isolated from a sediment sample from the Garga hot spring in the Barguzin Valley, Baikal Region, Russian Federation (54°19′3.72″N, 110°59′38.4″E). The sequenced and annotated genome is 2,838,680 bp and encodes 3,009 genes.
doi:10.1128/genomeA.01258-14
PMCID: PMC4256193  PMID: 25477412
18.  Genome Sequence of Anoxybacillus flavithermus Strain AK1, a Thermophile Isolated from a Hot Spring in Saudi Arabia 
Genome Announcements  2015;3(3):e00604-15.
Anoxybacillus flavithermus strain AK1 was isolated from Al-Ain Alhara, a thermal hot spring located 50 km southeast of the city of Gazan, Saudi Arabia (16°56ʹN, 43°15ʹE). The sequenced and annotated genome is 2,630,664 bp and encodes 2,799 genes.
doi:10.1128/genomeA.00604-15
PMCID: PMC4457075  PMID: 26044438
19.  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.
doi:10.1371/journal.pone.0063025
PMCID: PMC3648570  PMID: 23667565
20.  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.
doi:10.1128/AEM.02387-08
PMCID: PMC2675196  PMID: 19233950
21.  Molecular phylogenetic analysis of bacterial community and characterization of Cr(VI) reducers from the sediments of Tantloi hot spring, India 
Aquatic Biosystems  2014;10:7.
Background
A geothermal ecosystem located at Tantloi, India has been found to be an interesting habitat for microbes of diverse nature. However, the microbial diversity of this habitat is poorly explored. In this study, a detailed phylogenetic study has been carried out to understand the bacterial diversity of this habitat and to identify prospective metal reducers using culture independent approach. The bacterial diversity of the sediments, which contain undetectable levels of Cr(VI), was analysed with respect to chromium reduction and the strains highly resistant to and efficiently reducing chromium under aerobic conditions were isolated and characterized.
Results
16S rRNA gene sequence analysis of Tantloi hot spring microbial community revealed a significant bacterial diversity represented by at least ten taxonomic divisions of Bacteria with clear predominance of Thermus. Similar sequence analysis of rRNA gene library clones derived from bacterial consortia enriched from sediments in presence of Cr(VI) revealed the abundance of the family Bacillaceae. Under aerobic conditions at 65°C, the consortia reduced 1 mM of Cr(VI) completely within 24 h and 5 mM in 6 days. A complete reduction of 1 mM Cr(VI) has been shown by five of our isolates within 36 h. 16S rRNA gene sequences of all the isolates showed high degree of similarity (97-99%) to Bacillaceae with ten of them being affiliated to Anoxybacillus. Crude extract as well as the soluble fraction from isolates TSB-1 and TSB-9 readily reduced Cr(VI); TSB-1 showed higher chromium reductase activity.
Conclusion
Most of the Tantloi Spring Bacterial (TSB) sequences analyzed in different taxonomic divisions could be related to representatives with known metabolic traits which indicated presence of organisms involved in redox processes of a variety of elements including iron, sulphur and chromium. Approximately 80% of the sequences obtained in this study represented novel phylotypes indicating the possibility of discovery of bacteria with biotechnologically important new biomolecules. Again, highly chromium-resistant and remarkably active Cr(VI)-reducing Anoxybacillus strains isolated in this study could serve as potential candidates for designing chromium bioremediation strategies at high temperatures and also at high chromium concentrations.
doi:10.1186/2046-9063-10-7
PMCID: PMC4168125  PMID: 25243065
Phylogenetic analysis; Bacterial community; Hot spring; Chromium reduction; Bioremediation
22.  New insight into silica deposition in horsetail (Equisetum arvense) 
BMC Plant Biology  2011;11:112.
Background
The horsetails (Equisetum sp) are known biosilicifiers though the mechanism underlying silica deposition in these plants remains largely unknown. Tissue extracts from horsetails grown hydroponically and also collected from the wild were acid-digested in a microwave oven and their silica 'skeletons' visualised using the fluor, PDMPO, and fluorescence microscopy.
Results
Silica deposits were observed in all plant regions from the rhizome through to the stem, leaf and spores. Numerous structures were silicified including cell walls, cell plates, plasmodesmata, and guard cells and stomata at varying stages of differentiation. All of the major sites of silica deposition in horsetail mimicked sites and structures where the hemicellulose, callose is known to be found and these serendipitous observations of the coincidence of silica and callose raised the possibility that callose might be templating silica deposition in horsetail. Hydroponic culture of horsetail in the absence of silicic acid resulted in normal healthy plants which, following acid digestion, showed no deposition of silica anywhere in their tissues. To test the hypothesis that callose might be templating silica deposition in horsetail commercially available callose was mixed with undersaturated and saturated solutions of silicic acid and the formation of silica was demonstrated by fluorimetry and fluorescence microscopy.
Conclusions
The initiation of silica formation by callose is the first example whereby any biomolecule has been shown to induce, as compared to catalyse, the formation of silica in an undersaturated solution of silicic acid. This novel discovery allowed us to speculate that callose and its associated biochemical machinery could be a missing link in our understanding of biosilicification.
doi:10.1186/1471-2229-11-112
PMCID: PMC3160890  PMID: 21801378
Biosilicification; biogenic silica; silicic acid; horsetails; callose; PDMPO; fluorescence; acid digestion.
23.  A High Molecular-Mass Anoxybacillus sp. SK3-4 Amylopullulanase: Characterization and Its Relationship in Carbohydrate Utilization 
An amylopullulanase of the thermophilic Anoxybacillus sp. SK3-4 (ApuASK) was purified to homogeneity and characterized. Though amylopullulanases larger than 200 kDa are rare, the molecular mass of purified ApuASK appears to be approximately 225 kDa, on both SDS-PAGE analyses and native-PAGE analyses. ApuASK was stable between pH 6.0 and pH 8.0 and exhibited optimal activity at pH 7.5. The optimal temperature for ApuASK enzyme activity was 60 °C, and it retained 54% of its total activity for 240 min at 65 °C. ApuASK reacts with pullulan, starch, glycogen, and dextrin, yielding glucose, maltose, and maltotriose. Interestingly, most of the previously described amylopullulanases are unable to produce glucose and maltose from these substrates. Thus, ApuASK is a novel, high molecular-mass amylopullulanase able to produce glucose, maltose, and maltotriose from pullulan and starch. Based on whole genome sequencing data, ApuASK appeared to be the largest protein present in Anoxybacillus sp. SK3-4. The α-amylase catalytic domain present in all of the amylase superfamily members is present in ApuASK, located between the cyclodextrin (CD)-pullulan-degrading N-terminus and the α-amylase catalytic C-terminus (amyC) domains. In addition, the existence of a S-layer homology (SLH) domain indicates that ApuASK might function as a cell-anchoring enzyme and be important for carbohydrate utilization in a streaming hot spring.
doi:10.3390/ijms140611302
PMCID: PMC3709733  PMID: 23759984
Anoxybacillus; amylase; Bacillus; Geobacillus; glycoside hydrolase 13; pullulan; pullulanase; starch; thermostable enzyme
24.  Plant growth conditions alter phytolith carbon 
Many plants, including grasses and some important human food sources, accumulate, and precipitate silica in their cells to form opaline phytoliths. These phytoliths contain small amounts of organic matter (OM) that are trapped during the process of silicification. Previous work has suggested that plant silica is associated with compounds such as proteins, lipids, lignin, and carbohydrate complexes. It is not known whether these compounds are cellular components passively encapsulated as the cell silicifies, polymers actively involved in the precipitation process or random compounds assimilated by the plant and discarded into a “glass wastebasket.” Here, we used Raman spectroscopy to map the distribution of OM in phytoliths, and to analyze individual phytoliths isolated from Sorghum bicolor plants grown under different laboratory treatments. Using mapping, we showed that OM in phytoliths is distributed throughout the silica and is not related to dark spots visible in light microscopy, previously assumed to be the repository for phytolith OM. The Raman spectra exhibited common bands indicative of C-H stretching modes of general OM, and further more diagnostic bands consistent with carbohydrates, lignins, and other OM. These Raman spectra exhibited variability of spectral signatures and of relative intensities between sample treatments indicating that differing growth conditions altered the phytolith carbon. This may have strong implications for understanding the mechanism of phytolith formation, and for use of phytolith carbon isotope values in dating or paleoclimate reconstruction.
doi:10.3389/fpls.2015.00753
PMCID: PMC4585121  PMID: 26442066
phytolith; organic matter; Raman; silica; SRS; VCA
25.  Crystal structure of Anoxybacillus α-amylase provides insights into maltose binding of a new glycosyl hydrolase subclass 
Scientific Reports  2016;6:23126.
A new subfamily of glycosyl hydrolase family GH13 was recently proposed for α-amylases from Anoxybacillus species (ASKA and ADTA), Geobacillus thermoleovorans (GTA, Pizzo, and GtamyII), Bacillus aquimaris (BaqA), and 95 other putative protein homologues. To understand this new GH13 subfamily, we report crystal structures of truncated ASKA (TASKA). ASKA is a thermostable enzyme capable of producing high levels of maltose. Unlike GTA, biochemical analysis showed that Ca2+ ion supplementation enhances the catalytic activities of ASKA and TASKA. The crystal structures reveal the presence of four Ca2+ ion binding sites, with three of these binding sites are highly conserved among Anoxybacillus α-amylases. This work provides structural insights into this new GH13 subfamily both in the apo form and in complex with maltose. Furthermore, structural comparison of TASKA and GTA provides an overview of the conformational changes accompanying maltose binding at each subsite.
doi:10.1038/srep23126
PMCID: PMC4791539  PMID: 26975884

Results 1-25 (954036)