| stable sulfur isotope fractionation and discrimination between the sulfur atoms of thiosulfate during oxidation by halothiobacillus neapolitanus. | growing cultures and nongrowing suspensions of halothiobacillus neapolitanus selectively fractionated (32)s and (34)s during the oxidation of the sulfane- and sulfonate-sulfur atoms of thiosulfate. sulfate was enriched in (32)s, with delta(34)s reaching -6.3 per thousand relative to the precursor sulfonate-sulfur of thiosulfate, which was progressively resynthesized from the thiosulfate-sulfane-sulfur during thiosulfate metabolism. polythionates, principally trithionate, accumulated during thios ... | 2008 | 18373645 |
| co2 fixation kinetics of halothiobacillus neapolitanus mutant carboxysomes lacking carbonic anhydrase suggest the shell acts as a diffusional barrier for co2. | the widely accepted models for the role of carboxysomes in the carbon-concentrating mechanism of autotrophic bacteria predict the carboxysomal carbonic anhydrase to be a crucial component. the enzyme is thought to dehydrate abundant cytosolic bicarbonate and provide ribulose 1.5-bisphosphate carboxylase/oxygenase (rubisco) sequestered within the carboxysome with sufficiently high concentrations of its substrate, co(2), to permit its efficient fixation onto ribulose 1,5-bisphosphate. in this stud ... | 2008 | 18258595 |
| transcript analysis of the halothiobacillus neapolitanus cso operon. | carboxysomes are polyhedral microcompartments that sequester the co(2)-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase in many autotrophic bacteria. their protein constituents are encoded by a set of tightly clustered genes that are thought to form an operon (the cso operon). this study is the first to systematically address transcriptional regulation of carboxysome protein expression. quantification of transcript levels derived from the cso operon of halothiobacillus neapolitanus, ... | 2008 | 17899012 |
| the effect of silica fume on biodegradation of cement paste and its capacity to immobilize strontium during exposure to microbial sulfur oxidation. | the disposal of low-level radioactive waste containing isotopes such as strontium by immobilization in cement paste has become common practice. however, the stability of cement paste in the environment may be impaired by sulfuric acid produced by sulfur-oxidizing bacteria. since biodegradation rates in the environment of most radioactive waste burial sites are too low to be measured, determination of the degradation kinetics of cement paste is a difficult task. this study reports on the developm ... | 2008 | 17578671 |
| structural analysis of csos1a and the protein shell of the halothiobacillus neapolitanus carboxysome. | the carboxysome is a bacterial organelle that functions to enhance the efficiency of co2 fixation by encapsulating the enzymes ribulose bisphosphate carboxylase/oxygenase (rubisco) and carbonic anhydrase. the outer shell of the carboxysome is reminiscent of a viral capsid, being constructed from many copies of a few small proteins. here we describe the structure of the shell protein csos1a from the chemoautotrophic bacterium halothiobacillus neapolitanus. the csos1a protein forms hexameric units ... | 2007 | 17518518 |
| succession of sulfur-oxidizing bacteria in the microbial community on corroding concrete in sewer systems. | microbially induced concrete corrosion (micc) in sewer systems has been a serious problem for a long time. a better understanding of the succession of microbial community members responsible for the production of sulfuric acid is essential for the efficient control of micc. in this study, the succession of sulfur-oxidizing bacteria (sob) in the bacterial community on corroding concrete in a sewer system in situ was investigated over 1 year by culture-independent 16s rrna gene-based molecular tec ... | 2007 | 17142362 |
| structure of halothiobacillus neapolitanus carboxysomes by cryo-electron tomography. | carboxysomes are polyhedral bodies consisting of a proteinaceous shell filled with ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco). they are found in the cytoplasm of all cyanobacteria and some chemoautotrophic bacteria. previous studies of halothiobacillus neapolitanus and nitrobacter agilis carboxysomes suggest that the structures are either icosahedral or dodecahedral. to determine the protein shell structure more definitively, purified h. neapolitanus carboxysomes were re-examined ... | 2006 | 17028023 |
| inhibitory effects of sulfamic acid on three thiosulfate-oxidizing chemolithotrophs. | sulfamate is an analogue of thiosulfate, and the sodium and potassium salts of sulfamic acid inhibited the chemolithoautotrophic growth on thiosulfate of acidithiobacillus ferrooxidans and halothiobacillus neapolitanus. the chemo-organotrophic growth of paracoccus versutus on sucrose was similarly inhibited by sulfamate. thiosulfate oxidation by suspensions of h. neapolitanus was, however, unaffected by sulfamate, showing that sulfamate did not directly affect thiosulfate uptake, activation or o ... | 2006 | 17020550 |
| thiomicrospira halophila sp. nov., a moderately halophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium from hypersaline lakes. | enrichments at 2 m nacl and ph 7.5-8, with thiosulfate or sulfide as electron donor, inoculated with sediments from hypersaline chloride-sulfate lakes of the kulunda steppe (altai, russia) resulted in the domination of two different groups of moderately halophilic, chemolithoautotrophic, sulfur-oxidizing bacteria. under fully aerobic conditions with thiosulfate, bacteria belonging to the genus halothiobacillus dominated while, under microaerophilic conditions, a highly motile, short vibrio-shape ... | 2006 | 17012565 |
| characterization of the carboxysomal carbonic anhydrase csosca from halothiobacillus neapolitanus. | in cyanobacteria and many chemolithotrophic bacteria, the co(2)-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) is sequestered into polyhedral protein bodies called carboxysomes. the carboxysome is believed to function as a microcompartment that enhances the catalytic efficacy of rubisco by providing the enzyme with its substrate, co(2), through the action of the shell protein csosca, which is a novel carbonic anhydrase. in the work reported here, the biochemical properti ... | 2006 | 17012396 |
| diversity of culturable halophilic sulfur-oxidizing bacteria in hypersaline habitats. | unexpectedly high culturable diversity of moderately and extremely halophilic obligately chemolithoautotrophic sulfur-oxidizing bacteria (sob) was discovered in the sediments of various hypersaline habitats, including chloride-sulfate lakes in mongolia, russia and ukraine, a sea saltern in slovenia and a deep-sea salt brine from the mediterranean. six different groups of halophilic sob, including four new genera, all belonging to the gammaproteobacteria, were found. two groups of moderately halo ... | 2006 | 17005982 |
| the structure of beta-carbonic anhydrase from the carboxysomal shell reveals a distinct subclass with one active site for the price of two. | csosca (formerly csos3) is a bacterial carbonic anhydrase localized in the shell of a cellular microcompartment called the carboxysome, where it converts hco(3)(-) to co(2) for use in carbon fixation by ribulose-bisphosphate carboxylase/oxygenase (rubisco). csosca lacks significant sequence similarity to any of the four known classes of carbonic anhydrase (alpha, beta, gamma, or delta), and so it was initially classified as belonging to a new class, epsilon. the crystal structure of csosca from ... | 2006 | 16407248 |
| halothiobacillus neapolitanus strain oswa isolated from "the old sulphur well" at harrogate (yorkshire, england). | the "old sulphur well" has a subterranean input of water containing 5.5mm total sulfide, which would be inhibitory to the growth of most bacteria. the obligately chemolithoautotrophic halothiobacillus neapolitanus is a sulfur bacterium known to tolerate and metabolize high sulfide concentrations, and we report the isolation of h. neapolitanus strain oswa from this source. strain oswa grows well on thiosulfate and tetrathionate as energy sources, and tolerates at least 5mm sulfide. its specific g ... | 2005 | 16261864 |
| [corrosion of pipe steel samples and conjugated conversion of sulfur compounds by thiobacteria halothiobacillus neapolitanus dsm 15147]. | the kinetics of conversion of sulfur compounds by halothiobacillus neapolitanus dsm 15147 bacteria was studied in the presence of steel samples. it was shown that the presence of steel altered the known pathway of sulfur compound oxidation by thiobacteria. production of atomic hydrogen via the interaction between biogenic sulfuric acid and steel enhanced secondary production of intermediates and decreased the content of sulfate produced previously. the process was accompanied by ph elevation and ... | 2005 | 16240657 |
| thiovirga sulfuroxydans gen. nov., sp. nov., a chemolithoautotrophic sulfur-oxidizing bacterium isolated from a microaerobic waste-water biofilm. | a novel mesophilic, chemolithoautotrophic, sulfur-oxidizing bacterium, designated strain so07(t), was isolated from a microaerobic waste-water biofilm. chemolithoautotrophic growth was observed with elemental sulfur, sulfide and thiosulfate as sole electron donors and oxygen as electron acceptor. anaerobic and heterotrophic growth were not observed. nitrate was not used as a terminal electron acceptor. the optimum ph and temperature for growth were ph 7.5 and 30 degrees c, respectively. the majo ... | 2005 | 15879233 |
| accelerated biodegradation of cement by sulfur-oxidizing bacteria as a bioassay for evaluating immobilization of low-level radioactive waste. | disposal of low-level radioactive waste by immobilization in cement is being evaluated worldwide. the stability of cement in the environment may be impaired by sulfur-oxidizing bacteria that corrode the cement by producing sulfuric acid. since this process is so slow that it is not possible to perform studies of the degradation kinetics and to test cement mixtures with increased durability, procedures that accelerate the biodegradation are required. semicontinuous cultures of halothiobacillus ne ... | 2004 | 15466547 |
| isolation, characterization, and in situ detection of a novel chemolithoautotrophic sulfur-oxidizing bacterium in wastewater biofilms growing under microaerophilic conditions. | we successfully isolated a novel aerobic chemolithotrophic sulfur-oxidizing bacterium, designated strain so07, from wastewater biofilms growing under microaerophilic conditions. for isolation, the use of elemental sulfur (s(0)), which is the most abundant sulfur pool in the wastewater biofilms, as the electron donor was an effective measure to establish an enrichment culture of strain so07 and further isolation. 16s rrna gene sequence analysis revealed that newly isolated strain so07 was affilia ... | 2004 | 15128575 |
| a novel evolutionary lineage of carbonic anhydrase (epsilon class) is a component of the carboxysome shell. | a significant portion of the total carbon fixed in the biosphere is attributed to the autotrophic metabolism of prokaryotes. in cyanobacteria and many chemolithoautotrophic bacteria, co(2) fixation is catalyzed by ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco), most if not all of which is packaged in protein microcompartments called carboxysomes. these structures play an integral role in a cellular co(2)-concentrating mechanism and are essential components for autotrophic growth. here ... | 2004 | 14729686 |
| diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes from groundwater and aquifer microorganisms. | to test our hypothesis that microbial autotrophic co2 fixation plays an important role in subsurface systems of two large groundwater remediation projects, several anaerobic/microaerobic aquifer and groundwater samples were taken and used to investigate the distribution and phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) large-subunit genes. two primer sets were designed for amplifying partial-subunit genes of rubisco forms i and ii from the dna, directly extr ... | 2003 | 12704564 |
| halothiobacillus kellyi sp. nov., a mesophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium isolated from a shallow-water hydrothermal vent in the aegean sea, and emended description of the genus halothiobacillus. | a new mesophilic, chemolithoautotrophic, sulfur-oxidizing bacterium, strain milos-bii1t, was isolated from a sediment sample taken from a shallow-water hydrothermal vent in the aegean sea with thiosulfate as electron donor and co2 as carbon source. based on the almost complete sequence of the 16s rrna gene, strain milos-bii1t forms a phylogenetic cluster with thiobacillus hydrothermalis, thiobacillus neapolitanus, thiobacillus halophilus and thiobacillus sp. w5, all of which are obligately chemo ... | 2000 | 10843067 |
| identification and localization of the carboxysome peptide csos3 and its corresponding gene in thiobacillus neapolitanus. | four genes encoding carboxysome shell peptides (csos1a, csos1b, csos1c, csos2), the genes encoding the large and small subunits of rubisco (cbbl, cbbs), and three unidentified orfs constitute an operon in thiobacillus neapolitanus. an unidentified orf 1.54 kb in size is predicted from sequence analysis to encode a protein with a molecular mass of approximately 57 kda. when this orf was expressed in escherichia coli under the control of its endogenous ribosome-binding site, no peptide product was ... | 2000 | 10816046 |
| reclassification of some species of thiobacillus to the newly designated genera acidithiobacillus gen. nov., halothiobacillus gen. nov. and thermithiobacillus gen. nov. | the species of the genus 'thiobacillus' fall into the alpha-, beta- and gamma-subclasses of the proteobacteria, the type species thiobacillus thioparus being located in the beta-subclass. 'thiobacillus' species exhibit almost as much diversity in dna composition and physiology as is found collectively in all other proteobacterial groups. on the basis of physiological characters and 16s rrna gene sequence comparisons, eight of the existing thiobacillus species are proposed for reassignment to thr ... | 2000 | 10758854 |
| thiofaba tepidiphila gen. nov., sp. nov., a novel obligately chemolithoautotrophic, sulfur-oxidizing bacterium of the gammaproteobacteria isolated from a hot spring. | a novel obligately chemolithoautotrophic, sulfur-oxidizing bacterium designated strain bda453t was isolated from a hot spring in fukushima prefecture, japan. the cells were short-rod-shaped and possessed an inclusion, a gram-negative type cell wall and a single polar flagellum. strain bda453t grew by sulfur-oxidizing respiration with thiosulfate, elemental sulfur, sulfide and tetrathionate as electron donors and used only carbon dioxide as a carbon source. the optimum growth conditions were 45 d ... | 2008 | 18676474 |
| sulphide oxidation to elemental sulphur in a membrane bioreactor: performance and characterization of the selected microbial sulphur-oxidizing community. | in leather tanning industrial areas sulphide management represents a major problem. however, biological sulphide oxidation to sulphur represents a convenient solution to this problem. elemental sulphur is easy to separate and the process is highly efficient in terms of energy consumption and effluent quality. as the oxidation process is performed by specialized bacteria, selection of an appropriate microbial community is fundamental for obtaining a good yield. sulphur oxidizing bacteria (sob) re ... | 2008 | 18814984 |
| halothiobacillus neapolitanus carboxysomes sequester heterologous and chimeric rubisco species. | the carboxysome is a bacterial microcompartment that consists of a polyhedral protein shell filled with ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco), the enzyme that catalyzes the first step of co2 fixation via the calvin-benson-bassham cycle. | 2008 | 18974784 |
| methods for aligning and for averaging 3d volumes with missing data. | the visibility and resolution of a tomographic reconstruction containing multiple copies of discrete particles can be enhanced by averaging subtomograms after they are corrected aligned. however, the "missing wedge" in electron tomography can easily lead to erroneous alignment. we have explored a fourier space cross-correlation method with a proper weighting scheme to align and average different sets of volumetric data, each of which has different missing data due to the limited specimen tilts. ... | 2008 | 18299206 |
| microbial communities in subpermafrost saline fracture water at the lupin au mine, nunavut, canada. | we report the first investigation of a deep subpermafrost microbial ecosystem, a terrestrial analog for the martian subsurface. our multidisciplinary team analyzed fracture water collected at 890 and 1,130 m depths beneath a 540-m-thick permafrost layer at the lupin au mine (nunavut, canada). 14c, 3h, and noble gas isotope analyses suggest that the na-ca-cl, suboxic, fracture water represents a mixture of geologically ancient brine, approximately25-kyr-old, meteoric water and a minor modern tali ... | 2009 | 19568805 |
| phylogeny and distribution of the soxb gene among thiosulfate-oxidizing bacteria. | a pcr protocol for the detection of sulfur-oxidizing bacteria based on soxb genes that are essential for thiosulfate oxidation by sulfur-oxidizing bacteria of various phylogenetic groups which use the 'paracoccus sulfur oxidation' pathway was developed. five degenerate primers were used to specifically amplify fragments of soxb genes from different sulfur-oxidizing bacteria previously shown to oxidize thiosulfate. the pcr yielded a soxb fragment of approximately 1000 bp from most of the bacteria ... | 2001 | 11313131 |
| microbiology of a wetland ecosystem constructed to remediate mine drainage from a heavy metal mine. | a pilot passive treatment plant (pptp) was constructed to evaluate the potential of a composite wetland system to remediate acidic, metal-rich water draining the former wheal jane tin, in cornwall, england. the treatment plant consists of three separate and controllable composite systems, each of which comprises a series of aerobic wetlands for iron oxidation and precipitation, a compost bioreactor for removing chalcophilic metals and to generate alkalinity, and rock filter ponds for removing so ... | 2005 | 15680626 |
| quorum sensing in acinetobacter: an emerging pathogen. | acinetobacter is emerging as one of the major nosocomial infectious pathogens, facilitated by tolerance to desiccation and multidrug resistance. quorum sensing (autoinducer-receptor mechanism) plays role in biofilm formation in acinetobacter, though its role in regulation of other virulence factors is yet to be established. phylogenetic studies indicate that acinetobacter baumannii is closely related to burkholderia ambifaria but its quorum sensing genes (abai and abar) were acquired horizontall ... | 2010 | 20846031 |
| insights from multiple structures of the shell proteins from the beta-carboxysome. | carboxysomes are primitive bacterial organelles that function as a part of a carbon concentrating mechanism (ccm) under conditions where inorganic carbon is limiting. the carboxysome enhances the efficiency of cellular carbon fixation by encapsulating together carbonic anhydrase and the co(2)-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco). the carboxysome has a roughly icosahedral shape with an outer shell between 800 and 1500 a in diameter, which is constructed from a f ... | 2009 | 19177356 |
| the pentameric vertex proteins are necessary for the icosahedral carboxysome shell to function as a co2 leakage barrier. | carboxysomes are polyhedral protein microcompartments found in many autotrophic bacteria; they encapsulate the co(2) fixing enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) within a thin protein shell and provide an environment that enhances the catalytic capabilities of the enzyme. two types of shell protein constituents are common to carboxysomes and related microcompartments of heterotrophic bacteria, and the genes for these proteins are found in a large variety of bacteria. | 2009 | 19844578 |
| characterization of sulfide-oxidizing microbial mats developed inside a full-scale anaerobic digester employing biological desulfurization. | the microbial mats responsible for biological desulfurization from biogas in a full-scale anaerobic digester were characterized in terms of their structure, as well as their chemical and microbial properties. filament-shaped elemental sulfur 100-500-á++m in length was shown to cover the mats, which cover the entire headspace of the digester. this is the first report on filamentous sulfur production in a non-marine environment. the results of the analysis of the mats suggest that the key players ... | 2011 | 21735263 |
| The Sulfur Oxygenase Reductase from the Mesophilic Bacterium Halothiobacillus neapolitanus is a Highly Active Thermozyme. | A biochemical, biophysical and phylogenetic study of the sulfur oxygenase reductase (SOR) from the mesophilic Gammaproteobacterium Halothiobacillus neapolitanus (HnSOR) was performed in order to determine the structural and biochemical properties. SOR proteins from 14 predominantly chemolithoautotrophic bacterial and archaeal species are currently available in public databases. Sequence alignment and phylogenetic analysis showed that they form a coherent protein family. The HnSOR purified from E ... | 2011 | 22139503 |
| Phylogenetic assessment of culture collection strains of Thiobacillus thioparus, and definitive 16S rRNA gene sequences for T. thioparus, T. denitrificans, and Halothiobacillus neapolitanus. | The 16S rRNA gene sequences of 12 strains of Thiobacillus thioparus held by different culture collections have been compared. A definitive sequence for the reference type strain (Starkey; ATCC 8158(T)) was obtained. The sequences for four examples of the Starkey type strain were essentially identical, confirming their sustained identity after passage through different laboratories. One strain (NCIMB 8454) was reassigned as a strain of Halothiobacillus neapolitanus, and a second (NCIMB 8349) was ... | 2011 | 21858648 |
| ribulose-1,5-bisphosphate carboxylase/oxygenase genes as a functional marker for chemolithoautotrophic halophilic sulfur-oxidizing bacteria in hypersaline habitats. | the presence and diversity of the cbb genes encoding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) (a key enzyme of the calvin-benson cycle of autotrophic co(2) assimilation) were investigated in pure cultures of seven genera of halophilic chemolithoautotrophic sulfur-oxidizing bacteria (sob) and in sediments from a hypersaline lake in which such bacteria have been recently discovered. all of the halophilic sob strains (with the exception of thiohalomonas nitrati ... | 2010 | 20299400 |
| the murein of thiobacillus neapolitanus. | amino acid analysis of pure murein isolated from cells of t. neapolitanus revealed the typical constituents of most mureins form gram-negative bacteria. i.e. glutamic acid, alanine and diaminopimelic acid, but the molecular ratio ot these was unusual, being approximately 1: 1: 1. the reduced amount of alanine was explained by the absence of monomers containing tetrapeptide side chains, as revealed by h. p. 1. c. analysis, [(3)h]glutamic acid, [(3)h]diaminopimelic acid and [(3)h]n-acetylglucosami ... | 1991 | 21542392 |
| bacteria involved in sulfur amendment oxidation and acidification processes of alkaline 'alperujo' compost. | eight strains of sulfur oxidizing bacteria were isolated from alkaline 'alperujo' compost, seven being identified as paracoccus thiocyanatus and one as halothiobacillus neapolitanus. this was the first time that p. thiocyanatus was isolated from mature compost. acidification capability of isolated strains was compared with type strains h. neapolitanus cip104769, thiobacillus denitrificans cip104767 and thiomonas intermedia cip104401. indigenous p. thiocyanatus strains were as much as or more eff ... | 2010 | 20970324 |
| analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein csos1c. | lattice-translocation or crystal order-disorder phenomena occur when some layers or groups of molecules in a crystal are randomly displaced relative to other groups of molecules by a discrete set of vectors. in previous work, the effects of lattice translocation on diffraction intensities have been corrected by considering that the observed intensities are the product of the intensities from an ideal crystal (lacking disorder) multiplied by the squared magnitude of the fourier transform of the s ... | 2009 | 19690376 |