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David S. Holmes - One of the best experts on this subject based on the ideXlab platform.
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Reclassification of 'Thiobacillus prosperus' Huber and Stetter 1989 as Acidihalobacter prosperus gen. nov., sp. nov., a member of the family Ectothiorhodospiraceae.
International journal of systematic and evolutionary microbiology, 2015Co-Authors: Juan Pablo Cárdenas, Rodrigo Ortiz, Paul R. Norris, Elizabeth L.j. Watkin, David S. HolmesAbstract:Analysis of phylogenomic metrics of a recently released draft genome sequence of the halotolerant, acidophile ‘Thiobacillus prosperus’ DSM 5130 indicates that it is not a member of the genus Thiobacillus within the class Betaproteobacteria as originally proposed. Based on data from 16S rRNA gene phylogeny, and analyses of multiprotein phylogeny and average nucleotide identity (ANI), we show that it belongs to a new genus within the family Ectothiorhodospiraceae, for which we propose the name Acidihalobacter gen. nov. In accordance, it is proposed that ‘Thiobacillus prosperus’ DSM 5130 be named Acidihalobacter prosperus gen. nov., sp. nov. DSM 5130T ( = JCM 30709T) and that it becomes the type strain of the type species of this genus.
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functional analysis of gapped microbial genomes amino acid metabolism of Thiobacillus ferrooxidans
Proceedings of the National Academy of Sciences of the United States of America, 2000Co-Authors: Evgeni Selkov, David S. Holmes, Ross Overbeek, Yakov Kogan, Lien Chu, Veronika Vonstein, Simon Silver, Robert Haselkorn, Michael FonsteinAbstract:A gapped genome sequence of the biomining bacterium Thiobacillus ferrooxidans strain ATCC23270 was assembled from sheared DNA fragments (3.2-times coverage) into 1,912 contigs. A total of 2,712 potential genes (ORFs) were identified in 2.6 Mbp (megabase pairs) of Thiobacillus genomic sequence. Of these genes, 2,159 could be assigned functions by using the WIT-Pro/EMP genome analysis system, most with a high degree of certainty. Nine hundred of the genes have been assigned roles in metabolic pathways, producing an overview of cellular biosynthesis, bioenergetics, and catabolism. Sequence similarities, relative gene positions on the chromosome, and metabolic reconstruction (placement of gene products in metabolic pathways) were all used to aid gene assignments and for development of a functional overview. Amino acid biosynthesis was chosen to demonstrate the analytical capabilities of this approach. Only 10 expected enzymatic activities, of the nearly 150 involved in the biosynthesis of all 20 amino acids, are currently unassigned in the Thiobacillus genome. This result compares favorably with 10 missing genes for amino acid biosynthesis in the complete Escherichia coli genome. Gapped genome analysis can therefore give a decent picture of the central metabolism of a microorganism, equivalent to that of a complete sequence, at significantly lower cost.
Juan Pablo Cárdenas - One of the best experts on this subject based on the ideXlab platform.
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Reclassification of 'Thiobacillus prosperus' Huber and Stetter 1989 as Acidihalobacter prosperus gen. nov., sp. nov., a member of the family Ectothiorhodospiraceae.
International journal of systematic and evolutionary microbiology, 2015Co-Authors: Juan Pablo Cárdenas, Rodrigo Ortiz, Paul R. Norris, Elizabeth L.j. Watkin, David S. HolmesAbstract:Analysis of phylogenomic metrics of a recently released draft genome sequence of the halotolerant, acidophile ‘Thiobacillus prosperus’ DSM 5130 indicates that it is not a member of the genus Thiobacillus within the class Betaproteobacteria as originally proposed. Based on data from 16S rRNA gene phylogeny, and analyses of multiprotein phylogeny and average nucleotide identity (ANI), we show that it belongs to a new genus within the family Ectothiorhodospiraceae, for which we propose the name Acidihalobacter gen. nov. In accordance, it is proposed that ‘Thiobacillus prosperus’ DSM 5130 be named Acidihalobacter prosperus gen. nov., sp. nov. DSM 5130T ( = JCM 30709T) and that it becomes the type strain of the type species of this genus.
Hidehiko Tanaka - One of the best experts on this subject based on the ideXlab platform.
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purification and characterization of 3 isopropylmalate dehydrogenase from Thiobacillus thiooxidans
Journal of Bioscience and Bioengineering, 2000Co-Authors: Hiroshi Kawaguchi, Tatsuo Tano, Yumi Nakayama, Hideyuki Matsunami, Kenji Inagaki, Hidehiko TanakaAbstract:3-Isopropylmalate dehydrogenase was purified to homogeneity from the acidophilic autotroph Thiobacillus thiooxidans. The native enzyme was a dimer of molecular weight 40,000. The apparent Km values for 3-isopropylmalate and NAD+ were estimated to be 0.13 mM and 8.7 mM, respectively. The optimum pH for activity was 9.0 and the optimum temperature was 65°C. The properties of the enzyme were similar to those of the Thiobacillus ferrooxidans enzyme, expect for substrate specificity. T. thiooxidans 3-isopropylmalate dehydrogenase could not utilize malate as a substrate.
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purification and characterization of 3 isopropylmalate dehydrogenase of acidophilic autotroph Thiobacillus thiooxidans
Process Metallurgy, 1999Co-Authors: Hiroshi Kawaguchi, Tatsuo Tano, Yumi Nakayama, Hideyuki Matsunami, Kenji Inagaki, Hidehiko TanakaAbstract:3-Isopropylmalate dehydrogenase was purified to homogeneity from the acidophilic autotroph Thiobacillus thiooxidans . The native enzyme molecule is a dimer of molecular weight 40,000. The K m value for 3-isopropylmalate was estimated to be 0.13 mM and that for NAD + 8.7 mM. The optimum pH and temperature for the activity are 9.0 and 65, respectively. The properties of the enzyme are similar to those of the Thiobacillus ferrooxidans enzymes, except for substrate specificity. T. ferrooxidans 3-isopropylmalate dehydrogenase is able to utilize alkyl-malate as substrate in addition to 3-isopropylmalate. However, T. thiooxidans 3-isopropylmalate is not able to utilize malate as a substrate.
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overproduction and substrate specificity of 3 isopropylmalate dehydrogenase from Thiobacillus ferrooxidans
Bioscience Biotechnology and Biochemistry, 1998Co-Authors: Hideyuki Matsunami, Katsumi Kakinuma, Tadashi Eguchi, Kenji Inagaki, Hiroshi Kawaguchi, Hidehiko TanakaAbstract:We constructed an overexpression system in Escherichia coli of the leuB gene coding for 3-isopropylmalate dehydrogenase in Thiobacillus ferrooxidans. E. coli harboring the plasmid we constructed, pKK leuB1, produced 17-fold the enzyme protein of the expression system previously used for purification. The substrate specificity of the enzyme was analyzed with synthetic (2R, 3S)-3-alkylmalates. The 3-isopropylmalate dehydrogenase of Thiobacillus ferrooxidans had broad specificity toward the alkylmalates.
Scott C Brooks - One of the best experts on this subject based on the ideXlab platform.
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microbial and thiosulfate mediated dissolution of mercury sulfide minerals and transformation to gaseous mercury
Frontiers in Microbiology, 2015Co-Authors: Adiari I Vazquezrodriguez, Tong Zhang, Colleen M Hansel, Carl H Lamborg, Cara M Santelli, Samuel M Webb, Scott C BrooksAbstract:Mercury (Hg) is a toxic heavy metal that poses significant environmental and human health risks. Soils and sediments, where Hg can exist as the Hg sulfide mineral metacinnabar (β-HgS), represent major Hg reservoirs in aquatic environments. Metacinnabar has historically been considered a sink for Hg in all but severely acidic environments, and thus disregarded as a potential source of Hg back to aqueous or gaseous pools. Here, we conducted a combination of field and laboratory incubations to identify the potential for metacinnabar as a source of dissolved Hg within near neutral pH environments and the underpinning (a)biotic mechanisms at play. We show that the abundant and widespread sulfur-oxidizing bacteria of the genus Thiobacillus extensively colonized metacinnabar chips incubated within aerobic, near neutral pH creek sediments. Laboratory incubations of axenic Thiobacillus thioparus cultures led to the release of metacinnabar-hosted Hg(II) and subsequent volatilization to Hg(0). This dissolution and volatilization was greatly enhanced in the presence of thiosulfate, which served a dual role by enhancing HgS dissolution through Hg complexation and providing an additional metabolic substrate for Thiobacillus. These findings reveal a new coupled abiotic-biotic pathway for the transformation of metacinnabar-bound Hg(II) to Hg(0), while expanding the sulfide substrates available for neutrophilic chemosynthetic bacteria to Hg-laden sulfides. They also point to mineral-hosted Hg as an underappreciated source of gaseous elemental Hg to the environment.
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microbial and thiosulfate mediated dissolution of mercury sulfide minerals and transformation to gaseous mercury
Frontiers in Microbiology, 2015Co-Authors: Adiari I Vazquezrodriguez, Tong Zhang, Colleen M Hansel, Carl H Lamborg, Cara M Santelli, Samuel M Webb, Scott C BrooksAbstract:Mercury (Hg) is a toxic heavy metal that poses significant human and environmental health risks. Soils and sediments, where Hg can exist as the Hg sulfide mineral metacinnabar (β-HgS), represent major Hg reservoirs in aquatic environments. Metacinnabar has historically been considered a sink for Hg in all but severely acidic environments, and thus disregarded as a potential source of Hg back to aqueous or gaseous pools. Here, we conducted a combination of field and laboratory incubations to identify the potential for metacinnabar as a source of dissolved Hg within near neutral pH environments and the underpinning (a)biotic mechanisms at play. We show that the abundant and widespread sulfur-oxidizing bacterium Thiobacillus extensively colonized metacinnabar chips incubated within aerobic, near neutral pH creek sediments. Laboratory incubations of axenic Thiobacillus cultures lead to the release of metacinnabar-hosted Hg(II) and subsequent volatilization to Hg(0). This dissolution and volatilization was greatly enhanced in the presence of the sulfur intermediate, thiosulfate, which served a dual role by enhancing HgS dissolution and providing an additional metabolic substrate for Thiobacillus. These findings reveal a new coupled abiotic-biotic pathway for the transformation of metacinnabar-bound Hg(II) to Hg(0), while expanding the sulfide substrates available for neutrophilic chemosynthetic bacteria to Hg-laden sulfides. They also point to mineral-hosted Hg as an underappreciated source of gaseous elemental Hg to the environment.
Donovan P Kelly - One of the best experts on this subject based on the ideXlab platform.
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International Journal of Systematic and Evolutionary Microbiology (2000), 50, 547–550 Printed in Great Britain
2013Co-Authors: Donovan P Kelly, Ann P WoodAbstract:Confirmation of Thiobacillus denitrificans as a species of the genus Thiobacillus, in the β-subclass of the Proteobacteria, with strain NCIMB 9548 as the type strai
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Phylogenetic assessment of culture collection strains of Thiobacillus thioparus, and definitive 16S rRNA gene sequences for T. thioparus, T. denitrificans, and HaloThiobacillus neapolitanus
Archives of Microbiology, 2012Co-Authors: Rich Boden, David Cleland, Peter N. Green, Yoko Katayama, Yoshihito Uchino, J. Colin Murrell, Donovan P KellyAbstract: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 a species of ThermiThiobacillus . These two strains have been renamed in their catalog by the National Collection of Industrial and Marine Bacteria. The 16S rRNA gene sequence of the type strain of HaloThiobacillus neapolitanus (NCIMB 8539^T) was determined and used to confirm the identity of other culture collection strains of this species. The reference sequences for the type strains of Thiobacillus thioparus and HaloThiobacillus neapolitanus have been added to the online List of Prokaryotic Names with Standing in Nomenclature . Comparison of the 16S rRNA gene sequences available for strains of Thiobacillus denitrificans indicated that the sequence for the type strain (NCIMB 9548^T) should always be used as the reference sequence for new and existing isolates.
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Confirmation of Thiobacillus denitrificans as a species of the genus Thiobacillus, in the beta-subclass of the Proteobacteria, with strain NCIMB 9548 as the type strain.
International Journal of Systematic and Evolutionary Microbiology, 2000Co-Authors: Donovan P Kelly, Ann P WoodAbstract:Thiobacillus denitrificans is physiologically similar to the type species of the genus Thiobacillus, Thiobacillus Thioparus, and both are located in the beta-subclass of the Proteobacteria. T. denitrificans is distinguished from all other Thiobacillus species by its ability to grow as a facultatively anaerobic chemolithotroph, coupling the oxidation of inorganic sulfur compounds to the reduction of nitrate, nitrite and other oxidized nitrogen compounds to dinitrogen. A definitive description of this species is provided and strain NCIMB 9548T is designated as the type strain of the species, thereby correcting an earlier error in the literature.
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reclassification of some species of Thiobacillus to the newly designated genera acidiThiobacillus gen nov haloThiobacillus gen nov and thermiThiobacillus gen nov
International Journal of Systematic and Evolutionary Microbiology, 2000Co-Authors: Donovan P Kelly, Ann P WoodAbstract: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 three newly designated genera within the gamma-subclass of the Proteobacteria, namely AcidiThiobacillus, HaloThiobacillus and ThermiThiobacillus.
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oxidative metabolism of inorganic sulfur compounds by bacteria
Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 1997Co-Authors: Donovan P Kelly, Jasvinder K Shergill, Weiping Lu, Ann P WoodAbstract:The history of the elucidation of the microbiology and biochemistry of the oxidation of inorganic sulfur compounds in chemolithotrophic bacteria is briefly reviewed, and the contribution of Martinus Beijerinck to the study of sulfur-oxidizing bacteria highlighted. Recent developments in the biochemistry, enzymology and molecular biology of sulfur oxidation in obligately and facultatively lithotrophic bacteria are summarized, and the existence of at least two major pathways of thiosulfate (sulfur and sulfide) oxidation confirmed. These are identified as the ‘Paracoccus sulfur oxidation’ (or PSO) pathway and the ‘S4intermediate’ (or S4I) pathway respectively. The former occurs in organisms such as Paracoccus (Thiobacillus) versutus and P. denitrificans, and possibly in Thiobacillus novellus and Xanthobacter spp. The latter pathway is characteristic of the obligate chemolithotrophs (e.g. Thiobacillus tepidarius, T. neapolitanus, T. ferrooxidans, T. thiooxidans) and facultative species such as T. acidophilus and T. aquaesulis, all of which can produce or oxidize tetrathionate when grown on thiosulfate. The central problem, as yet incompletely resolved in all cases, is the enzymology of the conversion of sulfane-sulfur (as in the outer [S-] atom of thiosulfate [-S-SO3-]), or sulfur itself, to sulfate, and whether sulfite is involved as a free intermediate in this process in all, or only some, cases. The study of inorganic sulfur compound oxidation for energetic purposes in bacteria (i.e. chemolithotrophy and sulfur photolithotrophy) poses challenges for comparative biochemistry. It also provides evidence of convergent evolution among diverse bacterial groups to achieve the end of energy-yielding sulfur compound oxidation (to drive autotrophic growth on carbon dioxide) but using a variety of enzymological systems, which share some common features. Some new data are presented on the oxidation of 35S-thiosulfate, and on the effect of other anions (selenate, molybdate, tu ngstate, chromate, vanadate) on sulfur compound oxidation, including observations which relate to the roles of polythionates and elemental sulfur as intermediates.