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Dimitry Y. Sorokin - One of the best experts on this subject based on the ideXlab platform.
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trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase
Proceedings of the National Academy of Sciences of the United States of America, 2020Co-Authors: T. V. Tikhonova, Dimitry Y. Sorokin, Wilfred R Hagen, Maria G Khrenova, T V Rakitina, I G ShabalinAbstract:Biocatalytic copper centers are generally involved in the activation and reduction of dioxygen, with only few exceptions known. Here we report the discovery and characterization of a previously undescribed copper center that forms the active site of a copper-containing enzyme thiocyanate dehydrogenase (suggested EC 1.8.2.7) that was purified from the haloalkaliphilic Sulfur-Oxidizing Bacterium of the genus Thioalkalivibrio ubiquitous in saline alkaline soda lakes. The copper cluster is formed by three copper ions located at the corners of a near-isosceles triangle and facilitates a direct thiocyanate conversion into cyanate, elemental Sulfur, and two reducing equivalents without involvement of molecular oxygen. A molecular mechanism of catalysis is suggested based on high-resolution three-dimensional structures, electron paramagnetic resonance (EPR) spectroscopy, quantum mechanics/molecular mechanics (QM/MM) simulations, kinetic studies, and the results of site-directed mutagenesis.
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Structure of the flavocytochrome c sulfide dehydrogenase associated with the copper-binding protein CopC from the haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio paradoxusARh 1.
Acta crystallographica. Section D Structural biology, 2018Co-Authors: Eugeny M. Osipov, Dimitry Y. Sorokin, T. V. Tikhonova, Anastasia V. Lilina, Stanislav I. Tsallagov, T.n. Safonova, Vladimir O PopovAbstract:Flavocytochrome c sulfide dehydrogenase from Thioalkalivibrio paradoxus (TpFCC) is a heterodimeric protein consisting of flavin- and monohaem c-binding subunits. TpFCC was co-purified and co-crystallized with the dimeric copper-binding protein TpCopC. The structure of the TpFCC-(TpCopC)2 complex was determined by X-ray diffraction at 2.6 Å resolution. The flavin-binding subunit of TpFCC is structurally similar to those determined previously, and the structure of the haem-binding subunit is similar to that of the N-terminal domain of dihaem FCCs. According to classification based on amino-acid sequence, TpCopC belongs to a high-affinity CopC subfamily characterized by the presence of a conserved His1-Xxx-His3 motif at the N-terminus. Apparently, a unique α-helix which is present in each monomer of TpCopC at the interface with TpFCC plays a key role in complex formation. The structure of the copper-binding site in TpCopC is similar to those in other known CopC structures. His3 is not involved in binding to the copper ion and is 6-7 Å away from this ion. Therefore, the His1-Xxx-His3 motif cannot be considered to be a key factor in the high affinity of CopC for copper(II) ions. It is suggested that the TpFCC-(TpCopC)2 heterotetramer may be a component of a large periplasmic complex that is responsible for thiocyanate metabolism.
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analysis of the genes involved in thiocyanate oxidation during growth in continuous culture of the haloalkaliphilic Sulfur Oxidizing Bacterium thioalkalivibrio thiocyanoxidans arh 2t using transcriptomics
mSystems, 2017Co-Authors: Tom Berben, Dimitry Y. Sorokin, Cherel Balkema, Gerard MuyzerAbstract:ABSTRACT Thiocyanate (N=C−S − ) is a moderately toxic, inorganic Sulfur compound. It occurs naturally as a by-product of the degradation of glucosinolate-containing plants and is produced industrially in a number of mining processes. Currently, two pathways for the primary degradation of thiocyanate in bacteria are recognized, the carbonyl sulfide pathway and the cyanate pathway, of which only the former has been fully characterized. Use of the cyanate pathway has been shown in only 10 strains of Thioalkalivibrio , a genus of obligately haloalkaliphilic Sulfur-Oxidizing Gammaproteobacteria found in soda lakes. So far, only the key enzyme in this reaction, thiocyanate dehydrogenase (TcDH), has been purified and studied. To gain a better understanding of the other genes involved in the cyanate pathway, we conducted a transcriptomics experiment comparing gene expression during the growth of Thioalkalivibrio thiocyanoxidans ARh 2 T with thiosulfate with that during its growth with thiocyanate. Triplicate cultures were grown in continuous substrate-limited mode, followed by transcriptome sequencing (RNA-Seq) of the total mRNA. Differential expression analysis showed that a cluster of genes surrounding the gene for TcDH were strongly upregulated during growth with thiocyanate. This cluster includes genes for putative copper uptake systems ( copCD , ABC-type transporters), a putative electron acceptor ( fccAB ), and a two-component regulatory system (histidine kinase and a σ 54 -responsive Fis family transcriptional regulator). Additionally, we observed the increased expression of RuBisCO and some carboxysome shell genes involved in inorganic carbon fixation, as well as of aprAB , genes involved in sulfite oxidation through the reverse sulfidogenesis pathway. IMPORTANCE Thiocyanate is a moderately toxic and chemically stable Sulfur compound that is produced by both natural and industrial processes. Despite its significance as a pollutant, knowledge of the microbial degradation of thiocyanate is very limited. Therefore, investigation of thiocyanate oxidation in haloalkaliphiles such as the genus Thioalkalivibrio may lead to improved biotechnological applications in wastewater remediation.
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complete genome sequence of thioalkalivibrio paradoxus type strain arh 1t an obligately chemolithoautotrophic haloalkaliphilic Sulfur Oxidizing Bacterium isolated from a kenyan soda lake
Standards in Genomic Sciences, 2015Co-Authors: Tom Berben, Lynne A. Goodwin, Dimitry Y. Sorokin, Nikos C. Kyrpides, Natalia Ivanova, Amrita Pati, Tanja Woyke, Gerard MuyzerAbstract:Thioalkalivibrio paradoxus strain ARh 1T is a chemolithoautotrophic, non-motile, Gram-negative Bacterium belonging to the Gammaproteobacteria that was isolated from samples of haloalkaline soda lakes. It derives energy from the oxidation of reduced Sulfur compounds and is notable for its ability to grow on thiocyanate as its sole source of electrons, Sulfur and nitrogen. The full genome consists of 3,756,729 bp and comprises 3,500 protein-coding and 57 RNA-coding genes. This organism was sequenced as part of the community science program at the DOE Joint Genome Institute.
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Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1 T, a chemolithoautotrophic haloalkaliphilic Sulfur-Oxidizing Bacterium capable of complete denitrification
Standards in Genomic Sciences, 2015Co-Authors: Tom Berben, Lynne A. Goodwin, Dimitry Y. Sorokin, Nikos C. Kyrpides, Natalia Ivanova, Amrita Pati, Tanja WoykeAbstract:Thioalkalivibrio thiocyanodenitrificans strain ARhD 1T is a motile, Gram-negative Bacterium isolated from soda lakes that belongs to the Gammaproteobacteria. It derives energy for growth and carbon fixation from the oxidation of Sulfur compounds, most notably thiocyanate, and so is a chemolithoautotroph. It is capable of complete denitrification under anaerobic conditions. The draft genome sequence consists of 3,746,647 bp in 3 scaffolds, containing 3558 protein-coding and 121 RNA genes. T. thiocyanodenitrificans ARhD 1T was sequenced as part of the DOE Joint Genome Institute Community Science Program.
Manabu Fukui - One of the best experts on this subject based on the ideXlab platform.
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Sulfurimicrobium lacus gen. nov., sp. nov., a Sulfur oxidizer isolated from lake water, and review of the family Sulfuricellaceae to show that it is not a later synonym of Gallionellaceae
Archives of Microbiology, 2020Co-Authors: Hisaya Kojima, Mamoru Kanda, Kazuhiro Umezawa, Manabu FukuiAbstract:A facultatively anaerobic Sulfur-Oxidizing Bacterium, strain skT11^T, was isolated from anoxic lake water of a stratified freshwater lake. As electron donor for chemolithoautotrophic growth, strain skT11^T oxidized thiosulfate, tetrathionate, and elemental Sulfur under nitrate-reducing conditions. Oxygen-dependent growth was observed under microoxic conditions, but not under fully oxygenated conditions. Growth was observed at a temperature range of 5–37 °C, with optimum growth at 28 °C. Strain skT11^T grew at a pH range of 5.1–7.5, with optimum growth at pH 6.5–6.9. Heterotrophic growth was not observed. Major components in the cellular fatty acid profile were C_16:1 and C_16:0. The complete genome of strain skT11^T consisted of a circular chromosome with a size of 3.8 Mbp and G + C content of 60.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the strain skT11^T is related to Sulfur-Oxidizing bacteria of the genera Sulfuricella , Sulfurirhabdus, and Sulfuriferula , with sequence identities of 95.4% or lower. The analysis also indicated that these three genera should be excluded from the family Gallionellaceae , as members of another family. On the basis of its genomic and phenotypic properties, strain skT11^T (= DSM 110711^ T = NBRC 114323^ T) is proposed as the type strain of a new species in a new genus, Sulfurimicrobium lacus gen. nov., sp. nov. In addition, emended descriptions of the families Gallionellaceae and Sulfuricellaceae are proposed to declare that Sulfuricellaceae is not a later synonym of Gallionellaceae .
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Sulfuriferula nivalis sp nov a Sulfur oxidizer isolated from snow and emended description of Sulfuriferula plumbiphila
International Journal of Systematic and Evolutionary Microbiology, 2020Co-Authors: Hisaya Kojima, Jun Mochizuki, Manabu FukuiAbstract:A chemolithoautotrophic Sulfur-Oxidizing Bacterium, strain SGTMT was isolated from snow collected in Japan. As electron donors for growth, SGTMT oxidized thiosulfate, tetrathionate and elemental Sulfur. Heterotrophic growth was not observed. Growth of the novel isolate was observed at a temperature range of 5–28 °C, with optimum growth at 18 °C. SGTMT grew at a pH range of 4.3–7.4, with optimum growth at pH 6.1–7.1. Major components in the cellular fatty acid profile were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The complete genome of SGTMT consisted of a circular chromosome of approximately 3.4 Mbp and two plasmids. Phylogenetic analysis based on the 16S rRNA gene indicated that SGTMT represented a member of the genus Sulfuriferula , and its closest relative is Sulfuriferula thiophila mst6T with a sequence identity of 98 %. A comparative genome analysis showed dissimilarity between the genomes of SGTMT and S. thiophila mst6T, as low values of average nucleotide identity (74.9 %) and digital DNA–DNA hybridization (20.4%). On the basis of its genomic and phenotypic properties, SGTMT (=DSM 109609T=BCRC 81185T) is proposed as the type strain of a novel species, Sulfuriferula nivalis sp. nov. Some characteristics of another species in the same genus, Sulfuriferula plumbiphila , were also investigated to revise and supplement its description. The type strain of S. plumbiphila can grow on thiosulfate, tetrathionate and elemental Sulfur. The strain showed optimum growth at pH 6.3–7.0 and shared major cellular fatty acids with the other species of the genus Sulfuriferula .
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thiomicrorhabdus aquaedulcis sp nov a Sulfur Oxidizing Bacterium isolated from lake water
International Journal of Systematic and Evolutionary Microbiology, 2019Co-Authors: Hisaya Kojima, Manabu FukuiAbstract:Strain HaS4T is an aerobic Sulfur-Oxidizing Bacterium isolated from water of Lake Harutori in Japan. It was isolated and partially characterized in a previous study, but its taxonomic status has not been determined. The previous study revealed that the strain is an obligate chemolithoautotroph which grows at temperatures ranging from 0 to 25 °C (optimum, 22 °C) and pH from pH 6.2 to 8.8 (optimum, pH 6.6–7.4). In this study, further characterization of the strain was made to describe it as representative of a novel species. Cells of strain HaS4T are rod-shaped, 1.6–2.5 µm long, 0.7–0.9 µm wide and Gram-stain-negative. Major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. Phylogenetic analysis based on the 16S rRNA gene indicated that the strain is related to the genus Thiomicrorhabdus, but phylogenetically distinct from the type strains of existing species in the genus. On the basis of its phylogenetic and phenotypic properties, strain HaS4T (=NBRC 112315T=BCRC 81110T) is proposed as type strain of a new non-marine species of the genus Thiomicrorhabdus with the name Thiomicrorhabdus aquaedulcis sp. nov.
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Sulfuricaulis limicola gen nov sp nov a Sulfur oxidizer isolated from a lake
International Journal of Systematic and Evolutionary Microbiology, 2016Co-Authors: Hisaya Kojima, Tomohiro Watanabe, Manabu FukuiAbstract:A novel Sulfur-Oxidizing Bacterium, strain HA5T, was isolated from sediment of a lake in Japan. The cells were rod-shaped (0.3-0.5 × 1.2-6.0 μm) and Gram-stain-negative. The G+C content of the genomic DNA was 63 mol%. The major components in the cellular fatty acid profile were C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The strain oxidized thiosulfate, tetrathionate and elemental Sulfur as electron donors to support autotrophic growth. Growth was observed at a temperature range of 8-37 °C, with optimum growth at 28-32 °C. The pH range for growth was pH 6.1-9.2. Optimum growth of the isolate was observed in medium without NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs to the family Acidiferrobacteraceae in the class Gammaproteobacteria. The closest relative was Sulfurifustis variabilis skN76T with the highest 16S rRNA gene sequence similarity of 93 %. On the basis of phylogenetic and phenotypic properties, strain HA5T is proposed to represent a novel species of a new genus, Sulfuricaulis limicola gen. nov., sp. nov. The type strain of the type species is HA5T ( = DSM 100373T = NBRC 110752T).
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Sulfuriferula multivorans gen nov sp nov isolated from a freshwater lake reclassification of thiobacillus plumbophilus as Sulfuriferula plumbophilus sp nov and description of Sulfuricellaceae fam nov and Sulfuricellales ord nov
International Journal of Systematic and Evolutionary Microbiology, 2015Co-Authors: Tomohiro Watanabe, Hisaya Kojima, Manabu FukuiAbstract:A Sulfur-Oxidizing Bacterium, strain TTNT, was isolated from a Thioploca sample obtained from a freshwater lake in Japan. The isolate shared 97.1 % 16S rRNA gene sequence similarity with an obligately aerobic chemolithoautotroph, ‘Thiobacillus plumbophilus’ Gro7T. Cells were rods, motile, and Gram-stain-negative. The G+C content of the genomic DNA was approximately 66 mol%. Strain TTNT grew over a temperature range of 8–32 °C (optimum 22–25 °C), an NaCl concentration range of 0–133.3 mM (optimum 0–3.3 mM) and a pH range of 5.3–8.6 (optimum pH 6.4–7.0). Strain TTNT was facultatively anaerobic and could utilize nitrate as an electron acceptor. The isolate oxidized tetrathionate, thiosulfate and elemental Sulfur as the sole energy sources for autotrophic growth, and could also grow heterotrophically on a number of organic substrates. Based on its phylogenetic and phenotypic properties, strain TTNT represents a novel species of a novel genus, for which the name Sulfuriferula multivorans gen. nov., sp. nov. is proposed. The type strain is TTNT ( = NBRC 110683T = DSM 29343T). Along with this, the reclassification of ‘Thiobacillus plumbophilus’ as Sulfuriferula plumbophilus sp. nov. (type strain Gro7T = NBRC 107929T = DSM 6690T) is proposed. Based on the data obtained in this study, we describe the designations Sulfuricellaceae fam. nov. and Sulfuricellales ord. nov.
Gerard Muyzer - One of the best experts on this subject based on the ideXlab platform.
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analysis of the genes involved in thiocyanate oxidation during growth in continuous culture of the haloalkaliphilic Sulfur Oxidizing Bacterium thioalkalivibrio thiocyanoxidans arh 2t using transcriptomics
mSystems, 2017Co-Authors: Tom Berben, Dimitry Y. Sorokin, Cherel Balkema, Gerard MuyzerAbstract:ABSTRACT Thiocyanate (N=C−S − ) is a moderately toxic, inorganic Sulfur compound. It occurs naturally as a by-product of the degradation of glucosinolate-containing plants and is produced industrially in a number of mining processes. Currently, two pathways for the primary degradation of thiocyanate in bacteria are recognized, the carbonyl sulfide pathway and the cyanate pathway, of which only the former has been fully characterized. Use of the cyanate pathway has been shown in only 10 strains of Thioalkalivibrio , a genus of obligately haloalkaliphilic Sulfur-Oxidizing Gammaproteobacteria found in soda lakes. So far, only the key enzyme in this reaction, thiocyanate dehydrogenase (TcDH), has been purified and studied. To gain a better understanding of the other genes involved in the cyanate pathway, we conducted a transcriptomics experiment comparing gene expression during the growth of Thioalkalivibrio thiocyanoxidans ARh 2 T with thiosulfate with that during its growth with thiocyanate. Triplicate cultures were grown in continuous substrate-limited mode, followed by transcriptome sequencing (RNA-Seq) of the total mRNA. Differential expression analysis showed that a cluster of genes surrounding the gene for TcDH were strongly upregulated during growth with thiocyanate. This cluster includes genes for putative copper uptake systems ( copCD , ABC-type transporters), a putative electron acceptor ( fccAB ), and a two-component regulatory system (histidine kinase and a σ 54 -responsive Fis family transcriptional regulator). Additionally, we observed the increased expression of RuBisCO and some carboxysome shell genes involved in inorganic carbon fixation, as well as of aprAB , genes involved in sulfite oxidation through the reverse sulfidogenesis pathway. IMPORTANCE Thiocyanate is a moderately toxic and chemically stable Sulfur compound that is produced by both natural and industrial processes. Despite its significance as a pollutant, knowledge of the microbial degradation of thiocyanate is very limited. Therefore, investigation of thiocyanate oxidation in haloalkaliphiles such as the genus Thioalkalivibrio may lead to improved biotechnological applications in wastewater remediation.
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complete genome sequence of thioalkalivibrio paradoxus type strain arh 1t an obligately chemolithoautotrophic haloalkaliphilic Sulfur Oxidizing Bacterium isolated from a kenyan soda lake
Standards in Genomic Sciences, 2015Co-Authors: Tom Berben, Lynne A. Goodwin, Dimitry Y. Sorokin, Nikos C. Kyrpides, Natalia Ivanova, Amrita Pati, Tanja Woyke, Gerard MuyzerAbstract:Thioalkalivibrio paradoxus strain ARh 1T is a chemolithoautotrophic, non-motile, Gram-negative Bacterium belonging to the Gammaproteobacteria that was isolated from samples of haloalkaline soda lakes. It derives energy from the oxidation of reduced Sulfur compounds and is notable for its ability to grow on thiocyanate as its sole source of electrons, Sulfur and nitrogen. The full genome consists of 3,756,729 bp and comprises 3,500 protein-coding and 57 RNA-coding genes. This organism was sequenced as part of the community science program at the DOE Joint Genome Institute.
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DOI:10.4056/sigs.1483693 Complete genome sequence of “Thioalkalivibrio sulfidophilus” HL-EbGr7
2013Co-Authors: Gerard Muyzer, Natalia Ivanova, Amrita Pati, Tanja Woyke, Konstantinos Mavromatis, Alla Lapidus, Dimitry Yu Sorokin, Nikos C, Corresponding Gerard MuyzerAbstract:“Thioalkalivibrio sulfidophilus ” HL-EbGr7 is an obligately chemolithoautotrophic, haloalkaliphilic Sulfur-Oxidizing Bacterium (SOB) belonging to the Gammaproteobacteria. The strain was found to predominate a full-scale bioreactor, removing sulfide from biogas. Here we report the complete genome sequence of strain HL-EbGr7 and its annotation. The genome was sequenced within the Joint Genome Institute Community Sequencing Program, because of its relevance to the sustainable removal of sulfide from bio- and industrial waste gases
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thiomicrospira halophila sp nov a moderately halophilic obligately chemolithoautotrophic Sulfur Oxidizing Bacterium from hypersaline lakes
International Journal of Systematic and Evolutionary Microbiology, 2006Co-Authors: Dimitry Y. Sorokin, Tatjana V. Kolganova, Tatjana P. Tourova, Elizaveta M Spiridonova, Ivan A Berg, Gerard MuyzerAbstract: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-shaped phenotype outcompeted the halothiobacilli. Three genetically and phenotypically highly similar vibrio-shaped isolates were obtained in pure culture and one of them, strain HL 5T, was identified as a member of the Thiomicrospira crunogena cluster by 16S rRNA gene sequencing. The new isolates were able to grow with thiosulfate as electron donor within a broad salinity range from 0.5 to 3.5 M NaCl with an optimum at 1.5 M and within a pH range from 6.5 to 8.5 with an optimum at pH 7.5–7.8. Comparative analysis of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) gene sequences demonstrated that strain HL 5T possessed two genes, cbbL-1 and cbbL-2, of the form I RuBisCO and a cbbM gene of the form II RuBisCO, similar to the other members of the Thiomicrospira crunogena cluster. On the basis of phenotypic and genetic comparison, the new halophilic isolates are proposed to be placed into a novel species, Thiomicrospira halophila sp. nov. (type strain HL 5T=DSM 15072T=UNIQEM U 221T).
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thioclava pacifica gen nov sp nov a novel facultatively autotrophic marine Sulfur Oxidizing Bacterium from a near shore sulfidic hydrothermal area
International Journal of Systematic and Evolutionary Microbiology, 2005Co-Authors: Dimitry Y. Sorokin, Tatjana P. Tourova, Elizaveta M Spiridonova, Fred A Rainey, Gerard MuyzerAbstract:Strain TL 2T was isolated on mineral medium with thiosulfate from a near-shore sulfidic hydrothermal area in Matupi Harbour on the island of New Britain, Papua New Guinea. The cells varied from long filaments with swollen ends, often aggregated, to short rods, depending on the growth conditions. The Bacterium was obligately aerobic and grew autotrophically with thiosulfate as energy source or heterotrophically with organic acids and sugars. In thiosulfate-limited continuous culture, μ max and Y max for autotrophic growth were 0·1 h−1 and 3 g protein mol−1, respectively. From the various reduced Sulfur compounds tested, only thiosulfate and sulfide supported active respiration. Inorganic carbon was assimilated via the Calvin cycle. Presence of the ‘green’-type of form I RubisCO gene was detected. Growth was possible from 15 to 47 °C with an optimum at 35 °C, pH 6·5–8·5 with an optimum at pH 8·0, and between 10 and 90 g NaCl l−1 with an optimum at 35 g l−1. Phylogenetic analysis based on 16S rRNA and cbbL gene sequences demonstrated that strain TL 2T forms a separate lineage within the alpha-3 subdivision of the Proteobacteria, distantly related to the genera Rhodovulum and Rhodobacter. On the basis of these results, a novel genus and species, Thioclava pacifica gen. nov., sp. nov., is proposed to accommodate strain TL 2T (=DSM 10166T=UNIQEM 229T).
Hisaya Kojima - One of the best experts on this subject based on the ideXlab platform.
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Sulfurimicrobium lacus gen. nov., sp. nov., a Sulfur oxidizer isolated from lake water, and review of the family Sulfuricellaceae to show that it is not a later synonym of Gallionellaceae
Archives of Microbiology, 2020Co-Authors: Hisaya Kojima, Mamoru Kanda, Kazuhiro Umezawa, Manabu FukuiAbstract:A facultatively anaerobic Sulfur-Oxidizing Bacterium, strain skT11^T, was isolated from anoxic lake water of a stratified freshwater lake. As electron donor for chemolithoautotrophic growth, strain skT11^T oxidized thiosulfate, tetrathionate, and elemental Sulfur under nitrate-reducing conditions. Oxygen-dependent growth was observed under microoxic conditions, but not under fully oxygenated conditions. Growth was observed at a temperature range of 5–37 °C, with optimum growth at 28 °C. Strain skT11^T grew at a pH range of 5.1–7.5, with optimum growth at pH 6.5–6.9. Heterotrophic growth was not observed. Major components in the cellular fatty acid profile were C_16:1 and C_16:0. The complete genome of strain skT11^T consisted of a circular chromosome with a size of 3.8 Mbp and G + C content of 60.2 mol%. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the strain skT11^T is related to Sulfur-Oxidizing bacteria of the genera Sulfuricella , Sulfurirhabdus, and Sulfuriferula , with sequence identities of 95.4% or lower. The analysis also indicated that these three genera should be excluded from the family Gallionellaceae , as members of another family. On the basis of its genomic and phenotypic properties, strain skT11^T (= DSM 110711^ T = NBRC 114323^ T) is proposed as the type strain of a new species in a new genus, Sulfurimicrobium lacus gen. nov., sp. nov. In addition, emended descriptions of the families Gallionellaceae and Sulfuricellaceae are proposed to declare that Sulfuricellaceae is not a later synonym of Gallionellaceae .
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Sulfuriferula nivalis sp nov a Sulfur oxidizer isolated from snow and emended description of Sulfuriferula plumbiphila
International Journal of Systematic and Evolutionary Microbiology, 2020Co-Authors: Hisaya Kojima, Jun Mochizuki, Manabu FukuiAbstract:A chemolithoautotrophic Sulfur-Oxidizing Bacterium, strain SGTMT was isolated from snow collected in Japan. As electron donors for growth, SGTMT oxidized thiosulfate, tetrathionate and elemental Sulfur. Heterotrophic growth was not observed. Growth of the novel isolate was observed at a temperature range of 5–28 °C, with optimum growth at 18 °C. SGTMT grew at a pH range of 4.3–7.4, with optimum growth at pH 6.1–7.1. Major components in the cellular fatty acid profile were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The complete genome of SGTMT consisted of a circular chromosome of approximately 3.4 Mbp and two plasmids. Phylogenetic analysis based on the 16S rRNA gene indicated that SGTMT represented a member of the genus Sulfuriferula , and its closest relative is Sulfuriferula thiophila mst6T with a sequence identity of 98 %. A comparative genome analysis showed dissimilarity between the genomes of SGTMT and S. thiophila mst6T, as low values of average nucleotide identity (74.9 %) and digital DNA–DNA hybridization (20.4%). On the basis of its genomic and phenotypic properties, SGTMT (=DSM 109609T=BCRC 81185T) is proposed as the type strain of a novel species, Sulfuriferula nivalis sp. nov. Some characteristics of another species in the same genus, Sulfuriferula plumbiphila , were also investigated to revise and supplement its description. The type strain of S. plumbiphila can grow on thiosulfate, tetrathionate and elemental Sulfur. The strain showed optimum growth at pH 6.3–7.0 and shared major cellular fatty acids with the other species of the genus Sulfuriferula .
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thiomicrorhabdus aquaedulcis sp nov a Sulfur Oxidizing Bacterium isolated from lake water
International Journal of Systematic and Evolutionary Microbiology, 2019Co-Authors: Hisaya Kojima, Manabu FukuiAbstract:Strain HaS4T is an aerobic Sulfur-Oxidizing Bacterium isolated from water of Lake Harutori in Japan. It was isolated and partially characterized in a previous study, but its taxonomic status has not been determined. The previous study revealed that the strain is an obligate chemolithoautotroph which grows at temperatures ranging from 0 to 25 °C (optimum, 22 °C) and pH from pH 6.2 to 8.8 (optimum, pH 6.6–7.4). In this study, further characterization of the strain was made to describe it as representative of a novel species. Cells of strain HaS4T are rod-shaped, 1.6–2.5 µm long, 0.7–0.9 µm wide and Gram-stain-negative. Major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. Phylogenetic analysis based on the 16S rRNA gene indicated that the strain is related to the genus Thiomicrorhabdus, but phylogenetically distinct from the type strains of existing species in the genus. On the basis of its phylogenetic and phenotypic properties, strain HaS4T (=NBRC 112315T=BCRC 81110T) is proposed as type strain of a new non-marine species of the genus Thiomicrorhabdus with the name Thiomicrorhabdus aquaedulcis sp. nov.
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Sulfuricaulis limicola gen nov sp nov a Sulfur oxidizer isolated from a lake
International Journal of Systematic and Evolutionary Microbiology, 2016Co-Authors: Hisaya Kojima, Tomohiro Watanabe, Manabu FukuiAbstract:A novel Sulfur-Oxidizing Bacterium, strain HA5T, was isolated from sediment of a lake in Japan. The cells were rod-shaped (0.3-0.5 × 1.2-6.0 μm) and Gram-stain-negative. The G+C content of the genomic DNA was 63 mol%. The major components in the cellular fatty acid profile were C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The strain oxidized thiosulfate, tetrathionate and elemental Sulfur as electron donors to support autotrophic growth. Growth was observed at a temperature range of 8-37 °C, with optimum growth at 28-32 °C. The pH range for growth was pH 6.1-9.2. Optimum growth of the isolate was observed in medium without NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs to the family Acidiferrobacteraceae in the class Gammaproteobacteria. The closest relative was Sulfurifustis variabilis skN76T with the highest 16S rRNA gene sequence similarity of 93 %. On the basis of phylogenetic and phenotypic properties, strain HA5T is proposed to represent a novel species of a new genus, Sulfuricaulis limicola gen. nov., sp. nov. The type strain of the type species is HA5T ( = DSM 100373T = NBRC 110752T).
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Sulfuriferula multivorans gen nov sp nov isolated from a freshwater lake reclassification of thiobacillus plumbophilus as Sulfuriferula plumbophilus sp nov and description of Sulfuricellaceae fam nov and Sulfuricellales ord nov
International Journal of Systematic and Evolutionary Microbiology, 2015Co-Authors: Tomohiro Watanabe, Hisaya Kojima, Manabu FukuiAbstract:A Sulfur-Oxidizing Bacterium, strain TTNT, was isolated from a Thioploca sample obtained from a freshwater lake in Japan. The isolate shared 97.1 % 16S rRNA gene sequence similarity with an obligately aerobic chemolithoautotroph, ‘Thiobacillus plumbophilus’ Gro7T. Cells were rods, motile, and Gram-stain-negative. The G+C content of the genomic DNA was approximately 66 mol%. Strain TTNT grew over a temperature range of 8–32 °C (optimum 22–25 °C), an NaCl concentration range of 0–133.3 mM (optimum 0–3.3 mM) and a pH range of 5.3–8.6 (optimum pH 6.4–7.0). Strain TTNT was facultatively anaerobic and could utilize nitrate as an electron acceptor. The isolate oxidized tetrathionate, thiosulfate and elemental Sulfur as the sole energy sources for autotrophic growth, and could also grow heterotrophically on a number of organic substrates. Based on its phylogenetic and phenotypic properties, strain TTNT represents a novel species of a novel genus, for which the name Sulfuriferula multivorans gen. nov., sp. nov. is proposed. The type strain is TTNT ( = NBRC 110683T = DSM 29343T). Along with this, the reclassification of ‘Thiobacillus plumbophilus’ as Sulfuriferula plumbophilus sp. nov. (type strain Gro7T = NBRC 107929T = DSM 6690T) is proposed. Based on the data obtained in this study, we describe the designations Sulfuricellaceae fam. nov. and Sulfuricellales ord. nov.
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Sulfuricurvum kujiense gen nov sp nov a facultatively anaerobic chemolithoautotrophic Sulfur Oxidizing Bacterium isolated from an underground crude oil storage cavity
International Journal of Systematic and Evolutionary Microbiology, 2004Co-Authors: Yumiko Kodama, Kazuya WatanabeAbstract:A facultatively anaerobic, chemolithoautotrophic, Sulfur-Oxidizing Bacterium, strain YK-1T, was isolated from an underground crude-oil storage cavity at Kuji in Iwate, Japan. The cells were motile, curved rods and had a single polar flagellum. Optimum growth occurred in a low-strength salt medium at pH 7·0 and 25 °C. It utilized sulfide, elemental Sulfur, thiosulfate and hydrogen as the electron donors and nitrate as the electron acceptor under anaerobic conditions, but it did not use nitrite. Oxygen also served as the electron acceptor under the microaerobic condition (O2 in the head space 1 %). It did not grow on sugars, organic acids or hydrocarbons as carbon and energy sources. The DNA G+C content of strain YK-1T was 45 mol%. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that its closest relative was Thiomicrospira denitrificans in the ‘Epsilonproteobacteria’, albeit with low homology (90 %). On the basis of physiological and phylogenetic data, strain YK-1T should be classified into a novel genus and species, for which the name Sulfuricurvum kujiense gen. nov., sp. nov. is proposed. The type strain is YK-1T (=JCM 11577T=MBIC 06352T=ATCC BAA-921T).
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Sulfuricurvum kujiense gen nov sp nov a facultatively anaerobic chemolithoautotrophic Sulfur Oxidizing Bacterium isolated from an underground crude oil storage cavity
International Journal of Systematic and Evolutionary Microbiology, 2004Co-Authors: Yumiko Kodama, Kazuya WatanabeAbstract:A facultatively anaerobic, chemolithoautotrophic, Sulfur-Oxidizing Bacterium, strain YK-1(T), was isolated from an underground crude-oil storage cavity at Kuji in Iwate, Japan. The cells were motile, curved rods and had a single polar flagellum. Optimum growth occurred in a low-strength salt medium at pH 7.0 and 25 degrees C. It utilized sulfide, elemental Sulfur, thiosulfate and hydrogen as the electron donors and nitrate as the electron acceptor under anaerobic conditions, but it did not use nitrite. Oxygen also served as the electron acceptor under the microaerobic condition (O(2) in the head space 1 %). It did not grow on sugars, organic acids or hydrocarbons as carbon and energy sources. The DNA G+C content of strain YK-1(T) was 45 mol%. Phylogenetic analysis, based on the 16S rRNA gene sequence, showed that its closest relative was Thiomicrospira denitrificans in the 'Epsilonproteobacteria', albeit with low homology (90 %). On the basis of physiological and phylogenetic data, strain YK-1(T) should be classified into a novel genus and species, for which the name Sulfuricurvum kujiense gen. nov., sp. nov. is proposed. The type strain is YK-1(T) (=JCM 11577(T)=MBIC 06352(T)=ATCC BAA-921(T)).
