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Kathleen M Scott - One of the best experts on this subject based on the ideXlab platform.
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diversity in co 2 concentrating mechanisms among chemolithoautotrophs from the genera hydrogenovibrio thiomicrorhabdus and Thiomicrospira ubiquitous in sulfidic habitats worldwide
Applied and Environmental Microbiology, 2019Co-Authors: Kathleen M Scott, Edward M Haller, Rich Boden, Dale Chaput, Tara L Harmer, Juliana M Leonard, Clare Dennison, Abigail Anderson, Tiffany Arnold, Samantha BudensteinAbstract:Members of the genera Hydrogenovibrio, Thiomicrospira, and Thiomicrorhabdus fix carbon at hydrothermal vents, coastal sediments, hypersaline lakes, and other sulfidic habitats. The genome sequences of these ubiquitous and prolific chemolithoautotrophs suggest a surprising diversity of mechanisms for the uptake and fixation of dissolved inorganic carbon (DIC); these mechanisms are verified here. Carboxysomes are apparent in the transmission electron micrographs of most of these organisms but are lacking in Thiomicrorhabdus sp. strain Milos-T2 and Thiomicrorhabdus arctica, and the inability of Thiomicrorhabdus sp. strain Milos-T2 to grow under low-DIC conditions is consistent with the absence of carboxysome loci in its genome. For the remaining organisms, genes encoding potential DIC transporters from four evolutionarily distinct families (Tcr_0853 and Tcr_0854, Chr, SbtA, and SulP) are located downstream of carboxysome loci. Transporter genes collocated with carboxysome loci, as well as some homologs located elsewhere on the chromosomes, had elevated transcript levels under low-DIC conditions, as assayed by reverse transcription-quantitative PCR (qRT-PCR). DIC uptake was measureable via silicone oil centrifugation when a representative of each of the four types of transporter was expressed in Escherichia coli The expression of these genes in the carbonic anhydrase-deficient E. coli strain EDCM636 enabled it to grow under low-DIC conditions, a result consistent with DIC transport by these proteins. The results from this study expand the range of DIC transporters within the SbtA and SulP transporter families, verify DIC uptake by transporters encoded by Tcr_0853 and Tcr_0854 and their homologs, and introduce DIC as a potential substrate for transporters from the Chr family.IMPORTANCE Autotrophic organisms take up and fix DIC, introducing carbon into the biological portion of the global carbon cycle. The mechanisms for DIC uptake and fixation by autotrophic Bacteria and Archaea are likely to be diverse but have been well characterized only for "Cyanobacteria" Based on genome sequences, members of the genera Hydrogenovibrio, Thiomicrospira, and Thiomicrorhabdus have a variety of mechanisms for DIC uptake and fixation. We verified that most of these organisms are capable of growing under low-DIC conditions, when they upregulate carboxysome loci and transporter genes collocated with these loci on their chromosomes. When these genes, which fall into four evolutionarily independent families of transporters, are expressed in E. coli, DIC transport is detected. This expansion in known DIC transporters across four families, from organisms from a variety of environments, provides insight into the ecophysiology of autotrophs, as well as a toolkit for engineering microorganisms for carbon-neutral biochemistries of industrial importance.
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genomes of ubiquitous marine and hypersaline hydrogenovibrio thiomicrorhabdus and Thiomicrospira spp encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments
Environmental Microbiology, 2018Co-Authors: Kathleen M Scott, Tara L Harmer, Km Antonen, Gj Camper, John Williams, Sydney Russel, Cody M B Porter, John H Paul, Megan K Bridges, Ck CamplaAbstract:Chemolithoautotrophic bacteria from the genera Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira are common, sometimes dominant, isolates from sulfidic habitats including hydrothermal vents, soda and salt lakes and marine sediments. Their genome sequences confirm their membership in a deeply branching clade of the Gammaproteobacteria. Several adaptations to heterogeneous habitats are apparent. Their genomes include large numbers of genes for sensing and responding to their environment (EAL- and GGDEF-domain proteins and methyl-accepting chemotaxis proteins) despite their small sizes (2.1-3.1 Mbp). An array of sulfur-oxidizing complexes are encoded, likely to facilitate these organisms' use of multiple forms of reduced sulfur as electron donors. Hydrogenase genes are present in some taxa, including group 1d and 2b hydrogenases in Hydrogenovibrio marinus and H. thermophilus MA2-6, acquired via horizontal gene transfer. In addition to high-affinity cbb3 cytochrome c oxidase, some also encode cytochrome bd-type quinol oxidase or ba3 -type cytochrome c oxidase, which could facilitate growth under different oxygen tensions, or maintain redox balance. Carboxysome operons are present in most, with genes downstream encoding transporters from four evolutionarily distinct families, which may act with the carboxysomes to form CO2 concentrating mechanisms. These adaptations to habitat variability likely contribute to the cosmopolitan distribution of these organisms.
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Reclassification of Thiomicrospira hydrogeniphila (Watsuji et al. 2016) to Thiomicrorhabdus hydrogenophila comb. nov., with emended description of Thiomicrorhabdus (Boden et al., 2017)
International Journal of Systematic and Evolutionary Microbiology, 2017Co-Authors: Rich Boden, Kathleen M Scott, Lee P. HuttAbstract:The genus Thiomicrorhabdus (Tmr) in the Piskirickettsiaceae in the Thiotrichales of the Gammaproteobacteria contains four species of sulfur-oxidising obligate chemolithoautotroph with validly published names, all previously classified as Thiomicrospira (Tms) species. Here we demonstrate that Thiomicrospira hydrogeniphila , a recently published hydrogen-utilising chemolithoautotroph closely related to Thiomicrorhabdus frisia (type species of Thiomicrorhabdus ) should be classified as a member of the genus Thiomicrorhabdus and not Thiomicrospira , as Thiomicrorhabdus hydrogeniphila comb. nov., on the basis of comparative physiology and morphology as well as 16S rRNA (rrs) gene identity of Tms. hydrogeniphila MAS2T being closer to that of Tmr. frisia JB-A2T (99.1 %) than to Tms. pelophila DSM 1534T (90.5 %) or Hydrogenovibrio marinus MH-110T (94.1 %), and on the basis of the topology of 16S rRNA gene maximum likelihood trees, which clearly place Tms. hydrogeniphila within the genus Thiomicrorhabdus . It was also noted that thiosulfate-grown Thiomicrorhabdus spp. can be distinguished from Thiomicrospira spp. or Hydrogenovibrio spp. on the basis of the 3 dominant fatty acids (C16 : 1, C18 : 1 and C16 : 0), and from other Thiomicrorhabdus spp. on the basis of the fourth dominant fatty acid, which varies between the species of this genus – which could provide a useful diagnostic method. We provide an emended description of Thiomicrorhabdus (Boden R, Scott KM, Williams J, Russel S, Antonen K et al. Int J Syst Evol Microbiol 2017;67:1140–1151) to take into account the properties of Thiomicrorhabdus hydrogeniphila comb. nov.
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an evaluation of Thiomicrospira hydrogenovibrio and thioalkalimicrobium reclassification of four species of Thiomicrospira to each thiomicrorhabdus gen nov and hydrogenovibrio and reclassification of all four species of thioalkalimicrobium to Thiomicrospira
International Journal of Systematic and Evolutionary Microbiology, 2017Co-Authors: Rich Boden, Kathleen M Scott, John Williams, Sydney Russel, Kirsten Antonen, Alex W Rae, Lee P. HuttAbstract:Thiomicrospira(Tms) species are small sulfur-oxidizing chemolithoautotrophic members of the Gammaproteobacteria. Whilst the type species Tms. pelophila and closely related Tms. thyasirae exhibit canonical spiral morphology under sub-optimal growth conditions, most species are vibrios or rods. The 16S rRNA gene diversity is vast, with identities as low as 91.6 % for Tms. pelophila versus Tms. frisia, for example. Thiomicrospira was examined with closely related genera Hydrogenovibrio and Thioalkalimicrobium and, to rationalize organisms on the basis of the 16S rRNA gene phylogeny, physiology and morphology, we reclassify Tms. kuenenii, Tms. crunogena, Tms. thermophila and Tms. halophila to Hydrogenovibrio kuenenii comb. nov., H. crunogenus corrig. comb. nov., H. thermophilus corrig. comb. nov. and H. halophilus corrig. comb. nov. We reclassify Tms. frisia, Tms. arctica, Tms. psychrophila and Tms. chilensis to Thiomicrorhabdus (Tmr) gen. nov., as Tmr. frisia comb. nov., Tmr. arctica comb. nov., Tmr. psychrophila comb. nov. and Tmr. chilensis comb. nov. - the type species of Thiomicrorhabdus is Tmr. frisia. We demonstrate that Thioalkalimicrobium species fall within the genus Thiomicrospira sensu stricto, thus reclassifying them as Tms. aerophila corrig. comb. nov., Tms. microaerophila corrig. comb. nov., Tms. cyclica corrig. comb. nov. and Tms. sibirica corrig. comb. nov. We provide emended descriptions of the genera Thiomicrospira and Hydrogenovibrio and of Tms. thyasirae.
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Dissolved inorganic carbon uptake in Thiomicrospira crunogena XCL-2 is Δp- and ATP-sensitive and enhances RubisCO-mediated carbon fixation
Archives of Microbiology, 2016Co-Authors: Kristy J. Menning, Balaraj B. Menon, Kathleen M ScottAbstract:The gammaproteobacterium Thiomicrospira crunogena XCL-2 is an aerobic sulfur-oxidizing hydrothermal vent chemolithoautotroph that has a CO_2 concentrating mechanism (CCM), which generates intracellular dissolved inorganic carbon (DIC) concentrations much higher than extracellular, thereby providing substrate for carbon fixation at sufficient rate. This CCM presumably requires at least one active DIC transporter to generate the elevated intracellular concentrations of DIC measured in this organism. In this study, the half-saturation constant ( K _CO2) for purified carboxysomal RubisCO was measured (276 ± 18 µM) which was much greater than the K _CO2 of whole cells (1.03 µM), highlighting the degree to which the CCM facilitates CO_2 fixation under low CO_2 conditions. To clarify the bioenergetics powering active DIC uptake, cells were incubated in the presence of inhibitors targeting ATP synthesis (DCCD) or proton potential (CCCP). Incubations with each of these inhibitors resulted in diminished intracellular ATP, DIC, and fixed carbon, despite an absence of an inhibitory effect on proton potential in the DCCD-incubated cells. Electron transport complexes NADH dehydrogenase and the bc _1 complex were found to be insensitive to DCCD, suggesting that ATP synthase was the primary target of DCCD. Given the correlation of DIC uptake to the intracellular ATP concentration, the ABC transporter genes were targeted by qRT-PCR, but were not upregulated under low-DIC conditions. As the T. crunogena genome does not include orthologs of any genes encoding known DIC uptake systems, these data suggest that a novel, yet to be identified, ATP- and proton potential-dependent DIC transporter is active in this bacterium. This transporter serves to facilitate growth by T. crunogena and other Thiomicrospira s in the many habitats where they are found.
Daniel Barker - One of the best experts on this subject based on the ideXlab platform.
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comparison of the protein coding genomes of three deep sea sulfur oxidising bacteria candidatus ruthia magnifica candidatus vesicomyosocius okutanii and Thiomicrospira crunogena
BMC Research Notes, 2017Co-Authors: Susan Mcgill, Daniel BarkerAbstract:“ Candidatus Ruthia magnifica”, “Candidatus Vesicomyosocius okutanii” and Thiomicrospira crunogena are all sulfur-oxidising bacteria found in deep-sea vent environments. Recent research suggests that the two symbiotic organisms, “Candidatus R. magnifica” and “Candidatus V. okutanii”, may share common ancestry with the autonomously living species T. crunogena. We used comparative genomics to examine the genome-wide protein-coding content of all three species to explore their similarities. In particular, we used the OrthoMCL algorithm to sort proteins into groups of putative orthologs on the basis of sequence similarity. The OrthoMCL inflation parameter was tuned using biological criteria. Using the tuned value, OrthoMCL delimited 1070 protein groups. 63.5% of these groups contained one protein from each species. Two groups contained duplicate protein copies from all three species. 123 groups were unique to T. crunogena and ten groups included multiple copies of T. crunogena proteins but only single copies from the other species. “Candidatus R. magnifica” had one unique group, and had multiple copies in one group where the other species had a single copy. There were no groups unique to “Candidatus V. okutanii”, and no groups in which there were multiple “Candidatus V. okutanii” proteins but only single proteins from the other species. Results align with previous suggestions that all three species share a common ancestor. However this is not definitive evidence to make taxonomic conclusions and the possibility of horizontal gene transfer was not investigated. Methodologically, the tuning of the OrthoMCL inflation parameter using biological criteria provides further methods to refine the OrthoMCL procedure.
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Comparison of the protein-coding genomes of three deep-sea, sulfur-oxidising bacteria: “Candidatus Ruthia magnifica”, “Candidatus Vesicomyosocius okutanii” and Thiomicrospira crunogena
'Springer Science and Business Media LLC', 2017Co-Authors: Susan E. Mcgill, Daniel BarkerAbstract:Abstract Objective “ Candidatus Ruthia magnifica”, “Candidatus Vesicomyosocius okutanii” and Thiomicrospira crunogena are all sulfur-oxidising bacteria found in deep-sea vent environments. Recent research suggests that the two symbiotic organisms, “Candidatus R. magnifica” and “Candidatus V. okutanii”, may share common ancestry with the autonomously living species T. crunogena. We used comparative genomics to examine the genome-wide protein-coding content of all three species to explore their similarities. In particular, we used the OrthoMCL algorithm to sort proteins into groups of putative orthologs on the basis of sequence similarity. Results The OrthoMCL inflation parameter was tuned using biological criteria. Using the tuned value, OrthoMCL delimited 1070 protein groups. 63.5% of these groups contained one protein from each species. Two groups contained duplicate protein copies from all three species. 123 groups were unique to T. crunogena and ten groups included multiple copies of T. crunogena proteins but only single copies from the other species. “Candidatus R. magnifica” had one unique group, and had multiple copies in one group where the other species had a single copy. There were no groups unique to “Candidatus V. okutanii”, and no groups in which there were multiple “Candidatus V. okutanii” proteins but only single proteins from the other species. Results align with previous suggestions that all three species share a common ancestor. However this is not definitive evidence to make taxonomic conclusions and the possibility of horizontal gene transfer was not investigated. Methodologically, the tuning of the OrthoMCL inflation parameter using biological criteria provides further methods to refine the OrthoMCL procedure
Gerard Muyzer - One of the best experts on this subject based on the ideXlab platform.
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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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distribution and diversity of sulfur oxidizing Thiomicrospira spp at a shallow water hydrothermal vent in the aegean sea milos greece
Applied and Environmental Microbiology, 1999Co-Authors: Thorsten Brinkhoff, Stefan M Sievert, Jan Kuever, Gerard MuyzerAbstract:A shallow-water hydrothermal vent system in the Aegean Sea close to the island of Milos (Greece) was chosen to study the diversity and distribution of the chemolithoautotrophic sulfur-oxidizing bacterium Thiomicrospira. Cell numbers in samples from different regions around a solitary vent decreased toward the center of the vent (horizontal distribution), as well as with depth (vertical distribution), corresponding to an increase in temperature (from ca. 25 to 60 degrees C) and a decrease in pH (from ca. pH 7 to 5). Thiomicrospira was one of the most abundant culturable sulfur oxidizers and was even dominant in one region. Phylogenetic analysis of Thiomicrospira spp. present in the highest most-probable-number (MPN) dilutions revealed that most of the obtained sequences grouped in two new closely related clusters within the Thiomicrospira branch. Two different new isolates, i.e., Milos-T1 and Milos-T2, were obtained from high-dilution (10(-5)) enrichments. Phylogenetic analysis indicated that isolate Milos-T1 is related to the recently described Thiomicrospira kuenenii and Hydrogenovibrio marinus, whereas isolate Milos-T2 grouped with the MPN sequences of cluster 2. The predominance of strain Milos-T2 was indicated by its identification in several environmental samples by hybridization analysis of denaturing gradient gel electrophoresis (DGGE) patterns and by sequencing of one of the corresponding bands, i.e., ML-1, from the DGGE gel. The results shown in this paper support earlier indications that Thiomicrospira species are important members of hydrothermal vent communities.
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a polyphasic approach to study the diversity and vertical distribution of sulfur oxidizing Thiomicrospira species in coastal sediments of the german wadden sea
Ninth Annual V. M. Goldschmidt Conference, 1999Co-Authors: Thorsten Brinkhoff, Jan Kuever, Cecilia M Santegoeds, Kerstin Sahm, Gerard MuyzerAbstract:The rRNA approach (25, 26), which involves using rRNA as a molecular marker to detect and identify particular bacteria in their natural habitats (3) and to explore microbial diversity without cultivation (6, 7), is routinely used in microbial ecological studies. In some studies, the molecular approach has been combined with microbiological methods in an attempt to isolate the relevant microorganisms (13). In other studies molecular biological techniques have been used in combination with geochemical techniques or with microsensors (see reference 4 for an overview) to characterize environmental parameters. However, molecular biological techniques, microbiological methods, and geochemical techniques or microsensors have been used together in only a few studies (28, 37). Nevertheless, combining techniques and concepts from different disciplines is necessary to obtain a better understanding of the interactions between microorganisms and their natural environments, which is the aim of microbial ecology. Here we describe the use of a comprehensive approach to study the functional role of different closely related Thiomicrospira strains in one habitat, an intertidal mud flat. Thiomicrospira species are chemolithoautotrophic bacteria that use reduced sulfur compounds as energy sources and CO2 as a carbon source; they are obligate aerobes (18). 16S rRNA sequence comparisons have shown that these organisms form a monophyletic group within the gamma subdivision of the class Proteobacteria (8, 22). In a recent study we demonstrated the ubiquity of the genus Thiomicrospira in environments in which reduced sulfur compounds are present (8). In addition, we were able to isolate Thiomicrospira species from most of these habitats and demonstrated that the species diversity within this genus is high. Four isolates, strains JB-A1, JB-A1F, JB-A2, and JB-B2, were obtained from a sample taken from an intertidal coastal mud flat of the Jadebusen Bay, which is part of the German Wadden Sea. Comparative sequence analysis of their 16S rRNA genes demonstrated that these isolates were phylogenetically affiliated with different members of the genus Thiomicrospira. Two of the isolates from the Jadebusen sediment, strains JB-A1 and JB-A2, were biochemically and physiologically characterized and were recently described by Brinkhoff and coworkers (9) as members of two new species of the genus Thiomicrospira (17), Thiomicrospira kuenenii (JB-A1) and Thiomicrospira frisia (JB-A2). Another isolate, strain JB-A1F, had a 16S rRNA sequence that was identical to the 16S rRNA sequence of Thiomicrospira pelophila (17). The fourth isolate, JB-B2, was phylogenetically related to Thiomicrospira crunogena. In addition to our isolates, members of three Thiomicrospira species, T. pelophila (17), Thiomicrospira denitrificans (39), and Thiomicrospira thyasirae (46, 47), were isolated from this habitat. The presence in one habitat of several Thiomicrospira isolates that exhibited only minor differences in their genotypic and phenotypic features prompted us to study the abundance and vertical distribution of the organisms in the sediment in order to determine niche differentiation. To do this, we used tools and techniques from different disciplines. Microsensor measurements were performed with sediment cores to determine environmental parameters, such as oxygen and sulfide contents and pH (19, 31). In parallel, two additional cores were sliced, and the slices were used for molecular biological and microbiological analyses. The most-probable-number (MPN) technique was used to determine the relative abundance of chemolithoautotrophic sulfur-oxidizing bacteria. A genus-specific PCR (8) allowed us to detect Thiomicrospira species in the cultures. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S ribosomal DNA (rDNA) fragments (see reference 24 for an overview) obtained after enzymatic amplification with primers specific for the domain Bacteria, followed by hybridization analysis with a Thiomicrospira-specific oligonucleotide probe (8), was used to identify different Thiomicrospira strains in the MPN tubes. In addition, primers specific for Thiomicrospira 16S rDNA (8) were used to obtain DNA fragments for a sequence analysis. rRNA slot blot hybridization (29, 36) was performed to determine the abundance of 16S rRNA in different sediment layers and to infer the physiological status of the Thiomicrospira populations present. The results of this polyphasic approach showed that many different Thiomicrospira populations were present down to a depth of 40 mm. As a significant amount of Thiomicrospira-specific rRNA was present only in the oxic layer of the sediment, we concluded that only the Thiomicrospira populations living in the oxic part of the sediment were metabolically active.
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Thiomicrospira chilensis sp nov a mesophilic obligately chemolithoautotrophic sulfur oxidizing bacterium isolated from a thioploca mat
International Journal of Systematic and Evolutionary Microbiology, 1999Co-Authors: Thorsten Brinkhoff, Carl O. Wirsen, Gerard Muyzer, Jan KueverAbstract:A new member of the genus Thiomicrospira, which utilizes thiosulfate as the electron donor and CO2 as the carbon source, was isolated from a sediment sample dominated by the filamentous sulfur bacterium Thioploca. Although the physiological properties investigated are nearly identical to other described species of the genus, it is proposed that strain Ch-1Tis a member of new species, Thiomicrospira chilensis sp. nov., on the basis of differences in genotypic characteristics (16S rRNA sequence, DNA homology, G+C content). Strain Ch-1Twas highly motile with a slight tendency to form aggregates in the stationary growth phase. The organism was obligately autotrophic and strictly aerobic. Nitrate was not used as an electron acceptor. Chemolithoautotrophic growth was observed with thiosulfate, tetrathionate, sulfur and sulfide. The isolate was not able to grow heterotrophically. Growth of strain Ch-1Twas observed between pH 5·3 and 8·5 with an optimum at pH 7·0. The temperature range for growth was between 3·5 and 42 °C; the optimal growth temperature was between 32 and 37°C. The mean maximum growth rate on thiosulfate was 0·4 h-1. This is the second Thiomicrospira species described that has a rodshaped morphology; therefore discrimination between vibrio-shaped Thiomicrospira and rod-shaped Thiobacilli is no longer valid.
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Thiomicrospira kuenenii sp nov and Thiomicrospira frisia sp nov two mesophilic obligately chemolithoautotrophic sulfur oxidizing bacteria isolated from an intertidal mud flat
International Journal of Systematic and Evolutionary Microbiology, 1999Co-Authors: Thorsten Brinkhoff, Carl O. Wirsen, Gerard Muyzer, Jan KueverAbstract:Two new members of the genus Thiomicrospira were isolated from an intertidal mud flat sample with thiosulfate as the electron donor and CO2 as carbon source. On the basis of differences in genotypic and phenotypic characteristics, it is proposed that strain JB-A1T (= DSM 12350T) and strain JB-A2T (= DSM 12351T) are members of two new species, Thiomicrospira kuenenii and Thiomicrospira frisia, respectively. The cells were Gram-negative vibrios or slightly bent rods. Strain JB-A1T was highly motile, whereas strain JB-A2T showed a much lower degree of motility combined with a strong tendency to form aggregates. Both organisms were obligately autotrophic and strictly aerobic. Nitrate was not used as electron acceptor. Chemolithoautotrophic growth was observed with thiosulfate, tetrathionate, sulfur and sulfide. Neither isolate was able to grow heterotrophically. For strain JB-A1T, growth was observed between pH values of 4·0 and 7·5 with an optimum at pH 6·0, whereas for strain JB-A2T, growth was observed between pH 4·2 and 8·5 with an optimum at pH 6·5. The temperature limits for growth were between 3·5 and 42°C and 3·5 and 39 °C, respectively. The optimum growth temperature for strain JB-A1T was between 29 and 33·5 °C, whereas strain JB-A2T showed optimal growth between 32 and 35 °C. The mean maximum growth rate on thiosulfate was 0·35 h-1for strain JB-A1T and 0·45 h-1for strain JB-A2T.
Kazuya Watanabe - One of the best experts on this subject based on the ideXlab platform.
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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)).
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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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molecular characterization of bacterial populations in petroleum contaminated groundwater discharged from underground crude oil storage cavities
Applied and Environmental Microbiology, 2000Co-Authors: Kazuya Watanabe, Kazuaki Syutsubo, Yumiko Kodama, Kanako Watanabe, Shigeaki HarayamaAbstract:Petroleum-contaminated groundwater discharged from underground crude oil storage cavities (cavity groundwater) harbored more than 106 microorganisms ml−1, a density 100 times higher than the densities in groundwater around the cavities (control groundwater). To characterize bacterial populations growing in the cavity groundwater, 46 PCR-amplified almost full-length 16S ribosomal DNA (rDNA) fragments were cloned and sequenced, and 28 different sequences were obtained. All of the sequences were affiliated with the Proteobacteria; 25 sequences (43 clones) were affiliated with the epsilon subclass, 2 were affiliated with the beta subclass, and 1 was affiliated with the delta subclass. Two major clusters (designated clusters 1 and 2) were found for the epsilon subclass proteobacterial clones; cluster 1 (25 clones) was most closely related to Thiomicrospira denitrificans (88% identical in nucleotide sequence), while cluster 2 (11 clones) was closely related to Arcobacterspp. Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rDNA fragments showed that one band was detected most strongly in cavity groundwater profiles independent of storage oil type and season. The sequence of this major band was identical to the sequences of most of the cluster 1 clones. Fluorescence in situ hybridization (FISH) indicated that the cluster 1 population accounted for 12 to 24% of the total bacterial population. This phylotype was not detected in the control groundwater by DGGE and FISH analyses. These results indicate that the novel members of the epsilon subclass of the Proteobacteria grow as major populations in the petroleum-contaminated cavity groundwater.
Stefan M Sievert - One of the best experts on this subject based on the ideXlab platform.
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Calvin-Benson-Bassham Cycle Gene Organization in Proteobacteria
2013Co-Authors: Kathleen M Scott, Fereniki N Abril, Lois A Ball, Chantell J Barrett, Rodrigo A Blake, Amanda J Boller, Patrick S G Chain, Stefan M Sievert, Justine A Clark, Carisa R DavisAbstract:RubisCO genes (cbbLS and cbbM) are green, phosphoribulokinase genes (cbbP) are red, other genes encoding Calvin-Benson-Bassham cycle enzymes are black, and carboxysome structural genes are grey. For species in which cbbP is not near cbbLS or cbbM, the distance from the RubisCO gene to cbbP in kbp is indicated in parentheses. Thiob. denitrificans has two cbbP genes, so two distances are indicated for this species. Names of organisms that are unable to grow well as organoheterotrophs are boxed. Abbreviations and accession numbers for the 16S sequences used to construct the cladogram are as follows: A. ehrlichei, Alkalilimnicola ehrlichei, AF406554; Brady. sp., Bradyrhizobium sp., AF338169;B. japonicum, Bradyrhizobium japonicum, D13430; B. xenovorans, Burkholderia xenovorans, U86373; D. aromatica, Dechloromonas aromatica, AY032610; M. magneticum, Magnetospirillum magneticum, D17514; M. capsulatus, Methylococcus capsulatus BATH, AF331869; N. hamburgensis, Nitrobacter hamburgensis, L11663; N. winogradskyi, Nitrobacter winogradskyi, L11661; N. oceani, Nitrosococcus oceani, AF363287; N. europaea, Nitrosomonas europaea, BX321856; N. multiformis, Nitrosospira multiformis, L35509; P. denitrificans, Paracoccus denitrificans, X69159; R. sphaeroides, Rhodobacter sphaeroides, CP000144; R. ferrireducens, Rhodoferax ferrireducens, AF435948; R. palustris, Rhodopseudomonas palustris, NC 005296; R. rubrum, Rhodospirillum rubrum, D30778; R. gelatinosus, Rubrivivax gelatinosus, M60682; S. meliloti, Sinorhizobium meliloti, D14509; T. denitrificans, Thiobacillus denitrificans, AJ43144; T. crunogena, Thiomicrospira crunogena, AF064545. The cladogram was based on an alignment of 1,622 bp of the 16S rRNA genes, and is the most parsimonious tree (length 2,735) resulting from a heuristic search with 100 replicate random step-wise addition and TBR branch swapping (PAUP*4.0b10 [113]). Sequences were aligned using ClustalW [114], as implemented in BioEdit. Percent similarities and identities for cbbL, cbbM, and cbbP gene products, as well as gene locus tags, are provided as supporting information (Table S4).
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the genome of deep sea vent chemolithoautotroph Thiomicrospira crunogena xcl 2
PLOS Biology, 2006Co-Authors: Kathleen M Scott, Fereniki N Abril, Lois A Ball, Chantell J Barrett, Rodrigo A Blake, Amanda J Boller, Patrick S G Chain, Stefan M Sievert, Justine ClarkAbstract:Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 base pairs), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of coding sequences (CDSs) encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. Thiom. crunogena XCL-2 is unusual among obligate sulfur-oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.
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the genome of deep sea vent chemolithoautotroph Thiomicrospira crunogena xcl 2
Lawrence Berkeley National Laboratory, 2006Co-Authors: Kathleen M Scott, Fereniki N Abril, Lois A Ball, Chantell J Barrett, Rodrigo A Blake, Amanda J Boller, Patrick S G Chain, Stefan M Sievert, Justine ClarkAbstract:Presented here is the complete genome sequence of Thiomicrospira crunogena XCL-2, representative of ubiquitous chemolithoautotrophic sulfur-oxidizing bacteria isolated from deep-sea hydrothermal vents. This gammaproteobacterium has a single chromosome (2,427,734 bp), and its genome illustrates many of the adaptations that have enabled it to thrive at vents globally. It has 14 methyl-accepting chemotaxis protein genes, including four that may assist in positioning it in the redoxcline. A relative abundance of CDSs encoding regulatory proteins likely control the expression of genes encoding carboxysomes, multiple dissolved inorganic nitrogen and phosphate transporters, as well as a phosphonate operon, which provide this species with a variety of options for acquiring these substrates from the environment. T. crunogena XCL-2 is unusual among obligate sulfur oxidizing bacteria in relying on the Sox system for the oxidation of reduced sulfur compounds. A 38 kb prophage is present, and a high level of prophage induction was observed, which may play a role in keeping competing populations of close relatives in check. The genome has characteristics consistent with an obligately chemolithoautotrophic lifestyle, including few transporters predicted to have organic allocrits, and Calvin-Benson-Bassham cycle CDSs scattered throughout the genome.
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evidence for autotrophic co2 fixation via the reductive tricarboxylic acid cycle by members of the e subdivision of proteobacteria
Journal of Bacteriology, 2005Co-Authors: Stefan M Sievert, Carl O. Wirsen, Michael Hügler, Georg Fuchs, Craig D. TaylorAbstract:Based on 16S rRNA gene surveys, bacteria of the e subdivision of proteobacteria have been identified to be important members of microbial communities in a variety of environments, and quite a few have been demonstrated to grow autotrophically. However, no information exists on what pathway of autotrophic carbon fixation these bacteria might use. In this study, Thiomicrospira denitrificans and Candidatus Arcobacter sulfidicus, two chemolithoautotrophic sulfur oxidizers of the e subdivision of proteobacteria, were examined for activities of the key enzymes of the known autotrophic CO 2 fixation pathways. Both organisms contained activities of the key enzymes of the reductive tricarboxylic acid cycle, ATP citrate lyase, 2-oxoglutarate:ferredoxin oxidoreductase, and pyruvate:ferredoxin oxidoreductase. Furthermore, no activities of key enzymes of other CO 2 fixation pathways, such as the Calvin cycle, the reductive acetyl coenzyme A pathway, and the 3-hydroxypropionate cycle, could be detected. In addition to the key enzymes, the activities of the other enzymes involved in the reductive tricarboxylic acid cycle could be measured. Sections of the genes encoding the α- and β-subunits of ATP citrate lyase could be amplified from both organisms. These findings represent the first direct evidence for the operation of the reductive tricarboxylic acid cycle for autotrophic CO 2 fixation in e-proteobacteria. Since e-proteobacteria closely related to these two organisms are important in many habitats, such as hydrothermal vents, oxic-sulfidic interfaces, or oilfields, these results suggest that autotrophic CO 2 fixation via the reductive tricarboxylic acid cycle might be more important than previously considered.
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characterization of an autotrophic sulfide oxidizing marine arcobacter sp that produces filamentous sulfur
Applied and Environmental Microbiology, 2002Co-Authors: Carl O. Wirsen, Stefan M Sievert, Colleen M Cavanaugh, Stephen J Molyneaux, Azeem Ahmad, L T Taylor, Edward F Delong, Craig D. TaylorAbstract:A coastal marine sulfide-oxidizing autotrophic bacterium produces hydrophilic filamentous sulfur as a novel metabolic end product. Phylogenetic analysis placed the organism in the genus Arcobacter in the epsilon subdivision of the Proteobacteria. This motile vibrioid organism can be considered difficult to grow, preferring to grow under microaerophilic conditions in flowing systems in which a sulfide-oxygen gradient has been established. Purified cell cultures were maintained by using this approach. Essentially all 4′,6-diamidino-2-phenylindole dihydrochloride-stained cells in a flowing reactor system hybridized with Arcobacter-specific probes as well as with a probe specific for the sequence obtained from reactor-grown cells. The proposed provisional name for the coastal isolate is “Candidatus Arcobacter sulfidicus.” For cells cultured in a flowing reactor system, the sulfide optimum was higher than and the CO2 fixation activity was as high as or higher than those reported for other sulfur oxidizers, such as Thiomicrospira spp. Cells associated with filamentous sulfur material demonstrated nitrogen fixation capability. No ribulose 1,5-bisphosphate carboxylase/oxygenase could be detected on the basis of radioisotopic activity or by Western blotting techniques, suggesting an alternative pathway of CO2 fixation. The process of microbial filamentous sulfur formation has been documented in a number of marine environments where both sulfide and oxygen are available. Filamentous sulfur formation by “Candidatus Arcobacter sulfidicus” or similar strains may be an ecologically important process, contributing significantly to primary production in such environments.
