DOCSLIB.ORG

Permanent Draft Genome of Thiobacillus Thioparus DSM 505T, an Obligately Chemolithoautotrophic Member of the Betaproteobacteria

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Permanent Draft Genome of Thiobacillus Thioparus DSM 505T, an Obligately Chemolithoautotrophic Member of the Betaproteobacteria Hutt et al. Standards in Genomic Sciences (2017) 12:10 DOI 10.1186/s40793-017-0229-3 SHORT GENOME REPORT Open Access Permanent draft genome of Thiobacillus thioparus DSM 505T, an obligately chemolithoautotrophic member of the Betaproteobacteria Lee P. Hutt1,2, Marcel Huntemann3, Alicia Clum3, Manoj Pillay3, Krishnaveni Palaniappan3, Neha Varghese3, Natalia Mikhailova3, Dimitrios Stamatis3, Tatiparthi Reddy3, Chris Daum3, Nicole Shapiro3, Natalia Ivanova3, Nikos Kyrpides3, Tanja Woyke3 and Rich Boden1,2* Abstract Thiobacillus thioparus DSM 505T is one of first two isolated strains of inorganic sulfur-oxidising Bacteria. The original strain of T. thioparus was lost almost 100 years ago and the working type strain is Culture CT (=DSM 505T = ATCC 8158T) isolated by Starkey in 1934 from agricultural soil at Rutgers University, New Jersey, USA. It is an obligate chemolithoautotroph that conserves energy from the oxidation of reduced inorganic sulfur compounds using the Kelly-Trudinger pathway and uses it to fix carbon dioxide It is not capable of heterotrophic or mixotrophic growth. The strain has a genome size of 3,201,518 bp. Here we report the genome sequence, annotation and characteristics. The genome contains 3,135 protein coding and 62 RNA coding genes. Genes encoding the transaldolase variant of the Calvin-Benson-Bassham cycle were also identified and an operon encoding carboxysomes, along with Smith’s biosynthetic horseshoe in lieu of Krebs’ cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). There is a partial sox operon of the Kelly-Friedrich pathway of inorganic sulfur-oxidation that contains soxXYZAB genes but lacking soxCDEF, there is also a lack of the DUF302 gene previously noted in the sox operon of other members of the ‘Proteobacteria’ that can use trithionate as an energy source. In spite of apparently not growing anaerobically with denitrification, the nar, nir, nor and nos operons encoding enzymes of denitrification are found in the T. thioparus genome, in the same arrangements as in the true denitrifier T. denitrificans. Keywords: Thiobacillus thioparus, Betaproteobacteria, Sulfur oxidation, Chemolithoautotroph, Carboxysome, Denitrification Introduction Betaproteobacteria) and the type strain is an isolate from In 1902, Thiobacillus thioparus was one of the first two Starkey (1934) (= Culture CT = DSM 505T =ATCC obligately chemolithoautrophic sulfur-oxidizing Bacteria 8158T = CIP 104484T = JCM 3859T = NBRC 103402T) to be isolated, (along with what is now Halothiobacillus [3, 4]. Originally, the characteristic of utilizing inorganic neapolitanus), and was named in 1904 [1, 2]. The ori- sulfur compounds as an energy source was thought to ginal isolates were lost, but Thiobacillus thioparus is be a taxonomic trait unique to Thiobacillus and at its now the type species of the genus (a member of the height the genus contained in at least 32 different ‘spe- cies’ [4]. With phylogenetic methods however, many of * Correspondence: [email protected] these strains have since been reassigned to different, T 1School of Biological and Marine Sciences, University of Plymouth, Drake often new genera with T. thioparus DSM 505 being one Circus, Plymouth PL4 8AA, UK of four species with validly published names left in the 2Sustainable Earth Institute, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK genus. Compared to other inorganic sulfur-oxidisers, Full list of author information is available at the end of the article surprisingly little research has been conducted on T. © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Hutt et al. Standards in Genomic Sciences (2017) 12:10 Page 2 of 8 thioparus DSM 505T in terms of physiology and bio- electron acceptor – nitrate, nitrite, thiosulfate, sulfate, chemistry or genetics, possibly due to the low growth elementary sulfur and ferric iron do not support growth yields of this species when compared to T. denitrificans as terminal electron acceptors. The genomic DNA G + C and T. aquaesulis [5, 6] making it more challenging to content has been estimated using the thermal denatur- study. It may, however, give extended and contrasted in- ation [11] at 61–62 mol% [7, 10]. T. thioparus DSM sights into autotrophic sulfur-oxidation in the Bacteria. 505T does not grow on any organic carbon compound It was selected for genome sequencing as part of the De- tested, including sugars (glucose, ribose, fructose, su- partment of Energy DOE-CSP 2012 initiative – as type crose), intermediates of Krebs’ cycle (citrate, succinate, species of a genus. fumarate, malate, oxaloacetate), carboxylates (glycolate, formate, acetate, propionate, pyruvate), one-carbon com- Organism information pounds (monomethylamine, dimethylamine, trimethyla- Classification and features mine, methanol, methane), structural amino acids (all Thiobacillus thioparus DSM 505T was isolated from 20), substituted thiophenes (thiophene-2-carboxylate, sandy loam soil from the New Jersey Agricultural Ex- thiophene-3-carboxylate) or complex media (yeast ex- perimental Station planted with unspecified vegetable tract, nutrient broth, brain-heart infusion, Columbia crops using 20mM thiosulfate as sole energy source in sheep or horse blood agar, chocolate agar). Energy basal medium at pH 8.5 by Starkey (1934) [3] and is cur- sources that support autotrophic growth of DSM 505T rently one of four species with validly published names include thiosulfate, trithionate, tetrathionate, pentathio- within the genus. It forms small white colonies of 1– nate, hexathionate, thiocyanate and dithionate. Some 3 mm diameter after 2–3 days that turn pink or brown bone fide strains of T. thioparus (Tk-m and E6) grow au- with age and which become coated with yellow-ish totrophically on carbon disulfide, dimethylsulfide, elementary sulfur. When grown in liquid media, finely dimethyldisulfide and Admidate (O,O-dimethylpho- divided (white) elementary sulfur is formed during early sphoramidothioate) [4], but it is not known if the type stages of growth, particularly when thiosulfate is used as strain DSM 505T is capable of this. Autotrophic growth the energy source. This disappears when growth ap- is not supported by Fe(II), Mn(II), Cu(I), U(IV), sulfite, proaches stationary phase. Thiosulfate is oxidized stoi- dimethylsulfoxide, dimethylsulfone, pyrite or formate. chiometrically to tetrathionate after 24 h accompanied During batch growth on thiosulfate the intermediate by a rise in pH, characteristic of the Kelly-Trudinger production of tetrathionate is observed during early pathway. Tetrathionate is subsequently oxidized to sul- stages of growth, indicative of the Kelly-Trudinger path- fate with culture pH falling to pH 4.8 by stationary way [12]. Compared to the other two members of the phase. During continuous culture, no intermediates are genus [5, 6], T. thioparus DSM 505T has relatively low detected in the medium once steady-state has been growth yields on thiosulfate (Hutt and Boden, manu- established. If the dilution rate of a thiosulfate limited script in preparation) which may give insight into the chemostat is increased, a large production of elementary physiological variances of Kelly-Trudinger pathway or- sulfur is observed, which disappears as a new steady- ganisms even within one genus. state is established at the faster dilution rate. General features of T. thioparus DSM 505T are summarized in Genome sequencing information Table 1. A phylogenetic tree based on the 16S rRNA Genome project history gene sequence showing this organisms position within This organism was selected for sequencing on the basis the Betaproteobacteria and rooted with Thermithiobacil- of its role in sulfur cycling, physiological, biochemical, lus tepidarius is given in Fig. 1. evolutionary and biogeochemical importance, and is part Cells are 1.5–2.0 by 0.6 to 0.8 μm and stain Gram of the GEBA-KMG project at the U.S. Department of negative. They are motile by means of a single polar fla- Energy JGI. The genome project is deposited in the Ge- gellum between 6 and 10 μm in length, as shown in nomes OnLine Database [13] and a high-quality per- Fig. 2. The dominant respiratory quinone is ubiquione-8 manent draft genome sequence in IMG (the annotated [7–10] and fix carbon dioxide using the Calvin-Benson- genome is publically available in IMG under Genome ID Bassham cycle at the expense of inorganic sulfur oxida- 2515154076) [14]. Sequencing, finishing and annotation tion. Cells accumulate polyphosphate (‘volutin’) granules were performed by the JGI using state of the art sequen- in batch culture and to a lesser extent in an energy- cing technology [15]. A summary of the project informa- limited chemostat [8]. Carboxysomes are present in cells tion is given in Table 2. regardless of growth conditions employed (Fig. 1), but are apparently not found in T. denitrificans cells, at least Growth conditions and genomic DNA preparation
Load more

Recommended publications
  • Changes in Bacterioplankton Communities Resulting from Direct and Indirect Interactions with Trace Metal Gradients in an Urbaniz
    Changes in Bacterioplankton Communities Resulting From Direct and Indirect Interactions With Trace Metal Gradients in an Urbanized Marine Coastal Area Clément Coclet, Cédric Garnier, Gaël Durrieu, Dario Omanović, Sébastien d’Onofrio, Christophe Le Poupon, Jean-Ulrich Mullot, Jean-François Briand, Benjamin Misson To cite this version: Clément Coclet, Cédric Garnier, Gaël Durrieu, Dario Omanović, Sébastien d’Onofrio, et al.. Changes in Bacterioplankton Communities Resulting From Direct and Indirect Interactions With Trace Metal Gradients in an Urbanized Marine Coastal Area. Frontiers in Microbiology, Frontiers Media, 2019, 10, 10.3389/fmicb.2019.00257. hal-02049263 HAL Id: hal-02049263 https://hal.archives-ouvertes.fr/hal-02049263 Submitted on 26 Feb 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. fmicb-10-00257 February 20, 2019 Time: 17:14 # 1 ORIGINAL RESEARCH published: 22 February 2019 doi: 10.3389/fmicb.2019.00257 Changes in Bacterioplankton Communities Resulting From Direct and Indirect Interactions With Trace Metal Gradients in an Urbanized
    [Show full text]
  • Thiobacillus Denitrificans
    Nitrate-Dependent, Neutral pH Bioleaching of Ni from an Ultramafic Concentrate by Han Zhou A thesis submitted in conformity with the requirements for the degree of Master of Applied Science Chemical Engineering and Applied Chemistry University of Toronto © Copyright by Han Zhou 2014 ii Nitrate-Dependent, Neutral pH Bioleaching of Ni from an Ultramafic Concentrate Han Zhou Master of Applied Science Chemical Engineering and Applied Chemistry University of Toronto 2014 Abstract This study explores the possibility of utilizing bioleaching techniques for nickel extraction from a mixed sulfide ore deposit with high magnesium content. Due to the ultramafic nature of this material, well-studied bioleaching technologies, which rely on acidophilic bacteria, will lead to undesirable processing conditions. This is the first work that incorporates nitrate-dependent bacteria under pH 6.5 environments for bioleaching of base metals. Experiments with both defined bacterial strains and indigenous mixed bacterial cultures were conducted with nitrate as the electron acceptor and sulfide minerals as electron donors in a series of microcosm studies. Nitrate consumption, sulfate production, and Ni released into the aqueous phase were used to track the extent of oxidative sulfide mineral dissolution; taxonomic identification of the mixed culture community was performed using 16S rRNA gene sequencing. Nitrate-dependent microcosms that contained indigenous sulfur- and/or iron-oxidizing microorganisms were cultured, characterized, and provided a proof-of-concept basis for further bioleaching studies. iii Acknowledgments I would like to extend my most sincere gratitude toward both of my supervisors Dr. Vladimiros Papangelakis and Dr. Elizabeth Edwards. This work could not have been completed without your brilliant and patient guidance.
    [Show full text]
  • Bacterial Oxidases of the Cytochrome Bd Family: Redox Enzymes of Unique Structure, Function, and Utility As Drug Targets
    Published in "Antioxidants & Redox Signaling doi: 10.1089/ars.2020.8039, 2020" which should be cited to refer to this work. Bacterial Oxidases of the Cytochrome bd Family: Redox Enzymes of Unique Structure, Function, and Utility As Drug Targets Vitaliy B. Borisov,1 Sergey A. Siletsky,1 Alessandro Paiardini,2 David Hoogewijs,3 Elena Forte,2 Alessandro Giuffre`,4 and Robert K. Poole5 Abstract Significance: Cytochrome bd is a ubiquinol:oxygen oxidoreductase of many prokaryotic respiratory chains with a unique structure and functional characteristics. Its primary role is to couple the reduction of molecular oxygen, even at submicromolar concentrations, to water with the generation of a proton motive force used for adenosine triphosphate production. Cytochrome bd is found in many bacterial pathogens and, surprisingly, in bacteria for- mally denoted as anaerobes. It endows bacteria with resistance to various stressors and is a potential drug target. Recent Advances: We summarize recent advances in the biochemistry, structure, and physiological functions of cytochrome bd in the light of exciting new three-dimensional structures of the oxidase. The newly discovered roles of cytochrome bd in contributing to bacterial protection against hydrogen peroxide, nitric oxide, perox- ynitrite, and hydrogen sulfide are assessed. Critical Issues: Fundamental questions remain regarding the precise delineation of electron flow within this multihaem oxidase and how the extraordinarily high affinity for oxygen is accomplished, while endowing bacteria with resistance to other small ligands. Future Directions: It is clear that cytochrome bd is unique in its ability to confer resistance to toxic small molecules, a property that is significant for understanding the propensity of pathogens to possess this oxidase.
    [Show full text]
  • Downloaded 13 April 2017); Using Diamond
    bioRxiv preprint doi: https://doi.org/10.1101/347021; this version posted June 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 2 3 4 5 Re-evaluating the salty divide: phylogenetic specificity of 6 transitions between marine and freshwater systems 7 8 9 10 Sara F. Pavera, Daniel J. Muratorea, Ryan J. Newtonb, Maureen L. Colemana# 11 a 12 Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA 13 b School of Freshwater Sciences, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA 14 15 Running title: Marine-freshwater phylogenetic specificity 16 17 #Address correspondence to Maureen Coleman, [email protected] 18 bioRxiv preprint doi: https://doi.org/10.1101/347021; this version posted June 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 19 Abstract 20 Marine and freshwater microbial communities are phylogenetically distinct and transitions 21 between habitat types are thought to be infrequent. We compared the phylogenetic diversity of 22 marine and freshwater microorganisms and identified specific lineages exhibiting notably high or 23 low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA 24 gene tag-sequencing datasets. As expected, marine and freshwater microbial communities 25 differed in the relative abundance of major phyla and contained habitat-specific lineages; at the 26 same time, however, many shared taxa were observed in both environments. 27 Betaproteobacteria and Alphaproteobacteria sequences had the highest similarity between 28 marine and freshwater sample pairs.
    [Show full text]
  • Multi-Omic Understanding of the Evolution of Xenobiotic Tolerance in Bacterial Isolates and Communities
    Washington University in St. Louis Washington University Open Scholarship Arts & Sciences Electronic Theses and Dissertations Arts & Sciences Summer 8-15-2019 Multi-omic Understanding of the Evolution of Xenobiotic Tolerance in Bacterial Isolates and Communities Tayte Paul Campbell Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/art_sci_etds Part of the Bioinformatics Commons, Biology Commons, and the Microbiology Commons Recommended Citation Campbell, Tayte Paul, "Multi-omic Understanding of the Evolution of Xenobiotic Tolerance in Bacterial Isolates and Communities" (2019). Arts & Sciences Electronic Theses and Dissertations. 1888. https://openscholarship.wustl.edu/art_sci_etds/1888 This Dissertation is brought to you for free and open access by the Arts & Sciences at Washington University Open Scholarship. It has been accepted for inclusion in Arts & Sciences Electronic Theses and Dissertations by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS Division of Biology and Biomedical Sciences Plant and Microbial Biosciences Dissertation Examination Committee: Gautam Dantas, Chair Arpita Bose Andrew Kau Audrey Odom-John Himadri Pakrasi Fuzhong Zhang Multi-omic Understanding of the Evolution of Xenobiotic Tolerance in Bacterial Isolates and Communities by Tayte P. Campbell A dissertation presented to The Graduate School of Washington University in partial fulfillment
    [Show full text]
  • Evaluating the Biogeochemistry and Microbial Function in the Athabasca Oil Sands Region: Understanding Natural Baselines for Reclamation End-Points
    University of Windsor Scholarship at UWindsor Electronic Theses and Dissertations Theses, Dissertations, and Major Papers 2019 Evaluating the biogeochemistry and microbial function in the Athabasca Oil Sands region: Understanding natural baselines for reclamation end-points Thomas Reid University of Windsor Follow this and additional works at: https://scholar.uwindsor.ca/etd Recommended Citation Reid, Thomas, "Evaluating the biogeochemistry and microbial function in the Athabasca Oil Sands region: Understanding natural baselines for reclamation end-points" (2019). Electronic Theses and Dissertations. 7732. https://scholar.uwindsor.ca/etd/7732 This online database contains the full-text of PhD dissertations and Masters’ theses of University of Windsor students from 1954 forward. These documents are made available for personal study and research purposes only, in accordance with the Canadian Copyright Act and the Creative Commons license—CC BY-NC-ND (Attribution, Non-Commercial, No Derivative Works). Under this license, works must always be attributed to the copyright holder (original author), cannot be used for any commercial purposes, and may not be altered. Any other use would require the permission of the copyright holder. Students may inquire about withdrawing their dissertation and/or thesis from this database. For additional inquiries, please contact the repository administrator via email ([email protected]) or by telephone at 519-253-3000ext. 3208. Evaluating the biogeochemistry and microbial function in the Athabasca Oil Sands
    [Show full text]
  • In-Vitro Synthesis and Reconstitution of Cytochrome Bo3 Ubiquinol Oxidase in Artificial Membranes
    In-vitro Synthesis and Reconstitution of Cytochrome bo3 Ubiquinol Oxidase in Artificial Membranes Dissertation Zur Erlangung des Grades Doktor der Naturwissenschaften Am Fachbereich Biologie Der Johannes Gutenberg-Universität Mainz Ahu ARSLAN YILDIZ geboren am 20.12.1980 in Turkey Mainz, 2010 Dekan: Prof. Dr. Erwin Schmidt 1. Berichterstatter: Prof. Dr. Eva K. Sinner 2. Berichterstatter: Prof. Dr. Harald Paulsen 3. Prüfer: Prof. Dr. Wolfgang Knoll 4. Prüfer: Prof. Dr. Elmar Jaenicke Tag der mündlichen Prüfung: 29.01.2010 Abbreviations ATP Adenosine triphosphate PD Parkinson’s Disease Cyt-bo3 Cytochrome bo3 ubiquinol oxidase NADH Nicotinamide adenine dinucleotide UQ Ubiquinone UQH2 Ubiquinol Cyt-c Cytochrome c E.coli Escherichia coli Heme Heme or Haem molecule Cyt-bd Cytochrome bd ubiquinol oxidase cyo Cytochrome encoding operon CuA Copper site in subunit II CuB Copper of binuclear site CFPS Cell-free protein synthesis tRNA Transfer RNA GTP Guanidine triphosphate BLMs Black lipid membranes sBLM Supported bilayer lipid membrane tBLM Tethered lipid bilayer membrane SPR Surface Plasmon Resonance Spectroscopy SPFS Surface Plasmon Enhanced Fluorescence Spectroscopy θc Critical angle θm Minimum angle TIR Total internal reflection εd Dielectric constant n Refractive index CA Contact angle pJRHisA Subunit II histidine tagged enzyme with natural promoter pRCO3 Fused subunit II-I-III enzyme with natural promoter pETcyo Subunit II histidine tagged enzyme with T7 promoter LB Luria Bertani media ii KOH Potassium hydroxide PES Polyethylene sulfonate
    [Show full text]
  • Phosphorus Recovery from Sewage Sludge Using Acidithiobacilli
    International Journal of Environmental Research and Public Health Article Phosphorus Recovery from Sewage Sludge Using Acidithiobacilli Surendra K. Pradhan 1,* , Helvi Heinonen-Tanski 1, Anna-Maria Veijalainen 1, Sirpa Peräniemi 2 and Eila Torvinen 1 1 Department of Environmental and Biological Sciences, University of Eastern Finland, FI-70211 Kuopio, Finland; helvi.heinonentanski@uef.fi (H.H.-T.); anna-maria.veijalainen@uef.fi (A.-M.V.); eila.torvinen@uef.fi (E.T.) 2 Department of Pharmacy, University of Eastern Finland, FI-70211 Kuopio, Finland; sirpa.peraniemi@uef.fi * Correspondence: surendra.pradhan@uef.fi Abstract: Sewage sludge contains a significant amount of phosphorus (P), which could be recycled to address the global demand for this non-renewable, important plant nutrient. The P in sludge can be solubilized and recovered so that it can be recycled when needed. This study investigated the P solubilization from sewage sludge using Acidithiobacillus thiooxidans and Acidithiobacillus ferroox- idans. The experiment was conducted by mixing 10 mL of sewage sludge with 90 mL of different water/liquid medium/inoculum and incubated at 30 ◦C. The experiment was conducted in three semi-continuous phases by replacing 10% of the mixed incubated medium with fresh sewage sludge. In addition, 10 g/L elemental sulfur (S) was supplemented into the medium in the third phase. The pH of the A. thiooxidans and A. ferrooxidans treated sludge solutions was between 2.2 and 6.3 until day 42. In phase 3, after supplementing with S, the pH of A. thiooxidans treated sludge was reduced to 0.9, Citation: Pradhan, S.K.; which solubilized and extracted 92% of P.
    [Show full text]
  • A Survey of Carbon Fixation Pathways Through a Quantitative Lens
    Journal of Experimental Botany, Vol. 63, No. 6, pp. 2325–2342, 2012 doi:10.1093/jxb/err417 Advance Access publication 26 December, 2011 REVIEW PAPER A survey of carbon fixation pathways through a quantitative lens Arren Bar-Even, Elad Noor and Ron Milo* Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel * To whom correspondence should be addressed. E-mail: [email protected] Received 15 August 2011; Revised 4 November 2011; Accepted 8 November 2011 Downloaded from Abstract While the reductive pentose phosphate cycle is responsible for the fixation of most of the carbon in the biosphere, it http://jxb.oxfordjournals.org/ has several natural substitutes. In fact, due to the characterization of three new carbon fixation pathways in the last decade, the diversity of known metabolic solutions for autotrophic growth has doubled. In this review, the different pathways are analysed and compared according to various criteria, trying to connect each of the different metabolic alternatives to suitable environments or metabolic goals. The different roles of carbon fixation are discussed; in addition to sustaining autotrophic growth it can also be used for energy conservation and as an electron sink for the recycling of reduced electron carriers. Our main focus in this review is on thermodynamic and kinetic aspects, including thermodynamically challenging reactions, the ATP requirement of each pathway, energetic constraints on carbon fixation, and factors that are expected to limit the rate of the pathways. Finally, possible metabolic structures at Weizmann Institute of Science on July 3, 2016 of yet unknown carbon fixation pathways are suggested and discussed.
    [Show full text]
  • I. General Introduction
    SECTION 3 ACIDITHIOBACILLUS I. General Introduction This document presents information that is accepted in the literature about the known characteristics of bacteria in the genus Acidithiobacillus. Regulatory officials may find the technical information useful in evaluating properties of micro-organisms that have been derived for various environmental applications. Consequently, this document provides a wide range of information without prescribing when the information would or would not be relevant to a specific risk assessment. The document represents a snapshot of current information (end-2002) that may be potentially relevant to such assessments. In considering information that should be presented on this taxonomic grouping, the Task Group on Micro-organisms has discussed the list of topics presented in the “Blue Book” (i.e. Recombinant DNA Safety Considerations (OECD, 1986)) and attempted to pare down that list to eliminate duplications as well as those topics whose meaning is unclear, and to rearrange the presentation of the topics covered to be more easily understood (the Task Group met in Vienna, 15-16 June, 2000). This document is a first draft of a proposed Consensus Document for environmental applications involving organisms from the genus Acidithiobacillus. II. General Considerations 1. Subject of Document: Species Included and Taxonomic Considerations The four species of Acidithiobacillus covered in this document were formerly placed in the genus Thiobacillus Beijerinck. In recent years several members of Thiobacillus were transferred to other genera while the remainder became part of three newly created genera, Acidithiobacillus, Halothiobacillus, Thermithiobacillus, and to the revised genus Thiobacillus sensu stricto (Kelly and Harrison, 1989; Kelly and Wood, 2000).
    [Show full text]
  • Comparative Genome Analysis of Acidithiobacillus Ferrooxidans, A
    Hydrometallurgy 94 (2008) 180–184 Contents lists available at ScienceDirect Hydrometallurgy journal homepage: www.elsevier.com/locate/hydromet Comparative genome analysis of Acidithiobacillus ferrooxidans, A. thiooxidans and A. caldus: Insights into their metabolism and ecophysiology Jorge Valdés 1, Inti Pedroso, Raquel Quatrini, David S. Holmes ⁎ Center for Bioinformatics and Genome Biology, Life Science Foundation, MIFAB and Andrés Bello University, Santiago, Chile ARTICLE INFO ABSTRACT Available online 2 July 2008 Draft genome sequences of Acidthiobacillus thiooxidans and A. caldus have been annotated and compared to the previously annotated genome of A. ferrooxidans. This has allowed the prediction of metabolic and Keywords: regulatory models for each species and has provided a unique opportunity to undertake comparative Acidithiobacillus genomic studies of this group of related bioleaching bacteria. In this paper, the presence or absence of Bioinformatics predicted genes for eleven metabolic processes, electron transfer pathways and other phenotypic Comparative genomics fi Metabolic integration characteristics are reported for the three acidithiobacilli: CO2 xation, the TCA cycle, sulfur oxidation, sulfur reduction, iron oxidation, iron assimilation, quorum sensing via the acyl homoserine lactone mechanism, hydrogen oxidation, flagella formation, Che signaling (chemotaxis) and nitrogen fixation. Predicted transcriptional and metabolic interplay between pathways pinpoints possible coordinated responses to environmental signals such as energy source, oxygen and nutrient limitations. The predicted pathway for nitrogen fixation in A. ferrooxidans will be described as an example of such an integrated response. Several responses appear to be especially characteristic of autotrophic microorganisms and may have direct implications for metabolic processes of critical relevance to the understanding of how these microorganisms survive and proliferate in extreme environments, including industrial bioleaching operations.
    [Show full text]
  • 1 Characterization of Sulfur Metabolizing Microbes in a Cold Saline Microbial Mat of the Canadian High Arctic Raven Comery Mast
    Characterization of sulfur metabolizing microbes in a cold saline microbial mat of the Canadian High Arctic Raven Comery Master of Science Department of Natural Resource Sciences Unit: Microbiology McGill University, Montreal July 2015 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Master in Science © Raven Comery 2015 1 Abstract/Résumé The Gypsum Hill (GH) spring system is located on Axel Heiberg Island of the High Arctic, perennially discharging cold hypersaline water rich in sulfur compounds. Microbial mats are found adjacent to channels of the GH springs. This thesis is the first detailed analysis of the Gypsum Hill spring microbial mats and their microbial diversity. Physicochemical analyses of the water saturating the GH spring microbial mat show that in summer it is cold (9°C), hypersaline (5.6%), and contains sulfide (0-10 ppm) and thiosulfate (>50 ppm). Pyrosequencing analyses were carried out on both 16S rRNA transcripts (i.e. cDNA) and genes (i.e. DNA) to investigate the mat’s community composition, diversity, and putatively active members. In order to investigate the sulfate reducing community in detail, the sulfite reductase gene and its transcript were also sequenced. Finally, enrichment cultures for sulfate/sulfur reducing bacteria were set up and monitored for sulfide production at cold temperatures. Overall, sulfur metabolism was found to be an important component of the GH microbial mat system, particularly the active fraction, as 49% of DNA and 77% of cDNA from bacterial 16S rRNA gene libraries were classified as taxa capable of the reduction or oxidation of sulfur compounds.
    [Show full text]