DOCSLIB.ORG

Miami University

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Miami University MIAMI UNIVERSITY The Graduate School Certificate for Approving the Dissertation We hereby approve the Dissertation of Gengxin Zhang Candidate for the Degree: Doctor of Philosophy _______________________________________ Hailiang Dong, Director(Advisor) ________________________________________ John Rakovan, Reader ________________________________________ Jonathan Levy, Reader ______________________________________ Yildirim Dilek, Reader ______________________________________ Matthew W. Fields, Graduate School Representative ABSTRACT Geomicrobial Processes and Diversity in Ultra-High Pressure Metamorphic Rocks and Deep Fluids from Chinese Continental Scientific Deep Drilling By Gengxin Zhang This dissertation investigates the microbial communities and microbe-mineral interactions in ultra-high pressure metamorphic rocks and deep fluids from the Chinese Continental Scientific Drilling (CCSD) project by using geochemical, mineralogical, cultivation and molecular microbiology methods. The drilling site is located in the eastern part of the Dabie-Sulu ultra high-pressure metamorphic (UHPM) orogenic belt at the convergent plate boundary between the Sino-Korean and Yangtze Plates. This integrated approach conclusively demonstrates that microbes can survive in the deep continental subsurface (down to 3350 m) and they play important roles in mineral transformations and elemental cycling. The first half of this study focuses on geochemical conditions and diversity and metabolic functions of microbial community. Characterization of SSU rRNA genes indicated that the bacterial clone sequences shifted form a Proteobacteria-dominated community to a Firmicutes-dominated one with increased depth. From the ground surface to 2030 m, most clone sequences were related to nitrate reducers, with a saline, alkaline, and cold habitat. From 2290 to 3350 m most sequences were closely related to anaerobic, thermophilic, halophilic or alkaliphilic bacteria. The archaeal diversity was low. Most archaeal sequences from the ground surface to 3350m were not related to known cultivated species, but to environmental clone sequences recovered from subsurface marine environments. An important contribution of this research is an enrichment of a thermophilic (optimal temperature of 68oC) organism from 2450m with an ability to reduce Fe(III) and oxidize Fe(II) under different conditions. This enriched organism was capable of reducing Fe(III) in aqueous form and in the structure of clay minerals and iron oxides at acidic pH. This organism was also capable of oxidizing Fe(II) in aqueous form and in the structure of pyrite and siderite. The second half of this dissertation focuses on microbe-mineral interactions by using enriched and isolated cultures to react with clay and iron oxide minerals. Mesophilic and thermophilic iron-reducing bacteria were incubated with lactate as the electron donor and structural Fe(III) in solid minerals as the sole electron acceptor. Extensive mineral reaction took place. One important such reaction was the smectite to illite reaction promoted by mesophilic and thermophilic metal reducing bacteria. This particular reaction highlights the significant role of iron-reducing bacteria in promoting the smectite to illite reaction at high temperature. Geomicrobial Processes and Diversity in Ultra-High Pressure Metamorphic Rocks and Deep Fluids from Chinese Continental Scientific Deep Drilling A DISSERTATION Submitted to the Faculty of Miami University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Geology by Gengxin Zhang Miami University Oxford, Ohio 2006 Dissertation Director: Hailiang Dong, Ph.D. TABLE OF CONTENTS Chapter 1: Introduction 1 References 3 Chapter 2: Microbial Diversity in Ultra-High Pressure Rocks and Fluids 6 From the Chinese Continental Scientific Drilling in China Abstract 7 Body Text 8 References 31 Chapter 3: Unique Microbial Community in Drilling Fluids From 50 Chinese Continental Scientific Drilling Abstract 51 Body Text 52 References 71 Chapter 4: Evidence for Microbial-Mediated Iron Redox cycling 90 in the Deep Subsurface Abstract 91 Body Text 92 References 113 Chapter 5: Microbial Reduction of Structural Fe(III) in Nontronite 141 by Thermophilic Bacteria and Their Roles in Promoting the Smectite-Illite Reaction Abstract 142 Body Text 143 References 154 Chapter 6: Microbial Effects in Promoting the Smectite to Illite Reaction: 171 Role of Organic Matter Intercalated in the Interlayer Abstract 172 Body Text 173 References 187 Chapter 7: Summary 204 ii LIST OF TABLES Chapter 2: Microbial Diversity in Ultra-High Pressure Rocks and Fluids 6 From the Chinese Continental Scientific Drilling in China 1 - Summary of Anions, TOC and 13C isotope compositions for the 36 rocks and drilling fluids 2 - Chemical composition of the rock samples from CCSD 37 3 - Phylogenetic bacterial rDNA clone-type analysis 38 Chapter 3: Unique Microbial Community in Drilling Fluids From 50 Chinese Continental Scientific Drilling 1 - Anion and cation composition, pH, salinity and in-situ temperature 78 for the drilling fluid samples Chapter 4: Evidence for Microbial-Mediated Iron Redox Cycling 90 in the Deep Subsurface 1 - Composition of M1 and AG medium 122 2 - Anion and cation composition, pH, salinity and in-situ temperature for 123 the drilling fluid sample 3 - Experimental conditions and employed analysis methods 124 Chapter 5: Microbial Reduction of Structural Fe(III) in Nontronite 141 by Thermophilic Bacteria and Their Roles in Promoting the Smectite-Illite Reaction 1 - Experimental conditions used for nontronite reduction in bacterial 161 cultures and abiotic controls 2 - Change in pH and Eh as a result of Fe(III) bioreduction 162 Chapter 6: Microbial Effects in Promoting the Smectite to Illite 171 Reaction:Role of Organic Matter Intercalated in the Interlayer iii LIST OF FIGURES Chapter 2: Microbial Diversity in Ultra-High Pressure Rocks and Fluids 6 From the Chinese Continental Scientific Drilling in China 1 - A map showing general geology in the Dabie-Sulu orogen 43 of central-eastern China 2 - A back-scattered electron image showing fractures in garnet and pyroxene 44 3 - An optical micrograph showing various mineral/fluid inclusions in 45 the UHP rocks 4 - Neighbor-joining tree of nearly full-length sequences (~1400 bp) of 46 isolates and representative examples of bacterial clone sequences 5 - Typical electropherograms of bacterial T-RFLPs 47 6 - Phylogenetic relationships of representative phylotypes of bacterial 48 16S rRNA gene sequences 7 - Phylogenetic relationships of representative phylotypes of archaeal 49 16S rRNA gene sequences Chapter 3: Unique Microbial Community in Drilling Fluids From 50 Chinese Continental Scientific Drilling 1 - A map showing general geology in the Dabie-Sulu orogen 81 of central-eastern China 2 - PLFA profiles for the drilling fluid samples 82 3 - Neighbor-joining tree of nearly full-length sequences (~1400 bp) 83 of isolates and representative examples of bacterial clone sequences 4 - Ferrihydrite was reduced by CCSD_DF2290_FWA_60_ isolate1 84 5 – Nontronite was reduced by CCSD_DF2450_M1_68_ isolate6 85 6 - Phylogenetic relationships of representative phylotypes of bacterial 87 16S rRNA gene sequences 7 - Phylogenetic relationships of representative phylotypes of archaeal 88 16S rRNA gene sequences 8 - Stacked bar graph showing the contribution of each family of bacteria 89 iv in the clone libraries for the drilling fluid samples Chapter 4: Evidence for Microbially-Mediated Iron Redox 90 Cycling in the Deep Subsurface 1 - Change in 0.5 N HCl-extractable Fe(II) with time in the first 128 transfer from the enrichment culture in the M1 medium 2 - Changes of Fe(II) concentration, lactate, acetate Eh and pH 129 with time in the second transfer in AG medium 3 - Change in 0.5 M HCl-extractable Fe(II) with time in the 131 third transfer in AG medium with nontronite, ferric citrate or ferrihydrite 4 - Photographs of biological oxidized FeS and abiotic FeS control 133 5 - XRD patterns of bio-oxidized FeS, abiotic control and reference 134 6 – Secondary electron image showing that ferric citrate was reduced 135 to form vivianite and then partially oxidized in the third transfer in AG medium 7 – Secondary electron image showing ferrihydrite as an oxidation 136 products of FeS 8 – TEM micrographs of microbially oxidized FeS 137 9 – Mössbauer spectra of the bioreduced ferric citrate at different temperature 139 10 – Phylogenetic relationships of representative phylotypes of bacterial 140 16S rRNA gene sequences Chapter 5: Microbial Reduction of Structural Fe(III) in Nontronite 141 by Thermophilic Bacteria and Their Roles in Promoting the Smectite-Illite Reaction 1 - Production of biogenic Fe(II) from bioreduced nontronite samples 165 2 - XRD patterns for of nontronite samples 166 3 - Secondary electron images of bioreduced and nonreduced nontronite 167 4 - Secondary electron image showing evolution of illite crystal morphology 168 5 - TEM micrographs for bioreduced and nonreduced nontronite 169 v 6 - Histograms showing the distribution of layer spacings in bioreduced 170 and nonreduced nontronite Chapter 6: Microbial Effects in Promoting the Smectite to Illite 171 Reaction:Role of Organic Matter Intercalated in the Interlayer 1 - XRD patterns for oriented specimens of nontronite 194 2 - Comparison of FTIR spectra for nontronite, cysteine 195 and cysteine-NAu-2 complex 3 - Production of biogenic Fe(II) from bioreduced nontronite 196 4 - Secondary electron images
Load more

Recommended publications
  • Desulfuribacillus Alkaliarsenatis Gen. Nov. Sp. Nov., a Deep-Lineage
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Extremophiles (2012) 16:597–605 DOI 10.1007/s00792-012-0459-7 ORIGINAL PAPER Desulfuribacillus alkaliarsenatis gen. nov. sp. nov., a deep-lineage, obligately anaerobic, dissimilatory sulfur and arsenate-reducing, haloalkaliphilic representative of the order Bacillales from soda lakes D. Y. Sorokin • T. P. Tourova • M. V. Sukhacheva • G. Muyzer Received: 10 February 2012 / Accepted: 3 May 2012 / Published online: 24 May 2012 Ó The Author(s) 2012. This article is published with open access at Springerlink.com Abstract An anaerobic enrichment culture inoculated possible within a pH range from 9 to 10.5 (optimum at pH with a sample of sediments from soda lakes of the Kulunda 10) and a salt concentration at pH 10 from 0.2 to 2 M total Steppe with elemental sulfur as electron acceptor and for- Na? (optimum at 0.6 M). According to the phylogenetic mate as electron donor at pH 10 and moderate salinity analysis, strain AHT28 represents a deep independent inoculated with sediments from soda lakes in Kulunda lineage within the order Bacillales with a maximum of Steppe (Altai, Russia) resulted in the domination of a 90 % 16S rRNA gene similarity to its closest cultured Gram-positive, spore-forming bacterium strain AHT28. representatives. On the basis of its distinct phenotype and The isolate is an obligate anaerobe capable of respiratory phylogeny, the novel haloalkaliphilic anaerobe is suggested growth using elemental sulfur, thiosulfate (incomplete as a new genus and species, Desulfuribacillus alkaliar- T T reduction) and arsenate as electron acceptor with H2, for- senatis (type strain AHT28 = DSM24608 = UNIQEM mate, pyruvate and lactate as electron donor.
    [Show full text]
  • Dynamic Consolidated Bioprocessing for Innovative Lab-Scale Production of Bacterial Alkaline Phosphatase from Bacillus Paraliche
    www.nature.com/scientificreports OPEN Dynamic consolidated bioprocessing for innovative lab‑scale production of bacterial alkaline phosphatase from Bacillus paralicheniformis strain APSO Soad A. Abdelgalil1,2*, Nadia A. Soliman1, Gaber A. Abo‑Zaid1 & Yasser R. Abdel‑Fattah1 To meet the present and forecasted market demand, bacterial alkaline phosphatase (ALP) production must be increased through innovative and efcient production strategies. Using sugarcane molasses and biogenic apatite as low‑cost and easily available raw materials, this work demonstrates the scalability of ALP production from a newfound Bacillus paralicheniformis strain APSO isolated from a black liquor sample. Mathematical experimental designs including sequential Plackett– Burman followed by rotatable central composite designs were employed to select and optimize the concentrations of the statistically signifcant media components, which were determined to be molasses, (NH4)2NO3, and KCl. Batch cultivation in a 7‑L stirred‑tank bioreactor under uncontrolled pH conditions using the optimized medium resulted in a signifcant increase in both the volumetric and specifc productivities of ALP; the alkaline phosphatase throughput 6650.9 U L−1, and µ = 0.0943 ­h−1; respectively, were obtained after 8 h that, ameliorated more than 20.96, 70.12 and 94 folds compared to basal media, PBD, and RCCD; respectively. However, neither the increased cell growth nor enhanced productivity of ALP was present under the pH‑controlled batch cultivation. Overall, this work presents novel strategies for the statistical optimization and scaling up of bacterial ALP production using biogenic apatite. Te bioeconomy represents the value chain of sustainable manufacturing using renewable, low-cost biological resources to sustainably produce food, energy, and industrial products1.
    [Show full text]
  • Archaeoglobus Profundus Type Strain (AV18T)
    Standards in Genomic Sciences (2010) 2:327-346 DOI:10.4056/sigs.942153 Complete genome sequence of Archaeoglobus profundus type strain (AV18T) Mathias von Jan1, Alla Lapidus2, Tijana Glavina Del Rio2, Alex Copeland2, Hope Tice2, Jan-Fang Cheng2, Susan Lucas2, Feng Chen2, Matt Nolan2, Lynne Goodwin2,3, Cliff Han2,3, Sam Pitluck2, Konstantinos Liolios2, Natalia Ivanova2, Konstantinos Mavromatis2, Galina Ovchinnikova2, Olga Chertkov2, Amrita Pati2, Amy Chen4, Krishna Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Elizabeth Saunders2, Thomas Brettin2,3, John C. Detter2,3, Patrick Chain2,4, Konrad Eichinger6, Harald Huber6, Ste- fan Spring1, Manfred Rohde7, Markus Göker1, Reinhard Wirth6, Tanja Woyke2, Jim Bristow2, Jonathan A. Eisen2,8, Victor Markowitz4, Philip Hugenholtz2, Nikos C Kyrpides2, and Hans-Peter Klenk1* 1 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 University of Regensburg, Microbiology – Archaeenzentrum, Regensburg, Germany 7 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 8 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: hyperthermophilic, marine, strictly anaerobic, sulfate respiration, hydrogen utili- zation, hydrothermal systems, Archaeoglobaceae, GEBA Archaeoglobus profundus (Burggraf et al. 1990) is a hyperthermophilic archaeon in the eu- ryarchaeal class Archaeoglobi, which is currently represented by the single family Archaeog- lobaceae, containing six validly named species and two strains ascribed to the genus 'Geoglobus' which is taxonomically challenged as the corresponding type species has no va- lidly published name.
    [Show full text]
  • WO 2018/064165 A2 (.Pdf)
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/064165 A2 05 April 2018 (05.04.2018) W !P O PCT (51) International Patent Classification: Published: A61K 35/74 (20 15.0 1) C12N 1/21 (2006 .01) — without international search report and to be republished (21) International Application Number: upon receipt of that report (Rule 48.2(g)) PCT/US2017/053717 — with sequence listing part of description (Rule 5.2(a)) (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 62/400,372 27 September 2016 (27.09.2016) US 62/508,885 19 May 2017 (19.05.2017) US 62/557,566 12 September 2017 (12.09.2017) US (71) Applicant: BOARD OF REGENTS, THE UNIVERSI¬ TY OF TEXAS SYSTEM [US/US]; 210 West 7th St., Austin, TX 78701 (US). (72) Inventors: WARGO, Jennifer; 1814 Bissonnet St., Hous ton, TX 77005 (US). GOPALAKRISHNAN, Vanch- eswaran; 7900 Cambridge, Apt. 10-lb, Houston, TX 77054 (US). (74) Agent: BYRD, Marshall, P.; Parker Highlander PLLC, 1120 S. Capital Of Texas Highway, Bldg. One, Suite 200, Austin, TX 78746 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW.
    [Show full text]
  • Specific Enrichment of Hyperthermophilic Electroactive Archaea From
    bioRxiv preprint doi: https://doi.org/10.1101/272039; this version posted February 27, 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 Specific enrichment of hyperthermophilic electroactive Archaea from 2 deep-sea hydrothermal vent on electrically conductive support. 3 4 Guillaume Pillot1, Eléonore Frouin1, Emilie Pasero1, Anne Godfroy2, Yannick Combet-Blanc1, 5 Sylvain Davidson1 & Pierre-Pol Liebgott1* 6 1 Aix Marseille Université, IRD, Université de Toulon, CNRS, MIO UM 110, Marseille, France. 7 2 Laboratoire de Microbiologie des Environnements Extrêmes - UMR6197 IFREMER, CNRS, 8 UBO Centre de Brest–CS10070/IUEM, Plouzané, France. 9 *Corresponding author: [email protected]; Mediterranean Institute of 10 Oceanography, Campus de Luminy, Bâtiment OCEANOMED, 13288 Marseille Cedex 09. 11 Abstract 12 While more and more investigations are done to isolate hyperthermophilic exoelectrogenic 13 communities from environments, none have been performed yet on deep-sea hydrothermal vent. 14 Samples of black smoker chimney from Rainbow site on the Atlantic mid-oceanic ridge have 15 been harvested for enriching exoelectrogens in microbial electrolysis cells under hyperthermophilic 16 (80°C) condition. Two enrichments have been performed: one from direct inoculation of crushed 17 chimney and the other one from inoculation of a pre-cultivation on iron (III) oxide. In both 18 experiments, a current production was observed from 2.4 A/m² to 5.8 A/m² with a set anode 19 potential of +0.05 vs SHE. Taxonomic affiliation of the exoelectrogen communities obtained 20 exhibited a specific enrichment of Archaea from Thermococcales and Archeoglobales orders on the 21 electrode, even when both inocula were dominated by Bacteria.
    [Show full text]
  • Marine Extremophiles: a Source of Hydrolases for Biotechnological Applications
    Mar. Drugs 2015, 13, 1925-1965; doi:10.3390/md13041925 OPEN ACCESS marine drugs ISSN 1660-3397 www.mdpi.com/journal/marinedrugs Article Marine Extremophiles: A Source of Hydrolases for Biotechnological Applications Gabriel Zamith Leal Dalmaso 1,2, Davis Ferreira 3 and Alane Beatriz Vermelho 1,* 1 BIOINOVAR—Biotechnology laboratories: Biocatalysis, Bioproducts and Bioenergy, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, Brazil; E-Mail: [email protected] 2 Graduate Program in Plant Biotechnology, Health and Science Centre, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, Brazil 3 BIOINOVAR—Biotechnology Laboratories: Virus-Cell Interaction, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Av. Carlos Chagas Filho, 373, 21941-902 Rio de Janeiro, Brazil; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +55-(21)-3936-6743; Fax: +55-(21)-2560-8344. Academic Editor: Kirk Gustafson Received: 1 December 2014 / Accepted: 25 March 2015 / Published: 3 April 2015 Abstract: The marine environment covers almost three quarters of the planet and is where evolution took its first steps. Extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. The ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. Hydrolases including amylases, cellulases, peptidases and lipases from hyperthermophiles, psychrophiles, halophiles and piezophiles have been investigated for these reasons.
    [Show full text]
  • Prokaryotic Biodiversity of Halophilic Microorganisms Isolated from Sehline Sebkha Salt Lake (Tunisia)
    Vol. 8(4), pp. 355-367, 22 January, 2014 DOI: 10.5897/AJMR12.1087 ISSN 1996-0808 ©2014 Academic Journals African Journal of Microbiology Research http://www.academicjournals.org/AJMR Full Length Research Paper Prokaryotic biodiversity of halophilic microorganisms isolated from Sehline Sebkha Salt Lake (Tunisia) Abdeljabbar HEDI1,2*, Badiaa ESSGHAIER1, Jean-Luc CAYOL2, Marie-Laure FARDEAU2 and Najla SADFI1 1Laboratoire Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar 2092, Tunisie. 2Laboratoire de Microbiologie et de Biotechnologie des Environnements Chauds UMR180, IRD, Université de Provence et de la Méditerranée, ESIL case 925, 13288 Marseille cedex 9, France. Accepted 7 February, 2013 North of Tunisia consists of numerous ecosystems including extreme hypersaline environments in which the microbial diversity has been poorly studied. The Sehline Sebkha is an important source of salt for food. Due to its economical importance with regards to its salt value, a microbial survey has been conducted. The purpose of this research was to examine the phenotypic features as well as the physiological and biochemical characteristics of the microbial diversity of this extreme ecosystem, with the aim of screening for metabolites of industrial interest. Four samples were obtained from 4 saline sites for physico-chemical and microbiological analyses. All samples studied were hypersaline (NaCl concentration ranging from 150 to 260 g/L). A specific halophilic microbial community was recovered from each site and initial characterization of isolated microorganisms was performed by using both phenotypic and phylogenetic approaches. The 16S rRNA genes from 77 bacterial strains and two archaeal strains were isolated and phylogenetically analyzed and belonged to two phyla Firmicutes and gamma-proteobacteria of the domain Bacteria.
    [Show full text]
  • Access to Electronic Thesis
    Access to Electronic Thesis Author: Khalid Salim Al-Abri Thesis title: USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS Qualification: PhD This electronic thesis is protected by the Copyright, Designs and Patents Act 1988. No reproduction is permitted without consent of the author. It is also protected by the Creative Commons Licence allowing Attributions-Non-commercial-No derivatives. If this electronic thesis has been edited by the author it will be indicated as such on the title page and in the text. USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS By Khalid Salim Al-Abri Msc., University of Sultan Qaboos, Muscat, Oman Mphil, University of Sheffield, England Thesis submitted in partial fulfillment for the requirements of the Degree of Doctor of Philosophy in the Department of Molecular Biology and Biotechnology, University of Sheffield, England 2011 Introductory Pages I DEDICATION To the memory of my father, loving mother, wife “Muneera” and son “Anas”, brothers and sisters. Introductory Pages II ACKNOWLEDGEMENTS Above all, I thank Allah for helping me in completing this project. I wish to express my thanks to my supervisor Professor Milton Wainwright, for his guidance, supervision, support, understanding and help in this project. In addition, he also stood beside me in all difficulties that faced me during study. My thanks are due to Dr. D. J. Gilmour for his co-supervision, technical assistance, his time and understanding that made some of my laboratory work easier. In the Ministry of Regional Municipalities and Water Resources, I am particularly grateful to Engineer Said Al Alawi, Director General of Health Control, for allowing me to carry out my PhD study at the University of Sheffield.
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • Sulphate-Reducing Bacteria's Response to Extreme Ph Environments and the Effect of Their Activities on Microbial Corrosion
    applied sciences Review Sulphate-Reducing Bacteria’s Response to Extreme pH Environments and the Effect of Their Activities on Microbial Corrosion Thi Thuy Tien Tran 1 , Krishnan Kannoorpatti 1,* , Anna Padovan 2 and Suresh Thennadil 1 1 Energy and Resources Institute, College of Engineering, Information Technology and Environment, Charles Darwin University, Darwin, NT 0909, Australia; [email protected] (T.T.T.T.); [email protected] (S.T.) 2 Research Institute for the Environment and Livelihoods, College of Engineering, Information Technology and Environment, Charles Darwin University, Darwin, NT 0909, Australia; [email protected] * Correspondence: [email protected] Abstract: Sulphate-reducing bacteria (SRB) are dominant species causing corrosion of various types of materials. However, they also play a beneficial role in bioremediation due to their tolerance of extreme pH conditions. The application of sulphate-reducing bacteria (SRB) in bioremediation and control methods for microbiologically influenced corrosion (MIC) in extreme pH environments requires an understanding of the microbial activities in these conditions. Recent studies have found that in order to survive and grow in high alkaline/acidic condition, SRB have developed several strategies to combat the environmental challenges. The strategies mainly include maintaining pH homeostasis in the cytoplasm and adjusting metabolic activities leading to changes in environmental pH. The change in pH of the environment and microbial activities in such conditions can have a Citation: Tran, T.T.T.; Kannoorpatti, significant impact on the microbial corrosion of materials. These bacteria strategies to combat extreme K.; Padovan, A.; Thennadil, S. pH environments and their effect on microbial corrosion are presented and discussed.
    [Show full text]
  • Thèses Traditionnelles
    UNIVERSITÉ D’AIX-MARSEILLE FACULTÉ DE MÉDECINE DE MARSEILLE ECOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTÉ THÈSE Présentée et publiquement soutenue devant LA FACULTÉ DE MÉDECINE DE MARSEILLE Le 23 Novembre 2017 Par El Hadji SECK Étude de la diversité des procaryotes halophiles du tube digestif par approche de culture Pour obtenir le grade de DOCTORAT d’AIX-MARSEILLE UNIVERSITÉ Spécialité : Pathologie Humaine Membres du Jury de la Thèse : Mr le Professeur Jean-Christophe Lagier Président du jury Mr le Professeur Antoine Andremont Rapporteur Mr le Professeur Raymond Ruimy Rapporteur Mr le Professeur Didier Raoult Directeur de thèse Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR 7278 Directeur : Pr. Didier Raoult 1 Avant-propos : Le format de présentation de cette thèse correspond à une recommandation de la spécialité Maladies Infectieuses et Microbiologie, à l’intérieur du Master des Sciences de la Vie et de la Santé qui dépend de l’Ecole Doctorale des Sciences de la Vie de Marseille. Le candidat est amené à respecter des règles qui lui sont imposées et qui comportent un format de thèse utilisé dans le Nord de l’Europe et qui permet un meilleur rangement que les thèses traditionnelles. Par ailleurs, la partie introduction et bibliographie est remplacée par une revue envoyée dans un journal afin de permettre une évaluation extérieure de la qualité de la revue et de permettre à l’étudiant de commencer le plus tôt possible une bibliographie exhaustive sur le domaine de cette thèse. Par ailleurs, la thèse est présentée sur article publié, accepté ou soumis associé d’un bref commentaire donnant le sens général du travail.
    [Show full text]
  • Reclassification of Eubacterium Hallii As Anaerobutyricum Hallii Gen. Nov., Comb
    TAXONOMIC DESCRIPTION Shetty et al., Int J Syst Evol Microbiol 2018;68:3741–3746 DOI 10.1099/ijsem.0.003041 Reclassification of Eubacterium hallii as Anaerobutyricum hallii gen. nov., comb. nov., and description of Anaerobutyricum soehngenii sp. nov., a butyrate and propionate-producing bacterium from infant faeces Sudarshan A. Shetty,1,* Simone Zuffa,1 Thi Phuong Nam Bui,1 Steven Aalvink,1 Hauke Smidt1 and Willem M. De Vos1,2,3 Abstract A bacterial strain designated L2-7T, phylogenetically related to Eubacterium hallii DSM 3353T, was previously isolated from infant faeces. The complete genome of strain L2-7T contains eight copies of the 16S rRNA gene with only 98.0– 98.5 % similarity to the 16S rRNA gene of the previously described type strain E. hallii. The next closest validly described species is Anaerostipes hadrus DSM 3319T (90.7 % 16S rRNA gene similarity). A polyphasic taxonomic approach showed strain L2-7T to be a novel species, related to type strain E. hallii DSM 3353T. The experimentally observed DNA–DNA hybridization value between strain L2-7T and E. hallii DSM 3353T was 26.25 %, close to that calculated from the genomes T (34.3 %). The G+C content of the chromosomal DNA of strain L2-7 was 38.6 mol%. The major fatty acids were C16 : 0,C16 : 1 T cis9 and a component with summed feature 10 (C18 : 1c11/t9/t6c). Strain L2-7 had higher amounts of C16 : 0 (30.6 %) compared to E. hallii DSM 3353T (19.5 %) and its membrane contained phosphatidylglycerol and phosphatidylethanolamine, which were not detected in E.
    [Show full text]