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A Study on the Phototrophic Microbial Mat Communities of Sulphur Mountain Thermal Springs and Their Association with the Endangered, Endemic Snail Physella Johnsoni
A Study on the Phototrophic Microbial Mat Communities of Sulphur Mountain Thermal Springs and their Association with the Endangered, Endemic Snail Physella johnsoni By Michael Bilyj A thesis submitted to the Faculty of Graduate Studies in partial fulfillment of the requirements for the degree of Master of Science Department of Microbiology Faculty of Science University of Manitoba Winnipeg, Manitoba October 2011 © Copyright 2011, Michael A. Bilyj 1 Abstract The seasonal population fluctuation of anoxygenic phototrophs and the diversity of cyanobacteria at the Sulphur Mountain thermal springs of Banff, Canada were investigated and compared to the drastic population changes of the endangered snail Physella johnsoni. A new species and two strains of Rhodomicrobium were taxonomically characterized in addition to new species of Rhodobacter and Erythromicrobium. Major mat-forming organisms included Thiothrix-like species, oxygenic phototrophs of genera Spirulina, Oscillatoria, and Phormidium and purple nonsulfur bacteria Rhodobacter, Rhodopseudomonas and Rhodomicrobium. Aerobic anoxygenic phototrophs comprised upwards of 9.6 x 104 CFU/cm2 of mat or 18.9% of total aerobic heterotrophic bacterial isolates at certain sites, while maximal purple nonsulfur and purple sulfur bacteria were quantified at 3.2 x 105 and 2.0 x 106 CFU/cm2 of mat, respectively. Photosynthetic activity measurements revealed incredibly productive carbon fixation rates averaging 40.5 mg C/cm2/24 h. A temporal mismatch was observed for mat area and prokaryote-based organics to P. johnsoni population flux in a ―tracking inertia‖ manner. 2 Acknowledgements It is difficult to express sufficient gratitude to my supervisor Dr. Vladimir Yurkov for his unfaltering patience, generosity and motivation throughout this entire degree. -
Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz
Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 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. THÈSE Pour l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. -
17, 3203–3222, 2020 © Author(S) 2020
Biogeosciences, 17, 3203–3222, 2020 https://doi.org/10.5194/bg-17-3203-2020 © Author(s) 2020. This work is distributed under the Creative Commons Attribution 4.0 License. The contribution of microbial communities in polymetallic nodules to the diversity of the deep-sea microbiome of the Peru Basin (4130–4198 m depth) Massimiliano Molari1, Felix Janssen1,2, Tobias R. Vonnahme1,a, Frank Wenzhöfer1,2, and Antje Boetius1,2 1Max Planck Institute for Marine Microbiology, Bremen, Germany 2HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany apresent address: UiT the Arctic University of Tromsø, Tromsø, Norway Correspondence: Massimiliano Molari ([email protected]) Received: 16 January 2020 – Discussion started: 3 February 2020 Revised: 27 April 2020 – Accepted: 15 May 2020 – Published: 25 June 2020 Abstract. Industrial-scale mining of deep-sea polymetal- tween the Clarion–Clipperton Fracture Zone (CCZ) and the lic nodules will remove nodules in large areas of the sea Peru Basin suggest that changes in environmental setting floor. The regrowth of the nodules by metal precipita- (e.g. sedimentation rates) also play a significant role in struc- tion is estimated to take millions of years. Thus, for fu- turing the nodule microbiome. ture mining impact studies, it is crucial to understand the role of nodules in shaping microbial diversity and function in deep-sea environments. Here we investigated microbial- community composition based on 16S rRNA gene sequences 1 Introduction retrieved from sediments and nodules of the Peru Basin (4130–4198 m water depth). The nodule field of the Peru Polymetallic nodules (or manganese nodules) occur in Basin showed a typical deep-sea microbiome, with domi- abyssal plains (4000–6000 m water depth) and consist pri- nance of the classes Gammaproteobacteria, Alphaproteobac- marily of manganese and iron as well as many other metals teria, Deltaproteobacteria, and Acidimicrobiia. -
DNA and RNA-SIP Reveal Nitrospira Spp. As Key Drivers of Nitrification in 2 Groundwater-Fed Biofilters
bioRxiv preprint doi: https://doi.org/10.1101/703868; this version posted July 16, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 DNA and RNA-SIP reveal Nitrospira spp. as key drivers of nitrification in 2 groundwater-fed biofilters 3 4 Running title: Nitrospira drives nitrification in groundwater-fed biofilters 5 Authors: Arda Gülay1,4*, Jane Fowler1, Karolina Tatari1, Bo Thamdrup3, Hans-Jørgen Albrechtsen1, 6 Waleed Abu Al-Soud2, Søren J. Sørensen2 and Barth F. Smets1* 7 1 Department of Environmental Engineering, Technical University of Denmark, Building 113, Miljøvej, 2800 8 Kgs Lyngby, Denmark. Phone: +45 45251600. FAX: +45 45932850. e-mail: [email protected], jfow@ 9 env.dtu.dk, [email protected], [email protected]* 10 2 Department of Biology, University of Copenhagen, Universitetsparken 15, Building 1, 2100 Copenhagen, 11 Denmark. Phone: +45 35323710. FAX: +45 35322128. e-mail: [email protected], [email protected] 12 3 Nordic Center for Earth Evolution, Department of Biology, University of Southern Denmark, Campusvej 55, 13 5230 Odense, Denmark. Phone: +45 35323710. FAX: +45 35322128. e-mail: [email protected] 14 4 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States, 15 26 Oxford St, Cambridge, MA 02138, Phone: +1 (617)4951564. e-mail: [email protected] 16 17 *Corresponding authors 18 Keywords: Nitrification, comammox, Nitrospira, DNA SIP, RNA SIP 19 bioRxiv preprint doi: https://doi.org/10.1101/703868; this version posted July 16, 2019. -
Information to Users
INFORMATION TO USERS This manuscript has been reproduced from themicrofilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, prim bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note win indicate the deletion. Oversize materials (e.g^ maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. Each original is also photographed in one exposure and is included in reduced form at the back of the book. Photographs inchiried in the original manuscript have been reproduced xerographically in this copy. Higher quality 6" x 9" black and white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UMI directly to order. A Be<l & Howell Information Company 300 North ZeeO Road. Ann Arbor. Ml 48106-1346 USA 313.- 761-4700 800/ 521-0600 BACTERIA ASSOCIATED WITH WELL WATER: BIOGEOCHEMICAL TRANSFORMATION OF FE AND MN, AND CHARACTERIZATION AND CHEMOTAXIS OF A METHYLOTROPHIC HYPHOMICROBIUM SP. DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in the Graduate School of The Ohio State University By Laura Tuhela, B.S., M.S. -
Hyphal Proteobacteria, Hirschia Baltica Gen. Nov. , Sp. Nov
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Oct. 1990, p. 443451 Vol. 40. No. 4 0020-7713/9O/040443-O9$02.00/0 Copyright 0 1990, International Union of Microbiological Societies Taxonomic and Phylogenetic Studies on a New Taxon of Budding, Hyphal Proteobacteria, Hirschia baltica gen. nov. , sp. nov. HEINZ SCHLESNER," CHRISTINA BARTELS, MANUEL SITTIG, MATTHIAS DORSCH, AND ERKO STACKEBRANDTT Institut fur Allgemeine Mikrobiologie, Christian-Albrecht-Universitat, 2300 Kiel, Federal Republic of Germany Four strains of budding, hyphal bacteria, which had very similar chemotaxonomic properties, were isolated from the Baltic Sea. The results of DNA-DNA hybridization experiments, indicated that three of the new isolates were closely related, while the fourth was only moderately related to the other three. Sequence signature and higher-order structural detail analyses of the 16s rRNA of strain IFAM 141gT (T = type strain) indicated that this isolate is related to the alpha subclass of the class Proteobacteriu. Although our isolates resemble members of the genera Hyphomicrobium and Hyphomonas in morphology, assignment to either of these genera was excluded on the basis of their markedly lower DNA guanine-plus-cytosine contents. We propose that these organisms should be placed in a new genus, Hirschiu baltica is the type species of this genus, and the type strain of H. bdtica is strain IFAM 1418 (= DSM 5838). Since the first description of a hyphal, budding bacterium, no1 and formamide were tested at concentrations of 0.02 and Hyphomicrobium vulgare (53), only the following additional 0.1% (vol/vol). Utilization of nitrogen sources was tested in genera having this morphological type have been formally M9 medium containing glucose as the carbon source. -
Deterioration of an Etruscan Tomb by Bacteria from the Order Rhizobiales
OPEN Deterioration of an Etruscan tomb by SUBJECT AREAS: bacteria from the order Rhizobiales SOIL MICROBIOLOGY Marta Diaz-Herraiz1*, Valme Jurado1*, Soledad Cuezva2, Leonila Laiz1, Pasquino Pallecchi3, Piero Tiano4, MICROBIOLOGY TECHNIQUES Sergio Sanchez-Moral5 & Cesareo Saiz-Jimenez1 Received 1Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avda. Reina Mercedes 10, 41012 Sevilla, Spain, 2Departamento de 23 September 2013 Ciencias de la Tierra y del Medio Ambiente, Universidad de Alicante, 03690 San Vicente del Raspeig, Spain, 3Soprintendenza per i Beni Archeologici della Toscana, 50143 Firenze, Italy, 4CNR Istituto per la Conservazione e Valorizzazione dei Beni Culturali, Accepted 50019 Sesto Fiorentino, Italy, 5Museo Nacional de Ciencias Naturales, MNCN-CSIC, 28006 Madrid, Spain. 10 December 2013 Published The Etruscan civilisation originated in the Villanovan Iron Age in the ninth century BC and was absorbed by 9 January 2014 Rome in the first century BC. Etruscan tombs, many of which are subterranean, are one of the best representations of this culture. The principal importance of these tombs, however, lies in the wall paintings and in the tradition of rich burial, which was unique in the Mediterranean Basin, with the exception of Correspondence and Egypt. Relatively little information is available concerning the biodeterioration of Etruscan tombs, which is caused by a colonisation that covers the paintings with white, circular to irregular aggregates of bacteria or requests for materials biofilms that tend to connect each other. Thus, these colonisations sometimes cover extensive surfaces. Here should be addressed to we show that the colonisation of paintings in Tomba del Colle is primarily due to bacteria of the order C.S.-J. -
Supplementary Information
Supplementary Information Comparative Microbiome and Metabolome Analyses of the Marine Tunicate Ciona intestinalis from Native and Invaded Habitats Caroline Utermann 1, Martina Blümel 1, Kathrin Busch 2, Larissa Buedenbender 1, Yaping Lin 3,4, Bradley A. Haltli 5, Russell G. Kerr 5, Elizabeta Briski 3, Ute Hentschel 2,6, Deniz Tasdemir 1,6* 1 GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany 2 Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Duesternbrooker Weg 20, 24105 Kiel, Germany 3 Research Group Invasion Ecology, Research Unit Experimental Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Duesternbrooker Weg 20, 24105 Kiel, Germany 4 Chinese Academy of Sciences, Research Center for Eco-Environmental Sciences, 18 Shuangqing Rd., Haidian District, Beijing, 100085, China 5 Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada 6 Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, Kiel 24118, Germany * Corresponding author: Deniz Tasdemir ([email protected]) This document includes: Supplementary Figures S1-S11 Figure S1. Genotyping of C. intestinalis with the mitochondrial marker gene COX3-ND1. Figure S2. Influence of the quality filtering steps on the total number of observed read pairs from amplicon sequencing. Figure S3. Rarefaction curves of OTU abundances for C. intestinalis and seawater samples. Figure S4. Multivariate ordination plots of the bacterial community associated with C. intestinalis. Figure S5. Across sample type and geographic origin comparison of the C. intestinalis associated microbiome. -
Appendices Physico-Chemical
http://researchcommons.waikato.ac.nz/ Research Commons at the University of Waikato Copyright Statement: The digital copy of this thesis is protected by the Copyright Act 1994 (New Zealand). The thesis may be consulted by you, provided you comply with the provisions of the Act and the following conditions of use: Any use you make of these documents or images must be for research or private study purposes only, and you may not make them available to any other person. Authors control the copyright of their thesis. You will recognise the author’s right to be identified as the author of the thesis, and due acknowledgement will be made to the author where appropriate. You will obtain the author’s permission before publishing any material from the thesis. An Investigation of Microbial Communities Across Two Extreme Geothermal Gradients on Mt. Erebus, Victoria Land, Antarctica A thesis submitted in partial fulfilment of the requirements for the degree of Master’s Degree of Science at The University of Waikato by Emily Smith Year of submission 2021 Abstract The geothermal fumaroles present on Mt. Erebus, Antarctica, are home to numerous unique and possibly endemic bacteria. The isolated nature of Mt. Erebus provides an opportunity to closely examine how geothermal physico-chemistry drives microbial community composition and structure. This study aimed at determining the effect of physico-chemical drivers on microbial community composition and structure along extreme thermal and geochemical gradients at two sites on Mt. Erebus: Tramway Ridge and Western Crater. Microbial community structure and physico-chemical soil characteristics were assessed via metabarcoding (16S rRNA) and geochemistry (temperature, pH, total carbon (TC), total nitrogen (TN) and ICP-MS elemental analysis along a thermal gradient 10 °C–64 °C), which also defined a geochemical gradient. -
Advance View Proofs
Microbes Environ. Vol. 00, No. 0, 000-000, 2015 https://www.jstage.jst.go.jp/browse/jsme2 doi:10.1264/jsme2.ME14123 Bacterial Community Analysis of Drinking Water Biofilms in Southern Sweden KATHARINA LÜHRIG1,2, BJÖRN CANBÄCK3, CATHERINE J. PAUL1,4, TOMAS JOHANSSON3, KENNETH M. PERSSON2,4, and PETER RÅDSTRÖM1* 1Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; 2Sydvatten AB, Hyllie Stationstorg 21, SE-215 32 Malmö, Sweden; 3Microbial Ecology Group, Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden; and 4Water Resources Engineering, Department of Building and Environmental Technology, Lund University, P.O. Box 118, SE-221 00 Lund, Sweden (Received August 28, 2014—Accepted January 10, 2015—Published online February 21, 2015) Next-generation sequencing of the V1-V2 and V3 variable regions of the 16S rRNA gene generated a total of 674,116 reads that described six distinct bacterial biofilm communities from both water meters and pipes. A high degree of reproducibility was demonstrated for the experimental and analytical work-flow by analyzing the communities present in parallel water meters, the rare occurrence of biological replicates within a working drinking water distribution system. The communities observed in water meters from households that did not complain about their drinking water were defined by sequences representing Proteobacteria (82–87%), with 22–40% of all sequences being classified as Sphingomonadaceae. However, a water meter biofilm community from a household with consumer reports of red water and flowing water containing elevated levels of iron and manganese had fewer sequences representing Proteobacteria (44%); only 0.6% of all sequences were classified as Sphingomonadaceae; and, in contrast to the other water meter communities, markedly more sequences represented Nitrospira and Pedomicrobium. -
Lists of Names of Prokaryotic Candidatus Taxa
NOTIFICATION LIST: CANDIDATUS LIST NO. 1 Oren et al., Int. J. Syst. Evol. Microbiol. DOI 10.1099/ijsem.0.003789 Lists of names of prokaryotic Candidatus taxa Aharon Oren1,*, George M. Garrity2,3, Charles T. Parker3, Maria Chuvochina4 and Martha E. Trujillo5 Abstract We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, pro- posed between the mid- 1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evo- lutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current propos- als to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes. Introduction of the category called Candidatus was first pro- morphology, basis of assignment as Candidatus, habitat, posed by Murray and Schleifer in 1994 [1]. The provisional metabolism and more. However, no such lists have yet been status Candidatus was intended for putative taxa of any rank published in the journal. that could not be described in sufficient details to warrant Currently, the nomenclature of Candidatus taxa is not covered establishment of a novel taxon, usually because of the absence by the rules of the Prokaryotic Code. -
Compile.Xlsx
Silva OTU GS1A % PS1B % Taxonomy_Silva_132 otu0001 0 0 2 0.05 Bacteria;Acidobacteria;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un; otu0002 0 0 1 0.02 Bacteria;Acidobacteria;Acidobacteriia;Solibacterales;Solibacteraceae_(Subgroup_3);PAUC26f; otu0003 49 0.82 5 0.12 Bacteria;Acidobacteria;Aminicenantia;Aminicenantales;Aminicenantales_fa;Aminicenantales_ge; otu0004 1 0.02 7 0.17 Bacteria;Acidobacteria;AT-s3-28;AT-s3-28_or;AT-s3-28_fa;AT-s3-28_ge; otu0005 1 0.02 0 0 Bacteria;Acidobacteria;Blastocatellia_(Subgroup_4);Blastocatellales;Blastocatellaceae;Blastocatella; otu0006 0 0 2 0.05 Bacteria;Acidobacteria;Holophagae;Subgroup_7;Subgroup_7_fa;Subgroup_7_ge; otu0007 1 0.02 0 0 Bacteria;Acidobacteria;ODP1230B23.02;ODP1230B23.02_or;ODP1230B23.02_fa;ODP1230B23.02_ge; otu0008 1 0.02 15 0.36 Bacteria;Acidobacteria;Subgroup_17;Subgroup_17_or;Subgroup_17_fa;Subgroup_17_ge; otu0009 9 0.15 41 0.99 Bacteria;Acidobacteria;Subgroup_21;Subgroup_21_or;Subgroup_21_fa;Subgroup_21_ge; otu0010 5 0.08 50 1.21 Bacteria;Acidobacteria;Subgroup_22;Subgroup_22_or;Subgroup_22_fa;Subgroup_22_ge; otu0011 2 0.03 11 0.27 Bacteria;Acidobacteria;Subgroup_26;Subgroup_26_or;Subgroup_26_fa;Subgroup_26_ge; otu0012 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_5;Subgroup_5_or;Subgroup_5_fa;Subgroup_5_ge; otu0013 1 0.02 13 0.32 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_or;Subgroup_6_fa;Subgroup_6_ge; otu0014 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_un;Subgroup_6_un;Subgroup_6_un; otu0015 8 0.13 30 0.73 Bacteria;Acidobacteria;Subgroup_9;Subgroup_9_or;Subgroup_9_fa;Subgroup_9_ge;