DOCSLIB.ORG

Microbial Population Composition of Ochrous Biofilms and Water Samples Obtained from Technical Groundwater-Fed Systems

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Microbial Population Composition of Ochrous Biofilms and Water Samples Obtained from Technical Groundwater-Fed Systems Microbial population composition of ochrous biofilms and water samples obtained from technical groundwater-fed systems vorgelegt von Diplom-Biologin Josephin Schröder geb. in Schwedt/Oder von der Fakultät III - Prozesswissenschaften der Technischen Universität Berlin zur Erlangung des akademischen Grades Doktorin der Naturwissenschaften - Dr. rer. nat.- genehmigte Dissertation Promotionsausschuss: Vorsitzender: Prof. Dr.-Ing. Sven-Uwe Geißen Gutachter: Prof. Dr. rer. nat. Ulrich Szewzyk Gutachter: Prof. Dr. Flynn Picardal Tag der wissenschaftlichen Aussprache: 05. Februar 2018 Berlin 2018 Danksagung An erster Stelle danke ich Prof. Dr. Ulrich Szewzyk für die Möglichkeit an dem spannenden und anwendungsbezogenen Thema zu arbeiten sowie für die wissenschaftliche Betreuung. Flynn Picardal danke ich für Bereitschaft, trotz der langen Anreise, meine Arbeit zu begutachten. Ebenfalls ein besonderer Dank gilt Dr. Burga Braun für die wissenschaftliche Betreuung während der gesamten Zeit am Fachgebiet, ihre ständige Unterstützung und für das Lesen des Manuskripts sowie die vielen wertvollen Vorschläge. Des Weiteren möchte ich den Projektpartnern des Antiocker-Projektes danken, die mir bei der Probenahme, Organisation und fachlichen Auseinandersetzung mit dem Thema geholfen haben. Ein besonderer Dank gilt Henrik, der zum einem als Projektpartner hervorragende Arbeit geleistet hat, mich bei der Auswertung der vielen Daten unterstützt hat, aber auch immer als guter Freund beiseite stand. Des Weiteren möchte ich den Mitarbeiterinnen und Mitarbeitern der UMB danken. An dieser Stelle seien namentlich Anna, Micha, Heinz, Anja, Gaby, Bertram, Stefie, Bärbel und Marcella genannt sowie Stef für ihre kompetente Hilfe und freundschaftliche Arbeitsweise im Labor. Vielen Dank für eure Unterstützung, die fruchtvollen Gespräche und die netten Stunden. Allen nicht namentlich erwähnten alten und neuen Kollegen des Fachgebietes Umweltmikrobiologie danke ich für das angenehme Arbeitsklima und die vielfältige Unterstützung. Außerdem möchte ich allen Studenten danken, die ihre Bachelorarbeit im Rahmen des Dissertationsthemas angefertigt haben und somit einen wichtigen Teil zu meiner Arbeit beigetragen haben. Nicht zuletzt gilt mein besonderer Dank meinen lieben Eltern, Geschwistern, Freunden Annika, Luise, Josi, Ulli und Johanna sowie meinem Freund André für die andauernde Unterstützung, Geduld und den notwendigen Rückhalt während der letzten Jahre. Veröffentlichungen Auszüge der im Folgenden dargestellten Daten wurden bereits im Vorfeld in Fachpublikationen veröffentlicht. Fachpublikationen mit ordentlichen Begutachtungsverfahren Braun, B.1, Schröder, J.1, Knecht, H., & Szewzyk, U. (2016). Unravelling the microbial community of a cold groundwater catchment system. Water Research, 107, 113-126. 1These authors contributed equally to this work. Schröder, J., Braun, B., Liere, K., & Szewzyk, U. (2016). Draft genome sequence of Rheinheimera sp. strain SA_1 isolated from iron backwash sludge in Germany. Genome Announcements, 4(4), e00853-16. Braun, B.; Künzel, S.; Schroeder, J.; & Szewzyk, U. (2017). Draft Genome Sequence of strain R_RK_3, an iron-depositing isolate of the genus Rhodomicrobium isolated from a dewatering well of an opencast mine. Genome Announcements 5, A.00864-17. Andere Veröffentlichungen Schwarzmüller, H., Menz, C., Grützmacher, G., Gnierss, G., Jordan, V., Schröder, J., Braun, B., Szewzyk, U., Macheleidt, W. & Grischeck, T. Mikrobielle Verockerung in technischen Systemen (Teil 1): Probenahme aus dem Filterbereich eines Trinkwasserbrunnens mit neuartigem Unterwasserkamera- und Probenahme-System wwt Wasserwirtschaft-Wassertechnik, 31–33. 2014 III Schröder, J., Braun, B., Schwarzmüller, H., Menz, C., Grützmacher, G., Gnierss, G., Jordan, V., Macheleidt, W., Grischeck, T. & Szewzyk, U. Mikrobielle Verockerung in technischen Systemen (Teil 2): Molekularbiologische und mikrobiologische Untersuchungen von Ockerproben aus dem Filterbereich eines Trinkwasserbrunnens der Berliner Wasserbetreibe und von verschiedenen Proben der Betriebspumpe im Rahmen einer Instandhaltungsmaßnahme wwt Wasserwirtschaft-Wassertechnik, 33–36. 2014 Mikrobielle Verockerung in technischen Systemen 2015. Teilprojekt 1a: Mikrobiologie der Verockerung bei neutralem pH-Wert und deren Verhinderung. BMBF Projekt Förderkennzeichen: 02WT1185. Braun, B., Knecht, H., Neulinger, S., Schröder, J., & Szewzyk, U. (2017). Bakterienprofile in natürlichen und technischen Ökosystemen. BIOspektrum, 23(1), 46-48. Bachelorarbeiten im Rahmen des Dissertationsthemas Jan Phillip Samson (2013); Vergleichende Populationsanalysen der mikrobiellen Gemeinschaften einer russischen Wasserfassung Jens Blume (2013); Charakterisierung von Bakterien aus einer russischen Wasserfassung Anja Höhne (2014); Etablierung einer quantitativen Real-Time PCR zum spezifischen Nachweis von Crenothrix spp., Geothrix spp. und Gallionella spp. in einer russischen Wasserfassung Annelie Höhne (2014); Quantitativer Nachweis von Rhodoferax spp. in einer Wasserfassung mittels Real-Time PCR Regina Heick (2015); Untersuchungen zur kleinräumigen Heterogenität von Biofilmpopulationen auf verockerten Unterwassermotorpumpen IV Abstract Abstract This study assessed the abundance, composition, diversity and functional organisation of bacterial communities correlated to chemical water parameters in four technical groundwater-fed systems. Each sampling site was vulnerable to iron-clogging and was characterised by its own specific technical and hydrochemical conditions. Biofilm and groundwater samples were obtained and compared for drinking water wells in Berlin, a groundwater catchment area with a subsurface iron and manganese removal system in Russia, dewatering wells in the Rhenish lignite mining area and a lab-scale reactor with a natural ochrous formation due to groundwater abstraction. Each sampling site’s bacterial composition was analysed by 16S rRNA gene clone library construction or 454-pyrosequencing to determine the dominant bacterial groups and to compare the bacterial compositions across all of the sampling sites. Samples from all sites featured highly comparable distributions of phyla, and these mainly consisted of Proteobacteria. However, there were differences between the sites regarding the bacterial class. Sequences with a high homology to the class of Deltaproteobacteria were predominantly abundant in those samples obtained from the lab-scale reactor and the Berlin drinking water wells. In addition, sequences from those samples derived from the wells located at the Russian water catchment site were associated with Betaproteobacteria, while sequences from the dewatering wells at the opencast mining sites belonged to Gammaproteobacteria. A bacterial population analysis of the 16S rRNA gene did not reveal any shared core operational taxonomic units (OTUs) across all of the sampling sites; however, several OTUs, such as Geobacter, Rhodoferax, Gallionella and Geothrix, were found repeatedly often at most of the sampling sites, indicating that they had an influence on the iron-clogging processes. Those groups are all involved in iron oxidation and reduction reactions, and their biofilm formation potential became apparent. In addition, site-dependent characteristics, such as methane availability in groundwater, caused high abundances of methano- and methylotrophic bacterial V Abstract genera, such as Crenothrix and Methylobacter. Such microorganisms are common sources of water supply problems. In addition to methane’s influence on the microbial community composition, the groundwater dissolved organic carbon (DOC) concentration and the redox potential, which is affected by the availability of oxygen, indicated to play a major role. Additionally, total bacterial and species-specific quantitative real-time PCR (qPCR) enabled to calculate the relative abundance of major taxonomic groups within the samples. The gene copy numbers detected by qPCR for all biofilm samples obtained from water well equipment revealed high amounts of Gallionella-, Crenothrix-, Geothrix- and Rhodoferax-related genes (up to 1011 copies g-1). In addition, the richness values calculated by denaturing gradient gel electrophoresis (DGGE) indicated a high degree of diversity in almost all samples. The identification of parameters with an effect on the bacterial community structure will potentially help to prevent and remediate the clogging process in technical groundwater-fed systems. VI Zusammenfassung Zusammenfassung In dieser Arbeit wurden die Abundanz, Zusammensetzung, Diversität und funktionale Organisation (engl. functional organisation) der bakteriellen Gemeinschaften in vier technischen, mit Grundwasser gespeisten Systemen, untersucht. Zusätzlich wurden diese Daten mit den wasserchemischen Parametern korreliert. Alle untersuchten technischen Systeme zeigten Verockerungsablagerungen und waren durch standortspezifische, technische und hydrochemische Bedingungen charakterisiert. Die Biofilm- und Wasserproben stammten aus Trinkwasserbrunnen in Berlin, einer Trinkwasserfassung mit unterirdischer Enteisenung und Entmanganung in Russland, Sümpfungsbrunnen aus dem rheinischen Braunkohletagebaurevier und einem Brunnenreaktor im Labormaßstab. Die bakteriellen Gemeinschaften aller Standorte wurden auf der Ebene der 16S rDNA durch Erstellung einer Klonbibliothek und mittels 454- Pyrosequenzierungsanalyse untersucht, um die dominanten bakteriellen Gruppen zu detektieren und untereinander zu vergleichen. Das Phylum der Proteobacteria war die dominierende Gruppe
Load more

Recommended publications
  • Phototrophic Oxidation of Ferrous Iron by a Rhodomicrobium Vannielii Strain
    Phototrophic oxidation of ferrous iron by a Rhodomicrobium vannielii strain Silke Heising and Bernhard Schink Author for correspondence: Bernhard Schink. Tel: ­49 7531 882140. Fax: ­49 7531 882966. e-mail: Bernhard.Schink!uni-konstanz.de Fakulta$ tfu$r Biologie, Oxidation of ferrous iron was studied with the anaerobic phototrophic Universita$ t Konstanz, bacterial strain BS-1. Based on morphology, substrate utilization patterns, Postfach 5560, D-78434 Konstanz, Germany arrangement of intracytoplasmic membranes and the in vivo absorption spectrum, this strain was assigned to the known species Rhodomicrobium vannielii. Also, the type strain of this species oxidized ferrous iron in the light. Phototrophic growth of strain BS-1 with ferrous iron as electron donor was stimulated by the presence of acetate or succinate as cosubstrates. The ferric iron hydroxides produced precipitated on the cell surfaces as solid crusts which impeded further iron oxidation after two to three generations. The complexing agent nitrilotriacetate stimulated iron oxidation but the yield of cell mass did not increase stoichiometrically under these conditions. Other complexing agents inhibited cell growth. Ferric iron was not reduced in the dark, and manganese salts were neither oxidized nor reduced. It is concluded that ferrous iron oxidation by strain BS-1 is only a side activity of this bacterium that cannot support growth exclusively with this electron source over prolonged periods of time. Keywords: iron metabolism, phototrophic bacteria, Rhodomicrobium vannielii, iron complexation, nitrilotriacetate (NTA) INTRODUCTION anoxygenic purple bacteria, including a Rhodo- microbium vannielii-like isolate (Widdel et al., 1993). Iron is the fourth most important element in the Earth’s Other strains of purple phototrophs able to oxidize crust, making up about 5% of the total crust mass ferrous iron are strain L7, a non-motile rod with gas (Ehrlich, 1990).
    [Show full text]
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Which Organisms Are Used for Anti-Biofouling Studies
    Table S1. Semi-systematic review raw data answering: Which organisms are used for anti-biofouling studies? Antifoulant Method Organism(s) Model Bacteria Type of Biofilm Source (Y if mentioned) Detection Method composite membranes E. coli ATCC25922 Y LIVE/DEAD baclight [1] stain S. aureus ATCC255923 composite membranes E. coli ATCC25922 Y colony counting [2] S. aureus RSKK 1009 graphene oxide Saccharomycetes colony counting [3] methyl p-hydroxybenzoate L. monocytogenes [4] potassium sorbate P. putida Y. enterocolitica A. hydrophila composite membranes E. coli Y FESEM [5] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) K. pneumonia ATCC13883 P. aeruginosa BAA-1744 composite membranes E. coli Y SEM [6] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) graphene oxide E. coli ATCC25922 Y colony counting [7] S. aureus ATCC9144 P. aeruginosa ATCCPAO1 composite membranes E. coli Y measuring flux [8] (unspecified/unique sample type) graphene oxide E. coli Y colony counting [9] (unspecified/unique SEM sample type) LIVE/DEAD baclight S. aureus stain (unspecified/unique sample type) modified membrane P. aeruginosa P60 Y DAPI [10] Bacillus sp. G-84 LIVE/DEAD baclight stain bacteriophages E. coli (K12) Y measuring flux [11] ATCC11303-B4 quorum quenching P. aeruginosa KCTC LIVE/DEAD baclight [12] 2513 stain modified membrane E. coli colony counting [13] (unspecified/unique colony counting sample type) measuring flux S. aureus (unspecified/unique sample type) modified membrane E. coli BW26437 Y measuring flux [14] graphene oxide Klebsiella colony counting [15] (unspecified/unique sample type) P. aeruginosa (unspecified/unique sample type) graphene oxide P. aeruginosa measuring flux [16] (unspecified/unique sample type) composite membranes E.
    [Show full text]
  • The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro
    FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities.
    [Show full text]
  • 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.
    [Show full text]
  • Deoxyribonucleic Acid Base Sequence Homologies of Some Budding and Prosthecate Bacterla RICHARD L
    JOURNAL OF BACTERIOLOGY, Apr. 1972, p. 256-261 Vol. 110, No. 1 Copyright © 1972 American Society for Microbiology Printed in U.S.A. Deoxyribonucleic Acid Base Sequence Homologies of Some Budding and Prosthecate Bacterla RICHARD L. MOORE' AND PETER HIRSCH2 Department of Microbiology and Public Health, Michigan State University, East Lansing, Michigan 48823 Received for publication 21 December 1971 The genetic relatedness of a number of budding and prosthecate bacteria was determined by deoxyribonucleic acid (DNA) homology experiments of the di- rect binding type. Strains of Hyphomicrobium sp. isolated from aquatic habi- tats were found to have relatedness values ranging from 9 to 70% with strain "EA-617," a subculture of the Hyphomicrobium isolated by Mevius from river water. Strains obtained from soil enrichments had lower values with EA-617, ranging from 3 to 5%. Very little or no homology was detected between the amino acid-utilizing strain Hyphomicrobium neptunium and other Hyphomi- crobium strains, although significant homology was observed with the two Hyphomonas strains examined. No homology could be detected between pros- thecate bacteria of the genera Rhodomicrobium, Prosthecomicrobium, Ancal- omicrobium, or Caulobacter, and Hyphomicrobium strain EA-617 or H. nep- tunium LE-670. The grouping of Hyphomicrobium strains by their relatedness values agrees well with a grouping according to the base composition of their DNA species. It is concluded that bacteria possessing cellular extensions repre- sent a widely diverse group of organisms. Two genera of bacteria, Hyphomicrobium drum, P. pneumaticum, Ancalomicrobium adetum, and Rhodomicrobium, are listed under the and Caulobacter crescentus were obtained from J. T. family of Hyphomicrobiaceae in the seventh Staley (Seattle); Rhodomicrobium vannielii was re- edition of Bergey's Manual of Determinative ceived from H.
    [Show full text]
  • Research Collection
    Research Collection Doctoral Thesis Development and application of molecular tools to investigate microbial alkaline phosphatase genes in soil Author(s): Ragot, Sabine A. Publication Date: 2016 Permanent Link: https://doi.org/10.3929/ethz-a-010630685 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO.23284 DEVELOPMENT AND APPLICATION OF MOLECULAR TOOLS TO INVESTIGATE MICROBIAL ALKALINE PHOSPHATASE GENES IN SOIL A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (Dr. sc. ETH Zurich) presented by SABINE ANNE RAGOT Master of Science UZH in Biology born on 25.02.1987 citizen of Fribourg, FR accepted on the recommendation of Prof. Dr. Emmanuel Frossard, examiner PD Dr. Else Katrin Bünemann-König, co-examiner Prof. Dr. Michael Kertesz, co-examiner Dr. Claude Plassard, co-examiner 2016 Sabine Anne Ragot: Development and application of molecular tools to investigate microbial alkaline phosphatase genes in soil, c 2016 ⃝ ABSTRACT Phosphatase enzymes play an important role in soil phosphorus cycling by hydrolyzing organic phosphorus to orthophosphate, which can be taken up by plants and microorgan- isms. PhoD and PhoX alkaline phosphatases and AcpA acid phosphatase are produced by microorganisms in response to phosphorus limitation in the environment. In this thesis, the current knowledge of the prevalence of phoD and phoX in the environment and of their taxonomic distribution was assessed, and new molecular tools were developed to target the phoD and phoX alkaline phosphatase genes in soil microorganisms.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 1 Anoxygenic Phototrophic Chloroflexota Member Uses a Type
    Anoxygenic phototrophic Chloroflexota member uses a Type I reaction center Supplementary Materials J. M. Tsuji, N. A. Shaw, S. Nagashima, J. J. Venkiteswaran, S. L. Schiff, S. Hanada, M. Tank, J. D. Neufeld Correspondence to: [email protected]; [email protected]; [email protected] This PDF file includes: Materials and Methods Supplementary Text, Sections S1 to S4 Figs. S1 to S9 Tables S1 to S3 1 Materials and Methods Enrichment cultivation of ‘Ca. Chx. allophototropha’ To culture novel anoxygenic phototrophs, we sampled Lake 227, a seasonally anoxic and ferruginous Boreal Shield lake at the International Institute for Sustainable Development Experimental Lakes Area (IISD-ELA; near Kenora, Canada). Lake 227 develops up to ~100 μM concentrations of dissolved ferrous iron in its anoxic water column (31), and anoxia is more pronounced than expected naturally due to the long-term experimental eutrophication of the lake (32). The lake’s physico-chemistry has been described in detail previously (31). We collected water from the illuminated portion of the upper anoxic zone of Lake 227 in September 2017, at 3.875 and 5 m depth, and transported this water anoxically and chilled in 120 mL glass serum bottles, sealed with black rubber stoppers (Geo-Microbial Technology Company; Ochelata, Oklahoma, USA), to the laboratory. Water was supplemented with 2% v/v of a freshwater medium containing 8 mM ferrous chloride (33) and was distributed anoxically into 120 mL glass serum bottles, also sealed with black rubber stoppers (Geo-Microbial Technology Company), that had a headspace of dinitrogen gas at 1.5 atm final pressure.
    [Show full text]