DOCSLIB.ORG

Characterisation of the Symbiotic Bacterial Partners in Phototrophic

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Characterisation of the Symbiotic Bacterial Partners in Phototrophic Ludwig-Maximilians-Universität München Fakultät für Biologie CHARACTERIZATION OF THE SYMBIOTIC BACTERIAL PARTNERS IN PHOTOTROPHIC CONSORTIA Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades vorgelegt von Kristina Renate Pfannes Ludwig‐Maximilians‐Universität München Fakultät für Biologie Characterization of the symbiotic bacterial partners in phototrophic consortia Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades vorgelegt von Kristina Renate Pfannes aus Dettelbach München im Juli 2007 „WENN DU EIN SCHIFF BAUEN WILLST, DANN TROMMLE NICHT MÄNNER ZUSAMMEN, UM HOLZ ZU BESCHAFFEN, AUFGABEN ZU VERGEBEN UND DIE ARBEIT EINZUTEILEN, SONDERN LEHRE SIE DIE SEHNSUCHT NACH DEM WEITEN, ENDLOSEN MEER” ANTOINE DE SAINT-EXUPERY FRZ. FLIEGER & SCHRIFTSTELLER (1900-1944) 1. Gutachter: Prof. Dr. Jörg Overmann, LMU München 2. Gutachterin: Prof. Dr. Kirsten Jung, LMU München Tag der Abgabe: 31.07.2007 Tag des Promotionskolloquiums: 22.11.2007 PUBLICATIONS ORIGINATING FROM THIS THESIS CHAPTER 3 Kanzler BEM, Pfannes KR, Vogl K, Overmann J (2005) Molecular characterization of the nonphotosynthetic partner bacterium in the consortium “Chlorochromatium aggregatum”. Appl Environ Microbiol 71:7434‐7441 CHAPTER 4 Pfannes KR, Vogl K, Overmann J (2007) The heterotrophic symbionts of phototrophic consortia belong to a highly diverse subgroup of Betaproteobacteria characterized by a tandem rrn operon structure. Environ Microbiol 9:2782‐2794 CHAPTER 5 Vogl K, Glaeser J, Pfannes KR, Wanner G, Overmann J (2006) Chlorobium chlorochromatii sp. nov., a symbiotic green sulfur bacterium isolated from the phototrophic consortium “Chlorochromatium aggregatum”. Arch Microbiol 185:363‐372 CHAPTER 6 Pfannes KR, Müller JF, Zikeli K, Bayer AI, Vogl K, Wenter R, Hütz KA, Grossart H‐P, Sandmann G, Takaichi S, Overmann J (2007) Oxygen tolerance and physiological properties of symbiotic and free‐living green sulfur bacteria. (manuscript) CONTRIBUTIONS CHAPTER 3 The chemotaxis experiments were performed by Birgit Kanzler. She also did the in situ hybridization and the phylogenetic analyses under supervision of Kajetan Vogl. Kristina Pfannes established the enrichment and isolation of genomic DNA of the central bacterium via CsCl equilibrium density gradient centrifugation, determined the mol% G+C content and performed the real‐time PCR. CHAPTER 4 Kristina Pfannes performed the amplification and cloning of the rRNA operon. Moreover, she did the screening and analysis of the natural bacterial communities and conducted the in situ hybridization as well as the phylogenetical and statistical analyses. Kajetan Vogl developed the new cultivation approach of consortia cultures. CHAPTER 5 The epibiont was isolated and phylogenetically analysed by Kajetan Vogl in cooperation with Jens Glaeser. Kajetan Vogl also did the substrate test and the growth experiments (temperature optimum, light intensity optimum, pH optimum) and the pigment analyses. Prof. Dr. Gerhard Wanner took the electron microscopy pictures. The contributions of Kristina Pfannes were the determination of the cell surface hydrophobicity and the salinity optimum, the pigment extraction, the KOH‐string test and the Gram‐staining. CHAPTER 6 Kristina Pfannes, Kerstin Zikeli and Johannes Müller conducted the oxygen tolerance test. The enzyme assays were established and performed by Kristina Pfannes and Johannes Müller. Roland Wenter did the RT‐PCR. Kristina Pfannes performed the genome analyses and the phylogenetic studies. Also, she prepared the samples for the analysis of the carotenoids and the determination of the amino acid and carbohydrate excretion. Prof. Dr. Gerhard Sandmann and Prof. Dr. Shinichi Takaichi analysed the carotenoids. Kerstin Zikeli and Katharina Hütz were responsible for the chlorosome analysis. The carbohydrate excretion and the amino acid excretion was measured by Dr. Hans‐Peter Grossart and Prof. Dr. Meinhard Simon, respectively. Anne Bayer did the amino acid utilization experiment. I hereby confirm the above statements Kristina Pfannes Prof. Dr. Jörg Overmann TABLE OF CONTENTS I. ABBREVIATIONS.....................................................................................................................1 1 Summary.....................................................................................................................................1 2 Introduction ...............................................................................................................................3 2.1 Diversity of Symbioses ...........................................................................................................3 2.2 Significance of Prokaryotic Symbioses.................................................................................4 2.3 Photosynthesis and Phototrophy in Bacteria.......................................................................8 2.4 Green Sulfur Bacteria..........................................................................................................10 2.5 Phototrophic Consortia........................................................................................................13 2.6 "Chlorochromatium aggregatum" as a Model Organism..................................................18 2.7 Aim of this Work..................................................................................................................20 2.8 References .............................................................................................................................23 3 Molecular characterization of the non‐photosynthetic partner bacterium in the consortium “Chlorochromatium aggregatum”...................................................................35 3.1 Abstract.................................................................................................................................35 3.2 Introduction ..........................................................................................................................36 3.3 Material and Methods..........................................................................................................37 3.3.1 Source of organisms ........................................................................................................................ 37 3.3.2 Media and growth conditions .......................................................................................................... 37 3.3.3 Enrichment by chemotaxis .............................................................................................................. 38 3.3.4 PCR ................................................................................................................................................. 39 3.3.5 Quantitative PCR............................................................................................................................. 40 3.3.6 Denaturing gradient gel electrophoresis (DGGE)............................................................................ 40 3.3.7 Cloning ............................................................................................................................................ 40 3.3.8 Sequencing ...................................................................................................................................... 41 3.3.9 Phylogenetic analyses...................................................................................................................... 41 3.3.10 Fluorescence in situ hybridization (FISH) .................................................................................. 42 3.3.11 CsCl – bisbenzimidazole density gradient centrifugation ........................................................... 42 3.3.12 Accession numbers...................................................................................................................... 43 TABLE OF CONTENTS 3.4 Results and Discussion ........................................................................................................ 45 3.4.1 Improved chemotactic enrichment of intact phototrophic consortia................................................45 3.4.2 Analysis of the 16S rRNA gene sequence of the central bacterium of "C. aggregatum" ................46 3.4.3 Phylogenetic classification of the central rod ..................................................................................49 3.4.4 GC-content and enrichment of genomic DNA of the central bacterium..........................................50 3.4.5 Relevance for future studies.............................................................................................................53 3.5 Acknowledgements .............................................................................................................. 54 3.6 References ............................................................................................................................ 54 4 The heterotrophic symbionts of phototrophic consortia belong to a highly diverse subgroup of Betaproteobacteria characterized by a tandem rrn operon structure....... 61 4.1 Abstract ................................................................................................................................ 61 4.2 Introduction ......................................................................................................................... 62 4.3 Materials and Methods ....................................................................................................... 64 4.3.1 Source of organisms
Load more

Recommended publications
  • Novel Copper-Containing Membrane Monooxygenases (Cummos) Encoded by Alkane- Utilizing Betaproteobacteria
    Lawrence Berkeley National Laboratory Recent Work Title Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane- utilizing Betaproteobacteria. Permalink https://escholarship.org/uc/item/8z48x96q Journal The ISME journal, 14(3) ISSN 1751-7362 Authors Rochman, Fauziah F Kwon, Miye Khadka, Roshan et al. Publication Date 2020-03-01 DOI 10.1038/s41396-019-0561-2 Peer reviewed eScholarship.org Powered by the California Digital Library University of California 1 1 2 1Novel copper-containing membrane monooxygenases 2(CuMMOs) encoded by alkane-utilizing Betaproteobacteria 3 4Running title: Novel CuMMOs in Betaproteobacteria 5 6Fauziah F. Rochman1, Miye Kwon2, Roshan Khadka1, Ivica Tamas1,3, Azriel 7Abraham Lopez-Jauregui1,4, Andriy Sheremet1, Angela Smirnova1, Rex R. 8Malmstrom5, Sukhwan Yoon2, Tanja Woyke5, Peter F. Dunfield1*, Tobin J. 9Verbeke1 10 111 Department of Biological Sciences, University of Calgary, 2500 University 12Dr. NW Calgary AB Canada T2N 1N4 132 Department of Civil and Environmental Engineering, Korea Advanced 14Institute of Science and Technology, Daejeon, Korea 153Department of Biology and Ecology, University of Novi Sad Novi Sad, Serbia 164 Instituto Tecnologico y de Estudios Superiores de Monterrey, Chihuahua, 17Mexico 185 Department of Energy Joint Genome Institute, Walnut Creek, California, 19USA. 20 21*Corresponding author: [email protected]; 403-220-2469 22 3 2 4 23Competing interests: The authors declare that they have no competing 24interests. 5 3 6 25Abstract 26Copper-containing membrane monooxygenases (CuMMOs) are encoded by 27xmoCAB(D) gene clusters and catalyze the oxidation of methane, ammonia, 28or some short chain alkanes and alkenes. In a metagenome constructed from 29an oilsands tailings pond we detected an xmoCABD gene cluster with <59% 30derived amino acid identity to genes from known bacteria.
    [Show full text]
  • Response of Heterotrophic Stream Biofilm Communities to a Gradient of Resources
    The following supplement accompanies the article Response of heterotrophic stream biofilm communities to a gradient of resources D. J. Van Horn1,*, R. L. Sinsabaugh1, C. D. Takacs-Vesbach1, K. R. Mitchell1,2, C. N. Dahm1 1Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA 2Present address: Department of Microbiology & Immunology, University of British Columbia Life Sciences Centre, Vancouver BC V6T 1Z3, Canada *Email: [email protected] Aquatic Microbial Ecology 64:149–161 (2011) Table S1. Representative sequences for each OTU, associated GenBank accession numbers, and taxonomic classifications with bootstrap values (in parentheses), generated in mothur using 14956 reference sequences from the SILVA data base Treatment Accession Sequence name SILVA taxonomy classification number Control JF695047 BF8FCONT18Fa04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Cellvibrio(100);unclassified; Control JF695049 BF8FCONT18Fa12.b1 Bacteria(100);Proteobacteria(100);Alphaproteobacteria(100);Rhizobiales(100);Methylocystaceae(100);uncultured(100);unclassified; Control JF695054 BF8FCONT18Fc01.b1 Bacteria(100);Planctomycetes(100);Planctomycetacia(100);Planctomycetales(100);Planctomycetaceae(100);Isosphaera(50);unclassified; Control JF695056 BF8FCONT18Fc04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Xanthomonadales(100);Xanthomonadaceae(100);uncultured(64);unclassified; Control JF695057 BF8FCONT18Fc06.b1 Bacteria(100);Proteobacteria(100);Betaproteobacteria(100);Burkholderiales(100);Comamonadaceae(100);Ideonella(54);unclassified;
    [Show full text]
  • Introduction to Arthropod Groups What Is Entomology?
    Entomology 340 Introduction to Arthropod Groups What is Entomology? The study of insects (and their near relatives). Species Diversity PLANTS INSECTS OTHER ANIMALS OTHER ARTHROPODS How many kinds of insects are there in the world? • 1,000,0001,000,000 speciesspecies knownknown Possibly 3,000,000 unidentified species Insects & Relatives 100,000 species in N America 1,000 in a typical backyard Mostly beneficial or harmless Pollination Food for birds and fish Produce honey, wax, shellac, silk Less than 3% are pests Destroy food crops, ornamentals Attack humans and pets Transmit disease Classification of Japanese Beetle Kingdom Animalia Phylum Arthropoda Class Insecta Order Coleoptera Family Scarabaeidae Genus Popillia Species japonica Arthropoda (jointed foot) Arachnida -Spiders, Ticks, Mites, Scorpions Xiphosura -Horseshoe crabs Crustacea -Sowbugs, Pillbugs, Crabs, Shrimp Diplopoda - Millipedes Chilopoda - Centipedes Symphyla - Symphylans Insecta - Insects Shared Characteristics of Phylum Arthropoda - Segmented bodies are arranged into regions, called tagmata (in insects = head, thorax, abdomen). - Paired appendages (e.g., legs, antennae) are jointed. - Posess chitinous exoskeletion that must be shed during growth. - Have bilateral symmetry. - Nervous system is ventral (belly) and the circulatory system is open and dorsal (back). Arthropod Groups Mouthpart characteristics are divided arthropods into two large groups •Chelicerates (Scissors-like) •Mandibulates (Pliers-like) Arthropod Groups Chelicerate Arachnida -Spiders,
    [Show full text]
  • ( 12 ) United States Patent
    US010314866B2 (12 ) United States Patent (10 ) Patent No. : US 10 ,314 ,866 B2 Kovarik ( 45 ) Date of Patent: * Jun . 11, 2019 ( 54 ) METHOD OF REDUCING THE 61/ 919 , 297 , filed on Dec . 20 , 2013, provisional LIKELIHOOD OF SKIN CANCER IN AN application No . 61/ 467, 767 , filed on Mar . 25, 2011 . INDIVIDUAL HUMAN BEING (71 ) Applicant: Joseph E . Kovarik , Englewood , CO (51 ) Int. Cl. (US ) A61K 31 / 58 ( 2006 . 01 ) A61K 35 /00 (2006 . 01 ) (72 ) Inventor: Joseph E . Kovarik , Englewood , CO A61K 35 / 74 (2015 . 01 ) ( US ) A61K 38 / 17 ( 2006 .01 ) A61K 31 / 715 ( 2006 . 01 ) ( * ) Notice : Subject to any disclaimer , the term of this patent is extended or adjusted under 35 (32 ) U . S . Cl. CPC .. .. .. .. A61K 35 / 74 ( 2013 .01 ) ; A61K 31 /58 U . S . C . 154 ( b ) by 0 days . (2013 .01 ) ; A61K 31/ 715 (2013 . 01 ) ; A61K This patent is subject to a terminal dis 38 / 1709 (2013 . 01 ) ; A61K 38 / 1758 ( 2013 .01 ) ; claimer . A61K 2035 / 11 ( 2013 .01 ) (58 ) Field of Classification Search ( 21) Appl. No .: 16 / 160, 336 None (22 ) Filed : Oct . 15, 2018 See application file for complete search history . (65 ) Prior Publication Data ( 56 ) References Cited US 2019 / 0038680 A1 Feb . 7 , 2019 U . S . PATENT DOCUMENTS Related U . S . Application Data 3 , 178 , 341 A 4 / 1965 Hamill et al . 4 , 568 ,639 A 2 / 1986 Lew (63 ) Continuation of application No . 15 / 403 , 823 , filed on 4 ,687 , 841 A 8 / 1987 Spilburg et al. Jan . 11 , 2017 , now Pat. No. 10 , 111, 913 , which is a 4 , 720 ,486 A 1 / 1988 Spilburg et al .
    [Show full text]
  • Phylum Arthropod Silvia Rondon, and Mary Corp, OSU Extension Entomologist and Agronomist, Respectively Hermiston Research and Extension Center, Hermiston, Oregon
    Phylum Arthropod Silvia Rondon, and Mary Corp, OSU Extension Entomologist and Agronomist, respectively Hermiston Research and Extension Center, Hermiston, Oregon Member of the Phyllum Arthropoda can be found in the seas, in fresh water, on land, or even flying freely; a group with amazing differences of structure, and so abundant that all the other animals taken together are less than 1/6 as many as the arthropods. Well-known members of this group are the Kingdom lobsters, crayfish and crabs; scorpions, spiders, mites, ticks, Phylum Phylum Phylum Class the centipedes and millipedes; and last, but not least, the Order most abundant of all, the insects. Family Genus The Phylum Arthropods consist of the following Species classes: arachnids, chilopods, diplopods, crustaceans and hexapods (insects). All arthropods possess: • Exoskeleton. A hard protective covering around the outside of the body (divided by sutures into plates called sclerites). An insect's exoskeleton (integument) serves as a protective covering over the body, but also as a surface for muscle attachment, a water-tight barrier against desiccation, and a sensory interface with the environment. It is a multi-layered structure with four functional regions: epicuticle (top layer), procuticle, epidermis, and basement membrane. • Segmented body • Jointed limbs and jointed mouthparts that allow extensive specialization • Bilateral symmetry, whereby a central line can divide the body Insect molting or removing its into two identical halves, left and right exoesqueleton • Ventral nerve
    [Show full text]
  • Studies on the Role of the Keratinocytes in Cutaneous Immnity
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Repository of the Academy's Library Factors shaping the composition of the cutaneous microbiota K. Szabó1, L. Erdei2, B. Sz. Bolla2, G. Tax2, T. Bíró3, L. Kemény1,2 1. MTA-SZTE Dermatological Research Group, Szeged, Hungary 2. Department of Dermatology and Allergology, University of Szeged, Hungary 3. DE-MTA “Lendület” Cellular Physiology Research Group, Departments of Physiology and Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary Running head: Factors shaping the composition of the cutaneous microbiota Manuscript word count: Manuscript table count: none Manuscript figure count: none Corresponding author: Kornélia Szabó Tel: +36-62-545 799 Fax: +36-62-545 799 E-mail address: [email protected] Keywords: microbiota, cutaneous microbiota, Propionibacterium acnes, acne vulgaris, disappearing microbiota hypothesis What's already known about this topic: -Microbes are integral components of the human ecosystem. -The cutaneous microbiota plays an important role in the regulation of skin homeostasis. -The composition of skin microbiota is influenced by many factors. What does this study add? -The dominance of P. acnes in the postadolescent sebum-rich skin regions and its role in acne pathogenesis may be explained by the disappearing microbiota hypothesis. Funding sources: Hungarian Scientific Research Fund (OTKA NK105369), János Bolyai Research Scholarship from the Hungarian Academy of Sciences (for K. Sz). Conflict of interest: The authors declare no conflict of interest. 1 Abstract From our birth, we are constantly exposed to bacteria, fungi and viruses, some of which are capable of transiently or permanently inhabiting our different body parts as our microbiota.
    [Show full text]
  • Comparative Neuroanatomy of Mollusks and Nemerteans in the Context of Deep Metazoan Phylogeny
    Comparative Neuroanatomy of Mollusks and Nemerteans in the Context of Deep Metazoan Phylogeny Von der Fakultät für Mathematik, Informatik und Naturwissenschaften der RWTH Aachen University zur Erlangung des akademischen Grades einer Doktorin der Naturwissenschaften genehmigte Dissertation vorgelegt von Diplom-Biologin Simone Faller aus Frankfurt am Main Berichter: Privatdozent Dr. Rudolf Loesel Universitätsprofessor Dr. Peter Bräunig Tag der mündlichen Prüfung: 09. März 2012 Diese Dissertation ist auf den Internetseiten der Hochschulbibliothek online verfügbar. Contents 1 General Introduction 1 Deep Metazoan Phylogeny 1 Neurophylogeny 2 Mollusca 5 Nemertea 6 Aim of the thesis 7 2 Neuroanatomy of Minor Mollusca 9 Introduction 9 Material and Methods 10 Results 12 Caudofoveata 12 Scutopus ventrolineatus 12 Falcidens crossotus 16 Solenogastres 16 Dorymenia sarsii 16 Polyplacophora 20 Lepidochitona cinerea 20 Acanthochitona crinita 20 Scaphopoda 22 Antalis entalis 22 Entalina quinquangularis 24 Discussion 25 Structure of the brain and nerve cords 25 Caudofoveata 25 Solenogastres 26 Polyplacophora 27 Scaphopoda 27 i CONTENTS Evolutionary considerations 28 Relationship among non-conchiferan molluscan taxa 28 Position of the Scaphopoda within Conchifera 29 Position of Mollusca within Protostomia 30 3 Neuroanatomy of Nemertea 33 Introduction 33 Material and Methods 34 Results 35 Brain 35 Cerebral organ 38 Nerve cords and peripheral nervous system 38 Discussion 38 Peripheral nervous system 40 Central nervous system 40 In search for the urbilaterian brain 42 4 General Discussion 45 Evolution of higher brain centers 46 Neuroanatomical glossary and data matrix – Essential steps toward a cladistic analysis of neuroanatomical data 49 5 Summary 53 6 Zusammenfassung 57 7 References 61 Danksagung 75 Lebenslauf 79 ii iii 1 General Introduction Deep Metazoan Phylogeny The concept of phylogeny follows directly from the theory of evolution as published by Charles Darwin in The origin of species (1859).
    [Show full text]
  • The Arthropod Phylum Phyla a Major Groups of Organisms
    Lab 1: Arthropod Classification Name: _______________________________ Hierarchical Classification System Classification systems enable us to impart order to a complex environment. In biology, organisms may be grouped according to their overall similarity (a classification method known as phenetics) or according to their evolutionary relationships (a classification system known as cladistics). Most modern scientists tend to adopt a cladistic approach when classifying organisms. In biology, organisms are given a generic name (reflecting the genus of the organisms), and a specific name (reflecting the species of the organism). A genus is a group of closely related organisms. Genera which are closely related are grouped into a higher (less specific) category known as a family. Families are grouped into orders, and orders into classes. Classes of organisms are grouped into phyla, and phyla are grouped into kingdoms. Domains are the highest taxonomic rank of organisms. Domain Bacteria, Eubacteria, Eukarya Kingdom Plants, Animals, Fungus, Protists Phylum Cnidaria, Annelida, Arthropoda Class Insecta, Arachnida, Crustacea Order Coleoptera, Lepidoptera, Diptera Family Tipulidae, Apidae, Scarabeidae Genus Scaptia, Euglossa, Anastrangalia Species beyonceae, bazinga, laetifica Glossary of Phylogenetic Terms Phylogeny: interrelationships of organisms based on evolution Systematics: the study of the diversity of organisms, which attempts to organize or rationalize diversity in terms of phylogeny Taxonomy: the technical aspects of systematics, dealing with the formal description of species, establishing rankings of groups, and general principles of classification and naming Phylogenetic Tree (cladogram): a diagrammatic representation of the presumed line of descent of a group of organisms. Thus, a phylogenetic tree is actually a hypothesis regarding the evolutionary history of a group of organisms.
    [Show full text]
  • Onychophorology, the Study of Velvet Worms
    Uniciencia Vol. 35(1), pp. 210-230, January-June, 2021 DOI: http://dx.doi.org/10.15359/ru.35-1.13 www.revistas.una.ac.cr/uniciencia E-ISSN: 2215-3470 [email protected] CC: BY-NC-ND Onychophorology, the study of velvet worms, historical trends, landmarks, and researchers from 1826 to 2020 (a literature review) Onicoforología, el estudio de los gusanos de terciopelo, tendencias históricas, hitos e investigadores de 1826 a 2020 (Revisión de la Literatura) Onicoforologia, o estudo dos vermes aveludados, tendências históricas, marcos e pesquisadores de 1826 a 2020 (Revisão da Literatura) Julián Monge-Nájera1 Received: Mar/25/2020 • Accepted: May/18/2020 • Published: Jan/31/2021 Abstract Velvet worms, also known as peripatus or onychophorans, are a phylum of evolutionary importance that has survived all mass extinctions since the Cambrian period. They capture prey with an adhesive net that is formed in a fraction of a second. The first naturalist to formally describe them was Lansdown Guilding (1797-1831), a British priest from the Caribbean island of Saint Vincent. His life is as little known as the history of the field he initiated, Onychophorology. This is the first general history of Onychophorology, which has been divided into half-century periods. The beginning, 1826-1879, was characterized by studies from former students of famous naturalists like Cuvier and von Baer. This generation included Milne-Edwards and Blanchard, and studies were done mostly in France, Britain, and Germany. In the 1880-1929 period, research was concentrated on anatomy, behavior, biogeography, and ecology; and it is in this period when Bouvier published his mammoth monograph.
    [Show full text]
  • Coincidence of Photic Zone Euxinia and Impoverishment of Arthropods
    www.nature.com/scientificreports OPEN Coincidence of photic zone euxinia and impoverishment of arthropods in the aftermath of the Frasnian- Famennian biotic crisis Krzysztof Broda1*, Leszek Marynowski2, Michał Rakociński1 & Michał Zatoń1 The lowermost Famennian deposits of the Kowala quarry (Holy Cross Mountains, Poland) are becoming famous for their rich fossil content such as their abundant phosphatized arthropod remains (mostly thylacocephalans). Here, for the frst time, palaeontological and geochemical data were integrated to document abundance and diversity patterns in the context of palaeoenvironmental changes. During deposition, the generally oxic to suboxic conditions were interrupted at least twice by the onset of photic zone euxinia (PZE). Previously, PZE was considered as essential in preserving phosphatised fossils from, e.g., the famous Gogo Formation, Australia. Here, we show, however, that during PZE, the abundance of arthropods drastically dropped. The phosphorous content during PZE was also very low in comparison to that from oxic-suboxic intervals where arthropods are the most abundant. As phosphorous is essential for phosphatisation but also tends to fux of the sediment during bottom water anoxia, we propose that the PZE in such a case does not promote the fossilisation of the arthropods but instead leads to their impoverishment and non-preservation. Thus, the PZE conditions with anoxic bottom waters cannot be presumed as universal for exceptional fossil preservation by phosphatisation, and caution must be paid when interpreting the fossil abundance on the background of redox conditions. 1 Euxinic conditions in aquatic environments are defned as the presence of H2S and absence of oxygen . If such conditions occur at the chemocline in the water column, where light is available, they are defned as photic zone euxinia (PZE).
    [Show full text]
  • Shifts in Human Skin and Nares Microbiota of Healthy Children and Adults Julia Oh1, Sean Conlan1, Eric C Polley2, Julia a Segre1*† and Heidi H Kong3*†
    Oh et al. Genome Medicine 2012, 4:77 http://genomemedicine.com/content/4/10/77 RESEARCH Open Access Shifts in human skin and nares microbiota of healthy children and adults Julia Oh1, Sean Conlan1, Eric C Polley2, Julia A Segre1*† and Heidi H Kong3*† Abstract Background: Characterization of the topographical and temporal diversity of the microbial collective (microbiome) hosted by healthy human skin established a reference for studying disease-causing microbiomes. Physiologic changes occur in the skin as humans mature from infancy to adulthood. Thus, characterizations of adult microbiomes might have limitations when considering pediatric disorders such as atopic dermatitis (AD) or issues such as sites of microbial carriage. The objective of this study was to determine if microbial communities at several body sites in children differed significantly from adults. Methods: Using 16S-rRNA gene sequencing technology, we characterized and compared the bacterial communities of four body sites in relation to Tanner stage of human development. Body sites sampled included skin sites characteristically involved in AD (antecubital/popliteal fossae), a control skin site (volar forearm), and the nares. Twenty-eight healthy individuals aged from 2 to 40 years were evaluated at the outpatient dermatology clinic in the National Institutes of Health’s Clinical Center. Exclusion criteria included the use of systemic antibiotics within 6 months, current/prior chronic skin disorders, asthma, allergic rhinitis, or other chronic medical conditions. Results: Bacterial communities in the nares of children (Tanner developmental stage 1) differed strikingly from adults (Tanner developmental stage 5). Firmicutes (Streptococcaceae), Bacteroidetes, and Proteobacteria (b, g) were overrepresented in Tanner 1 compared to Tanner 5 individuals, where Corynebacteriaceae and Propionibacteriaceae predominated.
    [Show full text]
  • Pdf/77/5/636/2920651/Gsminmag.77.5.02-B.Pdf by Guest on 01 October 2021 Goldschmidt2013 Conference Abstracts 637
    636 Goldschmidt2013 Conference Abstracts Discovery and characterization of Using isotopic analysis of copper to contrasting siderophores produced by assess copper transport and related nitrogen fixing bacteria using partitioning in wetland systems high resolution LC-MS I. BABCSANYI*, F. CHABAUX, V.M. GRANET AND G. IMFELD* OLIVER BAAR, DAVID H. PERLMAN, ANNE M. L. KRAEPIEL AND FRANÇOIS M. M. MOREL* Laboratory of Hydrology and Geochemistry of Strasbourg (LHyGeS), University of Strasbourg/ENGEES, CNRS, 1, Princeton University, Princeton, NJ, USA rue Blessig, 67 084 Strasbourg CEDEX (*correspondence: [email protected]) (*correspondence: [email protected], [email protected]) Azotobacter vinelandii (AV) and Azotobacter chroococcum (AC) are closely related N fixing bacteria. 2 Copper isotopes (65Cu/63Cu) are potentially powerful new Whereas the structures and physiological functions of geochemical proxies for transport and oxidation–reduction siderophores produced by AV have been much studied, those processes in hydromorphic soils, rivers and lake sediments. of AC remain unidentified beyond a general chemical However, the integrative signal of !65Cu has not been used so characterization. Here we have exploited the characteristic far to investigate the transport and partitioning of copper in iron isotopic fingerprint to identify known and unknown wetland systems with respect to both hydrological and siderophores and characterize them structurally using ultra- biogeochemical conditions. Here we used copper isotopes to sensitive high-resolution nano-flow UPLC-MS on an LTQ- investigate the copper cycling in a stormwater wetland (as a Orbitrap XL platform. ‘natural laboratory’) that regularly received copper- Interrogation of preliminary data for AV revealed many contaminated runoff from a 42 ha vineyard catchment putative Fe-chelators with high abundances, including those (Rouffach, Alsace, France).
    [Show full text]