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University of Oklahoma
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D. -
Protocols for Monitoring Harmful Algal Blooms for Sustainable Aquaculture and Coastal Fisheries in Chile (Supplement Data)
Protocols for monitoring Harmful Algal Blooms for sustainable aquaculture and coastal fisheries in Chile (Supplement data) Provided by Kyoko Yarimizu, et al. Table S1. Phytoplankton Naming Dictionary: This dictionary was constructed from the species observed in Chilean coast water in the past combined with the IOC list. Each name was verified with the list provided by IFOP and online dictionaries, AlgaeBase (https://www.algaebase.org/) and WoRMS (http://www.marinespecies.org/). The list is subjected to be updated. Phylum Class Order Family Genus Species Ochrophyta Bacillariophyceae Achnanthales Achnanthaceae Achnanthes Achnanthes longipes Bacillariophyta Coscinodiscophyceae Coscinodiscales Heliopeltaceae Actinoptychus Actinoptychus spp. Dinoflagellata Dinophyceae Gymnodiniales Gymnodiniaceae Akashiwo Akashiwo sanguinea Dinoflagellata Dinophyceae Gymnodiniales Gymnodiniaceae Amphidinium Amphidinium spp. Ochrophyta Bacillariophyceae Naviculales Amphipleuraceae Amphiprora Amphiprora spp. Bacillariophyta Bacillariophyceae Thalassiophysales Catenulaceae Amphora Amphora spp. Cyanobacteria Cyanophyceae Nostocales Aphanizomenonaceae Anabaenopsis Anabaenopsis milleri Cyanobacteria Cyanophyceae Oscillatoriales Coleofasciculaceae Anagnostidinema Anagnostidinema amphibium Anagnostidinema Cyanobacteria Cyanophyceae Oscillatoriales Coleofasciculaceae Anagnostidinema lemmermannii Cyanobacteria Cyanophyceae Oscillatoriales Microcoleaceae Annamia Annamia toxica Cyanobacteria Cyanophyceae Nostocales Aphanizomenonaceae Aphanizomenon Aphanizomenon flos-aquae -
October-2009-Inoculum.Pdf
Supplement to Mycologia Vol. 60(5) October 2009 Newsletter of the Mycological Society of America — In This Issue — Feature Article Fungal zoospores are valuable food Fungal zoospores are valuable food resources in aquatic ecosystems resources in aquatic ecosystems MSA Business President’s Corner By Frank H. Gleason, Maiko Kagami, Secretary’s Email Express Agostina V. Marano and Telesphore Simi-Ngando MSA Officers 2009 –2010 MSA 2009 Annual Reports Fungal zoospores are known to contain large quantities Minutes of the 2009 MSA Annual Council Meeting Minutes of the MSA 2009 Annual Business Meeting of glycogen and lipids in the form of endogenous reserves. MSA 2009 Award Winners Lipids are considered to be high energy compounds, some of MSA 2009 Abstracts (Additional) which are important for energy storage. Lipids can be con - Mycological News A North American Flora for Mushroom-Forming Fungi tained in membrane bound vesicles called lipid globules Marine Mycology Class which can easily be seen in the cytoplasm of fungal Mycohistorybytes Peripatetic Mycology zoospores with both the light and electron microscopes Student Research Opportunities in Thailand (Munn et al . 1981; Powell 1993; Barr 2001). Koch (1968) MSA Meeting 2010 MycoKey version 3.2 and Bernstein (1968) both noted variation in the size and MycoRant numbers of lipoid globules within zoospores in the light mi - Dr Paul J Szaniszlo croscope. The ultrastructure of the lipid globule complex Symposium : Gondwanic Connections in Fungi Mycologist’s Bookshelf was carefully examined by Powell and Roychoudhury A Preliminary Checklist of Micromycetes in Poland (1992). Fungal Pathogenesis in Plants and Crops Pathogenic Fungi in the Cryphonectriaceae Preliminary studies reviewed by Cantino and Mills Recently Received Books (1976) revealed a rich supply of lipids in the cells of Blasto - Take a Break cladiella emersonii . -
Cutleriaceae, Phaeophyceae)Pre 651 241..248
bs_bs_banner Phycological Research 2012; 60: 241–248 Taxonomic revision of the genus Cutleria proposing a new genus Mutimo to accommodate M. cylindricus (Cutleriaceae, Phaeophyceae)pre_651 241..248 Hiroshi Kawai,1* Keita Kogishi,1 Takeaki Hanyuda1 and Taiju Kitayama2 1Kobe University Research Center for Inland Seas, Kobe, and 2Department of Botany, National Museum of Nature and Science, Amakubo, Tsukuba, Japan branched, compressed or cylindrical thalli (e.g., SUMMARY C. chilosa (Falkenberg) P.C. Silva, C. compressa Kützing, C. cylindrica Okamura and C. multifida Molecular phylogenetic analyses of representative Cut- (Turner) Greville); (ii) flat, fan-shaped thalli (e.g. C. leria species using mitochondrial cox3, chloroplast adspersa (Mertens ex Roth) De Notaris, C. hancockii psaA, psbA and rbcL gene sequences showed that E.Y. Dawson, C. kraftii Huisman and C. mollis Allender C. cylindrica Okamura was not included in the clade et Kraft). However, only a sporophytic generation is composed of other Cutleria species including the gen- reported for some taxa and the nature of their gameto- eritype C. multifida (Turner) Greville and the related phytic (erect) thalli are unclear (e.g. C. canariensis taxon Zanardinia typus (Nardo) P.C. Silva. Instead, (Sauvageau) I.A. Abbott et J.M. Huisman and C. irregu- C. cylindrica was sister to the clade composed of the laris I.A. Abbott & Huisman). Cutleria species typically two genera excluding C. cylindrica. Cutleria spp. have show a heteromorphic life history alternating between heteromophic life histories and their gametophytes are relatively large dioecious gametophytes of trichothallic rather diverse in gross morphology, from compressed or growth and small crustose sporophytes, considered cylindrical-branched to fan-shaped, whereas the sporo- characteristic of the order. -
Monitoreo De Microalgas De Ambientes Costeros De La Provincia De Buenos Aires Y Monitoreo De Toxinas En Moluscos Bivalvos
PROYECTO MARCO MONITOREO DE MICROALGAS DE AMBIENTES COSTEROS DE LA PROVINCIA DE BUENOS AIRES Y MONITOREO DE TOXINAS EN MOLUSCOS BIVALVOS Directora Científica: Eugenia A. Sar1 Coordinación Técnica: Andrea Lavigne2, Ramiro Duffard2 Grupo responsable: Inés Sunesen1, Andrea Lavigne2 Grupo responsable de muestreo: Inés Sunesen1, Andrea Lavigne2 1 Departamento Científico Ficología, Facultad de Ciencias Naturales y Museo, UNLP 2 Ministerio de Asuntos Agrarios, Dirección Provincial de Pesca. MORTANDAD MASIVA DE SARACAS (BREVOORTIA AUREA) EN LA PROVINCIA DE BUENOS AIRES INTRODUCCIÓN A partir del 4 de marzo se produjo una varazón masiva de saracas, Brevoortia aurea, en el área costera de la Provincia de Buenos Aires entre Samborombón y Mar Azul, República Argentina y en el área costera de los Departamentos de Canelones y Montevideo, República Oriental del Uruguay. Tanto el Instituto Nacional de Investigaciones y Desarrollo Pesquero (INIDEP) asesora de la Subsecretaría de Pesca y Acuicultura de la Nación (SSPyA), del Consejo Federal Pesquero (CFP) y de la Cancillería Argentina, Argentina, como la Dirección Nacional de Recursos Acuáticos (DINARA) dependiente del Ministerio de Agricultura Ganadería y Pesca de Uruguay determinaron que la presunción de que el evento se hubiera producido por un descarte de la flota pesquera comercial podía ser desestimada. La estimación de biomasa de peces muertos depositados en la costa argentina fue de 3000 toneladas (informe del INIDEP del 19 de marzo), sin embargo varazones menores continúan aún y fueron observadas en Mar Azul durante la campaña del del 30-03-15 (cuyo análisis de muestras está en procesamiento). Para esas fechas algunos peces llegaban vivos a la costa con señales de asfixia, por lo que no puede presumirse que hubieran muerto en aguas próximas a las playas tiempo antes. -
Fluorescence in Situ Hybridization Using 18S Rrna- Targeted Probe for Specific Detection of Thraustochytrids (Labyrinthulomycetes)
Plankton Benthos Res 2(2): 91–97, 2007 Plankton & Benthos Research © The Plankton Society of Japan Fluorescence in situ hybridization using 18S rRNA- targeted probe for specific detection of thraustochytrids (Labyrinthulomycetes) YOSHITAKE TAKAO1, YUJI TOMARU1, KEIZO NAGASAKI1, YUKARI SASAKURA2, RINKA YOKOYAMA2 & DAISKE HONDA2* 1 National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2–17–5 Maruishi, Hatsukaichi, Hiroshima 739–0452, Japan 2 Department of Biology, Faculty of Science and Engineering, Konan University, 8–9–1 Okamoto, Higashinada, Kobe 658–8501, Japan Received 5 December 2006; Accepted 13 March 2007 Abstract: Thraustochytrids are cosmopolitan osmotrophic or heterotrophic microorganisms that play, especially in coastal ecosystems, important roles as decomposers and producers of polyunsaturated fatty acids (PUFA), and are also known to be pathogens of mollusks and seaweeds. However, because of shortcomings in the current methods for detec- tion and enumeration of thraustochytrids, very little information is available concerning their natural dynamics and eco- logical roles. In this study, we propose a new method for detecting thraustochytrids using a fluorescent 18S ribosomal RNA (rRNA)-targeted oligonucleotide probe (Probe ThrFL1). Detection of thraustochytrids by means of the fluores- cence in situ hybridization (FISH) technique with ThrFL1 was specific; the probe did not react with the other stra- menopile organisms or with the dinoflagellate that was tested. Because of the high specificity and intense reactivity, the FISH protocol is expected to be a strong tool for examining ecological features of thraustochytrids. Key words: Aurantiochytrium, Decomposer, FISH method, Schizochytrium, Thraustochytrium tance as decomposers (Raghukumar et al. 2001). In addi- Introduction tion, due to their high productivity of PUFAs such as do- Thraustochytrids are cosmopolitan apochlorotic stra- cosahexaenoic acid and docosapentaenoic acid (Nakahara menopile protists classified in the class Labyrinthu- et al. -
SPECIAL PUBLICATION 6 the Effects of Marine Debris Caused by the Great Japan Tsunami of 2011
PICES SPECIAL PUBLICATION 6 The Effects of Marine Debris Caused by the Great Japan Tsunami of 2011 Editors: Cathryn Clarke Murray, Thomas W. Therriault, Hideaki Maki, and Nancy Wallace Authors: Stephen Ambagis, Rebecca Barnard, Alexander Bychkov, Deborah A. Carlton, James T. Carlton, Miguel Castrence, Andrew Chang, John W. Chapman, Anne Chung, Kristine Davidson, Ruth DiMaria, Jonathan B. Geller, Reva Gillman, Jan Hafner, Gayle I. Hansen, Takeaki Hanyuda, Stacey Havard, Hirofumi Hinata, Vanessa Hodes, Atsuhiko Isobe, Shin’ichiro Kako, Masafumi Kamachi, Tomoya Kataoka, Hisatsugu Kato, Hiroshi Kawai, Erica Keppel, Kristen Larson, Lauran Liggan, Sandra Lindstrom, Sherry Lippiatt, Katrina Lohan, Amy MacFadyen, Hideaki Maki, Michelle Marraffini, Nikolai Maximenko, Megan I. McCuller, Amber Meadows, Jessica A. Miller, Kirsten Moy, Cathryn Clarke Murray, Brian Neilson, Jocelyn C. Nelson, Katherine Newcomer, Michio Otani, Gregory M. Ruiz, Danielle Scriven, Brian P. Steves, Thomas W. Therriault, Brianna Tracy, Nancy C. Treneman, Nancy Wallace, and Taichi Yonezawa. Technical Editor: Rosalie Rutka Please cite this publication as: The views expressed in this volume are those of the participating scientists. Contributions were edited for Clarke Murray, C., Therriault, T.W., Maki, H., and Wallace, N. brevity, relevance, language, and style and any errors that [Eds.] 2019. The Effects of Marine Debris Caused by the were introduced were done so inadvertently. Great Japan Tsunami of 2011, PICES Special Publication 6, 278 pp. Published by: Project Designer: North Pacific Marine Science Organization (PICES) Lori Waters, Waters Biomedical Communications c/o Institute of Ocean Sciences Victoria, BC, Canada P.O. Box 6000, Sidney, BC, Canada V8L 4B2 Feedback: www.pices.int Comments on this volume are welcome and can be sent This publication is based on a report submitted to the via email to: [email protected] Ministry of the Environment, Government of Japan, in June 2017. -
Phylogeny and Morphology of a Chattonella (Raphidophyceae) Species from the Mediterranean Sea: What Is C
This article was downloaded by: [Stiftung Alfred Wegener Institute für Polar- und Meeresforschung ] On: 17 April 2013, At: 02:13 Publisher: Taylor & Francis Informa Ltd Registered in England and Wales Registered Number: 1072954 Registered office: Mortimer House, 37-41 Mortimer Street, London W1T 3JH, UK European Journal of Phycology Publication details, including instructions for authors and subscription information: http://www.tandfonline.com/loi/tejp20 Phylogeny and morphology of a Chattonella (Raphidophyceae) species from the Mediterranean Sea: what is C. subsalsa? Sascha Klöpper a , Uwe John a , Adriana Zingone b , Olga Mangoni c , Wiebe H.C.F. Kooistra b & Allan D. Cembella a a Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany b Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy c Department of Biological Sciences, University Federico II, Via Mezzocannone 8, 80138, Naples, Italy Version of record first published: 13 Mar 2013. To cite this article: Sascha Klöpper , Uwe John , Adriana Zingone , Olga Mangoni , Wiebe H.C.F. Kooistra & Allan D. Cembella (2013): Phylogeny and morphology of a Chattonella (Raphidophyceae) species from the Mediterranean Sea: what is C. subsalsa?, European Journal of Phycology, 48:1, 79-92 To link to this article: http://dx.doi.org/10.1080/09670262.2013.771412 PLEASE SCROLL DOWN FOR ARTICLE Full terms and conditions of use: http://www.tandfonline.com/page/terms-and-conditions This article may be used for research, teaching, and private study purposes. Any substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing, systematic supply, or distribution in any form to anyone is expressly forbidden. -
The Classification of Lower Organisms
The Classification of Lower Organisms Ernst Hkinrich Haickei, in 1874 From Rolschc (1906). By permission of Macrae Smith Company. C f3 The Classification of LOWER ORGANISMS By HERBERT FAULKNER COPELAND \ PACIFIC ^.,^,kfi^..^ BOOKS PALO ALTO, CALIFORNIA Copyright 1956 by Herbert F. Copeland Library of Congress Catalog Card Number 56-7944 Published by PACIFIC BOOKS Palo Alto, California Printed and bound in the United States of America CONTENTS Chapter Page I. Introduction 1 II. An Essay on Nomenclature 6 III. Kingdom Mychota 12 Phylum Archezoa 17 Class 1. Schizophyta 18 Order 1. Schizosporea 18 Order 2. Actinomycetalea 24 Order 3. Caulobacterialea 25 Class 2. Myxoschizomycetes 27 Order 1. Myxobactralea 27 Order 2. Spirochaetalea 28 Class 3. Archiplastidea 29 Order 1. Rhodobacteria 31 Order 2. Sphaerotilalea 33 Order 3. Coccogonea 33 Order 4. Gloiophycea 33 IV. Kingdom Protoctista 37 V. Phylum Rhodophyta 40 Class 1. Bangialea 41 Order Bangiacea 41 Class 2. Heterocarpea 44 Order 1. Cryptospermea 47 Order 2. Sphaerococcoidea 47 Order 3. Gelidialea 49 Order 4. Furccllariea 50 Order 5. Coeloblastea 51 Order 6. Floridea 51 VI. Phylum Phaeophyta 53 Class 1. Heterokonta 55 Order 1. Ochromonadalea 57 Order 2. Silicoflagellata 61 Order 3. Vaucheriacea 63 Order 4. Choanoflagellata 67 Order 5. Hyphochytrialea 69 Class 2. Bacillariacea 69 Order 1. Disciformia 73 Order 2. Diatomea 74 Class 3. Oomycetes 76 Order 1. Saprolegnina 77 Order 2. Peronosporina 80 Order 3. Lagenidialea 81 Class 4. Melanophycea 82 Order 1 . Phaeozoosporea 86 Order 2. Sphacelarialea 86 Order 3. Dictyotea 86 Order 4. Sporochnoidea 87 V ly Chapter Page Orders. Cutlerialea 88 Order 6. -
"Phycology". In: Encyclopedia of Life Science
Phycology Introductory article Ralph A Lewin, University of California, La Jolla, California, USA Article Contents Michael A Borowitzka, Murdoch University, Perth, Australia . General Features . Uses The study of algae is generally called ‘phycology’, from the Greek word phykos meaning . Noxious Algae ‘seaweed’. Just what algae are is difficult to define, because they belong to many different . Classification and unrelated classes including both prokaryotic and eukaryotic representatives. Broadly . Evolution speaking, the algae comprise all, mainly aquatic, plants that can use light energy to fix carbon from atmospheric CO2 and evolve oxygen, but which are not specialized land doi: 10.1038/npg.els.0004234 plants like mosses, ferns, coniferous trees and flowering plants. This is a negative definition, but it serves its purpose. General Features Algae range in size from microscopic unicells less than 1 mm several species are also of economic importance. Some in diameter to kelps as long as 60 m. They can be found in kinds are consumed as food by humans. These include almost all aqueous or moist habitats; in marine and fresh- the red alga Porphyra (also known as nori or laver), an water environments they are the main photosynthetic or- important ingredient of Japanese foods such as sushi. ganisms. They are also common in soils, salt lakes and hot Other algae commonly eaten in the Orient are the brown springs, and some can grow in snow and on rocks and the algae Laminaria and Undaria and the green algae Caulerpa bark of trees. Most algae normally require light, but some and Monostroma. The new science of molecular biology species can also grow in the dark if a suitable organic carbon has depended largely on the use of algal polysaccharides, source is available for nutrition. -
Algae from the Arid Southwestern United States: an Annotated Bibliography
SERI/TR-231-1947 UC Category: 61a DE83011976 Algae from the Arid Southwestern United States: An Annotated Bibliography A Subcontract Report W. H. Thomas S. R. Gaines Institute of Marine Resources Scripps Institute of Oceanography University of California, San Diego La Jolla, California 92092 June 1983 Prepared under Subcontract No. XK-09111-1 SERI Technical Monitor: M. Lowenstein Solar Energy Research Institute A Division of Midwest Research Institute 1617 Cole Boulevard Golden, Colorado 80401 Prepared for the U.S. Department of Energy Contract No. EG-77-C-01-4042 Printed in the United States of America Available from: National Technical Information service U.S. Department of Commerce 5285 Port Royal Road Springfield, VA 22161 Price: Microfiche $4.50 Printed Copy $14.50 NOTICE This report was prepared as an account of work sponsored by the United States Government. Neither the United States nor the United States Department of Energy, nor any ·of their employees, nor any of their contractors, subcontractors, or their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness or usefulness of any information, apparatus, product or process disclosed, or represents that its use would not infringe privately owned rights. FOREWORD This report is an annotated bibliography compiled by Scripps Institute of Oceanography for the Solar Energy Research Institute (SERI) under Subcontract XK-09111-1, using funds provided by the Biomass Energy Technology Divison of the Department of Energy. This report is provided to the research community in the hope that it will be an invaluable tool for future research in field collection and identification of microalgae in desert environments. -
Ambient Aquatic Life Water Quality Criteria for Tributyltin (TBT) - Final AMBIENT AQUATIC LIFE WATER QUALITY CRITERIA FOR
United States Office of Water EPA 822-R-03-031 Environmental Protection 4304T December 2003 Agency Ambient Aquatic Life Water Quality Criteria for Tributyltin (TBT) - Final AMBIENT AQUATIC LIFE WATER QUALITY CRITERIA FOR TRIBUTYLTIN CAS Registry Number (See Text) December 2003 U.S. ENVIRONMENTAL PROTECTION AGENCY OFFICE OF WATER OFFICE OF SCIENCE AND TECHNOLOGY HEALTH AND ECOLOGICAL CRITERIA DIVISION WASHINGTON D.C. NOTICES This document has been reviewed by the Health and Ecological Criteria Division, Office of Science and Technology, U.S. Environmental Protection Agency, and is approved for publication. Mention of trade names or commercial products does not constitute endorsement or recommendation for use. This document is available to the public through the National Technical Information Service (NTIS), 5285 Port Royal Road, Springfield, VA 22161. It is also available on EPA’s web site: http://www.epa.gov./waterscience/criteria/tributyltin. ii FOREWORD Section 304(a)(1) of the Clean Water Act of 1977 (P.L. 95-217) requires the Administrator of the Environmental Protection Agency to publish water quality criteria that accurately reflect the latest scientific knowledge on the kind and extent of all identifiable effects on health and welfare that might be expected from the presence of pollutants in any body of water, including ground water. This final document is a revision of proposed criteria based upon consideration of scientific input received from U.S. EPA staff, the public and independent peer reviewers. Criteria contained in this document replace any previously published EPA aquatic life criteria for tributyltin (TBT). The term "water quality criteria" is used in two sections of the Clean Water Act, section 304(a)(1) and section 303(c)(2).