Ecological Factors in the Inundative Use of Fungal Entomopathogens
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Old Woman Creek National Estuarine Research Reserve Management Plan 2011-2016
Old Woman Creek National Estuarine Research Reserve Management Plan 2011-2016 April 1981 Revised, May 1982 2nd revision, April 1983 3rd revision, December 1999 4th revision, May 2011 Prepared for U.S. Department of Commerce Ohio Department of Natural Resources National Oceanic and Atmospheric Administration Division of Wildlife Office of Ocean and Coastal Resource Management 2045 Morse Road, Bldg. G Estuarine Reserves Division Columbus, Ohio 1305 East West Highway 43229-6693 Silver Spring, MD 20910 This management plan has been developed in accordance with NOAA regulations, including all provisions for public involvement. It is consistent with the congressional intent of Section 315 of the Coastal Zone Management Act of 1972, as amended, and the provisions of the Ohio Coastal Management Program. OWC NERR Management Plan, 2011 - 2016 Acknowledgements This management plan was prepared by the staff and Advisory Council of the Old Woman Creek National Estuarine Research Reserve (OWC NERR), in collaboration with the Ohio Department of Natural Resources-Division of Wildlife. Participants in the planning process included: Manager, Frank Lopez; Research Coordinator, Dr. David Klarer; Coastal Training Program Coordinator, Heather Elmer; Education Coordinator, Ann Keefe; Education Specialist Phoebe Van Zoest; and Office Assistant, Gloria Pasterak. Other Reserve staff including Dick Boyer and Marje Bernhardt contributed their expertise to numerous planning meetings. The Reserve is grateful for the input and recommendations provided by members of the Old Woman Creek NERR Advisory Council. The Reserve is appreciative of the review, guidance, and council of Division of Wildlife Executive Administrator Dave Scott and the mapping expertise of Keith Lott and the late Steve Barry. -
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1 BROADLY SAMPLED TREE OF EUKARYOTIC LIFE Broadly Sampled Multigene Analyses Yield a Well-resolved Eukaryotic Tree of Life Laura Wegener Parfrey1†, Jessica Grant2†, Yonas I. Tekle2,6, Erica Lasek-Nesselquist3,4, Hilary G. Morrison3, Mitchell L. Sogin3, David J. Patterson5, Laura A. Katz1,2,* 1Program in Organismic and Evolutionary Biology, University of Massachusetts, 611 North Pleasant Street, Amherst, Massachusetts 01003, USA 2Department of Biological Sciences, Smith College, 44 College Lane, Northampton, Massachusetts 01063, USA 3Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA 4Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Providence, Rhode Island 02912, USA 5Biodiversity Informatics Group, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA 6Current address: Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut 06520, USA †These authors contributed equally *Corresponding author: L.A.K - [email protected] Phone: 413-585-3825, Fax: 413-585-3786 Keywords: Microbial eukaryotes, supergroups, taxon sampling, Rhizaria, systematic error, Excavata 2 An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level ‘supergroups’, many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Further, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduces power to evaluate hypotheses. -
Long Metabarcoding of the Eukaryotic Rdna Operon to Phylogenetically and Taxonomically Resolve Environmental Diversity
bioRxiv preprint doi: https://doi.org/10.1101/627828; this version posted May 5, 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. Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity Mahwash Jamy1, Rachel Foster2, Pierre Barbera3, Lucas Czech3, Alexey Kozlov3, Alexandros Stamatakis3,4, David Bass2,5*, Fabien Burki1,* 1Science for Life Laboratory, Program in Systematic Biology, Uppsala University, Uppsala, Sweden 2Department of Life Sciences, Natural History Museum, London, UK 3Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany 4Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany 5Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, Dorset, UK Corresponding authors: [email protected] [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/627828; this version posted May 5, 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. Abstract High-throughput environmental DNA metabarcoding has revolutionized the analysis of microbial diversity, but this approach is generally restricted to amplicon sizes below 500 base pairs. These short regions contain limited phylogenetic signal, which makes it impractical to use environmental DNA in full phylogenetic inferences. However, new long-read sequencing technologies such as the Pacific Biosciences platform may provide sufficiently large sequence lengths to overcome the poor phylogenetic resolution of short amplicons. -
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. -
Protista (PDF)
1 = Astasiopsis distortum (Dujardin,1841) Bütschli,1885 South Scandinavian Marine Protoctista ? Dingensia Patterson & Zölffel,1992, in Patterson & Larsen (™ Heteromita angusta Dujardin,1841) Provisional Check-list compiled at the Tjärnö Marine Biological * Taxon incertae sedis. Very similar to Cryptaulax Skuja Laboratory by: Dinomonas Kent,1880 TJÄRNÖLAB. / Hans G. Hansson - 1991-07 - 1997-04-02 * Taxon incertae sedis. Species found in South Scandinavia, as well as from neighbouring areas, chiefly the British Isles, have been considered, as some of them may show to have a slightly more northern distribution, than what is known today. However, species with a typical Lusitanian distribution, with their northern Diphylleia Massart,1920 distribution limit around France or Southern British Isles, have as a rule been omitted here, albeit a few species with probable norhern limits around * Marine? Incertae sedis. the British Isles are listed here until distribution patterns are better known. The compiler would be very grateful for every correction of presumptive lapses and omittances an initiated reader could make. Diplocalium Grassé & Deflandre,1952 (™ Bicosoeca inopinatum ??,1???) * Marine? Incertae sedis. Denotations: (™) = Genotype @ = Associated to * = General note Diplomita Fromentel,1874 (™ Diplomita insignis Fromentel,1874) P.S. This list is a very unfinished manuscript. Chiefly flagellated organisms have yet been considered. This * Marine? Incertae sedis. provisional PDF-file is so far only published as an Intranet file within TMBL:s domain. Diplonema Griessmann,1913, non Berendt,1845 (Diptera), nec Greene,1857 (Coel.) = Isonema ??,1???, non Meek & Worthen,1865 (Mollusca), nec Maas,1909 (Coel.) PROTOCTISTA = Flagellamonas Skvortzow,19?? = Lackeymonas Skvortzow,19?? = Lowymonas Skvortzow,19?? = Milaneziamonas Skvortzow,19?? = Spira Skvortzow,19?? = Teixeiromonas Skvortzow,19?? = PROTISTA = Kolbeana Skvortzow,19?? * Genus incertae sedis. -
Marine Biological Laboratory) Data Are All from EST Analyses
TABLE S1. Data characterized for this study. rDNA 3 - - Culture 3 - etK sp70cyt rc5 f1a f2 ps22a ps23a Lineage Taxon accession # Lab sec61 SSU 14 40S Actin Atub Btub E E G H Hsp90 M R R T SUM Cercomonadida Heteromita globosa 50780 Katz 1 1 Cercomonadida Bodomorpha minima 50339 Katz 1 1 Euglyphida Capsellina sp. 50039 Katz 1 1 1 1 4 Gymnophrea Gymnophrys sp. 50923 Katz 1 1 2 Cercomonadida Massisteria marina 50266 Katz 1 1 1 1 4 Foraminifera Ammonia sp. T7 Katz 1 1 2 Foraminifera Ovammina opaca Katz 1 1 1 1 4 Gromia Gromia sp. Antarctica Katz 1 1 Proleptomonas Proleptomonas faecicola 50735 Katz 1 1 1 1 4 Theratromyxa Theratromyxa weberi 50200 Katz 1 1 Ministeria Ministeria vibrans 50519 Katz 1 1 Fornicata Trepomonas agilis 50286 Katz 1 1 Soginia “Soginia anisocystis” 50646 Katz 1 1 1 1 1 5 Stephanopogon Stephanopogon apogon 50096 Katz 1 1 Carolina Tubulinea Arcella hemisphaerica 13-1310 Katz 1 1 2 Cercomonadida Heteromita sp. PRA-74 MBL 1 1 1 1 1 1 1 7 Rhizaria Corallomyxa tenera 50975 MBL 1 1 1 3 Euglenozoa Diplonema papillatum 50162 MBL 1 1 1 1 1 1 1 1 8 Euglenozoa Bodo saltans CCAP1907 MBL 1 1 1 1 1 5 Alveolates Chilodonella uncinata 50194 MBL 1 1 1 1 4 Amoebozoa Arachnula sp. 50593 MBL 1 1 2 Katz lab work based on genomic PCRs and MBL (Marine Biological Laboratory) data are all from EST analyses. Culture accession number is ATTC unless noted. GenBank accession numbers for new sequences (including paralogs) are GQ377645-GQ377715 and HM244866-HM244878. -
1 New Barcoded Primers for Efficient Retrieval of Cercozoan Sequences In
bioRxiv preprint doi: https://doi.org/10.1101/171611; this version posted August 2, 2017. 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 New barcoded primers for efficient retrieval of cercozoan sequences in high-throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts Anna Maria Fiore-Donno,a# Christian Rixen,b Martin Rippin,c Karin Glaser,d Elena Samolov,d Ulf Karsten,d Burkhard Becker,c Michael Bonkowskia Institute of Zoology, Terrestrial Ecology, Cluster of Excellence in Plant Sciences, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germanya; Institute for Snow and Avalanche Research SLF, Flüelastrasse 11, 7260 Davos Dorf, Switzerlandb; Institute of Botany, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germanyc; University of Rostock, Institute of Biological Sciences, Applied Ecology and Phycology, Albert-Einstein-Strasse 3, 18059 Rostock, Germanyd. Running title: New barcoded cercozoan primers Correspondence: Anna Maria Fiore-Donno, Institute of Zoology, Department of Terrestrial Ecology, University of Cologne, Zülpicher Str. 47b, 50674 Cologne, Germany; Fax: +492214705038; E-mail: [email protected]. Keywords: Cercozoa, environmental sampling, protists, metabarcoding, 18S V4 variable region. Abstract We describe the performance of a new metabarcoding approach to investigate the environmental diversity of a prominent group of widespread unicellular organisms, the Cercozoa. Cercozoa is an immensely large group of protists and although it may dominate in soil and aquatic ecosystems, its environmental diversity remains undersampled. -
Long Metabarcoding of the Eukaryotic Rdna Operon to Phylogenetically and Taxonomically Resolve Environmental Diversity
bioRxiv preprint doi: https://doi.org/10.1101/627828; this version posted May 5, 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. Long metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity Mahwash Jamy1, Rachel Foster2, Pierre Barbera3, Lucas Czech3, Alexey Kozlov3, Alexandros Stamatakis3,4, David Bass2,5*, Fabien Burki1,* 1Science for Life Laboratory, Program in Systematic Biology, Uppsala University, Uppsala, Sweden 2Department of Life Sciences, Natural History Museum, London, UK 3Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany 4Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany 5Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, Dorset, UK Corresponding authors: [email protected] [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/627828; this version posted May 5, 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. Abstract High-throughput environmental DNA metabarcoding has revolutionized the analysis of microbial diversity, but this approach is generally restricted to amplicon sizes below 500 base pairs. These short regions contain limited phylogenetic signal, which makes it impractical to use environmental DNA in full phylogenetic inferences. However, new long-read sequencing technologies such as the Pacific Biosciences platform may provide sufficiently large sequence lengths to overcome the poor phylogenetic resolution of short amplicons. -
Theratromyxa Weberi, an Amoeba Predatory on Plant-Parasitic Nematodes
258 Journal of Nematology, VoL 5, No. 4, October 1973 oxidase activity were increased by infection. 8.KRUSBERG, L. R. 1961. Studies on the culturing The reports of Chang (4) that lesion nematodes and parasitism of plant-parasitic nematodes, in were repelled and their respiration was particular Ditylenchus dipsaci and Aphelenchoides ritzemabosi on alfalfa tissues. significantly reduced by the oxidation products Nem atologica 6:181-200. of chlorogenic acid, strongly support this 9.MOUNTAIN, W. B. and Z. A. PATRICK. 1959. hypothesis. The peach replant problem in Ontario. VII. The pathogenicity of Pratylenchus penetrans (Cobb, LITERATURE CITED 1917) Filip. & Stek. 1941. Can. J. Bot. 37:459-470. 1.ACEDO, J. R. and R. A. ROHDE. 1971. 10. PATIL, S. S., R. L. POWELSON and R. R. YOUNG. Histochemical root pathology of Brassica 1964. Relation of chlorogenic acid and free oleracea capitata L. infected by Pratylenchus phenols in potato roots to infection by penetrans (Cobb) Filipjev and Verticillium albo-atrum. Phytopathology Schuurmans-Stekhoven (Nematoda: 54:531-535. Tylenchidae). J. Nematol. 3:62-68. ll.PITCHER, R. S., Z. A. PATRICK and W. B. 2.ARNOW, L. E. 1937. Colorimetric determination MOUNTAIN. 1960. Studies on the of the components of dopa and tyrosine host-parasite relations of Pratylenchus mixture. J. Biol. Chem. 118:531-537. penetrans (Cobb) to apple seedlings. I. 3.BLOCK, R. J., E. L. DURRUM and G. ZWEIG. Pathogenicity under sterile conditions. 1958. A manual of paper chromatography and Nematologica 5:309-314. paper electrophoresis. Academic Press, New 12.SMITH, I. 1960. Chromatographic and York. 710 p. electrophoretic technique. -
Kingdom Protozoa and Its 18Phyla
MICROBIOLOGICAL REVIEWS, Dec. 1993, p. 953-994 Vol. 57, No. 4 0146-0749/93/040953-42$02.00/0 Copyright © 1993, American Society for Microbiology Kingdom Protozoa and Its 18 Phyla T. CAVALIER-SMITH Evolutionary Biology Program of the Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 INTRODUCTION .......................................................................... 954 Changing Views of Protozoa as a Taxon.......................................................................... 954 EXCESSIVE BREADTH OF PROTISTA OR PROTOCTISTA ......................................................955 DISTINCTION BETWEEN PROTOZOA AND PLANTAE............................................................956 DISTINCTION BETWEEN PROTOZOA AND FUNGI ................................................................957 DISTINCTION BETWEEN PROTOZOA AND CHROMISTA .......................................................960 DISTINCTION BETWEEN PROTOZOA AND ANIMALIA ..........................................................962 DISTINCTION BETWEEN PROTOZOA AND ARCHEZOA.........................................................962 Transitional Problems in Narrowing the Definition of Protozoa ....................................................963 Exclusion of Parabasalia from Archezoa .......................................................................... 964 Exclusion of Entamoebia from Archezoa .......................................................................... 964 Are Microsporidia -
Biological Interference with Epidemics
CHAPTER 13 Biological Interference with Epidemics H. DARPOUX Station Centrale de Fathologie Vegetale, Centre National de Recherches Agronomiques, Versailles, France I. Introduction 521 II. Hyperparasitism: Parasites on Fungi 522 III. Bacteriophage 525 IV. Predators and Antagonistic Animals of Pathogens 527 V. Microbial Antagonisms 528 A. Phenomena of Antagonism 528 B. Microbial Antagonisms in Soil 531 C. Antagonism and Competition at the Time of Sowing the Seeds . 543 D. Antagonism on Fruit During the Storage 544 E. Antagonisms on a Level with Aerial Organs 544 VI. Interactions in the Fungal and Bacterial Diseases 547 VII. Complexes Associated with Nematodes 548 A. Hyperparasitism in the Nematodes 549 B. Predators of Phytophagous Nematodes 550 C. Action of Root Secretions on Nematodes 551 D. Interaction between Nematodes and Other Pathogenic Agents in Complex Diseases * 552 VIII. Interferences in the Virus Disease 554 A. Interaction between Viruses in the Host 554 B. Interactions between Strains of the Same Virus 555 IX. General Considerations 557 References 557 I. INTRODUCTION Various biological factors can influence the living pathogens of culti• vated plants and their hosts. The living world is a complex system where organisms fight for their existence, often to the prejudice of other organ• isms. Sometimes, however, beneficent associations are realized. In the natural biological medium, pathogens are submitted to the influence of neighboring organisms during their parasitic life, saprophytic phases, or during rest periods. Even the susceptibility of the host plant may be modified by biological factors. Sometimes the pathogen may be parasitized by another fungus or 521 522 Η. DARPOUX bacterium. The latter live at the expense of their hosts by drawing from them the materials necessary to their nutrition. -
The Phylogeny of Vampyrellid Amoebae Revisited
Shedding Light on Vampires: The Phylogeny of Vampyrellid Amoebae Revisited Sebastian Hess*, Nicole Sausen, Michael Melkonian Cologne Biocenter, Botanical Institute, University of Cologne, Cologne, Germany Abstract With the advent of molecular phylogenetic techniques the polyphyly of naked filose amoebae has been proven. They are interspersed in several supergroups of eukaryotes and most of them already found their place within the tree of life. Although the ‘vampire amoebae’ have attracted interest since the middle of the 19th century, the phylogenetic position and even the monophyly of this traditional group are still uncertain. In this study clonal co-cultures of eight algivorous vampyrellid amoebae and the respective food algae were established. Culture material was characterized morphologically and a molecular phylogeny was inferred using SSU rDNA sequence comparisons. We found that the limnetic, algivorous vampyrellid amoebae investigated in this study belong to a major clade within the Endomyxa CAVALIER-SMITH, 2002 (Cercozoa), grouping together with a few soil-dwelling taxa. They split into two robust clades, one containing species of the genus Vampyrella CIENKOWSKI, 1865, the other containing the genus Leptophrys HERTWIG &LESSER, 1874, together with terrestrial members. Supported by morphological data these clades are designated as the two families Vampyrellidae ZOPF, 1885, and Leptophryidae fam. nov. Furthermore the order Vampyrellida WEST, 1901 was revised and now corresponds to the major vampyrellid clade within the Endomyxa, comprising the Vampyrellidae and Leptophryidae as well as several environmental sequences. In the light of the presented phylogenetic analyses morphological and ecological aspects, the feeding strategy and nutritional specialization within the vampyrellid amoebae are discussed. Citation: Hess S, Sausen N, Melkonian M (2012) Shedding Light on Vampires: The Phylogeny of Vampyrellid Amoebae Revisited.