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Classification of Recently Discovered Amoeboid Protists

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Classification of Recently Discovered Amoeboid Protists Mississippi State University Scholars Junction Theses and Dissertations Theses and Dissertations 1-1-2018 Classification of Recently Discovered Amoeboid Protists Gabriel Schuler Follow this and additional works at: https://scholarsjunction.msstate.edu/td Recommended Citation Schuler, Gabriel, "Classification of Recently Discovered Amoeboid Protists" (2018). Theses and Dissertations. 1066. https://scholarsjunction.msstate.edu/td/1066 This Graduate Thesis - Open Access is brought to you for free and open access by the Theses and Dissertations at Scholars Junction. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of Scholars Junction. For more information, please contact [email protected]. Template C v3.0 (beta): Created by J. Nail 06/2015 Classification of recently discovered amoeboid protists. By TITLE PAGE Gabriel Schuler A Thesis Submitted to the Faculty of Mississippi State University in Partial Fulfillment of the Requirements for the Degree of Master of Science in Biological Science in the College of Arts and Sciences Mississippi State, Mississippi August 2018 Copyright by COPYRIGHT PAGE Gabriel Schuler 2018 Classification of recently discovered amoeboid protists. By APPROVAL PAGE Gabriel Schuler Approved: ____________________________________ Matthew W. Brown (Major Professor) ____________________________________ Diana C. Outlaw (Committee Member) ____________________________________ Jeffery D. Silberman (Committee Member) ____________________________________ Mark E. Welch (Graduate Coordinator) ____________________________________ Rick Travis Dean College of Arts & Sciences Name: Gabriel Schuler ABSTRACT Date of Degree: August 10, 2018 Institution: Mississippi State University Major Field: Biological Science Major Professor: Matthew W. Brown Title of Study: Classification of recently discovered amoeboid protists. Pages in Study 97 Candidate for Degree of Master of Science Many groups of protists, also known as microbial eukaryotes, remain understudied. One such group, the superfamily Sainouroidea in the supergroup Rhizaria has been shown to be a molecularly diverse and divergent clade by recent environmental sequencing. Here we isolated and analyzed cultures of Sainouroid amoebae using 18S rDNA sequencing, light microscopy, and TEM. Using a molecular species concept we described four novel genera and twelve novel species in Sainouroidea. Another understudied group Cutosea, in the supergroup Amoebozoa, contains the ATCC isolate PRA-29, which is an amoeba that has been used in many phylogenomic datasets. PRA- 29 was incorrectly identified as Pessonella sp. Here we studied PRA-29 in detail using light microscopy, TEM, and SEM and re-classify it as Armaparvus languidus novel genus, novel species. We show that a cell coat of microscales separated from the cell membrane is a unique trait found in all known Cutosean amoebae. DEDICATION This Master’s Thesis is dedicated to my daughter Eliza Bernadette Schuler and my wife Danielle Nicole Schuler. ii ACKNOWLEDGEMENTS I would like to thank Matthew W. Brown for support and guidance on this thesis. Additionally, I thank Alexander Tice and Jeffery D. Silberman for their large contribution to the project and their help with the writing in chapter two. I also thank Jared Stone, Rebecca A. Pearce, and Sarah Gammill for the work they contributed in their honors theses while in the lab of Jeffery Silberman at the University of Arkansas. I thank John D. Wilson and Chris Reading for the collection of snake feces for the project. Mississippi State University’s High Performance Computing Collaboratory provided some computational resources. Some data were collected while MWB was postdoctoral scholars in Prof. Andrew J. Roger’s lab in the Centre for Comparative Genomics and Evolutionary Bioinformatics at Dalhousie University. We thank Prof. Roger for his support on this project, Phil Vogrinc for handling snakes in the Wilson lab, the United Kingdom’s Forestry commission for unlimited access to Warum Forrest and Dr. Gabriela Jofré for aid in collecting European Grass snakes. We thank Eleni Gentekaki at the School of Science, Mae Fah Luang University, Chiang Rai, Thailand for aid in isolation of a strain. Electron microscopy images were acquired from the Institute for Imaging & Analytical Technologies (I2AT), which also provided technical support in particular from Amanda Lawrence. This project was supported in part by the National Science Foundation (NSF) Division of Environmental Biology (DEB) grant 1456054 (http://www.nsf.gov), awarded to MWB, Arkansas Biosciences Institute awarded to JDS, iii Arkansas Undergraduate Research Fellowships awarded to JS, RAP and University of Arkansas Honors awards for partial support of JS, RAP, SG (in the lab of JDS). iv TABLE OF CONTENTS DEDICATION .................................................................................................................... ii ACKNOWLEDGEMENTS ............................................................................................... iii LIST OF TABLES ............................................................................................................ vii LIST OF FIGURES ......................................................................................................... viii CHAPTER I. INTRODUCTION .................................................................................................1 II. PHYLOGENY AND CLASSIFICATION OF NOVEL DIVERSITY IN SAINOUROIDEA (CERCOZOA, RHIZARIA) SHEDS LIGHT ON A HIGHLY DIVERSE AND DIVERGENT CLADE ..............................................4 2.1 Abstract ......................................................................................................4 2.2 Introduction ...............................................................................................5 2.3 Results .......................................................................................................9 2.3.1 Molecular Phylogeny ...........................................................................9 2.3.2 Genus and Species Delineation .........................................................10 2.3.3 Light Microscopy ..............................................................................12 2.3.4 Transmission Electron Microscopy ...................................................14 2.4 Discussion ................................................................................................15 2.4.1 Genus and Species Delineation .........................................................15 2.4.2 Assignment of Guttulinopsis .............................................................17 2.4.3 Assignment of Rosculus ....................................................................18 2.4.4 Character Traits of Sainouroidea .......................................................22 2.4.5 Life History of Sainouroid Amoebae ................................................23 2.5 Conclusions .............................................................................................25 2.6 Methods ...................................................................................................26 2.6.1 Acquisition, Isolation, and Maintenance of Cultures ........................26 2.6.2 Light Microscopy ..............................................................................29 2.6.3 Morphology Comparison ...................................................................29 2.6.4 Transmission Electron Microscopy ...................................................29 2.6.5 18S rDNA Sequences ........................................................................30 2.6.6 Phylogenetic Analysis .......................................................................33 2.7 Taxonomic Summary ..............................................................................34 2.7.1 Taxonomy of Novel Genera and Species ..........................................34 v 2.8 Tables and Figures ...................................................................................45 III. DESCRIPTION OF ARMAPARVUS LANGUIDUS N. GEN. N. SP. CONFIRMS ULTRASTRUCTURAL UNITY OF CUTOSEA (AMOEBOZOA, EVOSEA) ...............................................................................64 3.1 Abstract ....................................................................................................64 3.2 Introduction .............................................................................................65 3.3 Methods ...................................................................................................69 3.3.1 Maintenance of Cultures ....................................................................69 3.3.2 Microscopy ........................................................................................69 3.3.3 Phylogeny ..........................................................................................70 3.4 Results .....................................................................................................71 3.4.1 Light Microscopy of A. languidus .....................................................71 3.4.2 Electron Microscopy of Cutosea .......................................................72 3.4.3 Phylogenetic Analysis .......................................................................73 3.5 Discussion ................................................................................................74 3.6 Taxonomic Summary ..............................................................................78
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