DOCSLIB.ORG

Downloaded from Genbank Using Custom Scripts

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Downloaded from Genbank Using Custom Scripts LABYRINTHULOMYCETES DIVERSITY META-ANALYSIS by Jingwen Pan A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Botany) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) January 2016 © Jingwen Pan, 2016 Abstract Labyrinthulomycetes are a group of ubiquitous stramenopiles that inhabit a wide range of habitats and play important ecological roles as nutrient recyclers and sometimes disease causing agents. Even though they have had a long history of being studied, their diversity has not yet been fully explored. The lack of a comprehensive reference database with up-to-date phylogeny also hinders any pursuits in understanding the ecological distribution of this group. This study was designed with the purpose of constructing a curated reference database and a phylogenetic tree based on existing 18S rDNA data, and then using this database to uncover any hidden diversity and novelty among Labyrinthulomycetes and provide a reference guidance for future identification. Using the newly-created reference database, I also analyzed high-throughput environmental sequencing data from two databases. My results reveal extensive diversity within the Labyrinthulomycetes, and recover many previously unknown environmental sequences, greatly expanding our knowledge of the ecological distribution of this group. The high- throughput environmental sequencing data analysis also shows some of the newly identified environmental clades to be particularly abundant in the ocean. The phylogenetic framework I have provided in this study, together with the metadata I have compiled, will serve as a useful tool for future ecological and evolutionary studies of this widespread lineage. ii Preface This thesis is original and unpublished. It is based on work designed by J. del Campo and I. I conducted all the analysis and J. del Campo provided supervisory guidance. I prepared all figures and wrote the manuscript, and J. del Campo and P.J. Keeling revised it. iii Table of Contents Abstract .................................................................................................................................................... ii Preface .................................................................................................................................................... iii Table of Contents ................................................................................................................................. iv List of Tables .......................................................................................................................................... v List of Figures ........................................................................................................................................ vi Acknowledgements ........................................................................................................................... vii Chapter 1: Introduction ...................................................................................................................... 1 1.1 Labyrinthulomycetes Introduction ...................................................................................................................... 1 1.1.1 Labyrinthulomycetes Classification ............................................................................................................ 1 1.1.2 Labyrinthulomycetes Morphology and Physiology .............................................................................. 3 1.1.3 Labyrinthulomycetes Ecology and Lifestyle ............................................................................................ 3 1.1.4 Summary ................................................................................................................................................................. 5 1.2 High-throughput Environmental Sequences Studies .................................................................................... 5 1.3 Goals ................................................................................................................................................................................... 7 Chapter 2: Materials and Methods .................................................................................................. 9 2.1 Reference Phylogenetic Tree Construction ....................................................................................................... 9 2.2 Reference Database Annotation ........................................................................................................................... 10 2.3 Labyrinthulomycetes V9 Reads Database ....................................................................................................... 11 2.4 Abundance and Richness Distribution Patterns ........................................................................................... 12 Chapter 3: Results ............................................................................................................................. 13 3.1 Phylogeny of Labyrinthulomycetes .................................................................................................................... 13 3.2 Examining Abundance and Richness using GenBank Sanger Sequences ........................................... 14 3.2.1 Host Association ................................................................................................................................................. 15 3.3 Abundance and Richness using V9 Reads ........................................................................................................ 16 Chapter 4: Discussion ....................................................................................................................... 19 4.1 Phylogeny and Classification ................................................................................................................................. 19 4.2 Environmental Distribution of Labyrinthulomycetes ................................................................................ 22 Chapter 5: Conclusion and Future Directions .......................................................................... 24 References ........................................................................................................................................... 34 iv List of Tables Table 1: List of previously described environmental clades (Collado-Mercado et al. 2010) and the new clades they now belong to according to the present phylogenetic study .... 30 Table 2: Total abundance and richness for the three Labyrinthulomycetes databases ....... 32 v List of Figures Figure 1: Diversity of Labyrinthulomycetes inferred from a maximum likelihood (RAxML) phylogenetic tree constructed using 18S rDNA sequences. ............................................ 26 Figure 2: Diversity of Labyrinthulomycetes (full version) ...................................................... 27 Figure 3: Abundance and richness for major groups of Labyrinthulomycetes .................... 31 Figure 4: Heatmap showing the abundance distribution of major groups of Labyrinthulomycetes according to different environmental parameters ..................... 33 vi Acknowledgements I would like to thank many people who made this thesis possible. First, I would like to express my sincere gratitude to my supervisor Patrick Keeling for his support, guidance and patience on my study. I also thank the members of my committee, Brian Leander, James Berger and Rosie Redfield for their advice. I am also grateful to all members from the Keeling lab, the Leander lab and the Fast lab for their help and inspiration along the way, and for creating such a wonderful working environment. I am also thankful to faculty and staff of UBC, especially Veronica Oxtoby, for general help. I own particular thanks to Javier del Campo, whose expertise and guidance have helped me in all the time of research and in writing of this thesis, and for being patient with me during stressful moments. Finally, I wish to thank my parents and friends for their love and continuous support throughout my study and my life. They have walked through every joyful and difficult moment with me. Special thanks to Fen Liu and Cuiyu Lin for their daily amusement and advice on Excel from the later. vii Chapter 1: Introduction 1.1 Labyrinthulomycetes Introduction Labyrinthulomycetes are a group of unicellular eukaryotic microorganisms commonly found in marine environments (Raghukumar 2002). The slime-like appearance of most of its members has resulted in previous misplacement of this group within Fungi, Oomycetes (Stramenopiles) and amoebae. Observations of mitochondria with tubular cristae and their heterokont, biflagellate zoospore production, together with support from 18S rRNA gene phylogenies eventually led to the placement of this group within the Stramenopiles, together with the photosynthetic Ochrophytes (diatom, brown algae, etc) and other non-photosynthetic groups, like the plant pathogenic Oomycetes (Cavalier-Smith et al. 1994; Tsui et al. 2009). Within the stramenopiles, the Labyrinthulomycetes is a monophyletic group and is characterized by having a cell wall made of scales containing proteins and sulphated polysaccharides, as well as the production of an ectoplasmic network (EN), which is a membrane-bound, branched network secreted through a unique organelle called bothrosome (sagenogenetosome). 1.1.1 Labyrinthulomycetes Classification
Load more

Recommended publications
  • METABOLIC EVOLUTION in GALDIERIA SULPHURARIA By
    METABOLIC EVOLUTION IN GALDIERIA SULPHURARIA By CHAD M. TERNES Bachelor of Science in Botany Oklahoma State University Stillwater, Oklahoma 2009 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY May, 2015 METABOLIC EVOLUTION IN GALDIERIA SUPHURARIA Dissertation Approved: Dr. Gerald Schoenknecht Dissertation Adviser Dr. David Meinke Dr. Andrew Doust Dr. Patricia Canaan ii Name: CHAD M. TERNES Date of Degree: MAY, 2015 Title of Study: METABOLIC EVOLUTION IN GALDIERIA SULPHURARIA Major Field: PLANT SCIENCE Abstract: The thermoacidophilic, unicellular, red alga Galdieria sulphuraria possesses characteristics, including salt and heavy metal tolerance, unsurpassed by any other alga. Like most plastid bearing eukaryotes, G. sulphuraria can grow photoautotrophically. Additionally, it can also grow solely as a heterotroph, which results in the cessation of photosynthetic pigment biosynthesis. The ability to grow heterotrophically is likely correlated with G. sulphuraria ’s broad capacity for carbon metabolism, which rivals that of fungi. Annotation of the metabolic pathways encoded by the genome of G. sulphuraria revealed several pathways that are uncharacteristic for plants and algae, even red algae. Phylogenetic analyses of the enzymes underlying the metabolic pathways suggest multiple instances of horizontal gene transfer, in addition to endosymbiotic gene transfer and conservation through ancestry. Although some metabolic pathways as a whole appear to be retained through ancestry, genes encoding individual enzymes within a pathway were substituted by genes that were acquired horizontally from other domains of life. Thus, metabolic pathways in G. sulphuraria appear to be composed of a ‘metabolic patchwork’, underscored by a mosaic of genes resulting from multiple evolutionary processes.
    [Show full text]
  • The Planktonic Protist Interactome: Where Do We Stand After a Century of Research?
    bioRxiv preprint doi: https://doi.org/10.1101/587352; this version posted May 2, 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. Bjorbækmo et al., 23.03.2019 – preprint copy - BioRxiv The planktonic protist interactome: where do we stand after a century of research? Marit F. Markussen Bjorbækmo1*, Andreas Evenstad1* and Line Lieblein Røsæg1*, Anders K. Krabberød1**, and Ramiro Logares2,1** 1 University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, N- 0316 Oslo, Norway 2 Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain * The three authors contributed equally ** Corresponding authors: Ramiro Logares: Institute of Marine Sciences (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain. Phone: 34-93-2309500; Fax: 34-93-2309555. [email protected] Anders K. Krabberød: University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, N-0316 Oslo, Norway. Phone +47 22845986, Fax: +47 22854726. [email protected] Abstract Microbial interactions are crucial for Earth ecosystem function, yet our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2,500 ecological interactions from ~500 publications, spanning the last 150 years.
    [Show full text]
  • 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.
    [Show full text]
  • An Integrative Approach Sheds New Light Onto the Systematics
    www.nature.com/scientificreports OPEN An integrative approach sheds new light onto the systematics and ecology of the widespread ciliate genus Coleps (Ciliophora, Prostomatea) Thomas Pröschold1*, Daniel Rieser1, Tatyana Darienko2, Laura Nachbaur1, Barbara Kammerlander1, Kuimei Qian1,3, Gianna Pitsch4, Estelle Patricia Bruni4,5, Zhishuai Qu6, Dominik Forster6, Cecilia Rad‑Menendez7, Thomas Posch4, Thorsten Stoeck6 & Bettina Sonntag1 Species of the genus Coleps are one of the most common planktonic ciliates in lake ecosystems. The study aimed to identify the phenotypic plasticity and genetic variability of diferent Coleps isolates from various water bodies and from culture collections. We used an integrative approach to study the strains by (i) cultivation in a suitable culture medium, (ii) screening of the morphological variability including the presence/absence of algal endosymbionts of living cells by light microscopy, (iii) sequencing of the SSU and ITS rDNA including secondary structures, (iv) assessment of their seasonal and spatial occurrence in two lakes over a one‑year cycle both from morphospecies counts and high‑ throughput sequencing (HTS), and, (v) proof of the co‑occurrence of Coleps and their endosymbiotic algae from HTS‑based network analyses in the two lakes. The Coleps strains showed a high phenotypic plasticity and low genetic variability. The algal endosymbiont in all studied strains was Micractinium conductrix and the mutualistic relationship turned out as facultative. Coleps is common in both lakes over the whole year in diferent depths and HTS has revealed that only one genotype respectively one species, C. viridis, was present in both lakes despite the diferent lifestyles (mixotrophic with green algal endosymbionts or heterotrophic without algae).
    [Show full text]
  • And Macro-Algae: Utility for Industrial Applications
    MICRO- AND MACRO-ALGAE: UTILITY FOR INDUSTRIAL APPLICATIONS Outputs from the EPOBIO project September 2007 Prepared by Anders S Carlsson, Jan B van Beilen, Ralf Möller and David Clayton Editor: Dianna Bowles cplpressScience Publishers EPOBIO: Realising the Economic Potential of Sustainable Resources - Bioproducts from Non-food Crops © September 2007, CNAP, University of York EPOBIO is supported by the European Commission under the Sixth RTD Framework Programme Specific Support Action SSPE-CT-2005-022681 together with the United States Department of Agriculture. Legal notice: Neither the University of York nor the European Commission nor any person acting on their behalf may be held responsible for the use to which information contained in this publication may be put, nor for any errors that may appear despite careful preparation and checking. The opinions expressed do not necessarily reflect the views of the University of York, nor the European Commission. Non-commercial reproduction is authorized, provided the source is acknowledged. Published by: CPL Press, Tall Gables, The Sydings, Speen, Newbury, Berks RG14 1RZ, UK Tel: +44 1635 292443 Fax: +44 1635 862131 Email: [email protected] Website: www.cplbookshop.com ISBN 13: 978-1-872691-29-9 Printed in the UK by Antony Rowe Ltd, Chippenham CONTENTS 1 INTRODUCTION 1 2 HABITATS AND PRODUCTION SYSTEMS 4 2.1 Definition of terms 4 2.2 Macro-algae 5 2.2.1 Habitats for red, green and brown macro-algae 5 2.2.2 Production systems 6 2.3 Micro-algae 9 2.3.1 Applications of micro-algae 9 2.3.2 Production
    [Show full text]
  • Safety of Oil from Schizochytrium Limacinum (Strain FCC-3204) for Use in Infant and Follow-On Formula As a Novel Food Pursuant to Regulation (EU) 2015/2283
    SCIENTIFIC OPINION ADOPTED: 24 November 2020 doi: 10.2903/j.efsa.2021.6344 Safety of oil from Schizochytrium limacinum (strain FCC-3204) for use in infant and follow-on formula as a novel food pursuant to Regulation (EU) 2015/2283 EFSA Panel on Nutrition, Novel Foods and Food Allergens (NDA), Dominique Turck, Jacqueline Castenmiller, Stefaan De Henauw, Karen Ildico Hirsch-Ernst, John Kearney, Alexandre Maciuk, Inge Mangelsdorf, Harry J McArdle, Androniki Naska, Carmen Pelaez, Kristina Pentieva, Alfonso Siani, Frank Thies, Sophia Tsabouri, Marco Vinceti, Francesco Cubadda, Thomas Frenzel, Marina Heinonen, Rosangela Marchelli, Monika Neuhauser-Berthold,€ Morten Poulsen, Miguel Prieto Maradona, Josef Rudolf Schlatter, Henk van Loveren, Emanuela Turla and Helle Katrine Knutsen Abstract Following a request from the European Commission, the EFSA Panel on Nutrition, Novel Foods and Food Allergens (NDA) was asked to deliver an opinion on the safety of Schizochytrium sp. oil as a novel food (NF) pursuant to Regulation (EU) 2015/2283. Schizochytrium sp. is a single-cell microalga. The strain FCC- 3204, used by the applicant (Fermentalg), belongs to the species Schizochytrium limacinum. The NF, an oil rich in docosahexaenoic acid (DHA), is obtained from microalgae after enzymatic lysis. The applicant proposed to use the NF in infant formulae (IF) and follow-on formulae (FOF). The use level defined by the applicant was derived from Regulation (EU) 2016/127, which states the mandatory addition of DHA to IF and FOF at the level of 20–50 mg/100 kcal. The intake of DHA resulting from the use of the NF in IF and FOF is not expected to pose safety concerns.
    [Show full text]
  • Plenary Lecture & Symposium
    PLENARY LECTURE & SYMPOSIUM SYMPOSIuM From genomics to flagellar and ciliary struc - MONDAY 29 JulY tures and cytoskeleton dynamics (by FEPS) PlENARY lECTuRE (ISoP Honorary Member lECTuRE) Chairs (by ISoP) Cristina Miceli , University of Camerino, Camerino, Italy Helena Soares , University of Lisbon and Gulbenkian Foun - Introduction - John Dolan , CNRS-Sorbonne University, Ville - dation, Lisbon, Portugal franche-sur-Mer, France. Jack Sunter - Oxford Brookes University, Oxford, UK- Genome Tom Fenchel University of Copenhagen, Copenhagen, Den - wide tagging in trypanosomes uncovers flagellum asymmetries mark Dorota Wloga - Nencki Institute of Experimental Biology, War - ISoP Honorary Member saw, Poland - Deciphering the molecular mechanisms that coor - dinate ciliary outer doublet complexes – search for “missing Size, Shape and Function among Protozoa links” Helena Soares - University of Lisbon and Polytechnic Institute of Lisbon, Lisbon, Portugal - From centrosomal microtubule an - SYMPOSIuM on ciliate biology and taxonomy in memory choring and organization to basal body positioning: TBCCD1 an of Denis lynn (by FEPS/ISoP) elusive protein Chairs Pierangelo luporini , University of Camerino, Camerino, Italy Roberto Docampo , University of Georgia, Athens, Georgia TuESDAY 30 JulY Alan Warren - Natural History Museum, London, UK. The bio - logy and systematics of peritrich ciliates: old concepts and new PlENARY lECTuRE (PAST-PRESIDENT LECTURE, by ISoP) findings Rebecca Zufall - University of Houston, Houston, USA. Amitosis Introduction - Avelina Espinosa , Roger Williams University, and the Evolution of Asexuality in Tetrahymena Ciliates Bristol, USA Sabine Agatha - University of Salzburg, Salzburg, Austria. The biology and systematics of oligotrichean ciliates: new findings David Bass and old concepts Natural History Museum London, London & Cefas, Weymouth, laura utz - School of Sciences, PUCRS, Porto Alegre, Brazil.
    [Show full text]
  • Microalgae-Blend Tilapia Feed Eliminates Fishmeal and Fish Oil
    www.nature.com/scientificreports * Oreochromis niloticus Nannochloropsis oculata Schizochytriump p Aquaculture, the world’s most e!cient producer of edible protein, continues to grow faster than any other major food sector in the world, in response to the rapidly increasing global demand for "sh and seafood 1,2. Feed inputs for aquaculture production represent 40–75% of aquaculture production costs and are a key market driver for aquaculture production1. #e aquafeed market is expected to grow 8–10% per annum and is production of compound feeds is projected to reach 73.15 million tonne (mt) in 2025 2–9. Ocean-derived "shmeal (FM) and "sh oil (FO) in aquafeeds has raised sustainability concerns as the supply of wild marine forage "sh will not meet growing demand and will constrain aquaculture growth 1,2,10,11. Moreo- ver, competition for FM and FO from pharmaceuticals, nutraceuticals, and feeds for other animals6,12 further exacerbates a supply–demand squeeze 2,13. #e use of forage "sh (such as herrings, sardines, and anchovies) for FMFO production also a$ects human food security because approximately 16.9 million of the 29 mt of forage "sh that is caught globally for aquaculture feed is directed away from human consumption every year 14. More than 90 percent of these "sh are considered food grade and could be directly consumed by humans, especially food insecure people in developing countries 15. Although more prevalent in aquafeeds for high-trophic "n"sh and crustaceans, FM and FO is also routinely incorporated (inclusion rates of 3–10%) in aquafeeds for low-trophic "n"sh like tilapia to enhance growth1,6,16–18.
    [Show full text]
  • Prospects on the Use of Schizochytrium Sp. to Develop Oral Vaccines
    REVIEW published: 25 October 2018 doi: 10.3389/fmicb.2018.02506 Prospects on the Use of Schizochytrium sp. to Develop Oral Vaccines Abel Ramos-Vega 1†, Sergio Rosales-Mendoza 2,3*†, Bernardo Bañuelos-Hernández 4 and Carlos Angulo 1* 1 Grupo de Inmunología and Vacunología, Centro de Investigaciones Biológicas del Noroeste, La Paz, Mexico, 2 Laboratorio de Biofarmacéuticos Recombinantes, Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico, 3 Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico, 4 Escuela de Agronomía y Veterinaria, Universidad De La Salle Bajío, León, México Although oral subunit vaccines are highly relevant in the fight against widespread diseases, their high cost, safety and proper immunogenicity are attributes that have yet to be addressed in many cases and thus these limitations should be considered in the development of new oral vaccines. Prominent examples of new platforms proposed to address these limitations are plant cells and microalgae. Schizochytrium Edited by: sp. constitutes an attractive expression host for vaccine production because of its Aleš Berlec, Jožef Stefan Institute (IJS), Slovenia high biosynthetic capacity, fast growth in low cost culture media, and the availability Reviewed by: of processes for industrial scale production. In addition, whole Schizochytrium sp. Saul Purton, cells may serve as delivery vectors; especially for oral vaccines since Schizochytrium University College London, United Kingdom sp. is safe for oral consumption, produces immunomodulatory compounds, and may Vanvimon Saksmerprome, provide bioencapsulation to the antigen, thus increasing its bioavailability. Remarkably, National Science and Technology Schizochytrium sp.
    [Show full text]
  • Proposal for Practical Multi-Kingdom Classification of Eukaryotes Based on Monophyly 2 and Comparable Divergence Time Criteria
    bioRxiv preprint doi: https://doi.org/10.1101/240929; this version posted December 29, 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 4.0 International license. 1 Proposal for practical multi-kingdom classification of eukaryotes based on monophyly 2 and comparable divergence time criteria 3 Leho Tedersoo 4 Natural History Museum, University of Tartu, 14a Ravila, 50411 Tartu, Estonia 5 Contact: email: [email protected], tel: +372 56654986, twitter: @tedersoo 6 7 Key words: Taxonomy, Eukaryotes, subdomain, phylum, phylogenetic classification, 8 monophyletic groups, divergence time 9 Summary 10 Much of the ecological, taxonomic and biodiversity research relies on understanding of 11 phylogenetic relationships among organisms. There are multiple available classification 12 systems that all suffer from differences in naming, incompleteness, presence of multiple non- 13 monophyletic entities and poor correspondence of divergence times. These issues render 14 taxonomic comparisons across the main groups of eukaryotes and all life in general difficult 15 at best. By using the monophyly criterion, roughly comparable time of divergence and 16 information from multiple phylogenetic reconstructions, I propose an alternative 17 classification system for the domain Eukarya to improve hierarchical taxonomical 18 comparability for animals, plants, fungi and multiple protist groups. Following this rationale, 19 I propose 32 kingdoms of eukaryotes that are treated in 10 subdomains. These kingdoms are 20 further separated into 43, 115, 140 and 353 taxa at the level of subkingdom, phylum, 21 subphylum and class, respectively (http://dx.doi.org/10.15156/BIO/587483).
    [Show full text]
  • Controlled Sampling of Ribosomally Active Protistan Diversity in Sediment-Surface Layers Identifies Putative Players in the Marine Carbon Sink
    The ISME Journal (2020) 14:984–998 https://doi.org/10.1038/s41396-019-0581-y ARTICLE Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink 1,2 1 1 3 3 Raquel Rodríguez-Martínez ● Guy Leonard ● David S. Milner ● Sebastian Sudek ● Mike Conway ● 1 1 4,5 6 7 Karen Moore ● Theresa Hudson ● Frédéric Mahé ● Patrick J. Keeling ● Alyson E. Santoro ● 3,8 1,9 Alexandra Z. Worden ● Thomas A. Richards Received: 6 October 2019 / Revised: 4 December 2019 / Accepted: 17 December 2019 / Published online: 9 January 2020 © The Author(s) 2020. This article is published with open access Abstract Marine sediments are one of the largest carbon reservoir on Earth, yet the microbial communities, especially the eukaryotes, that drive these ecosystems are poorly characterised. Here, we report implementation of a sampling system that enables injection of reagents into sediments at depth, allowing for preservation of RNA in situ. Using the RNA templates recovered, we investigate the ‘ribosomally active’ eukaryotic diversity present in sediments close to the water/sediment interface. We 1234567890();,: 1234567890();,: demonstrate that in situ preservation leads to recovery of a significantly altered community profile. Using SSU rRNA amplicon sequencing, we investigated the community structure in these environments, demonstrating a wide diversity and high relative abundance of stramenopiles and alveolates, specifically: Bacillariophyta (diatoms), labyrinthulomycetes and ciliates. The identification of abundant diatom rRNA molecules is consistent with microscopy-based studies, but demonstrates that these algae can also be exported to the sediment as active cells as opposed to dead forms.
    [Show full text]
  • Short Communication on the Classification of The
    SHORT COMMUNICATION ON THE CLASSIFICATION OF THE GENERA Labyrinthula, Schizochytrium AND Thraustochytrium (Labyrinthulids AND Thraustochytrids) Øjvind Moestrup Biological Institute, University of Copenhagen Universitetsparken 4 , DK- 2100 Copenhagen, Denmark E-mail: [email protected] Citation as: Moestrup Øjvind, 2019. On the classification of the genera Labyrinthula, Schizochytrium and Thraustochytrium (Labyrinthulids and Thraustochytrids). Tap chi Sinh hoc, 41(2): xx–xx. https://doi.org/10.15625/0866-7160/v41n2.xxxxx Species of the genera Labyrinthula, Schizochytrium, Thraustochytrium and related organisms have recently attracted attention in biotechnology, and here is a short note on how to classify these rather special organisms. The labyrinthulids and thraustochytrids belong to the heterokonts, a large group of very diverse organisms, from microscopic unicells to metre-long brown algae. The heterokonts comprise species that were formerly classified as algae, fungi and/or protozoa. Many heterokonts are autotrophic and contain chloroplasts, and such organisms are often classified as algae (golden algae, brown algae). Labyrinthulids and thraustochytrids, however, are heterotrophic and lack chloroplasts. They were until recently known as Labyrinthulomycetes or Labyrinthulea , indeed the new classification of Adl et al. (2019) uses the first of these names. It is an unfortunate name as it gives the misleading impression that they are fungi. Honigberg et al. (1964) and others considered them protozoa. Are heterokonts algae, protozoa or fungi? And, more specifically, what are labyrinthulids and thraustochytrids? The heterokonts are thought to be a very old group (probably precambrian), and this may account for their huge morphological diversity. In the WORMS list (World Register of Marine Species) heterokonts are classified as the Infrakingdom Heterokonta .
    [Show full text]