DOCSLIB.ORG

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Journal of Eukaryotic Microbiology ISSN 1066-5234 ORIGINAL ARTICLE Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes Sina M. Adl a, * , David Bass b,c , Christopher E. Lane d, Julius Luke se,f , Conrad L. Schoch g, Alexey Smirnov h, Sabine Agatha i, Cedric Berney j , Matthew W. Brown k,l , Fabien Burki m, Paco C ardenas n , Ivan Cepi cka o, Lyudmila Chistyakova p, Javier del Campo q, Micah Dunthorn r,s , Bente Edvardsen t , Yana Eglit u, Laure Guillou v, Vladim ır Hampl w, Aaron A. Heiss x, Mona Hoppenrath y, Timothy Y. James z, Anna Karn- kowska aa , Sergey Karpov h,ab , Eunsoo Kim x, Martin Kolisko e, Alexander Kudryavtsev h,ab , Daniel J.G. Lahr ac , Enrique Lara ad,ae , Line Le Gall af , Denis H. Lynn ag,ah , David G. Mann ai,aj , Ramon Massana q, Edward A.D. Mitchell ad,ak , Christine Morrow al , Jong Soo Park am , Jan W. Pawlowski an , Martha J. Powell ao , Daniel J. Richter ap , Sonja Rueckert aq , Lora Shadwick ar , Satoshi Shimano as , Frederick W. Spiegel ar , Guifr e Torruella at , Noha Youssef au , Vasily Zlatogursky h,av & Qianqian Zhang aw a Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, S7N 5A8, SK, Canada b Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom c Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Barrack Road, The Nothe, Weymouth, Dorset, DT4 8UB, United Kingdom d Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, 02881, USA e Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Cesk e Bud ejovice, 37005, Czechia f Faculty of Science, University of South Bohemia, Cesk e Bud ejovice, 37005, Czechia g National Institute for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, 20892, USA h Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, 199034, Russia i Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, Salzburg, A-5020, Austria j CNRS, UMR 7144 (AD2M), Groupe Evolution des Protistes et Ecosyst emes P elagiques, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, 29680, France k Department of Biological Sciences, Mississippi State University, Starkville, 39762, Mississippi, USA l Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Starkville, 39762, Mississippi, USA m Department of Organismal Biology, Program in Systematic Biology, Science for Life Laboratory, Uppsala University, Uppsala, 75236, Sweden n Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC Box 574, Uppsala, SE-75123, Sweden o Department of Zoology, Faculty of Science, Charles University, Vinicna 7, Prague, 128 44, Czechia p Core Facility Centre for Culture Collection of Microorganisms, Saint Petersburg State University, Saint Petersburg, 198504, Russia q Institut de Ci encies del Mar, CSIC, Passeig Mar ıtim de la Barceloneta, 37-49, Barcelona, 08003, Catalonia, Spain r Department of Ecology, University of Kaiserslautern, Erwin-Schroedinger Street, Kaiserslautern, D-67663, Germany s Department of Eukaryotic Microbiology, University of Duisburg-Essen, Universit atsstrasse€ 5, Essen, D-45141, Germany t Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, Oslo, 0316, Norway u Department of Biology, Dalhousie University, Halifax, B3H 4R2, NS, Canada v Sorbonne Universit e, Universit e Pierre et Marie Curie - Paris 6, CNRS, UMR 7144 (AD2M), Station Biologique de Roscoff, Place Georges Teis- sier, CS90074, Roscoff, 29688, France w Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Pr umyslov a 595, Vestec, 252 42, Czechia x Department of Invertebrate Zoology, American Museum of Natural History, New York City, New York, 10024, USA y Senckenbe rg am Meer, DZMB – German Centre for Marine Biodiversity Research, Wilhelmshaven, 26382, Germany z Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA aa Department of Molecular Phylogenetics and Evolution, University of Warsaw, Warsaw, 02-089, Poland ab Laboratory of Parasitic Worms and Protistology, Zoological Institute RAS, Saint Petersburg, 199034, Russia ac Department of Zoology, Institute of Biosciences, University of Sao Paulo, Matao Travessa 14 Cidade Universitaria, Sao Paulo, 05508-090, Sao Paulo, Brazil ad Laboratory of Soil Biodiversity, University of Neuch atel,^ Rue Emile-Argand 11, Neuch atel,^ 2000, Switzerland ae Real Jard ın Bot anico, CSIC, Plaza de Murillo 2, Madrid, 28014, Spain af Institut de Syst ematique, Evolution, Biodiversit e, Mus eum National d’Histoire Naturelle, Sorbonne Universit es, 57 rue Cuvier, CP 39, Paris, 75005, France ag Department of Integrative Biology, University of Guelph, Summerlee Science Complex, Guelph, ON, N1G 2W1, Canada ah Department of Zoology, University of British Columbia, 4200-6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada ai Royal Botanic Garden, Edinburgh, EH3 5LR, United Kingdom aj Institute for Agrifood Research and Technology, C/Poble Nou km 5.5, Sant Carles de La R apita, E-43540, Spain ak Jardin Botanique de Neuch atel,^ Chemin du Perthuis-du-Sault 58, Neuch atel,^ 2000, Switzerland al Department of Natural Sciences, National Museums Northern Ireland, 153 Bangor Road, Holywood, BT18 OEU, United Kingdom © 2018 The Authors Journal of Eukaryotic Microbiology published by Wiley Periodicals, Inc. on behalf of International Society of Protistologists 4 Journal of Eukaryotic Microbiology 2019, 66 , 4–119 This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Adl et al. Classification of Eukaryotes am Department of Oceanography and Kyungpook Institute of Oceanography, School of Earth System Sciences, Kyungpook National University, Daegu, Korea an Department of Genetics and Evolution, University of Geneva, 1211, Geneva 4, Switzerland ao Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, 35487, USA ap Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Mar ıtim de la Barceloneta 37-49, Barcelona, 08003, Catalonia, Spain aq School of Applied Sciences, Edinburgh Napier University, Edinburgh, EH11 4BN, United Kingdom ar Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, AR 72701, USA as Science Research Centre, Hosei University, 2-17-1 Fujimi, Chiyoda-ku, Tokyo, 102-8160, Japan at Laboratoire Evolution et Syst ematique, Universit e Paris-XI, Orsay, 91405, France au Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, 74074, USA av Department of Organismal Biology, Systematic Biology Program, Uppsala University, Uppsala, SE-752 36, Sweden aw Yantai Institute of Coastal Zone Research, Chinese Academy of Science, Yantai, 264003, China Keywords ABSTRACT Algae; amoebae; biodiversity; ciliate; ecol- ogy; flagellate; fungus; microbiology; para- This revision of the classification of eukaryotes follows that of Adl et al., 2012 site; plankton; protozoa; systematics; [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since taxonomy. have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, Correspondence environmental sampling in the intervening years has massively increased the S.M. Adl, Department of Soil Sciences, genetic information at hand. Consequently, we have discovered novel clades, College of Agriculture and Bioresources, exciting new genera and uncovered a massive species level diversity beyond University of Saskatchewan, 51 Campus the morphological species descriptions. Several clades known from environ- Drive, Saskatoon, SK, S7N 5A8 Canada mental samples only have now found their home. Sampling soils, deeper mar- Telephone number: 306 966 6866 ine waters and the deep sea will continue to fill us with surprises. The main e-mail: [email protected] changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Hap- Received: 2 September 2018; accepted tista and Cryptista. We provide suggested primer sets for DNA sequences September 4, 2018. from environmental samples that are effective for each clade. We have pro- vided a guide to trophic functional guilds in an appendix, to facilitate the inter- doi:10.1111/jeu.12691 pretation of environmental samples, and a standardized taxonomic guide for East Asian users. THIS revision of the classification of eukaryotes updates background information, and to Adl et al. 2007 for a dis- that of the International Society of Protistologists (Adl cussion. Briefly, we adopted a hierarchical system with- et al. 2012). Since then, there has been a massive out formal rank designations. The hierarchy is increase in DNA sequence information of phylogenetic rel- represented by indented paragraphs. The nomenclatural evance from environmental samples. We now have a priority is given to the oldest name (and its authority) that much better sense of the undescribed biodiversity in our correctly assembled genera or higher groups together environment (De Vargas et al. 2015; Pawlowski et al. into a clade, except where its composition was substan- 2012). While significant,
Recommended publications
  • Fmicb-11-542372 September 28, 2020 Time: 18:7 # 1

    Fmicb-11-542372 September 28, 2020 Time: 18:7 # 1

    UvA-DARE (Digital Academic Repository) Seasonal and Geographical Transitions in Eukaryotic Phytoplankton Community Structure in the Atlantic and Pacific Oceans Choi, C.J.; Jimenez, V.; Needham, D.M.; Poirier, C.; Bachy, C.; Alexander, H.; Wilken, S.; Chavez, F.P.; Sudek, S.; Giovannoni, S.J.; Worden, A.Z. DOI 10.3389/fmicb.2020.542372 Publication date 2020 Document Version Final published version Published in Frontiers in Microbiology License CC BY Link to publication Citation for published version (APA): Choi, C. J., Jimenez, V., Needham, D. M., Poirier, C., Bachy, C., Alexander, H., Wilken, S., Chavez, F. P., Sudek, S., Giovannoni, S. J., & Worden, A. Z. (2020). Seasonal and Geographical Transitions in Eukaryotic Phytoplankton Community Structure in the Atlantic and Pacific Oceans. Frontiers in Microbiology, 11, [542372]. https://doi.org/10.3389/fmicb.2020.542372 General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible.

  • Molecular Data and the Evolutionary History of Dinoflagellates by Juan Fernando Saldarriaga Echavarria Diplom, Ruprecht-Karls-Un

    Molecular data and the evolutionary history of dinoflagellates by Juan Fernando Saldarriaga Echavarria Diplom, Ruprecht-Karls-Universitat Heidelberg, 1993 A THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES Department of Botany We accept this thesis as conforming to the required standard THE UNIVERSITY OF BRITISH COLUMBIA November 2003 © Juan Fernando Saldarriaga Echavarria, 2003 ABSTRACT New sequences of ribosomal and protein genes were combined with available morphological and paleontological data to produce a phylogenetic framework for dinoflagellates. The evolutionary history of some of the major morphological features of the group was then investigated in the light of that framework. Phylogenetic trees of dinoflagellates based on the small subunit ribosomal RNA gene (SSU) are generally poorly resolved but include many well- supported clades, and while combined analyses of SSU and LSU (large subunit ribosomal RNA) improve the support for several nodes, they are still generally unsatisfactory. Protein-gene based trees lack the degree of species representation necessary for meaningful in-group phylogenetic analyses, but do provide important insights to the phylogenetic position of dinoflagellates as a whole and on the identity of their close relatives. Molecular data agree with paleontology in suggesting an early evolutionary radiation of the group, but whereas paleontological data include only taxa with fossilizable cysts, the new data examined here establish that this radiation event included all dinokaryotic lineages, including athecate forms. Plastids were lost and replaced many times in dinoflagellates, a situation entirely unique for this group. Histones could well have been lost earlier in the lineage than previously assumed.
  • Universidad Autónoma De Nuevo León Facultad De Ciencias Biológicas

    Universidad Autónoma De Nuevo León Facultad De Ciencias Biológicas

    UNIVERSIDAD AUTÓNOMA DE NUEVO LEÓN FACULTAD DE CIENCIAS BIOLÓGICAS TESIS TAXONOMÍA, DISTRIBUCIÓN E IMPORTANCIA DE LAS ALGAS DE NUEVO LEÓN POR DIANA ELENA AGUIRRE CAVAZOS COMO REQUISITO PARCIAL PARA OBTENER EL GRADO DE DOCTOR EN CIENCIAS CON ACENTUACIÓN EN MANEJO Y ADMINISTRACIÓN DE RECURSOS VEGETALES MAYO, 2018 TAXONOMÍA, DISTRIBUCIÓN E IMPORTANCIA DE LAS ALGAS DE NUEVO LEÓN Comité de Tesis Presidente: Dr. Sergio Manuel Salcedo Martínez. Secretario: Dr. Sergio Moreno Limón. Vocal 1: Hugo Alberto Luna Olvera. Vocal 2: Dr. Marco Antonio Alvarado Vázquez. Vocal 3: Dra. Alejandra Rocha Estrada. TAXONOMÍA, DISTRIBUCIÓN E IMPORTANCIA DE LAS ALGAS DE NUEVO LEÓN Dirección de Tesis Director: Dr. Sergio Manuel Salcedo Martínez. AGRADECIMIENTOS A Dios, por guiar siempre mis pasos y darme fortaleza ante las dificultades. Al Dr. Sergio Manuel Salcedo Martínez, por su disposición para participar como director de este proyecto, por sus consejos y enseñanzas que siempre tendré presente tanto en mi vida profesional como personal; pero sobre todo por su dedicación, paciencia y comprensión que hicieron posible la realización de este trabajo. A la Dra. Alejandra Rocha Estrada, El Dr. Marco Antonio Alvarado Vázquez, el Dr. Sergio Moreno Limón y el Dr. Hugo Alberto Luna Olvera por su apoyo y aportaciones para la realización de este trabajo. Al Dr. Eberto Novelo, por sus valiosas aportaciones para enriquecer el listado taxonómico. A la M.C. Cecilia Galicia Campos, gracias Cecy, por hacer tan amena la estancia en el laboratorio y en el Herbario; por esas pláticas interminables y esas “riso terapias” que siempre levantaban el ánimo. A mis entrañables amigos, “los biólogos”, “los cacos”: Brenda, Libe, Lula, Samy, David, Gera, Pancho, Reynaldo y Ricardo.
  • Patrons De Biodiversité À L'échelle Globale Chez Les Dinoflagellés

    Patrons De Biodiversité À L'échelle Globale Chez Les Dinoflagellés

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emerciements* ! Remerciements* A!l'issue!de!ce!travail!de!recherche!et!de!sa!rédaction,!j’ai!la!preuve!que!la!thèse!est!loin!d'être!un!travail! solitaire.! En! effet,! je! n'aurais! jamais! pu! réaliser! ce! travail! doctoral! sans! le! soutien! d'un! grand! nombre! de! personnes!dont!l’amitié,!la!générosité,!la!bonne!humeur%et%l'intérêt%manifestés%à%l'égard%de%ma%recherche%m'ont% permis!de!progresser!dans!cette!phase!délicate!de!«!l'apprentiGchercheur!».!
  • Protistology Mitochondrial Genomes of Amoebozoa

    Protistology Mitochondrial Genomes of Amoebozoa

    Protistology 13 (4), 179–191 (2019) Protistology Mitochondrial genomes of Amoebozoa Natalya Bondarenko1, Alexey Smirnov1, Elena Nassonova1,2, Anna Glotova1,2 and Anna Maria Fiore-Donno3 1 Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia 2 Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS, 194064 Saint Petersburg, Russia 3 University of Cologne, Institute of Zoology, Terrestrial Ecology, 50674 Cologne, Germany | Submitted November 28, 2019 | Accepted December 10, 2019 | Summary In this mini-review, we summarize the current knowledge on mitochondrial genomes of Amoebozoa. Amoebozoa is a major, early-diverging lineage of eukaryotes, containing at least 2,400 species. At present, 32 mitochondrial genomes belonging to 18 amoebozoan species are publicly available. A dearth of information is particularly obvious for two major amoebozoan clades, Variosea and Tubulinea, with just one mitochondrial genome sequenced for each. The main focus of this review is to summarize features such as mitochondrial gene content, mitochondrial genome size variation, and presence or absence of RNA editing, showing if they are unique or shared among amoebozoan lineages. In addition, we underline the potential of mitochondrial genomes for multigene phylogenetic reconstruction in Amoebozoa, where the relationships among lineages are not fully resolved yet. With the increasing application of next-generation sequencing techniques and reliable protocols, we advocate mitochondrial
  • Sex Is a Ubiquitous, Ancient, and Inherent Attribute of Eukaryotic Life

    Sex Is a Ubiquitous, Ancient, and Inherent Attribute of Eukaryotic Life

    PAPER Sex is a ubiquitous, ancient, and inherent attribute of COLLOQUIUM eukaryotic life Dave Speijera,1, Julius Lukešb,c, and Marek Eliášd,1 aDepartment of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands; bInstitute of Parasitology, Biology Centre, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, 370 05 Ceské Budejovice, Czech Republic; cCanadian Institute for Advanced Research, Toronto, ON, Canada M5G 1Z8; and dDepartment of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic Edited by John C. Avise, University of California, Irvine, CA, and approved April 8, 2015 (received for review February 14, 2015) Sexual reproduction and clonality in eukaryotes are mostly Sex in Eukaryotic Microorganisms: More Voyeurs Needed seen as exclusive, the latter being rather exceptional. This view Whereas absence of sex is considered as something scandalous for might be biased by focusing almost exclusively on metazoans. a zoologist, scientists studying protists, which represent the ma- We analyze and discuss reproduction in the context of extant jority of extant eukaryotic diversity (2), are much more ready to eukaryotic diversity, paying special attention to protists. We accept that a particular eukaryotic group has not shown any evi- present results of phylogenetically extended searches for ho- dence of sexual processes. Although sex is very well documented mologs of two proteins functioning in cell and nuclear fusion, in many protist groups, and members of some taxa, such as ciliates respectively (HAP2 and GEX1), providing indirect evidence for (Alveolata), diatoms (Stramenopiles), or green algae (Chlor- these processes in several eukaryotic lineages where sex has oplastida), even serve as models to study various aspects of sex- – not been observed yet.
  • University of Oklahoma

    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.
  • Multigene Eukaryote Phylogeny Reveals the Likely Protozoan Ancestors of Opis- Thokonts (Animals, Fungi, Choanozoans) and Amoebozoa

    Multigene Eukaryote Phylogeny Reveals the Likely Protozoan Ancestors of Opis- Thokonts (Animals, Fungi, Choanozoans) and Amoebozoa

    Accepted Manuscript Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opis- thokonts (animals, fungi, choanozoans) and Amoebozoa Thomas Cavalier-Smith, Ema E. Chao, Elizabeth A. Snell, Cédric Berney, Anna Maria Fiore-Donno, Rhodri Lewis PII: S1055-7903(14)00279-6 DOI: http://dx.doi.org/10.1016/j.ympev.2014.08.012 Reference: YMPEV 4996 To appear in: Molecular Phylogenetics and Evolution Received Date: 24 January 2014 Revised Date: 2 August 2014 Accepted Date: 11 August 2014 Please cite this article as: Cavalier-Smith, T., Chao, E.E., Snell, E.A., Berney, C., Fiore-Donno, A.M., Lewis, R., Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa, Molecular Phylogenetics and Evolution (2014), doi: http://dx.doi.org/10.1016/ j.ympev.2014.08.012 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. 1 1 Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts 2 (animals, fungi, choanozoans) and Amoebozoa 3 4 Thomas Cavalier-Smith1, Ema E. Chao1, Elizabeth A. Snell1, Cédric Berney1,2, Anna Maria 5 Fiore-Donno1,3, and Rhodri Lewis1 6 7 1Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
  • A Revised Classification of Naked Lobose Amoebae (Amoebozoa

    A Revised Classification of Naked Lobose Amoebae (Amoebozoa

    Protist, Vol. 162, 545–570, October 2011 http://www.elsevier.de/protis Published online date 28 July 2011 PROTIST NEWS A Revised Classification of Naked Lobose Amoebae (Amoebozoa: Lobosa) Introduction together constitute the amoebozoan subphy- lum Lobosa, which never have cilia or flagella, Molecular evidence and an associated reevaluation whereas Variosea (as here revised) together with of morphology have recently considerably revised Mycetozoa and Archamoebea are now grouped our views on relationships among the higher-level as the subphylum Conosa, whose constituent groups of amoebae. First of all, establishing the lineages either have cilia or flagella or have lost phylum Amoebozoa grouped all lobose amoe- them secondarily (Cavalier-Smith 1998, 2009). boid protists, whether naked or testate, aerobic Figure 1 is a schematic tree showing amoebozoan or anaerobic, with the Mycetozoa and Archamoe- relationships deduced from both morphology and bea (Cavalier-Smith 1998), and separated them DNA sequences. from both the heterolobosean amoebae (Page and The first attempt to construct a congruent molec- Blanton 1985), now belonging in the phylum Per- ular and morphological system of Amoebozoa by colozoa - Cavalier-Smith and Nikolaev (2008), and Cavalier-Smith et al. (2004) was limited by the the filose amoebae that belong in other phyla lack of molecular data for many amoeboid taxa, (notably Cercozoa: Bass et al. 2009a; Howe et al. which were therefore classified solely on morpho- 2011). logical evidence. Smirnov et al. (2005) suggested The phylum Amoebozoa consists of naked and another system for naked lobose amoebae only; testate lobose amoebae (e.g. Amoeba, Vannella, this left taxa with no molecular data incertae sedis, Hartmannella, Acanthamoeba, Arcella, Difflugia), which limited its utility.
  • Resource Partitioning Between Phytoplankton and Bacteria in the Coastal Baltic Sea Frontiers in Marine Science, 7: 1-19

    Resource Partitioning Between Phytoplankton and Bacteria in the Coastal Baltic Sea Frontiers in Marine Science, 7: 1-19

    http://www.diva-portal.org This is the published version of a paper published in Frontiers in Marine Science. Citation for the original published paper (version of record): Sörenson, E., Lindehoff, E., Farnelid, H., Legrand, C. (2020) Resource Partitioning Between Phytoplankton and Bacteria in the Coastal Baltic Sea Frontiers in Marine Science, 7: 1-19 https://doi.org/10.3389/fmars.2020.608244 Access to the published version may require subscription. N.B. When citing this work, cite the original published paper. Permanent link to this version: http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-99520 ORIGINAL RESEARCH published: 25 November 2020 doi: 10.3389/fmars.2020.608244 Resource Partitioning Between Phytoplankton and Bacteria in the Coastal Baltic Sea Eva Sörenson, Hanna Farnelid, Elin Lindehoff and Catherine Legrand* Department of Biology and Environmental Science, Linnaeus University Centre of Ecology and Evolution and Microbial Model Systems, Linnaeus University, Kalmar, Sweden Eutrophication coupled to climate change disturbs the balance between competition and coexistence in microbial communities including the partitioning of organic and inorganic nutrients between phytoplankton and bacteria. Competition for inorganic nutrients has been regarded as one of the drivers affecting the productivity of the eutrophied coastal Baltic Sea. Yet, it is unknown at the molecular expression level how resources are competed for, by phytoplankton and bacteria, and what impact this competition has on the community composition. Here we use metatranscriptomics and amplicon sequencing and compare known metabolic pathways of both phytoplankton and bacteria co-occurring during a summer bloom in the archipelago of Åland in the Baltic Sea to examine phytoplankton bacteria resource partitioning.
  • Ciliate Diversity, Community Structure, and Novel Taxa in Lakes of the Mcmurdo Dry Valleys, Antarctica

    Ciliate Diversity, Community Structure, and Novel Taxa in Lakes of the Mcmurdo Dry Valleys, Antarctica

    Reference: Biol. Bull. 227: 175–190. (October 2014) © 2014 Marine Biological Laboratory Ciliate Diversity, Community Structure, and Novel Taxa in Lakes of the McMurdo Dry Valleys, Antarctica YUAN XU1,*†, TRISTA VICK-MAJORS2, RACHAEL MORGAN-KISS3, JOHN C. PRISCU2, AND LINDA AMARAL-ZETTLER4,5,*࿣ 1Laboratory of Protozoology, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China; 2Montana State University, Department of Land Resources and Environmental Sciences, 334 Leon Johnson Hall, Bozeman, Montana 59717; 3Department of Microbiology, Miami University, Oxford, Ohio 45056; 4The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543; and 5Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, Rhode Island 02912 Abstract. We report an in-depth survey of next-genera- trends in dissolved oxygen concentration and salinity may tion DNA sequencing of ciliate diversity and community play a critical role in structuring ciliate communities. A structure in two permanently ice-covered McMurdo Dry PCR-based strategy capitalizing on divergent eukaryotic V9 Valley lakes during the austral summer and autumn (No- hypervariable region ribosomal RNA gene targets unveiled vember 2007 and March 2008). We tested hypotheses on the two new genera in these lakes. A novel taxon belonging to relationship between species richness and environmental an unknown class most closely related to Cryptocaryon conditions
  • Molecular Identification of Fungi

    Molecular Identification of Fungi

    Molecular Identification of Fungi Youssuf Gherbawy l Kerstin Voigt Editors Molecular Identification of Fungi Editors Prof. Dr. Youssuf Gherbawy Dr. Kerstin Voigt South Valley University University of Jena Faculty of Science School of Biology and Pharmacy Department of Botany Institute of Microbiology 83523 Qena, Egypt Neugasse 25 [email protected] 07743 Jena, Germany [email protected] ISBN 978-3-642-05041-1 e-ISBN 978-3-642-05042-8 DOI 10.1007/978-3-642-05042-8 Springer Heidelberg Dordrecht London New York Library of Congress Control Number: 2009938949 # Springer-Verlag Berlin Heidelberg 2010 This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Cover design: WMXDesign GmbH, Heidelberg, Germany, kindly supported by ‘leopardy.com’ Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Dedicated to Prof. Lajos Ferenczy (1930–2004) microbiologist, mycologist and member of the Hungarian Academy of Sciences, one of the most outstanding Hungarian biologists of the twentieth century Preface Fungi comprise a vast variety of microorganisms and are numerically among the most abundant eukaryotes on Earth’s biosphere.