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Functional Traits and Spatio-Temporal Structure of a Major Group of Soil Protists (Rhizaria: Cercozoa) in a Temperate Grassland
fmicb-10-01332 June 8, 2019 Time: 10:19 # 1 ORIGINAL RESEARCH published: 11 June 2019 doi: 10.3389/fmicb.2019.01332 Functional Traits and Spatio-Temporal Structure of a Major Group of Soil Protists (Rhizaria: Cercozoa) in a Temperate Grassland Anna Maria Fiore-Donno1,2*, Tim Richter-Heitmann3, Florine Degrune4,5, Kenneth Dumack1,2, Kathleen M. Regan6, Sven Marhan7, Runa S. Boeddinghaus7, Matthias C. Rillig4,5, Michael W. Friedrich3, Ellen Kandeler7 and Michael Bonkowski1,2 1 Terrestrial Ecology Group, Institute of Zoology, University of Cologne, Cologne, Germany, 2 Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany, 3 Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany, 4 Institute of Biology, Plant Ecology, Freie Universität Berlin, Berlin, Germany, 5 Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany, 6 The Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA, United States, 7 Department of Soil Biology, Institute of Soil Science and Land Evaluation, University of Hohenheim, Stuttgart, Germany Edited by: Soil protists are increasingly appreciated as essential components of soil foodwebs; Jaak Truu, University of Tartu, Estonia however, there is a dearth of information on the factors structuring their communities. Reviewed by: Here we investigate the importance of different biotic and abiotic factors as key Anne Winding, drivers of spatial and seasonal distribution of protistan communities. We conducted Aarhus University, Denmark 2 Ida Karlsson, an intensive survey of a 10 m grassland plot in Germany, focusing on a major group Swedish University of Agricultural of protists, the Cercozoa. From 177 soil samples, collected from April to November, Sciences, Sweden we obtained 694 Operational Taxonomy Units representing 6 million Illumina reads. -
Rare Phytomyxid Infection on the Alien Seagrass Halophila Stipulacea In
Research Article Mediterranean Marine Science Indexed in WoS (Web of Science, ISI Thomson) and SCOPUS The journal is available on line at http://www.medit-mar-sc.net DOI: http://dx.doi.org/10.12681/mms.14053 Rare phytomyxid infection on the alien seagrass Halophila stipulacea in the southeast Aegean Sea MARTIN VOHNÍK1,2, ONDŘEJ BOROVEC1,2, ELIF ÖZGÜR ÖZBEK3 and EMINE ŞÜKRAN OKUDAN ASLAN4 1 Department of Mycorrhizal Symbioses, Institute of Botany, Czech Academy of Sciences, Průhonice, 25243 Czech Republic 2 Department of Plant Experimental Biology, Faculty of Science, Charles University, Prague, 12844 Czech Republic 3 Marine Biology Museum, Antalya Metropolitan Municipality, Antalya, Turkey 4 Department of Marine Biology, Faculty of Fisheries, Akdeniz University, Antalya, Turkey Corresponding author: [email protected] Handling Editor: Athanasios Athanasiadis Received: 31 May 2017; Accepted: 9 October 2017; Published on line: 8 December 2017 Abstract Phytomyxids (Phytomyxea) are obligate endosymbionts of many organisms such as algae, diatoms, oomycetes and higher plants including seagrasses. Despite their supposed significant roles in the marine ecosystem, our knowledge of their marine diversity and distribution as well as their life cycles is rather limited. Here we describe the anatomy and morphology of several developmental stages of a phytomyxid symbiosis recently discovered on the petioles of the alien seagrass Halophila stipulacea at a locality in the southeast Aegean Sea. Its earliest stage appeared as whitish spots already on the youngest leaves at the apex of the newly formed rhizomes. The infected host cells grew in volume being filled with plasmodia which resulted in the formation of characteristic macroscopic galls. -
Protist Phylogeny and the High-Level Classification of Protozoa
Europ. J. Protistol. 39, 338–348 (2003) © Urban & Fischer Verlag http://www.urbanfischer.de/journals/ejp Protist phylogeny and the high-level classification of Protozoa Thomas Cavalier-Smith Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK; E-mail: [email protected] Received 1 September 2003; 29 September 2003. Accepted: 29 September 2003 Protist large-scale phylogeny is briefly reviewed and a revised higher classification of the kingdom Pro- tozoa into 11 phyla presented. Complementary gene fusions reveal a fundamental bifurcation among eu- karyotes between two major clades: the ancestrally uniciliate (often unicentriolar) unikonts and the an- cestrally biciliate bikonts, which undergo ciliary transformation by converting a younger anterior cilium into a dissimilar older posterior cilium. Unikonts comprise the ancestrally unikont protozoan phylum Amoebozoa and the opisthokonts (kingdom Animalia, phylum Choanozoa, their sisters or ancestors; and kingdom Fungi). They share a derived triple-gene fusion, absent from bikonts. Bikonts contrastingly share a derived gene fusion between dihydrofolate reductase and thymidylate synthase and include plants and all other protists, comprising the protozoan infrakingdoms Rhizaria [phyla Cercozoa and Re- taria (Radiozoa, Foraminifera)] and Excavata (phyla Loukozoa, Metamonada, Euglenozoa, Percolozoa), plus the kingdom Plantae [Viridaeplantae, Rhodophyta (sisters); Glaucophyta], the chromalveolate clade, and the protozoan phylum Apusozoa (Thecomonadea, Diphylleida). Chromalveolates comprise kingdom Chromista (Cryptista, Heterokonta, Haptophyta) and the protozoan infrakingdom Alveolata [phyla Cilio- phora and Miozoa (= Protalveolata, Dinozoa, Apicomplexa)], which diverged from a common ancestor that enslaved a red alga and evolved novel plastid protein-targeting machinery via the host rough ER and the enslaved algal plasma membrane (periplastid membrane). -
The Revised Classification of Eukaryotes
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/231610049 The Revised Classification of Eukaryotes Article in Journal of Eukaryotic Microbiology · September 2012 DOI: 10.1111/j.1550-7408.2012.00644.x · Source: PubMed CITATIONS READS 961 2,825 25 authors, including: Sina M Adl Alastair Simpson University of Saskatchewan Dalhousie University 118 PUBLICATIONS 8,522 CITATIONS 264 PUBLICATIONS 10,739 CITATIONS SEE PROFILE SEE PROFILE Christopher E Lane David Bass University of Rhode Island Natural History Museum, London 82 PUBLICATIONS 6,233 CITATIONS 464 PUBLICATIONS 7,765 CITATIONS SEE PROFILE SEE PROFILE Some of the authors of this publication are also working on these related projects: Biodiversity and ecology of soil taste amoeba View project Predator control of diversity View project All content following this page was uploaded by Smirnov Alexey on 25 October 2017. The user has requested enhancement of the downloaded file. The Journal of Published by the International Society of Eukaryotic Microbiology Protistologists J. Eukaryot. Microbiol., 59(5), 2012 pp. 429–493 © 2012 The Author(s) Journal of Eukaryotic Microbiology © 2012 International Society of Protistologists DOI: 10.1111/j.1550-7408.2012.00644.x The Revised Classification of Eukaryotes SINA M. ADL,a,b ALASTAIR G. B. SIMPSON,b CHRISTOPHER E. LANE,c JULIUS LUKESˇ,d DAVID BASS,e SAMUEL S. BOWSER,f MATTHEW W. BROWN,g FABIEN BURKI,h MICAH DUNTHORN,i VLADIMIR HAMPL,j AARON HEISS,b MONA HOPPENRATH,k ENRIQUE LARA,l LINE LE GALL,m DENIS H. LYNN,n,1 HILARY MCMANUS,o EDWARD A. D. -
A Functional Approach to Resolving the Biogeocomplexity of Two Extreme Environments Haydn Rubelmann III University of South Florida, [email protected]
University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School 11-12-2014 A Functional Approach to Resolving the Biogeocomplexity of Two Extreme Environments Haydn Rubelmann III University of South Florida, [email protected] Follow this and additional works at: https://scholarcommons.usf.edu/etd Part of the Marine Biology Commons, and the Microbiology Commons Scholar Commons Citation Rubelmann, Haydn III, "A Functional Approach to Resolving the Biogeocomplexity of Two Extreme Environments" (2014). Graduate Theses and Dissertations. https://scholarcommons.usf.edu/etd/5432 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. A Functional Approach to Resolving the Biogeocomplexity of Two Extreme Environments by Haydn Rubelmann III A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Cell Biology, Microbiology and Molecular Biology College of Arts and Sciences University of South Florida Major Professor: James R. Garey, Ph.D. Randy Larsen, Ph.D. Kathleen Scott, Ph.D. David Merkler, Ph.D. Date of Approval: November 12, 2014 Keywords: environmental microbiology, extremophiles, shallow-water hydrothermal vents, anoxic marine pits Copyright © 2014, Haydn Rubelmann III DEDICATION I would like to dedicate this dissertation to three of my personal champions: my grandfather, Haydn Rubelmann Sr. (1929 - 2004), who encouraged me to pursue an academic career; my stepfather, Dale Jones (1954 - 2008), who was the best father anyone could ever hope for, and my husband, Eduardo Godoy, who suffered through not only 8 years of my doctoral tenure, but a grueling civil liberty injustice that almost wedged the Caribbean Sea between us. -
Studies of Pathogenicity in Plasmodiophora Brassicae and Segregation of Clubroot Resistance Genes from Brassica Rapa Subsp
Studies of pathogenicity in Plasmodiophora brassicae and segregation of clubroot resistance genes from Brassica rapa subsp. rapifera by Junye Jiang A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Plant Science Department of Agricultural, Food and Nutritional Science University of Alberta © Junye Jiang, 2020 Abstract The planting of clubroot resistant (CR) canola (Brassica napus) is the most effective method to manage clubroot, a soilborne disease caused by Plasmodiophora brassicae. In recent years, many P. brassicae isolates capable of overcoming resistance have been detected, often in mixtures with avirulent isolates. To improve understanding of the effect of low concentrations of virulent isolates on host resistance, three CR canola cultivars (‘45H29’, ‘L135C’ and ‘L241C’) were inoculated with pairs of isolates representing virulent/avirulent pathotypes (2*/2, 3*/3 and 5*/5) of P. brassicae, collected after or before the introduction of CR canola, respectively. Clubroot severity was significantly higher in all nine experimental treatments (low virulent + high avirulent) than in the negative control NC1 (high avirulent), and higher in seven of nine experimental treatments than in the negative control NC2 (low virulent). Disease severity was positively correlated with P. brassicae biomass in planta, as determined by quantitative PCR analysis 28 - 35 days after inoculation (dai). These results suggest that low concentrations of virulent isolates compromised the clubroot resistance in canola, facilitating infection by avirulent isolates. In a second study, the expression of 205 P. brassicae genes encoding putative secreted proteins was compared following inoculation of the canola ‘45H29’ with pathotypes 5I (avirulent) and 5X (virulent) of the pathogen. -
Phylogenomics Supports the Monophyly of the Cercozoa T ⁎ Nicholas A.T
Molecular Phylogenetics and Evolution 130 (2019) 416–423 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Phylogenomics supports the monophyly of the Cercozoa T ⁎ Nicholas A.T. Irwina, , Denis V. Tikhonenkova,b, Elisabeth Hehenbergera,1, Alexander P. Mylnikovb, Fabien Burkia,2, Patrick J. Keelinga a Department of Botany, University of British Columbia, Vancouver V6T 1Z4, British Columbia, Canada b Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia ARTICLE INFO ABSTRACT Keywords: The phylum Cercozoa consists of a diverse assemblage of amoeboid and flagellated protists that forms a major Cercozoa component of the supergroup, Rhizaria. However, despite its size and ubiquity, the phylogeny of the Cercozoa Rhizaria remains unclear as morphological variability between cercozoan species and ambiguity in molecular analyses, Phylogeny including phylogenomic approaches, have produced ambiguous results and raised doubts about the monophyly Phylogenomics of the group. Here we sought to resolve these ambiguities using a 161-gene phylogenetic dataset with data from Single-cell transcriptomics newly available genomes and deeply sequenced transcriptomes, including three new transcriptomes from Aurigamonas solis, Abollifer prolabens, and a novel species, Lapot gusevi n. gen. n. sp. Our phylogenomic analysis strongly supported a monophyletic Cercozoa, and approximately-unbiased tests rejected the paraphyletic topologies observed in previous studies. The transcriptome of L. gusevi represents the first transcriptomic data from the large and recently characterized Aquavolonidae-Treumulida-'Novel Clade 12′ group, and phyloge- nomics supported its position as sister to the cercozoan subphylum, Endomyxa. These results provide insights into the phylogeny of the Cercozoa and the Rhizaria as a whole. -
Author's Manuscript (764.7Kb)
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. -
Complex Communities of Small Protists and Unexpected Occurrence Of
Complex communities of small protists and unexpected occurrence of typical marine lineages in shallow freshwater systems Marianne Simon, Ludwig Jardillier, Philippe Deschamps, David Moreira, Gwendal Restoux, Paola Bertolino, Purificación López-García To cite this version: Marianne Simon, Ludwig Jardillier, Philippe Deschamps, David Moreira, Gwendal Restoux, et al.. Complex communities of small protists and unexpected occurrence of typical marine lineages in shal- low freshwater systems. Environmental Microbiology, Society for Applied Microbiology and Wiley- Blackwell, 2015, 17 (10), pp.3610-3627. 10.1111/1462-2920.12591. hal-03022575 HAL Id: hal-03022575 https://hal.archives-ouvertes.fr/hal-03022575 Submitted on 24 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Europe PMC Funders Group Author Manuscript Environ Microbiol. Author manuscript; available in PMC 2015 October 26. Published in final edited form as: Environ Microbiol. 2015 October ; 17(10): 3610–3627. doi:10.1111/1462-2920.12591. Europe PMC Funders Author Manuscripts Complex communities of small protists and unexpected occurrence of typical marine lineages in shallow freshwater systems Marianne Simon, Ludwig Jardillier, Philippe Deschamps, David Moreira, Gwendal Restoux, Paola Bertolino, and Purificación López-García* Unité d’Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, 91405 Orsay, France Summary Although inland water bodies are more heterogeneous and sensitive to environmental variation than oceans, the diversity of small protists in these ecosystems is much less well-known. -
That Is Missing from Sequence Databases
Reticulamoeba Is a Long-Branched Granofilosean (Cercozoa) That Is Missing from Sequence Databases David Bass1*, Akinori Yabuki2¤,Se´bastien Santini3, Sarah Romac4,Ce´dric Berney1 1 Department of Life Sciences, The Natural History Museum, London, United Kingdom, 2 Department of Zoology, University of Oxford, Oxford, United Kingdom, 3 Structural and Genomic Information Laboratory, CNRS, UMR 7256, Mediterranean Institute of Microbiology, Aix-Marseille University, Marseille, France, 4 CNRS, UMR 7144, Equipe Evolution du Plancton et Paleo-Oceans, Roscoff, France Abstract We sequenced the 18S ribosomal RNA gene of seven isolates of the enigmatic marine amoeboflagellate Reticulamoeba Grell, which resolved into four genetically distinct Reticulamoeba lineages, two of which correspond to R. gemmipara Grell and R. minor Grell, another with a relatively large cell body forming lacunae, and another that has similarities to both R. minor and R. gemmipara but with a greater propensity to form cell clusters. These lineages together form a long-branched clade that branches within the cercozoan class Granofilosea (phylum Cercozoa), showing phylogenetic affinities with the genus Mesofila. The basic morphology of Reticulamoeba is a roundish or ovoid cell with a more or less irregular outline. Long and branched reticulopodia radiate from the cell. The reticulopodia bear granules that are bidirectionally motile. There is also a biflagellate dispersal stage. Reticulamoeba is frequently observed in coastal marine environmental samples. PCR primers specific to the Reticulamoeba clade confirm that it is a frequent member of benthic marine microbial communities, and is also found in brackish water sediments and freshwater biofilm. However, so far it has not been found in large molecular datasets such as the nucleotide database in NCBI GenBank, metagenomic datasets in Camera, and the marine microbial eukaryote sampling and sequencing consortium BioMarKs, although closely related lineages can be found in some of these datasets using a highly targeted approach. -
Marteilia Refringens and Marteilia Pararefringens Sp
Parasitology Marteilia refringens and Marteilia pararefringens sp. nov. are distinct parasites cambridge.org/par of bivalves and have different European distributions Research Article 1,2 1,2,3 1 4 5 Cite this article: Kerr R et al (2018). Marteilia R. Kerr , G. M. Ward , G. D. Stentiford , A. Alfjorden , S. Mortensen , refringens and Marteilia pararefringens sp. nov. J. P. Bignell1,S.W.Feist1, A. Villalba6,7, M. J. Carballal6, A. Cao6, I. Arzul8, are distinct parasites of bivalves and have different European distributions. Parasitology D. Ryder1 and D. Bass1,3 145, 1483–1492. https://doi.org/10.1017/ S003118201800063X 1Pathology and Microbial Systematics Theme, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth Laboratory, Weymouth, Dorset DT4 8UB, UK; 2Biosciences, College of Life and Environmental Sciences, Received: 19 July 2017 3 Revised: 16 January 2018 Stocker Road, University of Exeter, Exeter EX4 4QD, UK; Department of Life Sciences, The Natural History 4 Accepted: 8 February 2018 Museum, Cromwell Road, SW7 5BD, London, UK; Division of fish, Department of animal health and antimicrobial First published online: 11 June 2018 strategies, National Veterinary Institute (SVA), Sweden; 5Institute of Marine Research, PO. Box 1870, Nordnes, 5817 Bergen, Norway; 6Centro de Investigacións Mariñas, Consellería do Mar da Xunta de Galicia, 36620 Vilanova de Key words: Arousa, Spain; 7Department of Life Sciences, University of Alcalá, 28871 Alcalá de Henares, Spain and 8Institut Marteilia refringens; Marteilia pararefringens; Français de Recherche pour l’Exploitation de la Mer (Ifremer), Laboratoire de Génétique et Pathologie des ITS1 rDNA; IGS rDNA; Paramyxida; Mollusques Marins, Avenue de Mus de Loup, 17390 La Tremblade, France Ascetosporea; Mytilus edulis; Ostrea edulis Author for correspondence: Abstract Grant D. -
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).