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Unfolding the Secrets of Coral–Algal Symbiosis
The ISME Journal (2015) 9, 844–856 & 2015 International Society for Microbial Ecology All rights reserved 1751-7362/15 www.nature.com/ismej ORIGINAL ARTICLE Unfolding the secrets of coral–algal symbiosis Nedeljka Rosic1, Edmund Yew Siang Ling2, Chon-Kit Kenneth Chan3, Hong Ching Lee4, Paulina Kaniewska1,5,DavidEdwards3,6,7,SophieDove1,8 and Ove Hoegh-Guldberg1,8,9 1School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia; 2University of Queensland Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia; 3School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, Australia; 4The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; 5Australian Institute of Marine Science, Townsville, Queensland, Australia; 6School of Plant Biology, University of Western Australia, Perth, Western Australia, Australia; 7Australian Centre for Plant Functional Genomics, The University of Queensland, St Lucia, Queensland, Australia; 8ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, Queensland, Australia and 9Global Change Institute and ARC Centre of Excellence for Coral Reef Studies, The University of Queensland, St Lucia, Queensland, Australia Dinoflagellates from the genus Symbiodinium form a mutualistic symbiotic relationship with reef- building corals. Here we applied massively parallel Illumina sequencing to assess genetic similarity and diversity among four phylogenetically diverse dinoflagellate clades (A, B, C and D) that are commonly associated with corals. We obtained more than 30 000 predicted genes for each Symbiodinium clade, with a majority of the aligned transcripts corresponding to sequence data sets of symbiotic dinoflagellates and o2% of sequences having bacterial or other foreign origin. -
<I>Chlorella</I> Strain
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Kenneth Nickerson Papers Papers in the Biological Sciences 7-2016 Comparative genomics, transcriptomics, and physiology distinguish symbiotic from free-living Chlorella strains Cristian F. Quispe University of Nebraska-Lincoln, [email protected] Olivia Sonderman University of Nebraska–Lincoln Maya Khasin University of Nebraska–Lincoln, [email protected] Wayne R. Riekhof University of Nebraska–Lincoln, [email protected] James L. Van Etten University of Nebraska-Lincoln, [email protected] SeFoe nelloxtw pa thige fors aaddndition addal aitutionhorsal works at: https://digitalcommons.unl.edu/bioscinickerson Part of the Computational Biology Commons, Environmental Microbiology and Microbial Ecology Commons, Genomics Commons, Marine Biology Commons, Molecular Genetics Commons, Other Genetics and Genomics Commons, Other Life Sciences Commons, Pathogenic Microbiology Commons, and the Plant Pathology Commons Quispe, Cristian F.; Sonderman, Olivia; Khasin, Maya; Riekhof, Wayne R.; Van Etten, James L.; and Nickerson, Kenneth, "Comparative genomics, transcriptomics, and physiology distinguish symbiotic from free-living Chlorella strains" (2016). Kenneth Nickerson Papers. 15. https://digitalcommons.unl.edu/bioscinickerson/15 This Article is brought to you for free and open access by the Papers in the Biological Sciences at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Kenneth Nickerson Papers by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James L. Van Etten, and Kenneth Nickerson This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/bioscinickerson/15 Published in Algal Research 18 (2016), pp 332–340. doi 10.1016/j.algal.2016.06.001 Copyright © 2016 Elsevier B.V. -
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. -
Symbiodinium Genomes Reveal Adaptive Evolution of Functions Related to Symbiosis
bioRxiv preprint doi: https://doi.org/10.1101/198762; this version posted October 5, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Article 2 Symbiodinium genomes reveal adaptive evolution of 3 functions related to symbiosis 4 Huanle Liu1, Timothy G. Stephens1, Raúl A. González-Pech1, Victor H. Beltran2, Bruno 5 Lapeyre3,4, Pim Bongaerts5, Ira Cooke3, David G. Bourne2,6, Sylvain Forêt7,*, David J. 6 Miller3, Madeleine J. H. van Oppen2,8, Christian R. Voolstra9, Mark A. Ragan1 and Cheong 7 Xin Chan1,10,† 8 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, 9 Australia 10 2Australian Institute of Marine Science, Townsville, QLD 4810, Australia 11 3ARC Centre of Excellence for Coral Reef Studies and Department of Molecular and Cell 12 Biology, James Cook University, Townsville, QLD 4811, Australia 13 4Laboratoire d’excellence CORAIL, Centre de Recherches Insulaires et Observatoire de 14 l’Environnement, Moorea 98729, French Polynesia 15 5Global Change Institute, The University of Queensland, Brisbane, QLD 4072, Australia 16 6College of Science and Engineering, James Cook University, Townsville, QLD 4811, 17 Australia 18 7Research School of Biology, Australian National University, Canberra, ACT 2601, Australia 19 8School of BioSciences, The University of Melbourne, VIC 3010, Australia 1 bioRxiv preprint doi: https://doi.org/10.1101/198762; this version posted October 5, 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. -
The Symbiotic Life of Symbiodinium in the Open Ocean Within a New Species of Calcifying Ciliate (Tiarina Sp.)
The ISME Journal (2016) 10, 1424–1436 © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.) Solenn Mordret1,2,5, Sarah Romac1,2, Nicolas Henry1,2, Sébastien Colin1,2, Margaux Carmichael1,2, Cédric Berney1,2, Stéphane Audic1,2, Daniel J Richter1,2, Xavier Pochon3,4, Colomban de Vargas1,2 and Johan Decelle1,2,6 1EPEP—Evolution des Protistes et des Ecosystèmes Pélagiques—team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Roscoff, France; 2CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France; 3Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand and 4Institute of Marine Science, University of Auckland, Auckland, New Zealand Symbiotic partnerships between heterotrophic hosts and intracellular microalgae are common in tropical and subtropical oligotrophic waters of benthic and pelagic marine habitats. The iconic example is the photosynthetic dinoflagellate genus Symbiodinium that establishes mutualistic symbioses with a wide diversity of benthic hosts, sustaining highly biodiverse reef ecosystems worldwide. Paradoxically, although various species of photosynthetic dinoflagellates are prevalent eukaryotic symbionts in pelagic waters, Symbiodinium has not yet been reported in symbiosis within oceanic plankton, despite its high propensity for the symbiotic lifestyle. Here we report a new pelagic photosymbiosis between a calcifying ciliate host and the microalga Symbiodinium in surface ocean waters. Confocal and scanning electron microscopy, together with an 18S rDNA-based phylogeny, showed that the host is a new ciliate species closely related to Tiarina fusus (Colepidae). -
Pusillus Poseidon's Guide to Protozoa
Pusillus Poseidon’s guide to PROTOZOA GENERAL NOTES ABOUT PROTOZOANS Protozoa are also called protists. The word “protist” is the more general term and includes all types of single-celled eukaryotes, whereas “protozoa” is more often used to describe the protists that are animal-like (as opposed to plant-like or fungi-like). Protists are measured using units called microns. There are 1000 microns in one millimeter. A millimeter is the smallest unit on a metric ruler and can be estimated with your fingers: The traditional way of classifying protists is by the way they look (morphology), by the way they move (mo- tility), and how and what they eat. This gives us terms such as ciliates, flagellates, ameboids, and all those colors of algae. Recently, the classification system has been overhauled and has become immensely complicated. (Infor- mation about DNA is now the primary consideration for classification, rather than how a creature looks or acts.) If you research these creatures on Wikipedia, you will see this new system being used. Bear in mind, however, that the categories are constantly shifting as we learn more and more about protist DNA. Here is a visual overview that might help you understand the wide range of similarities and differences. Some organisms fit into more than one category and some don’t fit well into any category. Always remember that classification is an artificial construct made by humans. The organisms don’t know anything about it and they don’t care what we think! CILIATES Eats anything smaller than Blepharisma looks slightly pink because it Blepharisma itself, even smaller Bleph- makes a red pigment that senses light (simi- arismas. -
Symbiodinium Genomes Reveal Adaptive Evolution of Functions Related to Coral-Dinoflagellate Symbiosis
Corrected: Publisher correction ARTICLE DOI: 10.1038/s42003-018-0098-3 OPEN Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis Huanle Liu1, Timothy G. Stephens1, Raúl A. González-Pech1, Victor H. Beltran2, Bruno Lapeyre3,4,12, Pim Bongaerts5,6, Ira Cooke4, Manuel Aranda7, David G. Bourne2,8, Sylvain Forêt3,9, David J. Miller3,4, Madeleine J.H. van Oppen2,10, Christian R. Voolstra7, Mark A. Ragan1 & Cheong Xin Chan1,11 1234567890():,; Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world’s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp) to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families (containing 5% of Symbiodinium genes) that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identify extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding of Symbiodinium biology and the coral-algal symbiosis. 1 Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia. 2 Australian Institute of Marine Science, Townsville, QLD 4810, Australia. 3 ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia. -
Volume 19 Winter 2002 the Coral Hind, Lapu Lapu, Or Miniata
FREE ISSN 1045-3520 Volume 19 Winter 2002 Introducing a Zonal Based Natural Photo by Robert Fenner Filtration System for Reef Aquariums by Steve Tyree Quite a few natural based filtration systems have been devised by reef aquarists and scientists in the past twenty years. Some systems utilized algae to remove organic and inorganic pollutants from the reef aquarium; others utilized sediment beds. The natural filtration system that I have been researching and designing is drastically different from both of these types. No external algae are used. I believe that all the algae a functional reef requires are already growing in the reef, even if they are not apparent. They include micro-algae, turf algae, coralline algae, single-cell algae within photosynthetic corals, and cyanobacteria with photosynthetic capabilities. Most of the systems that I have set up to research this concept have not included sediment beds. All organic matter and pollutants are recycled and processed within the system by macro-organisms. Sediment beds have not been utilized to process excess Miniata Grouper, Cephalopholis miniata organic debris, but that does not prevent other aquarists from adding them. The main concept behind my system is the use of living sponges, sea squirts, and filter feeders for filtration. Sponges consume bacteria, can reach about twenty inches in length in the wild, and dissolved and colloidal organic material, micro-plankton, The Coral Hind, Lapu about half that in captivity. It is undoubtedly the most and fine particulate matter. Sea squirts consume large Lapu, or Miniata prized member of the genus for the aquarium trade. -
Genetic Diversity of Symbiotic Green Algae of Paramecium Bursaria Syngens Originating from Distant Geographical Locations
plants Article Genetic Diversity of Symbiotic Green Algae of Paramecium bursaria Syngens Originating from Distant Geographical Locations Magdalena Greczek-Stachura 1, Patrycja Zagata Le´snicka 1, Sebastian Tarcz 2 , Maria Rautian 3 and Katarzyna Mozd˙ ze˙ ´n 1,* 1 Institute of Biology, Pedagogical University of Krakow, Podchor ˛azych˙ 2, 30-084 Kraków, Poland; [email protected] (M.G.-S.); [email protected] (P.Z.L.) 2 Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Krakow, Poland; [email protected] 3 Laboratory of Protistology and Experimental Zoology, Faculty of Biology and Soil Science, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia; [email protected] * Correspondence: [email protected] Abstract: Paramecium bursaria (Ehrenberg 1831) is a ciliate species living in a symbiotic relationship with green algae. The aim of the study was to identify green algal symbionts of P. bursaria originating from distant geographical locations and to answer the question of whether the occurrence of en- dosymbiont taxa was correlated with a specific ciliate syngen (sexually separated sibling group). In a comparative analysis, we investigated 43 P. bursaria symbiont strains based on molecular features. Three DNA fragments were sequenced: two from the nuclear genomes—a fragment of the ITS1-5.8S rDNA-ITS2 region and a fragment of the gene encoding large subunit ribosomal RNA (28S rDNA), Citation: Greczek-Stachura, M.; as well as a fragment of the plastid genome comprising the 30rpl36-50infA genes. The analysis of two Le´snicka,P.Z.; Tarcz, S.; Rautian, M.; Mozd˙ ze´n,K.˙ Genetic Diversity of ribosomal sequences showed the presence of 29 haplotypes (haplotype diversity Hd = 0.98736 for Symbiotic Green Algae of Paramecium ITS1-5.8S rDNA-ITS2 and Hd = 0.908 for 28S rDNA) in the former two regions, and 36 haplotypes 0 0 bursaria Syngens Originating from in the 3 rpl36-5 infA gene fragment (Hd = 0.984). -
23.3 Groups of Protists
Chapter 23 | Protists 639 cysts that are a protective, resting stage. Depending on habitat of the species, the cysts may be particularly resistant to temperature extremes, desiccation, or low pH. This strategy allows certain protists to “wait out” stressors until their environment becomes more favorable for survival or until they are carried (such as by wind, water, or transport on a larger organism) to a different environment, because cysts exhibit virtually no cellular metabolism. Protist life cycles range from simple to extremely elaborate. Certain parasitic protists have complicated life cycles and must infect different host species at different developmental stages to complete their life cycle. Some protists are unicellular in the haploid form and multicellular in the diploid form, a strategy employed by animals. Other protists have multicellular stages in both haploid and diploid forms, a strategy called alternation of generations, analogous to that used by plants. Habitats Nearly all protists exist in some type of aquatic environment, including freshwater and marine environments, damp soil, and even snow. Several protist species are parasites that infect animals or plants. A few protist species live on dead organisms or their wastes, and contribute to their decay. 23.3 | Groups of Protists By the end of this section, you will be able to do the following: • Describe representative protist organisms from each of the six presently recognized supergroups of eukaryotes • Identify the evolutionary relationships of plants, animals, and fungi within the six presently recognized supergroups of eukaryotes • Identify defining features of protists in each of the six supergroups of eukaryotes. In the span of several decades, the Kingdom Protista has been disassembled because sequence analyses have revealed new genetic (and therefore evolutionary) relationships among these eukaryotes. -
New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life
bioRxiv preprint doi: https://doi.org/10.1101/403329; this version posted August 30, 2018. 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. New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life Jürgen F. H. Strassert1, Mahwash Jamy1, Alexander P. Mylnikov2, Denis V. Tikhonenkov2, Fabien Burki1,* 1Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden 2Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Region, Russia *Corresponding author: E-mail: [email protected] Keywords: TSAR, Telonemia, phylogenomics, eukaryotes, tree of life, protists bioRxiv preprint doi: https://doi.org/10.1101/403329; this version posted August 30, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract The broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these ‘orphan’ groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. -
Eighth International Conference on Modern and Fossil Dinoflagellates
0 DINO8 Eighth International Conference on Modern and Fossil Dinoflagellates May 4 to May 10, 2008 Université du Québec à Montréal Complexe des Sciences Pierre Dansereau Building SH, 200 Sherbrooke Street West, Montreal, Quebec, Canada Abstracts 1 TABLE OF CONTENTS ABSTRACTS……………………………………………………………………………………...2 LIST OF PARTICIPANTS………………………………………………………………………66 Organizing commitee Organizers : Anne de Vernal GEOTOP-UQAM, Canada ([email protected]) André Rochon ISMER-UQAR, Canada ([email protected]) Scientific committee: Susan Carty, Heidelberg College, Ohio, USA ([email protected]) Lucy Edwards, US Geological Survey ([email protected]) Marianne Ellegaard, University of Copenhagen, Denmark ([email protected]) Martin J. Head, Brock University, Canada ([email protected]) Alexandra Kraberg, Alfred Wegener Institute for Polar and Marine Research, Germany ([email protected] ) Jane Lewis, University of Westminster, UK ([email protected] ) Fabienne Marret, University of Liverpool, UK ([email protected] ) Kazumi Matsuoka, University of Nagasaki, Japan ([email protected] ) Jens Matthiessen, Alfred Wegener Institute for Polar and Marine Research, Germany ([email protected] ) Edwige Masure, Université Pierre et Marie Curie, France ([email protected] ) Marina Montresor, Stazione zoologica "Anton Dohrn" di Napoli, Italy ([email protected] ) Vera Pospelova, University of Victoria, Canada ([email protected] ) Suzanne Roy, ISMER-UQAR, Canada ([email protected]) Karin Zonneveld, University of Bremen, Germany ([email protected]) 2 ABSTRACTS Toxic blooms of Alexandrium fundyense in the Monitoring of the regional abundance of cysts may Gulf of Maine: the role of cysts in population thus hold the key to interannual forecasts of A. dynamics and long-term patterns of shellfish fundyense bloom severity in this region.