And Micro-Algae Using Comparative Metabolomics
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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. -
Safety Assessment of Red Algae-Derived Ingredients As Used in Cosmetics
Safety Assessment of Red Algae-Derived Ingredients as Used in Cosmetics Status: Draft Report for Panel Review Release Date: August 21, 2020 Panel Meeting Date: September 14 – 15, 2020 The Expert Panel for Cosmetic Ingredient Safety members are: Chair, Wilma F. Bergfeld, M.D., F.A.C.P.; Donald V. Belsito, M.D.; Curtis D. Klaassen, Ph.D.; Daniel C. Liebler, Ph.D.; James G. Marks, Jr., M.D.; Lisa A. Peterson, Ph.D.; Ronald C. Shank, Ph.D.; Thomas J. Slaga, Ph.D.; and Paul W. Snyder, D.V.M., Ph.D. The Cosmetic Ingredient Review (CIR) Executive Director is Bart Heldreth, Ph.D. This safety assessment was prepared by Priya Cherian, Scientific Analyst/Writer, CIR. © Cosmetic Ingredient Review 1620 L Street, NW, Suite 1200 ♢ Washington, DC 20036-4702 ♢ ph 202.331.0651 ♢ fax 202.331.0088 ♢ [email protected] Algal diversity and application. Rex L. Lowe Bowling Green State University Presentation Roadmap What are these things called algae? Species diversity & properties Ecosystem services, Ecosystem hazards Algal communities might look homogeneous but are very complex A stone this size may contain hundreds of species in a very complex community. A complex community of epilithic algae A complex community of epiphytic algae on Cladophora Ra = Rhoicosphenia abbreviata Esp = Epithemia sp. Es = Epithemia sorex Am = Achnanthidium minutissimum Cp = Cocconeis pediculus Cpl = Cocconeis placentula C = Cladophora What are algae? Algos = Latin seaweed Phycos = Greek seaweed ♦Thalloid organisms bearing chlorophyll a, lacking multicellular gametangia and their colorless relatives. ♦Morphologically diverse: ♦Prokaryotes, mesokaryotes, eukaryotes ♦Largest to smallest phototrophs (0.5µm-220 m) ♦Physiologically diverse: autotrophs, facultative heterotrophs, obligate heterotrophs (molecules or particles), parasites). -
Biology and Systematics of Heterokont and Haptophyte Algae1
American Journal of Botany 91(10): 1508±1522. 2004. BIOLOGY AND SYSTEMATICS OF HETEROKONT AND HAPTOPHYTE ALGAE1 ROBERT A. ANDERSEN Bigelow Laboratory for Ocean Sciences, P.O. Box 475, West Boothbay Harbor, Maine 04575 USA In this paper, I review what is currently known of phylogenetic relationships of heterokont and haptophyte algae. Heterokont algae are a monophyletic group that is classi®ed into 17 classes and represents a diverse group of marine, freshwater, and terrestrial algae. Classes are distinguished by morphology, chloroplast pigments, ultrastructural features, and gene sequence data. Electron microscopy and molecular biology have contributed signi®cantly to our understanding of their evolutionary relationships, but even today class relationships are poorly understood. Haptophyte algae are a second monophyletic group that consists of two classes of predominately marine phytoplankton. The closest relatives of the haptophytes are currently unknown, but recent evidence indicates they may be part of a large assemblage (chromalveolates) that includes heterokont algae and other stramenopiles, alveolates, and cryptophytes. Heter- okont and haptophyte algae are important primary producers in aquatic habitats, and they are probably the primary carbon source for petroleum products (crude oil, natural gas). Key words: chromalveolate; chromist; chromophyte; ¯agella; phylogeny; stramenopile; tree of life. Heterokont algae are a monophyletic group that includes all (Phaeophyceae) by Linnaeus (1753), and shortly thereafter, photosynthetic organisms with tripartite tubular hairs on the microscopic chrysophytes (currently 5 Oikomonas, Anthophy- mature ¯agellum (discussed later; also see Wetherbee et al., sa) were described by MuÈller (1773, 1786). The history of 1988, for de®nitions of mature and immature ¯agella), as well heterokont algae was recently discussed in detail (Andersen, as some nonphotosynthetic relatives and some that have sec- 2004), and four distinct periods were identi®ed. -
BROWN ALGAE [147 Species] (
CHECKLIST of the SEAWEEDS OF IRELAND: BROWN ALGAE [147 species] (http://seaweed.ucg.ie/Ireland/Check-listPhIre.html) PHAEOPHYTA: PHAEOPHYCEAE ECTOCARPALES Ectocarpaceae Acinetospora Bornet Acinetospora crinita (Carmichael ex Harvey) Kornmann Dichosporangium Hauck Dichosporangium chordariae Wollny Ectocarpus Lyngbye Ectocarpus fasciculatus Harvey Ectocarpus siliculosus (Dillwyn) Lyngbye Feldmannia Hamel Feldmannia globifera (Kützing) Hamel Feldmannia simplex (P Crouan et H Crouan) Hamel Hincksia J E Gray - Formerly Giffordia; see Silva in Silva et al. (1987) Hincksia granulosa (J E Smith) P C Silva - Synonym: Giffordia granulosa (J E Smith) Hamel Hincksia hincksiae (Harvey) P C Silva - Synonym: Giffordia hincksiae (Harvey) Hamel Hincksia mitchelliae (Harvey) P C Silva - Synonym: Giffordia mitchelliae (Harvey) Hamel Hincksia ovata (Kjellman) P C Silva - Synonym: Giffordia ovata (Kjellman) Kylin - See Morton (1994, p.32) Hincksia sandriana (Zanardini) P C Silva - Synonym: Giffordia sandriana (Zanardini) Hamel - Only known from Co. Down; see Morton (1994, p.32) Hincksia secunda (Kützing) P C Silva - Synonym: Giffordia secunda (Kützing) Batters Herponema J Agardh Herponema solitarium (Sauvageau) Hamel Herponema velutinum (Greville) J Agardh Kuetzingiella Kornmann Kuetzingiella battersii (Bornet) Kornmann Kuetzingiella holmesii (Batters) Russell Laminariocolax Kylin Laminariocolax tomentosoides (Farlow) Kylin Mikrosyphar Kuckuck Mikrosyphar polysiphoniae Kuckuck Mikrosyphar porphyrae Kuckuck Phaeostroma Kuckuck Phaeostroma pustulosum Kuckuck -
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. -
Genetic Tool Development in Marine Protists: Emerging Model Organisms for Experimental Cell Biology
RESOURCE https://doi.org/10.1038/s41592-020-0796-x Genetic tool development in marine protists: emerging model organisms for experimental cell biology Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of pro- tists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways. he ocean represents the largest continuous planetary ecosys- Results tem, hosting an enormous variety of organisms, which include Overview of taxa in the EMS initiative. Taxa were selected from Tmicroscopic biota such as unicellular eukaryotes (protists). multiple eukaryotic supergroups1,7 to maximize the potential of cel- Despite their small size, protists play key roles in marine biogeo- lular biology and to evaluate the numerous unigenes with unknown chemical cycles and harbor tremendous evolutionary diversity1,2. functions found in marine protists (Fig. 1). Before the EMS initia- Notwithstanding their significance for understanding the evolution tive, reproducible transformation of marine protists was limited to of life on Earth and their role in marine food webs, as well as driv- only a few species such as Thalassiosira pseudonana, Phaeodactylum ing biogeochemical cycles to maintain habitability, little is known tricornutum and Ostreococcus tauri (Supplementary Table 1). -
Genetic Tool Development in Marine Protists: Emerging Model Organisms for Experimental Cell Biology
UC Santa Cruz UC Santa Cruz Previously Published Works Title Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Permalink https://escholarship.org/uc/item/9x78x702 Journal Nature methods, 17(5) ISSN 1548-7091 Authors Faktorová, Drahomíra Nisbet, R Ellen R Fernández Robledo, José A et al. Publication Date 2020-05-01 DOI 10.1038/s41592-020-0796-x Peer reviewed eScholarship.org Powered by the California Digital Library University of California RESOURCE https://doi.org/10.1038/s41592-020-0796-x Genetic tool development in marine protists: emerging model organisms for experimental cell biology Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of pro- tists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways. he ocean represents the largest continuous planetary ecosys- Results tem, hosting an enormous variety of organisms, which include Overview of taxa in the EMS initiative. Taxa were selected from Tmicroscopic biota such as unicellular eukaryotes (protists). -
Genetic Tool Development in Marine Protists
bioRxiv preprint doi: https://doi.org/10.1101/718239; this version posted April 8, 2020. 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 4.0 International license. 1 Genetic tool development in marine protists: 2 Emerging model organisms for experimental cell biology 3 4 Drahomíra Faktorová1,#,*, R. Ellen R. Nisbet2,#, %, José A. Fernández Robledo3,#, Elena 5 Casacuberta4,#, Lisa Sudek5,#, Andrew E. Allen6,7, Manuel Ares Jr.8, Cristina Aresté4, Cecilia 6 Balestreri9, Adrian C. Barbrook2, Patrick Beardslee10, Sara Bender11, David S. Booth12, 7 François-Yves Bouget13, Chris Bowler14, Susana A. Breglia15, Colin Brownlee9, Gertraud 8 Burger16, Heriberto Cerutti10, Rachele Cesaroni17, Miguel A. Chiurillo18, Thomas Clemente10, 9 Duncan B. Coles3, Jackie L. Collier19, Elizabeth C. Cooney20, Kathryn Coyne21, Roberto 10 Docampo18, Christopher L. Dupont7, Virginia Edgcomb22, Elin Einarsson2, Pía A. 11 Elustondo15,$, Fernan Federici23, Veronica Freire-Beneitez24,25, Nastasia J. Freyria3, Kodai 12 Fukuda26, Paulo A. García27, Peter R. Girguis28, Fatma Gomaa28, Sebastian G. Gornik29, Jian 13 Guo5,8, Vladimír Hampl30, Yutaka Hanawa31, Esteban R. Haro-Contreras15, Elisabeth 14 Hehenberger20, Andrea Highfield9, Yoshihisa Hirakawa31, Amanda Hopes32, Christopher J. 15 Howe2, Ian Hu2, Jorge Ibañez23, Nicholas A.T. Irwin20, Yuu Ishii33, Natalia Ewa Janowicz30, 16 Adam C. Jones11, Ambar Kachale1, Konomi Fujimura-Kamada34, Binnypreet Kaur1, Jonathan 17 Z. Kaye11, Eleanna Kazana24,25, Patrick J. Keeling20, Nicole King12, Lawrence A. 18 Klobutcher35, Noelia Lander18, Imen Lassadi2, Zhuhong Li18, Senjie Lin35, Jean-Claude 19 Lozano13, Fulei Luan10, Shinichiro Maruyama33, Tamara Matute23, Cristina Miceli36, Jun 20 Minagawa34,37, Mark Moosburner6,7, Sebastián R. -
Article Is Available the Coccolithophore Emiliania Huxleyi, Limnol
Clim. Past, 16, 1007–1025, 2020 https://doi.org/10.5194/cp-16-1007-2020 © Author(s) 2020. This work is distributed under the Creative Commons Attribution 4.0 License. Can morphological features of coccolithophores serve as a reliable proxy to reconstruct environmental conditions of the past? Giulia Faucher1, Ulf Riebesell2, and Lennart Thomas Bach3 1Dipartimento di Scienze della Terra “Ardito Desio”, Università degli Studi di Milano, Milan 20133, Italy 2Biological Oceanography, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel 24105, Germany 3Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia Correspondence: Giulia Faucher ([email protected]) Received: 9 July 2019 – Discussion started: 15 July 2019 Revised: 16 April 2020 – Accepted: 6 May 2020 – Published: 9 June 2020 Abstract. Morphological changes in coccoliths, tiny cal- changing light intensity, Mg=Ca ratio, nutrient availability, cite platelets covering the outer surface of coccolithophores, and temperature in terms of coccolith morphology. The lack can be induced by physiological responses to environmental of a common response reveals the difficulties in using coc- changes. Coccoliths recovered from sedimentary successions colith morphology as a paleo-proxy for these environmen- may therefore provide information on paleo-environmental tal drivers. However, a common response was observed un- conditions prevailing at the time when the coccolithophores der changing seawater carbonate chemistry (i.e., rising CO2), were alive. To calibrate the biomineralization responses of which consistently induced malformations. This commonal- ancient coccolithophore to environmental changes, studies ity provides some confidence that malformations found in the often compared the biological responses of living coccol- sedimentary record could be indicative of adverse carbonate ithophore species with paleo-data from calcareous nannofos- chemistry conditions. -
Amelia G6mez Garreta Taxonomy of Phaeophyceae with Particular
Amelia G6mez Garreta Taxonomy of Phaeophyceae with particular reference to Mediterranean species Abstract G6mez Garreta, A.: Taxonomy of Phaeophyceae with particular reference to Mediterranean species. ~ Bocconea 16(1): 199-207. 2003. ~ ISSN 1120-4060. At present the taxonomy of Phaeophyceae is based not only on morphological characters, but also in uItrastructural and biochemical characters and in molecular data. Although molecular techniques have allowed us to clariry the taxonomy of brown algae, many problems remain unresolved. The main changes that the taxonomy of Phaeophyceae has undergone in recent years, particularly conceming Mediterranean taxa, and the problems that remain without solu tion are presented. Introduction The c1ass Phaeophyceae contains about 265 genera and 1500-2000 species (Hoek & al. 1995). In the Mediterranean Sea this c1ass are represented by 86 genera and 265 species (Ribera & al. 1992). They are almost ali marine; only a few species live in estuaries and freshwater habitats. Most of the brown algae grow in the eulittoral and the upper sublit toral zones and are dominant members ofthe marine flora in many parts ofthe world, spe cially in cold and temperate waters. The main characteristics of the brown algae are: yellow-brown plastids due to carotenoid pigments, in particular fucoxanthine, in addition to chlorophylls a and c; plas tids with 3-thylakoid lamellae and chloroplast endoplasmic reticulum confluent with nuc1ear envelope; laminaran as food storage; alginic acid, fucoidine and cellulose in the celi walls; mitochondria with tubular cristae; physodes containing phlorotannins; two het erokont lateral flagella only present in reproductive cells. The taxonomy of Phaeophyceae has been based classically on morphological charac ters: construction of the macroscopic plant (haplostichous or filamentous thallus/polystic hous or parenchymatous thallus), type of growth (diffuse growth/meristematic growth), life history (isomorfic/heteromorphic/diplontic) and sexual reproduction (iso-or-anisoga mous/oogamus). -
Marine Biological Laboratory) Data Are All from EST Analyses
TABLE S1. Data characterized for this study. rDNA 3 - - Culture 3 - etK sp70cyt rc5 f1a f2 ps22a ps23a Lineage Taxon accession # Lab sec61 SSU 14 40S Actin Atub Btub E E G H Hsp90 M R R T SUM Cercomonadida Heteromita globosa 50780 Katz 1 1 Cercomonadida Bodomorpha minima 50339 Katz 1 1 Euglyphida Capsellina sp. 50039 Katz 1 1 1 1 4 Gymnophrea Gymnophrys sp. 50923 Katz 1 1 2 Cercomonadida Massisteria marina 50266 Katz 1 1 1 1 4 Foraminifera Ammonia sp. T7 Katz 1 1 2 Foraminifera Ovammina opaca Katz 1 1 1 1 4 Gromia Gromia sp. Antarctica Katz 1 1 Proleptomonas Proleptomonas faecicola 50735 Katz 1 1 1 1 4 Theratromyxa Theratromyxa weberi 50200 Katz 1 1 Ministeria Ministeria vibrans 50519 Katz 1 1 Fornicata Trepomonas agilis 50286 Katz 1 1 Soginia “Soginia anisocystis” 50646 Katz 1 1 1 1 1 5 Stephanopogon Stephanopogon apogon 50096 Katz 1 1 Carolina Tubulinea Arcella hemisphaerica 13-1310 Katz 1 1 2 Cercomonadida Heteromita sp. PRA-74 MBL 1 1 1 1 1 1 1 7 Rhizaria Corallomyxa tenera 50975 MBL 1 1 1 3 Euglenozoa Diplonema papillatum 50162 MBL 1 1 1 1 1 1 1 1 8 Euglenozoa Bodo saltans CCAP1907 MBL 1 1 1 1 1 5 Alveolates Chilodonella uncinata 50194 MBL 1 1 1 1 4 Amoebozoa Arachnula sp. 50593 MBL 1 1 2 Katz lab work based on genomic PCRs and MBL (Marine Biological Laboratory) data are all from EST analyses. Culture accession number is ATTC unless noted. GenBank accession numbers for new sequences (including paralogs) are GQ377645-GQ377715 and HM244866-HM244878. -
Molecular Phylogeny of Two Unusual Brown Algae, Phaeostrophion Irregulare and Platysiphon Glacialis, Proposal of the Stschapoviales Ord
J. Phycol. 51, 918–928 (2015) © 2015 The Authors. Journal of Phycology published by Wiley Periodicals, Inc. on behalf of Phycological Society of America. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. DOI: 10.1111/jpy.12332 MOLECULAR PHYLOGENY OF TWO UNUSUAL BROWN ALGAE, PHAEOSTROPHION IRREGULARE AND PLATYSIPHON GLACIALIS, PROPOSAL OF THE STSCHAPOVIALES ORD. NOV. AND PLATYSIPHONACEAE FAM. NOV., AND A RE-EXAMINATION OF DIVERGENCE TIMES FOR BROWN ALGAL ORDERS1 Hiroshi Kawai,2 Takeaki Hanyuda Kobe University Research Center for Inland Seas, Rokkodai, Kobe 657-8501, Japan Stefano G. A. Draisma Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand Robert T. Wilce University of Massachusetts, Amherst, Massachusetts, USA and Robert A. Andersen Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington 98250, USA The molecular phylogeny of brown algae was results, we propose that the development of examined using concatenated DNA sequences of heteromorphic life histories and their success in the seven chloroplast and mitochondrial genes (atpB, temperate and cold-water regions was induced by the psaA, psaB, psbA, psbC, rbcL, and cox1). The study was development of the remarkable seasonality caused by carried out mostly from unialgal cultures; we the breakup of Pangaea. Most brown algal orders had included Phaeostrophion irregulare and Platysiphon diverged by roughly 60 Ma, around the last mass glacialis because their ordinal taxonomic positions extinction event during the Cretaceous Period, and were unclear.