Harmful Algal Blooms (HABS) Along Mexican Coasts
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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. -
FIRST RECORD of Erythropsidinium Agile (GYMNODINIALES: WARNOWIACEAE) in the MEXICAN PACIFIC
CICIMAR Oceánides 25(2): 137-142 (2010) FIRST RECORD OF Erythropsidinium agile (GYMNODINIALES: WARNOWIACEAE) IN THE MEXICAN PACIFIC Primer registro de Erythropsidinium agile et Swezy, 1921, Proterythropsis Kofoid et Swezy, (Gymnodiniales: Warnowiaceae) en el 1921, Warnowia Lindemann, 1928, Greuetodinium Pacífico Mexicano Loeblich III, 1980, and Erythropsidinium P.C. Silva, 1960. Ten species of Erythropsidinium have been RESUMEN. Se registra por primera vez Erythropsi- described from warm and temperate seas. However, dinium agile, un dinoflagelado de la Familia Warno- a taxonomical study based on the changes in struc- wiaceae para el Pacífico Mexicano, dentro de Bahía ture, position, and coloration of the ocelloid in the de La Paz (Golfo de California). Se observaron 26 course of the cell division or individual development ejemplares de E. agile, principalmente en muestras revealed that some species had different morpho- de fitoplancton de red para el periodo de estudio (Ju- types (Elbrächter, 1979). At present the valid species nio, 2006 a Junio, 2010). En muestras de botella se currently considered to belong to this genus are: estimaron densidades entre 80 y 1000 cél. L–1. Los ejemplares de E. agile mostraron gran variación en E. agile (Hertwig, 1884) P.C. Silva, 1960, E. cochlea forma, tamaño y coloración; se presentaron princi- (Schütt, 1895) P.C. Silva, 1960, E. extrudens (Ko- palmente en el período invierno-primavera, cuando foid et Swezy, 1921) P.C. Silva, 1960, and E. minus la columna del agua está homogénea, a temperatu- (Kofoid et Swezy, 1921) P.C. Silva, 1960. For the ras entre 19 y 22 °C y rica en nutrientes. -
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. -
Dinoflagelados (Dinophyta) De Los Órdenes Prorocentrales Y Dinophysiales Del Sistema Arrecifal Veracruzano, México
Symbol.dfont in 8/10 pts abcdefghijklmopqrstuvwxyz ABCDEFGHIJKLMNOPQRSTUVWXYZ Symbol.dfont in 10/12 pts abcdefghijklmopqrstuvwxyz ABCDEFGHIJKLMNOPQRSTUVWXYZ Symbol.dfont in 12/14 pts abcdefghijklmopqrstuvwxyz ABCDEFGHIJKLMNOPQRSTUVWXYZ Dinoflagelados (Dinophyta) de los órdenes Prorocentrales y Dinophysiales del Sistema Arrecifal Veracruzano, México Dulce Parra-Toriz1,3, María de Lourdes Araceli Ramírez-Rodríguez1 & David Uriel Hernández-Becerril2 1. Facultad de Biología, Universidad Veracruzana, Circuito Gonzalo Beltrán s/n, Zona Universitaria, Xalapa, Veracruz, 91090 México; [email protected] 2. Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México (UNAM). Apartado Postal 70-305, México D.F. 04510 México; [email protected] 3. Posgrado en Ciencias del Mar. Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México (UNAM). Apartado Postal 70-305, México D.F. 04510 México; [email protected] Recibido 12-III-2010. Corregido 24-VIII-2010. Aceptado 23-IX-2010. Abstract: Dinoflagellates (Dinophyta) of orders Dinophysiales and Prorocentrales of the Veracruz Reef System, Mexico. Dinoflagellates are a major taxonomic group in marine phytoplankton communities in terms of diversity and biomass. Some species are also important because they form blooms and/or produce toxins that may cause diverse problems. The composition of planktonic dinoflagellates of the orders Prorocentrales and Dinophysiales, in the Veracruz Reef System, were obtained during the period of October 2006 to January 2007. For this, samples were taken from the surface at 10 stations with net of 30µm mesh, and were analyzed by light and scanning electron microscopy. Each species was described and illustrated, measured and their dis- tribution and ecological data is also given. A total of nine species were found and identified, belonging to four genera: Dinophysis was represented by three species; Prorocentrum by three, Phalacroma by two, and only one species of Ornithocercus was detected. -
Seasonal and Interannual Changes in Ciliate and Dinoflagellate
ORIGINAL RESEARCH published: 07 February 2017 doi: 10.3389/fmars.2017.00016 Seasonal and Interannual Changes in Ciliate and Dinoflagellate Species Assemblages in the Arctic Ocean (Amundsen Gulf, Beaufort Sea, Canada) Edited by: Deo F. L. Onda 1, 2, 3, Emmanuelle Medrinal 1, 3, André M. Comeau 1, 3 †, Mary Thaler 1, 2, 3, George S. Bullerjahn, Marcel Babin 1, 2 and Connie Lovejoy 1, 2, 3* Bowling Green State University, USA Reviewed by: 1 Département de Biologie and Québec-Océan, Université Laval, Quebec, QC, Canada, 2 Takuvik, Joint International Rebecca Gast, Laboratory, UMI 3376, Centre National de la Recherche Scientifique (CNRS, France) and Université Laval, Québec, QC, Woods Hole Oceanographic Canada, 3 Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada Institution, USA Alison Clare Cleary, Independent Researcher, San Recent studies have focused on how climate change could drive changes in Francisco, United States phytoplankton communities in the Arctic. In contrast, ciliates and dinoflagellates that can *Correspondence: contribute substantially to the mortality of phytoplankton have received less attention. Connie Lovejoy Some dinoflagellate and ciliate species can also contribute to net photosynthesis, [email protected] which suggests that species composition could reflect food web complexity. To identify †Present Address: André M. Comeau, potential seasonal and annual species occurrence patterns and to link species with Centre for Comparative Genomics and environmental conditions, we first examined the seasonal pattern of microzooplankton Evolutionary Bioinformatics-Integrated Microbiome Resource, Department of and then performed an in-depth analysis of interannual species variability. We used Pharmacology, Dalhousie University, high-throughput amplicon sequencing to identify ciliates and dinoflagellates to the lowest Canada taxonomic level using a curated Arctic 18S rRNA gene database. -
Metagenomic Characterization of Unicellular Eukaryotes in the Urban Thessaloniki Bay
Metagenomic characterization of unicellular eukaryotes in the urban Thessaloniki Bay George Tsipas SCHOOL OF ECONOMICS, BUSINESS ADMINISTRATION & LEGAL STUDIES A thesis submitted for the degree of Master of Science (MSc) in Bioeconomy Law, Regulation and Management May, 2019 Thessaloniki – Greece George Tsipas ’’Metagenomic characterization of unicellular eukaryotes in the urban Thessaloniki Bay’’ Student Name: George Tsipas SID: 268186037282 Supervisor: Prof. Dr. Savvas Genitsaris I hereby declare that the work submitted is mine and that where I have made use of another’s work, I have attributed the source(s) according to the Regulations set in the Student’s Handbook. May, 2019 Thessaloniki - Greece Page 2 of 63 George Tsipas ’’Metagenomic characterization of unicellular eukaryotes in the urban Thessaloniki Bay’’ 1. Abstract The present research investigates through metagenomics sequencing the unicellular protistan communities in Thermaikos Gulf. This research analyzes the diversity, composition and abundance in this marine environment. Water samples were collected monthly from April 2017 to February 2018 in the port of Thessaloniki (Harbor site, 40o 37’ 55 N, 22o 56’ 09 E). The extraction of DNA was completed as well as the sequencing was performed, before the downstream read processing and the taxonomic classification that was assigned using PR2 database. A total of 1248 Operational Taxonomic Units (OTUs) were detected but only 700 unicellular eukaryotes were analyzed, excluding unclassified OTUs, Metazoa and Streptophyta. In this research-based study the most abundant and diverse taxonomic groups were Dinoflagellata and Protalveolata. Specifically, the most abundant groups of all samples are Dinoflagellata with 190 OTUs (27.70%), Protalveolata with 139 OTUs (20.26%) Ochrophyta with 73 OTUs (10.64%), Cercozoa with 67 OTUs (9.77%) and Ciliophora with 64 OTUs (9.33%). -
Manual for Phytoplankton Sampling and Analysis in the Black Sea
Manual for Phytoplankton Sampling and Analysis in the Black Sea Dr. Snejana Moncheva Dr. Bill Parr Institute of Oceanology, Bulgarian UNDP-GEF Black Sea Ecosystem Academy of Sciences, Recovery Project Varna, 9000, Dolmabahce Sarayi, II. Hareket P.O.Box 152 Kosku 80680 Besiktas, Bulgaria Istanbul - TURKEY Updated June 2010 2 Table of Contents 1. INTRODUCTION........................................................................................................ 5 1.1 Basic documents used............................................................................................... 1.2 Phytoplankton – definition and rationale .............................................................. 1.3 The main objectives of phytoplankton community analysis ........................... 1.4 Phytoplankton communities in the Black Sea ..................................................... 2. SAMPLING ................................................................................................................. 9 2.1 Site selection................................................................................................................. 2.2 Depth ............................................................................................................................... 2.3 Frequency and seasonality ....................................................................................... 2.4 Algal Blooms................................................................................................................. 2.4.1 Phytoplankton bloom detection -
PROTISTS Shore and the Waves Are Large, Often the Largest of a Storm Event, and with a Long Period
(seas), and these waves can mobilize boulders. During this phase of the storm the rapid changes in current direction caused by these large, short-period waves generate high accelerative forces, and it is these forces that ultimately can move even large boulders. Traditionally, most rocky-intertidal ecological stud- ies have been conducted on rocky platforms where the substrate is composed of stable basement rock. Projec- tiles tend to be uncommon in these types of habitats, and damage from projectiles is usually light. Perhaps for this reason the role of projectiles in intertidal ecology has received little attention. Boulder-fi eld intertidal zones are as common as, if not more common than, rock plat- forms. In boulder fi elds, projectiles are abundant, and the evidence of damage due to projectiles is obvious. Here projectiles may be one of the most important defi ning physical forces in the habitat. SEE ALSO THE FOLLOWING ARTICLES Geology, Coastal / Habitat Alteration / Hydrodynamic Forces / Wave Exposure FURTHER READING Carstens. T. 1968. Wave forces on boundaries and submerged bodies. Sarsia FIGURE 6 The intertidal zone on the north side of Cape Blanco, 34: 37–60. Oregon. The large, smooth boulders are made of serpentine, while Dayton, P. K. 1971. Competition, disturbance, and community organi- the surrounding rock from which the intertidal platform is formed zation: the provision and subsequent utilization of space in a rocky is sandstone. The smooth boulders are from a source outside the intertidal community. Ecological Monographs 45: 137–159. intertidal zone and were carried into the intertidal zone by waves. Levin, S. A., and R. -
Ecological Characterization of Bioluminescence in Mangrove Lagoon, Salt River Bay, St. Croix, USVI
Ecological Characterization of Bioluminescence in Mangrove Lagoon, Salt River Bay, St. Croix, USVI James L. Pinckney (PI)* Dianne I. Greenfield Claudia Benitez-Nelson Richard Long Michelle Zimberlin University of South Carolina Chad S. Lane Paula Reidhaar Carmelo Tomas University of North Carolina - Wilmington Bernard Castillo Kynoch Reale-Munroe Marcia Taylor University of the Virgin Islands David Goldstein Zandy Hillis-Starr National Park Service, Salt River Bay NHP & EP 01 January 2013 – 31 December 2013 Duration: 1 year * Contact Information Marine Science Program and Department of Biological Sciences University of South Carolina Columbia, SC 29208 (803) 777-7133 phone (803) 777-4002 fax [email protected] email 1 TABLE OF CONTENTS INTRODUCTION ............................................................................................................................................... 4 BACKGROUND: BIOLUMINESCENT DINOFLAGELLATES IN CARIBBEAN WATERS ............................................... 9 PROJECT OBJECTIVES ..................................................................................................................................... 19 OBJECTIVE I. CONFIRM THE IDENTIY OF THE BIOLUMINESCENT DINOFLAGELLATE(S) AND DOMINANT PHYTOPLANKTON SPECIES IN MANGROVE LAGOON ........................................................................ 22 OBJECTIVE II. COLLECT MEASUREMENTS OF BASIC WATER QUALITY PARAMETERS (E.G., TEMPERATURE, SALINITY, DISSOLVED O2, TURBIDITY, PH, IRRADIANCE, DISSOLVED NUTRIENTS) FOR CORRELATION WITH PHYTOPLANKTON -
Molecular Phylogeny of Prorocentrum (Dinoflagellata) from the Pacific Coast of Mexico Based on the Parsimony Analysis of Fragments of Lsurdna and Ssurdna
International Journal of Plant Physiology and Biochemistry Vol. 2(3), pp.29-37, July 2010 Available online at http://www.academicjournals.org/ijppb ISSN 2141 - 2162 ©2010 Academic Journals Full Length Research Paper Molecular phylogeny of Prorocentrum (Dinoflagellata) from the Pacific Coast of Mexico based on the parsimony analysis of fragments of LSUrDNA and SSUrDNA Eréndira J. Cohen-Fernández*, Francisco F. Pedroche, Mónica Rodríguez Palacios, Sergio Álvarez Hernández and Esther Meave del Castillo Departamento de Hidrobiología, Universidad Autónoma Metropolitana - Iztapalapa, Apartado Postal 55-535, México D. F. 09340, México. Accepted 13 May, 2010 A phylogenetic analysis of the Prorocentrum species is presented, that includes the sequences of the large and small ribosomal RNA subunits from 19 cultures from 13 of the 20 species reported in the Pacific coast of Mexico; the results showed that P. micans, P. gracile and P. mexicanum were the closest of species, that planktonic may be more recent than epibenthonic species and it is suggested that the probable ancestor of the Prorocentrum genus could be a round cell without apical spine, toxic and epibenthonic. Key words: Prorocentrum , parsimony analysis, dinoflagellates, LSUrDNA, SSUrDNA. INTRODUCTION Phylogenetic relationships between dinoflagellates based many new descriptions appearing during the last part of on DNA sequences of the small and large subunits of the 1800s until the 1970s when many synonyms were ribosomal RNA (SSUrDNA and LSUrDNA), have showed established and only one genus Prorocentrum was that this group of organisms consists of several recognized; until now, four genera are accepted (Guiry paraphyletic orders, one of which is Prorocentrales. and Guiry, 2007). -
Mixotrophy Among Dinoflagellates1
J Eukaryn Microbiol.. 46(4). 1999 pp. 397-401 0 1999 by the Society of Protozoologists Mixotrophy among Dinoflagellates’ DIANE K. STOECKER University of Maryland Center for Environmentul Science, Horn Point Laboratory, P.O. Box 775, Cambridge, Marylund 21613, USA ABSTRACT. Mixotrophy, used herein for the combination of phototrophy and phagotrophy, is widespread among dinoflagellates. It occurs among most, perhaps all, of the extant orders, including the Prorocentrales, Dinophysiales, Gymnodiniales, Noctilucales, Gon- yaulacales, Peridiniales, Blastodiniales, Phytodiniales, and Dinamoebales. Many cases of mixotrophy among dinoflagellates are probably undocumented. Primarily photosynthetic dinoflagellates with their “own” plastids can often supplement their nutrition by preying on other cells. Some primarily phagotrophic species are photosynthetic due to the presence of kleptochloroplasts or algal endosymbionts. Some parasitic dinoflagellates have plastids and are probably mixotrophic. For most mixotrophic dinoflagellates, the relative importance of photosynthesis, uptake of dissolved inorganic nutrients, and feeding are unknown. However, it is apparent that mixotrophy has different functions in different physiological types of dinoflagellates. Data on the simultaneous regulation of photosynthesis, assimilation of dissolved inorganic and organic nutrients, and phagotophy by environmental parameters (irradiance, availablity of dissolved nutrients, availability of prey) and by life history events are needed in order to understand the diverse -
The Windblown: Possible Explanations for Dinophyte DNA
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.07.242388; this version posted August 10, 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-ND 4.0 International license. The windblown: possible explanations for dinophyte DNA in forest soils Marc Gottschlinga, Lucas Czechb,c, Frédéric Mahéd,e, Sina Adlf, Micah Dunthorng,h,* a Department Biologie, Systematische Botanik und Mykologie, GeoBio-Center, Ludwig- Maximilians-Universität München, D-80638 Munich, Germany b Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, D- 69118 Heidelberg, Germany c Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA d CIRAD, UMR BGPI, F-34398, Montpellier, France e BGPI, Université de Montpellier, CIRAD, IRD, Montpellier SupAgro, Montpellier, France f Department of Soil Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, S7N 5A8, SK, Canada g Eukaryotic Microbiology, Faculty of Biology, Universität Duisburg-Essen, D-45141 Essen, Germany h Centre for Water and Environmental Research (ZWU), Universität Duisburg-Essen, D- 45141 Essen, Germany Running title: Dinophytes in soils Correspondence M. Dunthorn, Eukaryotic Microbiology, Faculty of Biology, Universität Duisburg-Essen, Universitätsstrasse 5, D-45141 Essen, Germany Telephone number: +49-(0)-201-183-2453; email: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.08.07.242388; this version posted August 10, 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.