Bioproductivity and Biodiversity in Shallow
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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. -
The Plankton Lifeform Extraction Tool: a Digital Tool to Increase The
Discussions https://doi.org/10.5194/essd-2021-171 Earth System Preprint. Discussion started: 21 July 2021 Science c Author(s) 2021. CC BY 4.0 License. Open Access Open Data The Plankton Lifeform Extraction Tool: A digital tool to increase the discoverability and usability of plankton time-series data Clare Ostle1*, Kevin Paxman1, Carolyn A. Graves2, Mathew Arnold1, Felipe Artigas3, Angus Atkinson4, Anaïs Aubert5, Malcolm Baptie6, Beth Bear7, Jacob Bedford8, Michael Best9, Eileen 5 Bresnan10, Rachel Brittain1, Derek Broughton1, Alexandre Budria5,11, Kathryn Cook12, Michelle Devlin7, George Graham1, Nick Halliday1, Pierre Hélaouët1, Marie Johansen13, David G. Johns1, Dan Lear1, Margarita Machairopoulou10, April McKinney14, Adam Mellor14, Alex Milligan7, Sophie Pitois7, Isabelle Rombouts5, Cordula Scherer15, Paul Tett16, Claire Widdicombe4, and Abigail McQuatters-Gollop8 1 10 The Marine Biological Association (MBA), The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK. 2 Centre for Environment Fisheries and Aquacu∑lture Science (Cefas), Weymouth, UK. 3 Université du Littoral Côte d’Opale, Université de Lille, CNRS UMR 8187 LOG, Laboratoire d’Océanologie et de Géosciences, Wimereux, France. 4 Plymouth Marine Laboratory, Prospect Place, Plymouth, PL1 3DH, UK. 5 15 Muséum National d’Histoire Naturelle (MNHN), CRESCO, 38 UMS Patrinat, Dinard, France. 6 Scottish Environment Protection Agency, Angus Smith Building, Maxim 6, Parklands Avenue, Eurocentral, Holytown, North Lanarkshire ML1 4WQ, UK. 7 Centre for Environment Fisheries and Aquaculture Science (Cefas), Lowestoft, UK. 8 Marine Conservation Research Group, University of Plymouth, Drake Circus, Plymouth, PL4 8AA, UK. 9 20 The Environment Agency, Kingfisher House, Goldhay Way, Peterborough, PE4 6HL, UK. 10 Marine Scotland Science, Marine Laboratory, 375 Victoria Road, Aberdeen, AB11 9DB, UK. -
Fig.S1. the Pairwise Aligments of High Scoring Pairs of Recognizable Pseudogenes
LysR transcriptional regulator Identities = 57/164 (35%), Positives = 82/164 (50%), Gaps = 13/164 (8%) 70530- SNQAIKTYLMPK*LRLLRQK*SPVEFQLQVHLIKKIRLNIVIRDINLTIIEN-TPVKLKI -70354 ++Q TYLMP+ + L RQK V QLQVH ++I ++ INL II P++LK 86251- ASQTTGTYLMPRLIGLFRQKYPQVAVQLQVHSTRRIAWSVANGHINLAIIGGEVPIELKN -86072 70353- FYTLLRMKERI*H*YCLGFL------FQFLIAYKKKNLYGLRLIKVDIPFPIRGIMNNP* -70192 + E L + F L + +K++LY LR I +D IR +++ 86071- MLQVTSYAED-----ELALILPKSHPFSMLRSIQKEDLYRLRFIALDRQSTIRKVIDKVL -85907 70191- IKTELIPRNLN-EMELSLFKPIKNAV*PGLNVTLIFVSAIAKEL -70063 + + EMEL+ + IKNAV GL + VSAIAKEL 85906- NQNGIDSTRFKIEMELNSVEAIKNAVQSGLGAAFVSVSAIAKEL -85775 ycf3 Photosystem I assembly protein Identities = 25/59 (42%), Positives = 39/59 (66%), Gaps = 3/59 (5%) 19162- NRSYML-SIQCM-PNNSDYVNTLKHCR*ALDLSSKL-LAIRNVTISYYCQDIIFSEKKD -19329 +RSY+L +I + +N +YV L++ ALDL+S+L AI N+ + Y+ Q + SEKKD 19583- DRSYILYNIGLIYASNGEYVKALEYYHQALDLNSRLPPAINNIAVIYHYQGVKASEKKD -19759 Fig.S1. The pairwise aligments of high scoring pairs of recognizable pseudogenes. The upper amino acid sequences indicates Cryptomonas sp. SAG977-2f. The lower sequences are corresponding amino acid sequences of homologs in C. curvata CCAP979/52. Table S1. Presence/absence of protein genes in the plastid genomes of Cryptomonas and representative species of Cryptomonadales. Note; y indicates pseudogenes. Photosynthetic Non-Photosynthetic Guillardia Rhodomonas Cryptomonas C. C. curvata C. curvata parameciu Guillardia Rhodomonas FBCC300 CCAP979/ SAG977 CCAC1634 m theta salina -2f B 012D 52 CCAP977/2 a rps2 + + + + -
Biovolumes and Size-Classes of Phytoplankton in the Baltic Sea
Baltic Sea Environment Proceedings No.106 Biovolumes and Size-Classes of Phytoplankton in the Baltic Sea Helsinki Commission Baltic Marine Environment Protection Commission Baltic Sea Environment Proceedings No. 106 Biovolumes and size-classes of phytoplankton in the Baltic Sea Helsinki Commission Baltic Marine Environment Protection Commission Authors: Irina Olenina, Centre of Marine Research, Taikos str 26, LT-91149, Klaipeda, Lithuania Susanna Hajdu, Dept. of Systems Ecology, Stockholm University, SE-106 91 Stockholm, Sweden Lars Edler, SMHI, Ocean. Services, Nya Varvet 31, SE-426 71 V. Frölunda, Sweden Agneta Andersson, Dept of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden, Umeå Marine Sciences Centre, Umeå University, SE-910 20 Hörnefors, Sweden Norbert Wasmund, Baltic Sea Research Institute, Seestr. 15, D-18119 Warnemünde, Germany Susanne Busch, Baltic Sea Research Institute, Seestr. 15, D-18119 Warnemünde, Germany Jeanette Göbel, Environmental Protection Agency (LANU), Hamburger Chaussee 25, D-24220 Flintbek, Germany Slawomira Gromisz, Sea Fisheries Institute, Kollataja 1, 81-332, Gdynia, Poland Siv Huseby, Umeå Marine Sciences Centre, Umeå University, SE-910 20 Hörnefors, Sweden Maija Huttunen, Finnish Institute of Marine Research, Lyypekinkuja 3A, P.O. Box 33, FIN-00931 Helsinki, Finland Andres Jaanus, Estonian Marine Institute, Mäealuse 10 a, 12618 Tallinn, Estonia Pirkko Kokkonen, Finnish Environment Institute, P.O. Box 140, FIN-00251 Helsinki, Finland Iveta Ledaine, Inst. of Aquatic Ecology, Marine Monitoring Center, University of Latvia, Daugavgrivas str. 8, Latvia Elzbieta Niemkiewicz, Maritime Institute in Gdansk, Laboratory of Ecology, Dlugi Targ 41/42, 80-830, Gdansk, Poland All photographs by Finnish Institute of Marine Research (FIMR) Cover photo: Aphanizomenon flos-aquae For bibliographic purposes this document should be cited to as: Olenina, I., Hajdu, S., Edler, L., Andersson, A., Wasmund, N., Busch, S., Göbel, J., Gromisz, S., Huseby, S., Huttunen, M., Jaanus, A., Kokkonen, P., Ledaine, I. -
HIGH-THROUGHPUT SEQUENCING REVEALS UNEXPECTED PHYTOPLANKTON PREY of an ESTUARINE COPEPOD a Thesis Submitted to the Faculty of Sa
HIGH-THROUGHPUT SEQUENCING REVEALS UNEXPECTED PHYTOPLANKTON PREY OF AN ESTUARINE COPEPOD A Thesis submitted to the faculty of San Francisco State University In partial fulfillment of z o l i the requirements for OL the Degree • Hk ^ Master of Science In Biology: Ecology, Evolution, and Conservation Biology by Ann Elisabeth Holmes San Francisco, California Copyright by Ann Elisabeth Holmes 2018 CERTIFICATION OF APPROVAL I certify that I have read High-throughput sequencing reveals unexpected phytoplankton prey of an estuarine copepod by Ann Elisabeth Holmes, and that in my opinion this work meets the criteria for approving a thesis submitted in partial fulfillment of the requirement for the degree Master of Science in Biology: Ecology, Evolution and Conservation Biology at San Francisco State University. Wim Kimmerer, PhD Professor Jopathon Stillman, PhD Professor Andrea Swei, PhD Assistant Professor HIGH-THROUGHPUT SEQUENCING REVEALS UNEXPECTED PHYTOPLANKTON PREY OF AN ESTUARINE COPEPOD Ann Elisabeth Holmes San Francisco, California 2018 Selective feeding by copepods has important ecological implications such as food web length, nutrient limitation, and control of algal blooms. Traditional methods for investigating copepod feeding in natural waters (e.g. stable isotope and fatty acid tracers or microdissection) have low taxonomic specificity or significant biases. We used high- throughput genetic sequencing (HTS) to identify in situ the phytoplankton prey of Pseudodiaptomus forbesi (Copepoda: Calanoida) in the San Francisco Estuary. Amplicons of the 16s rRNA gene were sequenced on an Illumina MiSeq. Cyanobacteria were the most frequently detected prey taxon, a result not predicted due to expected low nutritional value. In contrast, prey taxa expected to have high nutritional value for copepods (diatoms and cryptophytes) were not detected as frequently as anticipated based on the expectations generated using traditional approaches. -
Bangor University DOCTOR of PHILOSOPHY
Bangor University DOCTOR OF PHILOSOPHY Studies on micro algal fine-structure, taxonomy and systematics : cryptophyceae and bacillariophyceae. Novarino, Gianfranco Award date: 1990 Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Download date: 02. Oct. 2021 Studies on microalgal fine-structure, taxonomy, and systematics: Cryptopbyceae and Bacillariopbyceae In Two Volumes Volume I (Text) ,, ý,ý *-ýýI Twl by Gianfranco Novarino, Dottore in Scienze Biologiche (Rom) A Thesis submitted to the University of Wales in candidature for the degree of Philosophiae Doctor University of Wales (Bangor) School of Ocean Sciences Marine Science Laboratories Menai Bridge, Isle of Anglesey, United Kingdom December 1990 Lýýic. JýýVt. BEST COPY AVAILABLE Acknowledge mehts Dr I. A. N. Lucas, who supervised this work, kindly provided his helpful guidance, sharing his knowledge and expertise with patience and concern, critically reading the manuscripts of papers on the Cryptophyceae, and supplying many starter cultures of the strains studied here. -
Växtplankton I Fem Sjöar I Örebro Län 2016 Statusbedömning Av Miljötillståndet
Växtplankton i fem sjöar i Örebro län 2016 Statusbedömning av miljötillståndet Länsstyrelsen – en samlande kraft Sverige är indelat i 21 län och varje län har en länsstyrelse och en landshövding. Länsstyrelsen är regeringens ombud i länet och ska både förverkliga den nationella politiken och samtidigt ta hänsyn till regionala förhållanden och förutsättningar. Länsstyrelsen är alltså en viktig länk mellan länets kommuner och dess invånare å ena sidan och regeringen, riksdagen och de centrala myndigheterna å den andra sidan. Titel: Växtplankton i fem sjöar i Örebro län 2016 - Statusbedömning av miljötillståndet Utgivare: Länsstyrelsen i Örebro län Författare: Åsa Garberg, Medins Havs och Vattenkonsulter AB Kontaktperson: Pelle Grahn Publikationsnummer: 2016:45 Bilder: Länsstyrelsen (Rapportens framsida), Allt bildmaterial i rapporten omfattas av © Medins Havs- och Vattenkonsulter AB, om inte annat anges. Förord I denna rapport redovisas resultat från provtagningar av växtplankton i fem sjöar i Örebro län. Provtagningarna utfördes under augusti 2016 av Mikael Nyberg, Länsstyrelsen i Örebro län och genomfördes i enlighet med Natur- vårdsverkets handledning för miljöövervakning. Projektledare har varit Pelle Grahn, Länsstyrelsen i Örebro län. Undersökningarna utfördes som ett led i Länsstyrelsens arbete med att kart- lägga länets vatten i enlighet med EU:s ramdirektiv för vatten. Resultaten har använts som stöd vid bedömningar av vattendragens kemiska och ekologiska status, men kan också komma att fungera som underlag för framtida under- söknings- -
Improved Methodology for Identification of Cryptomonads: Combining Light Microscopy and PCR Amplification
J. Microbiol. Biotechnol. (2013), 23(3), 289–296 http://dx.doi.org/10.4014/jmb.1203.03057 First published online November 24, 2012 pISSN 1017-7825 eISSN 1738-8872 Improved Methodology for Identification of Cryptomonads: Combining Light Microscopy and PCR Amplification Xia, Shuang1,2, Yingyin Cheng3, Huan Zhu1,2, Guoxiang Liu1*, and Zhengyu Hu1 1Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China 2Graduate School of Chinese Academy of Sciences, Beijing 100039, China 3Center for Water Environment and Human Health, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China Received: March 26, 2012 / Revised: August 6, 2012 / Accepted: October 16, 2012 Cryptomonads are unicellular, biflagellate algae. Generally, Key words: Cryptomonad, fixative, glutaraldehyde, Lugol’s cryptomonad cells cannot be preserved well because of solution, morphology, PCR amplification their fragile nature, and an improved methodology should be developed to identify cryptomonads from natural habitats. In this study, we tried using several cytological Cryptomonads are unicellular, biflagellate algae, which are fixatives, including glutaraldehyde, formaldehyde, and cosmopolitan in distribution, living as important primary their combinations to preserve field samples collected producers in both freshwater and marine habitats [4, 15, from various waters, and the currently used fixative, 25, 26, 32, 37]. They often assume dominant phytoplankton Lugol’s solution was tested for comparison. Results status in various waters [27], and sometimes even form showed that among the fixatives tested, glutaraldehyde nuisance blooms [1, 9, 34]. However, the cell density of preserved the samples best, and the optimal concentration cryptomonads was low in preserved samples and their of glutaraldehyde was 2%. -
Nanoplankton Protists from the Western Mediterranean Sea. II. Cryptomonads (Cryptophyceae = Cryptomonadea)*
sm69n1047 4/3/05 20:30 Página 47 SCI. MAR., 69 (1): 47-74 SCIENTIA MARINA 2005 Nanoplankton protists from the western Mediterranean Sea. II. Cryptomonads (Cryptophyceae = Cryptomonadea)* GIANFRANCO NOVARINO Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, U.K. E-mail: [email protected] SUMMARY: This paper is an electron microscopical account of cryptomonad flagellates (Cryptophyceae = Cryptomon- adea) in the plankton of the western Mediterranean Sea. Bottle samples collected during the spring-summer of 1998 in the Sea of Alboran and Barcelona coastal waters contained a total of eleven photosynthetic species: Chroomonas (sensu aucto- rum) sp., Cryptochloris sp., 3 species of Hemiselmis, 3 species of Plagioselmis including Plagioselmis nordica stat. nov/sp. nov., Rhinomonas reticulata (Lucas) Novarino, Teleaulax acuta (Butcher) Hill, and Teleaulax amphioxeia (Conrad) Hill. Identification was based largely on cell surface features, as revealed by scanning electron microscopy (SEM). Cells were either dispersed in the water-column or associated with suspended particulate matter (SPM). Plagioselmis prolonga was the most common species both in the water-column and in association with SPM, suggesting that it might be a key primary pro- ducer of carbon. Taxonomic keys are given based on SEM. Key words: Cryptomonadea, cryptomonads, Cryptophyceae, flagellates, nanoplankton, taxonomy, ultrastructure. RESUMEN: PROTISTAS NANOPLANCTÓNICOS DEL MAR MEDITERRANEO NOROCCIDENTAL II. CRYPTOMONADALES (CRYPTOPHY- CEAE = CRYPTOMONADEA). – Este estudio describe a los flagelados cryptomonadales (Cryptophyceae = Cryptomonadea) planctónicos del Mar Mediterraneo Noroccidental mediante microscopia electrónica. La muestras recogidas en botellas durante la primavera-verano de 1998 en el Mar de Alboran y en aguas costeras de Barcelona, contenian un total de 11 espe- cies fotosintéticas: Chroomonas (sensu auctorum) sp., Cryptochloris sp., 3 especies de Hemiselmis, 3 especies de Plagio- selmis incluyendo Plagioselmis nordica stat. -
Microalgal Structure and Diversity in Some Canals Near Garbage Dumps of Bobongo Basin in the City of Douala, Cameroun
GSC Biological and Pharmaceutical Sciences, 2020, 10(02), 048–061 Available online at GSC Online Press Directory GSC Biological and Pharmaceutical Sciences e-ISSN: 2581-3250, CODEN (USA): GBPSC2 Journal homepage: https://www.gsconlinepress.com/journals/gscbps (RESEARCH ARTICLE) Microalgal structure and diversity in some canals near garbage dumps of Bobongo basin in the city of Douala, Cameroun Ndjouondo Gildas Parfait 1, *, Mekoulou Ndongo Jerson 2, Kojom Loïc Pradel 3, Taffouo Victor Désiré 4, Dibong Siegfried Didier 5 1 Department of Biology, High Teacher Training College, The University of Bamenda, P.O. BOX 39 Bambili, Cameroon. 2 Department of Animal organisms, Faculty of Science, The University of Douala, PO.BOX 24157 Douala, Cameroon. 3 Department of Animal organisms, Faculty of Science, The University of Douala, PO.BOX 24157 Douala, Cameroon. 4 Department of Botany, Faculty of Science, The University of Douala, PO.BOX 24157 Douala, Cameroon. 5 Department of Botany, Faculty of Science, The University of Douala, PO.BOX 24157 Douala, Cameroon. Publication history: Received on 14 January 2020; revised on 06 February 2020; accepted on 10 February 2020 Article DOI: https://doi.org/10.30574/gscbps.2020.10.2.0013 Abstract Anarchical and galloping anthropization is increasingly degrading the wetlands. This study aimed at determining the structure, diversity and spatiotemporal variation of microalgae from a few canals in the vicinity of garbage dumps of the Bobongo basin to propose methods of ecological management of these risk areas. Sampling took place from March 2016 to April 2019. Pelagic algae as well as those attached to stones and macrophytes were sampled in 25 stations. -
Lake Spokane Dissolved Oxygen Water Quality Attainment Plan Five Year Report
AVISTA CORPORATION LAKE SPOKANE DISSOLVED OXYGEN WATER QUALITY ATTAINMENT PLAN FIVE YEAR REPORT WASHINGTON 401 CERTIFICATION FERC LICENSE APPENDIX B, SECTION 5.6 SPOKANE RIVER HYDROELECTRIC PROJECT FERC PROJECT NO. 2545 Prepared By: March 24, 2017 [Page intentionally left blank] TABLE OF CONTENTS 1.0 INTRODUCTION ........................................................................................................ 1 2.0 BASELINE MONITORING ........................................................................................ 3 2.1 2016 Monitoring Results .............................................................................................. 3 2.2 Assessment of Lake Spokane Water Quality (2010 – 2016) ........................................ 7 2.3 Monitoring Recommendations ..................................................................................... 8 3.0 IMPLEMENTATION ACTIVITIES ........................................................................... 9 3.1 Studies .......................................................................................................................... 9 3.1.1 Carp Population Reduction Program ...................................................................... 10 3.1.2 Aquatic Weed Management .................................................................................... 10 3.2 2016 Implementation Measures .................................................................................. 11 3.2.1 Carp ........................................................................................................................ -
Cation and Anion Channelrhodopsins: Sequence Motifs and Taxonomic 2 Distribution
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.23.436664; this version posted March 23, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Cation and anion channelrhodopsins: Sequence motifs and taxonomic 2 distribution 3 Elena G. Govorunova1, Oleg A. Sineshchekov1, Hai Li1, Yumei Wang1, Leonid S. Brown2, Alyssa 4 Palmateer2, Michael Melkonian3, Shifeng Cheng4, Eric Carpenter5, Jordan Patterson5, Gane K.-S. 5 Wong5,6, and John L. Spudich1# 6 1Center for Membrane Biology, Department of Biochemistry & Molecular Biology, The 7 University of Texas Health Science Center at Houston McGovern Medical School, Houston, 8 Texas, USA 9 2Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, 10 Ontario, Canada 11 3Max Planck Institute for Plant Breeding Research, Integrative Bioinformatics, Cologne, 12 Germany 13 4Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 14 Shenzhen, China 15 5Departments of Biological Sciences and of Medicine, University of Alberta, Edmonton, Alberta, 16 Canada 17 6Beijing Genomics Institute-Shenzhen, Shenzhen, China 18 Running title: Cation and anion channelrhodopsins 19 #Address correspondence to John L. Spudich, [email protected]. 20 Word count Abstract: 227 21 Word count Text: 4,360 22 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.23.436664; this version posted March 23, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 23 ABSTRACT 24 Cation and anion channelrhodopsins (CCRs and ACRs, respectively) primarily from two algal 25 species, Chlamydomonas reinhardtii and Guillardia theta, have become widely used as 26 optogenetic tools to control cell membrane potential with light.