Identification of Benthic Diatoms Isolated from the Eastern Tidal Flats of the Yellow Sea: Comparison Between Morphological and Molecular Approaches
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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. -
Benthic and Planktonic Microalgal Community Structure and Primary Productivity in Lower Chesapeake Bay Matthew Reginald Semcheski Old Dominion University
Old Dominion University ODU Digital Commons Biological Sciences Theses & Dissertations Biological Sciences Spring 2014 Benthic and Planktonic Microalgal Community Structure and Primary Productivity in Lower Chesapeake Bay Matthew Reginald Semcheski Old Dominion University Follow this and additional works at: https://digitalcommons.odu.edu/biology_etds Part of the Biology Commons, Ecology and Evolutionary Biology Commons, Environmental Sciences Commons, and the Marine Biology Commons Recommended Citation Semcheski, Matthew R.. "Benthic and Planktonic Microalgal Community Structure and Primary Productivity in Lower Chesapeake Bay" (2014). Doctor of Philosophy (PhD), dissertation, Biological Sciences, Old Dominion University, DOI: 10.25777/j7nz-k382 https://digitalcommons.odu.edu/biology_etds/79 This Dissertation is brought to you for free and open access by the Biological Sciences at ODU Digital Commons. It has been accepted for inclusion in Biological Sciences Theses & Dissertations by an authorized administrator of ODU Digital Commons. For more information, please contact [email protected]. BENTHIC AND PLANKTONIC MICROALGAL COMMUNITY STRUCTURE AND PRIMARY PRODUCTIVITY IN LOWER CHESAPEAKE BAY by Matthew Reginald Semcheski B.S. May 2003, East Stroudsburg University M.S. August 2008, Old Dominion University A Dissertation Submitted to the Faculty of Old Dominion University in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY ECOLOGICAL SCIENCES OLD DOMINION UNIVERSITY MAY 2014 Approved by: Harold G. Marshall Kneeland K. Nesius (Member) John R. McConaugha (Member) ABSTRACT BENTHIC AND PLANKTONIC MICROALGAL COMMUNITY STRUCTURE AND PRIMARY PRODUCTIVITY IN LOWER CHESAPEAKE BAY Matthew Reginald Semcheski Old Dominion University, 2014 Director: Dr. Harold G. Marshall Microalgal populations are trophically important to a variety of micro- and macroheterotrophs in marine and estuarine systems. -
Towards a Digital Diatom: Image Processing and Deep Learning Analysis of Bacillaria Paradoxa Dynamic Morphology
bioRxiv preprint doi: https://doi.org/10.1101/2019.12.21.885897; this version posted December 23, 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 4.0 International license. Towards a Digital Diatom: image processing and deep learning analysis of Bacillaria paradoxa dynamic morphology Bradly Alicea1,2, Richard Gordon3,4, Thomas Harbich5, Ujjwal Singh6, Asmit Singh6, Vinay Varma7 Abstract Recent years have witnessed a convergence of data and methods that allow us to approximate the shape, size, and functional attributes of biological organisms. This is not only limited to traditional model species: given the ability to culture and visualize a specific organism, we can capture both its structural and functional attributes. We present a quantitative model for the colonial diatom Bacillaria paradoxa, an organism that presents a number of unique attributes in terms of form and function. To acquire a digital model of B. paradoxa, we extract a series of quantitative parameters from microscopy videos from both primary and secondary sources. These data are then analyzed using a variety of techniques, including two rival deep learning approaches. We provide an overview of neural networks for non-specialists as well as present a series of analysis on Bacillaria phenotype data. The application of deep learning networks allow for two analytical purposes. Application of the DeepLabv3 pre-trained model extracts phenotypic parameters describing the shape of cells constituting Bacillaria colonies. Application of a semantic model trained on nematode embryogenesis data (OpenDevoCell) provides a means to analyze masked images of potential intracellular features. -
Proceedings of National Seminar on Biodiversity And
BIODIVERSITY AND CONSERVATION OF COASTAL AND MARINE ECOSYSTEMS OF INDIA (2012) --------------------------------------------------------------------------------------------------------------------------------------------------------- Patrons: 1. Hindi VidyaPracharSamiti, Ghatkopar, Mumbai 2. Bombay Natural History Society (BNHS) 3. Association of Teachers in Biological Sciences (ATBS) 4. International Union for Conservation of Nature and Natural Resources (IUCN) 5. Mangroves for the Future (MFF) Advisory Committee for the Conference 1. Dr. S. M. Karmarkar, President, ATBS and Hon. Dir., C B Patel Research Institute, Mumbai 2. Dr. Sharad Chaphekar, Prof. Emeritus, Univ. of Mumbai 3. Dr. Asad Rehmani, Director, BNHS, Mumbi 4. Dr. A. M. Bhagwat, Director, C B Patel Research Centre, Mumbai 5. Dr. Naresh Chandra, Pro-V. C., University of Mumbai 6. Dr. R. S. Hande. Director, BCUD, University of Mumbai 7. Dr. Madhuri Pejaver, Dean, Faculty of Science, University of Mumbai 8. Dr. Vinay Deshmukh, Sr. Scientist, CMFRI, Mumbai 9. Dr. Vinayak Dalvie, Chairman, BoS in Zoology, University of Mumbai 10. Dr. Sasikumar Menon, Dy. Dir., Therapeutic Drug Monitoring Centre, Mumbai 11. Dr, Sanjay Deshmukh, Head, Dept. of Life Sciences, University of Mumbai 12. Dr. S. T. Ingale, Vice-Principal, R. J. College, Ghatkopar 13. Dr. Rekha Vartak, Head, Biology Cell, HBCSE, Mumbai 14. Dr. S. S. Barve, Head, Dept. of Botany, Vaze College, Mumbai 15. Dr. Satish Bhalerao, Head, Dept. of Botany, Wilson College Organizing Committee 1. Convenor- Dr. Usha Mukundan, Principal, R. J. College 2. Co-convenor- Deepak Apte, Dy. Director, BNHS 3. Organizing Secretary- Dr. Purushottam Kale, Head, Dept. of Zoology, R. J. College 4. Treasurer- Prof. Pravin Nayak 5. Members- Dr. S. T. Ingale Dr. Himanshu Dawda Dr. Mrinalini Date Dr. -
Holocene) Diatoms (Bacillariophyta
U.S. DEPARTMENT OF THE INTERIOR U.S. GEOLOGICAL SURVEY Taxonomy of recent and fossil (Holocene) diatoms (Bacillariophyta) from northern Willapa Bay, Washington by Eileen Hemphill-Haley1 OPEN-FILE REPORT 93-289 This report is preliminary and has not been reviewed for conformity with Geological Survey editorial standards or with the North American Stratigraphic Code. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. 1. Menlo Park, CA 94025 TABLE OF CONTENTS ABSTRACT........................................................................................................................! INTRODUCTION..............................................................................................................^ Background for the Study .......................................................................................1 Related Studies......................................................................................................2 METHODS........................................................................................................................^ FLORAL LIST.....................................................................................................................4 ACKNOWLEDGMENTS......................................................................................................120 REFERENCES...................................................................................................................121 FIGURES Figure 1. Sample -
Phylogeny of the Bacillariaceae with Emphasis on the Genus Pseudo-Nitzschia (Bacillariophyceae) Based on Partial LSU Rdna
Eur. J. Phycol. (2002), 37: 115–134. # 2002 British Phycological Society 115 DOI: 10.1017\S096702620100347X Printed in the United Kingdom Phylogeny of the Bacillariaceae with emphasis on the genus Pseudo-nitzschia (Bacillariophyceae) based on partial LSU rDNA NINA LUNDHOLM, NIELS DAUGBJERG AND ØJVIND MOESTRUP Department of Phycology, Botanical Institute, University of Copenhagen, Øster Farimagsgade 2D, 1353 Copenhagen K, Denmark (Received 10 July 2001; accepted 18 October 2001) In order to elucidate the phylogeny and evolutionary history of the Bacillariaceae we conducted a phylogenetic analysis of 42 species (sequences were determined from more than two strains of many of the Pseudo-nitzschia species) based on the first 872 base pairs of nuclear-encoded large subunit (LSU) rDNA, which include some of the most variable domains. Four araphid genera were used as the outgroup in maximum likelihood, parsimony and distance analyses. The phylogenetic inferences revealed the Bacillariaceae as monophyletic (bootstrap support ! 90%). A clade comprising Pseudo-nitzschia, Fragilariopsis and Nitzschia americana (clade A) was supported by high bootstrap values (! 94%) and agreed with the morphological features revealed by electron microscopy. Data for 29 taxa indicate a subdivision of clade A, one clade comprising Pseudo-nitzschia species, a second clade consisting of Pseudo-nitzschia species and Nitzschia americana, and a third clade comprising Fragilariopsis species. Pseudo-nitzschia as presently defined is paraphyletic and emendation of the genus is probably needed. The analyses suggested that Nitzschia is not monophyletic, as expected from the great morphological diversity within the genus. A cluster characterized by possession of detailed ornamentation on the frustule is indicated. Eighteen taxa (16 within the Bacillariaceae) were tested for production of domoic acid, a neurotoxic amino acid. -
Exploring Species Boundaries in the Diatom Genus Rhoicosphenia Using Morphology, Phylogeny, Ecology, and Biogeography Evan William Thomas
University of Colorado, Boulder CU Scholar Ecology & Evolutionary Biology Graduate Theses & Ecology & Evolutionary Biology Dissertations Spring 1-1-2016 Exploring Species Boundaries in the Diatom Genus Rhoicosphenia Using Morphology, Phylogeny, Ecology, and Biogeography Evan William Thomas Follow this and additional works at: http://scholar.colorado.edu/ebio_gradetds Part of the Ecology and Evolutionary Biology Commons, Environmental Microbiology and Microbial Ecology Commons, Molecular Biology Commons, and the Systems Biology Commons This Dissertation is brought to you for free and open access by Ecology & Evolutionary Biology at CU Scholar. It has been accepted for inclusion in Ecology & Evolutionary Biology Graduate Theses & Dissertations by an authorized administrator of CU Scholar. For more information, please contact [email protected]. i EXPLORING SPECIES BOUNDARIES IN THE DIATOM GENUS RHOICOSPHENIA USING MORPHOLOGY, PHYLOGENY, ECOLOGY, AND BIOGEOGRAPHY by EVAN WILLIAM THOMAS B.A., University of Michigan, 2005 M.S., Bowling Green State University, 2007 A thesis submitted to the Faculty of the Graduate School of the University of Colorado in partial fulfillment of the requirement for the degree of Doctor of Philosophy Department of Ecology and Evolutionary Biology 2016 ii This thesis entitled: Exploring species boundaries in the diatom genus Rhoicosphenia using morphology, phylogeny, ecology, and biogeography written by Evan William Thomas has been approved for the Department of Ecology and Evolutionary Biology ––––––––––––––––––––––––––––––––––– -
Duckweed Relationships
The Ecology and Palaeoecology of Diatom – Duckweed Relationships Thesis submitted for the degree of Doctor of Philosophy University College London by David Emson Department of Geography University College London and Department of Botany Natural History Museum February, 2015 1 I, David Emson confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. David Emson 2 Abstract This thesis focuses on the ecology and palaeoecology of diatom-duckweed relationships and utilises a combined experimental, ecological and palaeoecological approach. In particular, the study sought to determine the potential of the epiphytic diatom Lemnicola hungarica to be utilised as a proxy indicator of past dominance of duckweed (Lemna) in small ponds. To this end, contemporary sampling of epiphytic diatom assemblages from a variety of macrophytes (including multiple samples of free-floating plants) were collected from around the world and analysed for diatom epiphytes. In this study, even despite significant environmental gradients, L. hungarica showed a significant association with free-floating plants (including Lemna spp.) as did Sellaphora seminulum. To determine whether this relationship might be used to infer Lemna- dominance in sediment cores, diatom assemblages were analysed in surface sediments from English Lemna and non-Lemna covered ponds and in a core from a pond (Bodham Rail Pit, eastern England) known to have exhibited periods of Lemna-dominance in the past. In both cases, the data suggested that both L. hungarica and S. seminulum were excellent predictors of past Lemna-dominance. Finally, to infer the consequences of Lemna-dominance for the long-term biological structure and ecosystem function of the Bodham Rail Pit, the sedimentary remains of diatoms, plant pigments, and plant and animal macrofossils were enumerated from two sediment cores. -
Heterothallic Sexual Reproduction in the Model Diatom Cylindrotheca
Eur. J. Phycol. (2013), 48(1):93–105 Heterothallic sexual reproduction in the model diatom Cylindrotheca PIETER VANORMELINGEN1, BART VANELSLANDER1, SHINYA SATO2, JEROEN GILLARD3, ROSA TROBAJO4, KOEN SABBE1 AND WIM VYVERMAN1 1Laboratory of Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281 S8, 9000 Gent, Belgium 2Royal Botanic Garden, Edinburgh EH3 5LR, UK 3J. Craig Venter Institute, San Diego, California 92121, USA 4Aquatic Ecosystems, Institute for Food and Agricultural Research and Technology (IRTA) Crta Poble Nou s/n, 43540, St Carles de la Rapita, Catalonia, Spain (Received 8 June 2012; revised 26 September 2012; accepted 30 January 2013) Cylindrotheca is one of the main model diatoms for ecophysiological and silicification research and is among the few diatoms for which a transformation protocol is available. Knowledge of its life cycle is not available, however, although sexual reproduction has been described for several related genera. In this study, 16 Cylindrotheca closterium strains from a single rbcL lineage were used to describe the life cycle of this marine diatom, including the sexual process and mating system. Similar to other Bacillariaceae, sexual reproduction was induced by the presence of a suitable mating partner, with two gametes produced per gametangium, resulting in two auxospores per gametangial pair. Differences with other Bacillariaceae include details of cell pairing, gamete behaviour, auxospore orientation and chloroplast configuration, and perizonium structure. The mating system is heterothallic, since strains fell into two mating type groups, with several strains of one mating type occasionally displaying intraclonal auxosporulation. Initial cell lengths were on average 95–100 µm, the sexual size threshold was at least 66 µm, and the minimal viable cell length c. -
Defining Phylogenetic Relationships of Ochrophyta Using 18S Rrna
Euglena: 2013 Defining Phylogenetic Relationships of Ochrophyta Using 18S rRNA: Existence of Three Major Clades in Which Bacillariophyta is Basal Kaitryn Ronning, Emily Beliveau, Emily McCaffery, Cierra Omlor, and Ellie Rosenblum Department of Biology, Susquehanna University, Selinsgrove, PA 17870. Abstract This paper presents an analysis of the phylogenetic relationships amongst the Ochrophyta, the photosynthetic heterokonts, using 18S rRNA gene sequences and maximum likelihood analysis. Three maximum likelihood (ML) cladograms were produced using Kimura 2- parameter, Tamura-Nei and Tamura 3-parameter best fit models. These cladograms were nearly identical, and strongly suggest that Bacillariophyta is a basal group within the Ochrophyta. Additionally, we raise questions regarding the phylogenetic placement of Silicoflagellata and Pinguiophyta. Please cite this article as: Ronning, K., E. Beliveau, E. McCaffery, C. Omlor, and E. Rosenblum. 2013. Defining phylogenetic relationships of Ochrophyta using 18S rRNA: existence of three major clades in which Bacillariophyta is basal. Euglena. doi:/euglena. 1(2): 52-59. Introduction 1980’s, when Medlin began to use 18s rRNA gene Heterokontae, also called the straminopiles, sequences to resolve the grouping of diatoms (Medlin is a Kingdom containing many diverse taxa, ranging et al.1988 and Beszteri et al. 2001). Using from large multicellular species to small unicellular morphological characters alone has been misleading species. They can be found in freshwater, marine, because convergent evolution may have played a role and terrestrial habitats. Cavalier-Smith (1986) in the similarities of certain taxa, which could lead to established Heterokontae as a phylum in 1986. Then, misidentification (Medlin et al. 2000). For example, Cavalier-Smith (1986) raised Heterokontae to an silica frustules of diatoms appear to be very similar infrakingdom split into two main groups: the among species, which would suggest that the species Ochrophyta (a photosynthetic group consisting of are closely related. -
A New Diatom Species Found in an Alkaline Mountain
bioRxiv preprint doi: https://doi.org/10.1101/452110; this version posted October 26, 2018. 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. PINNULARIA BAETICA SP. NOV. Pinnularia baetica sp. nov. (Bacillarophyceae): a new diatom species found in an alkaline mountain lagoon in the south of Europe (Granada, Spain) DAVID FERNÁDEZ-MORENO1,2, ANA T. LUÍS3,4, PEDRO M. SÁNCHEZ- CASTILLO2 1Dnota Medio Ambiente, Granada, C/Baza, 6, Poligono Juncaril, 18220 Albolote. Granada, Spain. 2Department of Botany, Campus Fuentenueva, University of Granada, 18071 Granada, Spain. 3Universidade de Aveiro, Department of Geosciences, Geobiotec – Geobiosciences, Technologies and Engineering, Campus de Santiago, P–3810–193 Aveiro, Portugal 4CESAM Associated Lab – Department of Biology, Campus de Santiago, 3810-193 Aveiro, Portugal corresponding author's e-mail: [email protected] Phylum Ochrophyta Caval.-Sm. (Cavalier-Smith 1995) Class Bacillariophyceae Haeckel emend. Medlin & Kaczmarska (Medlin & Kaczmarska 2004) Subclass Bacillariophycidae Round (Round et al. 1990) Order Naviculales (Bessey 1907 sensu emend) Family Pinnulariaceae D.G. Mann, 1990 Genus Pinnularia C.G. Ehrenberg, 1843 Pinnularia baetica Fernández Moreno & Sánchez Castillo sp. nov 1 bioRxiv preprint doi: https://doi.org/10.1101/452110; this version posted October 26, 2018. 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. Abstract A new benthic freshwater diatom species belonging to the genus Pinnularia was found in Laguna Seca of Sierra Seca in the north of the province of Granada, Spain. -
MONOGRAPH on MARINE PLANKTON of EAST COAST of INDIA a Cruise Report
MONOGRAPH ON MARINE PLANKTON OF EAST COAST OF INDIA A Cruise Report Published by Indian National Centre for Ocean Information Services (INCOIS), Ocean Valley, Pragathi Nagar (B.O.), Nizampet (S.O.) Hyderabad - 500 090, India Phone: +91-40-23895000 Fax : +91-40-23895001 Email: [email protected] Citation: K.C. Sahu, S.K. Baliarsingh, S. Srichandan, Aneesh A. Lotliker, T.S. Kumar. 2013. Monograph on Marine Plankton of East Coast of India-A Cruise Report. Indian National Centre for Ocean Information Services, Hyderabad, 146 pp. Cover design: S.K. Baliarsingh ©2013, Indian National Centre for Ocean Information Services, Hyderabad, India All rights reserved. No part of this publication may be reproduced in any form or by any means, without the prior written permission of the publishers. ISBN: 978-81-923474-2-4 Document design: Aneesh A. Lotliker & S.K. Baliarsingh Author Information Prof. K.C Sahu Dept. of Marine Sciences, Berhampur University, Odisha-760007, India Email: [email protected] S.K. Baliarsingh Dept. of Marine Sciences, Berhampur University, Odisha-760007, India Email: [email protected] S. Srichandan Dept. of Marine Sciences, Berhampur University, Odisha-760007, India Email: [email protected] Aneesh A. Lotliker, Ph.D Advisory Services and Satellite Oceanography Group (ASG) Indian national Centre for Ocean information Services (INCOIS), Hyderabad-500090, India Email: [email protected] T. Srinivasa Kumar, Ph.D Advisory Services and Satellite Oceanography Group (ASG) Indian national Centre for Ocean information Services (INCOIS), Hyderabad-500090, India Email: [email protected] PREFACE This monograph is an attempt to document the plankton encountered during the cruise program conducted during the period from 1.4.2011 to 8.4.2011.