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The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service. -
The Diatoms Big Significance of Tiny Glass Houses
GENERAL ¨ ARTICLE The Diatoms Big Significance of Tiny Glass Houses Aditi Kale and Balasubramanian Karthick Diatoms are unique microscopic algae having intricate cell walls made up of silica. They are the major phytoplankton in aquatic ecosystems and account for 20–25% of the oxygen release and carbon fixation in the world. Their most charac- teristic features are mechanisms they have evolved to utilize silica. Due to their distinctive adaptations and ecology, they (left) Aditi Kale is a PhD student with the are used in various fields like biomonitoring, paleoecology, Biodiversity and nanotechnology and forensics. Paleobiology group of Agharkar Research Introduction Institute. She is studying the biogeography of Diatoms (Class: Bacillariophyceae) are unique microscopic al- freshwater diatoms in gae containing silica and having distinct geometrical shapes. Western Ghats for her They are unicellular, eukaryotic and photosynthetic organisms. thesis. Their cell size ranges between 5 µm–0.5 mm. They occur in wet (right) Balasubramanian or moist places where photosynthesis is possible. Diatoms are Karthick is Scientist with Biodiversity and either planktonic (free-floating) or benthic (attached to a substra- Paleobiology group of tum) in Nature (Figure 1). The individuals are solitary or some- Agharkar Research times form colonies. Diatoms are mostly non-motile; however, Institute. His interests some benthic diatoms have a specialized raphe system1 that include diatom taxonomy and ecology, microbial secretes mucilage to attach or glide along a surface. They are also biogeography,andaquatic known to form biofilms, i. e., layers of tightly attached cells of ecology. microorganisms. Biofilms are formed on a solid surface and are often surrounded by extra-cellular fluids. -
Diatoms Shape the Biogeography of Heterotrophic Prokaryotes in Early Spring in the Southern Ocean
Diatoms shape the biogeography of heterotrophic prokaryotes in early spring in the Southern Ocean Yan Liu, Pavla Debeljak, Mathieu Rembauville, Stéphane Blain, Ingrid Obernosterer To cite this version: Yan Liu, Pavla Debeljak, Mathieu Rembauville, Stéphane Blain, Ingrid Obernosterer. Diatoms shape the biogeography of heterotrophic prokaryotes in early spring in the Southern Ocean. Environmental Microbiology, Society for Applied Microbiology and Wiley-Blackwell, 2019, 21 (4), pp.1452-1465. 10.1111/1462-2920.14579. hal-02383818 HAL Id: hal-02383818 https://hal.archives-ouvertes.fr/hal-02383818 Submitted on 28 Nov 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Diatoms shape the biogeography of heterotrophic prokaryotes in early spring in the Southern Ocean 5 Yan Liu1, Pavla Debeljak1,2, Mathieu Rembauville1, Stéphane Blain1, Ingrid Obernosterer1* 1 Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, F-66650 10 Banyuls-sur-Mer, France 2 Department of Limnology and Bio-Oceanography, University of Vienna, A-1090 Vienna, Austria -
Effects of the Filter-Feeding Benthic Bivalve Corbicula Fluminea
water Article Effects of the Filter-Feeding Benthic Bivalve Corbicula fluminea on Plankton Community and Water Quality in Aquatic Ecosystems: A Mesocosm Study Yuqin Rong 1,2, Yali Tang 1,2,† , Lijuan Ren 1,2, William D Taylor 3 , Vladimir Razlutskij 4, Luigi Naselli-Flores 5 , Zhengwen Liu 1,6,7,* and Xiufeng Zhang 1,2,* 1 Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou 510632, China; [email protected] (Y.R.); [email protected] (Y.T.); [email protected] (L.R.) 2 Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Guangzhou 510632, China 3 Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; [email protected] 4 State Scientific and Production Amalgamation Scientific-Practical Center of the National Academy of Sciences of Belarus for Biological Resources, 220072 Minsk, Belarus; [email protected] 5 Department STEBICEF, University of Palermo, 90123 Palermo, Italy; [email protected] 6 Sino-Danish Centre for Education and Research (SDC), Beijing 100070, China 7 State Key Laboratory of Lake Science and Environment, Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China * Correspondence: [email protected] (Z.L.); [email protected] (X.Z.) † The author contributed equally to this work. Abstract: The influence of filter-feeding bivalves on plankton communities, nutrients, and water Citation: Rong, Y.; Tang, Y.; Ren, L.; quality in a given aquatic ecosystem is so profound that they can be considered ecosystem engineers. Taylor, W.D; Razlutskij, V.; In a 70-day mesocosm experiment, we tested the hypothesis that Corbicula fluminea would change Naselli-Flores, L.; Liu, Z.; Zhang, X. -
Four Hundred Million Years of Silica Biomineralization in Land Plants
Four hundred million years of silica biomineralization in land plants Elizabeth Trembath-Reicherta,1, Jonathan Paul Wilsonb, Shawn E. McGlynna,c, and Woodward W. Fischera aDivision of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125; bDepartment of Biology, Haverford College, Haverford, PA 19041; and cGraduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo 192-0397, Japan Edited by Thure E. Cerling, University of Utah, Salt Lake City, UT, and approved February 20, 2015 (received for review January 7, 2015) Biomineralization plays a fundamental role in the global silicon Silica is widely used within plants for structural support and cycle. Grasses are known to mobilize significant quantities of Si in pathogen defense (19–21), but it remains a poorly understood the form of silica biominerals and dominate the terrestrial realm aspect of plant biology. Recent work on the angiosperm Oryza today, but they have relatively recent origins and only rose to sativa demonstrated that silica accumulation is facilitated by taxonomic and ecological prominence within the Cenozoic Era. transmembrane proteins expressed in root cells (21–24). Phy- This raises questions regarding when and how the biological silica logenetic analysis revealed that these silicon transport proteins cycle evolved. To address these questions, we examined silica were derived from a diverse family of modified aquaporins that abundances of extant members of early-diverging land plant include arsenite and glycerol transporters (19, 21, 25, 26). A clades, which show that silica biomineralization is widespread different member of this aquaporin family was recently identi- across terrestrial plant linages. Particularly high silica abundances fied that enables silica uptake in the horsetail Equisetum,an are observed in lycophytes and early-diverging ferns. -
Exploring Bacteria Diatom Associations Using Single-Cell
Vol. 72: 73–88, 2014 AQUATIC MICROBIAL ECOLOGY Published online April 4 doi: 10.3354/ame01686 Aquat Microb Ecol FREEREE ACCESSCCESS Exploring bacteria–diatom associations using single-cell whole genome amplification Lydia J. Baker*, Paul F. Kemp Department of Oceanography, University of Hawai’i at Manoa, 1950 East West Road, Center for Microbial Oceanography: Research and Education (C-MORE), Honolulu, Hawai’i 96822, USA ABSTRACT: Diatoms are responsible for a large fraction of oceanic and freshwater biomass pro- duction and are critically important for sequestration of carbon to the deep ocean. As with most surfaces present in aquatic systems, bacteria colonize the exterior of diatom cells, and they inter- act with the diatom and each other. The ecology of diatoms may be better explained by conceptu- alizing them as composite organisms consisting of the host cell and its bacterial associates. Such associations could have collective properties that are not predictable from the properties of the host cell alone. Past studies of these associations have employed culture-based, whole-population methods. In contrast, we examined the composition and variability of bacterial assemblages attached to individual diatoms. Samples were collected in an oligotrophic system (Station ALOHA, 22° 45’ N, 158° 00’ W) at the deep chlorophyll maximum. Forty eukaryotic host cells were isolated by flow cytometry followed by multiple displacement amplification, including 26 Thalassiosira spp., other diatoms, dinoflagellates, coccolithophorids, and flagellates. Bacteria were identified by amplifying, cloning, and sequencing 16S rDNA using primers that select against chloroplast 16S rDNA. Bacterial sequences were recovered from 32 of 40 host cells, and from parallel samples of the free-living and particle-associated bacteria. -
Phytoplankton As Key Mediators of the Biological Carbon Pump: Their Responses to a Changing Climate
sustainability Review Phytoplankton as Key Mediators of the Biological Carbon Pump: Their Responses to a Changing Climate Samarpita Basu * ID and Katherine R. M. Mackey Earth System Science, University of California Irvine, Irvine, CA 92697, USA; [email protected] * Correspondence: [email protected] Received: 7 January 2018; Accepted: 12 March 2018; Published: 19 March 2018 Abstract: The world’s oceans are a major sink for atmospheric carbon dioxide (CO2). The biological carbon pump plays a vital role in the net transfer of CO2 from the atmosphere to the oceans and then to the sediments, subsequently maintaining atmospheric CO2 at significantly lower levels than would be the case if it did not exist. The efficiency of the biological pump is a function of phytoplankton physiology and community structure, which are in turn governed by the physical and chemical conditions of the ocean. However, only a few studies have focused on the importance of phytoplankton community structure to the biological pump. Because global change is expected to influence carbon and nutrient availability, temperature and light (via stratification), an improved understanding of how phytoplankton community size structure will respond in the future is required to gain insight into the biological pump and the ability of the ocean to act as a long-term sink for atmospheric CO2. This review article aims to explore the potential impacts of predicted changes in global temperature and the carbonate system on phytoplankton cell size, species and elemental composition, so as to shed light on the ability of the biological pump to sequester carbon in the future ocean. -
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. -
Does a Latitudinal Gradient Exist?
Notes 1813 Limnol. Oceatzogr., 38(8). 1993, 1813-1818 (0 1993, by the Ameruzan Society of Limnology and Oceanography. Inc Chlorophyll a concentrations in the North Pacific: Does a latitudinal gradient exist? Abstract -Chlorophyll a concentrations were tion properties of glass-fiber and membrane measured as a function of depth from 28 to 48”N filters have demonstrated that glass-fiber filters along 152”W in March 199 1 with Whatman GF/F and 0.2~pm Nuclepore filters. Surface Chl a concen- inadequately retain < 1-pm-diameter cells due trations measured with 0.2~ym Nuclepore filters were to their large nominal pore size (0.7 and 1.2 up to fourfold higher than those measured with pm for Whatman GF/F and GF/C filters). Low Whatman GF/F filters. The largest difference be- retention efficiencies of glass-fiber filters result tween the two filter types was found in subtropical waters, where picoplankton were a major constituent when Chl a concentrations are low (<0.5-l .O of the phytoplankton assemblage. Chl a concentra- pg Chl a liter-‘) and when picoplankton are a tions integrated from 0 to 175 m showed a threefold dominant fraction of the phytoplankton as- increase (9-26 mg Chl a m-I) between 28 and 48”N semblage (Phinney and Yentsch 1985; Taguchi when Whatman GF/F filters were used. However, integrated Chl a concentrations based on measure- and Laws 1988). Under such conditions the ments with 0.2~pm Nuclepore filters were nearly con- use of membrane filters with submicron pore stant (25-3 1 mg Chl a mpZ) over the transect. -
Biological Oceanography - Legendre, Louis and Rassoulzadegan, Fereidoun
OCEANOGRAPHY – Vol.II - Biological Oceanography - Legendre, Louis and Rassoulzadegan, Fereidoun BIOLOGICAL OCEANOGRAPHY Legendre, Louis and Rassoulzadegan, Fereidoun Laboratoire d'Océanographie de Villefranche, France. Keywords: Algae, allochthonous nutrient, aphotic zone, autochthonous nutrient, Auxotrophs, bacteria, bacterioplankton, benthos, carbon dioxide, carnivory, chelator, chemoautotrophs, ciliates, coastal eutrophication, coccolithophores, convection, crustaceans, cyanobacteria, detritus, diatoms, dinoflagellates, disphotic zone, dissolved organic carbon (DOC), dissolved organic matter (DOM), ecosystem, eukaryotes, euphotic zone, eutrophic, excretion, exoenzymes, exudation, fecal pellet, femtoplankton, fish, fish lavae, flagellates, food web, foraminifers, fungi, harmful algal blooms (HABs), herbivorous food web, herbivory, heterotrophs, holoplankton, ichthyoplankton, irradiance, labile, large planktonic microphages, lysis, macroplankton, marine snow, megaplankton, meroplankton, mesoplankton, metazoan, metazooplankton, microbial food web, microbial loop, microheterotrophs, microplankton, mixotrophs, mollusks, multivorous food web, mutualism, mycoplankton, nanoplankton, nekton, net community production (NCP), neuston, new production, nutrient limitation, nutrient (macro-, micro-, inorganic, organic), oligotrophic, omnivory, osmotrophs, particulate organic carbon (POC), particulate organic matter (POM), pelagic, phagocytosis, phagotrophs, photoautotorphs, photosynthesis, phytoplankton, phytoplankton bloom, picoplankton, plankton, -
Marine Plankton Diatoms of the West Coast of North America
MARINE PLANKTON DIATOMS OF THE WEST COAST OF NORTH AMERICA BY EASTER E. CUPP UNIVERSITY OF CALIFORNIA PRESS BERKELEY AND LOS ANGELES 1943 BULLETIN OF THE SCRIPPS INSTITUTION OF OCEANOGRAPHY OF THE UNIVERSITY OF CALIFORNIA LA JOLLA, CALIFORNIA EDITORS: H. U. SVERDRUP, R. H. FLEMING, L. H. MILLER, C. E. ZoBELL Volume 5, No.1, pp. 1-238, plates 1-5, 168 text figures Submitted by editors December 26,1940 Issued March 13, 1943 Price, $2.50 UNIVERSITY OF CALIFORNIA PRESS BERKELEY, CALIFORNIA _____________ CAMBRIDGE UNIVERSITY PRESS LONDON, ENGLAND [CONTRIBUTION FROM THE SCRIPPS INSTITUTION OF OCEANOGRAPHY, NEW SERIES, No. 190] PRINTED IN THE UNITED STATES OF AMERICA Taxonomy and taxonomic names change over time. The names and taxonomic scheme used in this work have not been updated from the original date of publication. The published literature on marine diatoms should be consulted to ensure the use of current and correct taxonomic names of diatoms. CONTENTS PAGE Introduction 1 General Discussion 2 Characteristics of Diatoms and Their Relationship to Other Classes of Algae 2 Structure of Diatoms 3 Frustule 3 Protoplast 13 Biology of Diatoms 16 Reproduction 16 Colony Formation and the Secretion of Mucus 20 Movement of Diatoms 20 Adaptations for Flotation 22 Occurrence and Distribution of Diatoms in the Ocean 22 Associations of Diatoms with Other Organisms 24 Physiology of Diatoms 26 Nutrition 26 Environmental Factors Limiting Phytoplankton Production and Populations 27 Importance of Diatoms as a Source of food in the Sea 29 Collection and Preparation of Diatoms for Examination 29 Preparation for Examination 30 Methods of Illustration 33 Classification 33 Key 34 Centricae 39 Pennatae 172 Literature Cited 209 Plates 223 Index to Genera and Species 235 MARINE PLANKTON DIATOMS OF THE WEST COAST OF NORTH AMERICA BY EASTER E. -
Three New Licmophora Species (Bacillariophyta: Fragilariophyceae) from Guam, Two with an Axial Wave in the Valve Ella M
Macatugal et al. Marine Biodiversity Records (2019) 12:4 https://doi.org/10.1186/s41200-019-0161-x RESEARCH Open Access Three new Licmophora species (Bacillariophyta: Fragilariophyceae) from Guam, two with an axial wave in the valve Ella M. S. Macatugal1, Bernadette G. Tharngan1 and Christopher S. Lobban2* Abstract Background: Diatoms in genus Licmophora are found as epiphytes on marine shores and are members of fouling communities. They can be abundant on natural coral reef substrates such as filamentous algae and as fringes on Halimeda. Biodiversity of benthic tropical diatoms is generally poorly known. Several new species of Licmophora have been reported from Guam but many are still undescribed. Methods: Samples of seaweeds with evident diatom coatings were collected during scuba dives, examined live, preserved in formalin, and processed with nitric acid cleaning following standard practice. Cleaned samples were examined in LM and SEM. Results: We describe two species unusual in having an axial wave in the valve, and a further long, straight species. L. repanda n. sp. and L. undulata n. sp. were of similar lengths (ca. 200 μm long) and both had axial waves but L. undulata was more slender with an inflated basal pole, had colonies on mucilage pads vs. long, single-stranded mucilage stalks. In addition, L. undulata had one apical rimoportula vs. two, elongated areolae along the midrib vs. uniform areolae, and the valvocopular advalvar striae ended halfway along, whereas in L. repanda they continued to the end. L. joymaciae n. sp. grew on long, single-stranded mucilage stalks with valves 300–400 μm long, with two apical rimoportulae, and basal pole not inflated.