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Protocols for Monitoring Harmful Algal Blooms for Sustainable Aquaculture and Coastal Fisheries in Chile (Supplement Data)
Protocols for monitoring Harmful Algal Blooms for sustainable aquaculture and coastal fisheries in Chile (Supplement data) Provided by Kyoko Yarimizu, et al. Table S1. Phytoplankton Naming Dictionary: This dictionary was constructed from the species observed in Chilean coast water in the past combined with the IOC list. Each name was verified with the list provided by IFOP and online dictionaries, AlgaeBase (https://www.algaebase.org/) and WoRMS (http://www.marinespecies.org/). The list is subjected to be updated. Phylum Class Order Family Genus Species Ochrophyta Bacillariophyceae Achnanthales Achnanthaceae Achnanthes Achnanthes longipes Bacillariophyta Coscinodiscophyceae Coscinodiscales Heliopeltaceae Actinoptychus Actinoptychus spp. Dinoflagellata Dinophyceae Gymnodiniales Gymnodiniaceae Akashiwo Akashiwo sanguinea Dinoflagellata Dinophyceae Gymnodiniales Gymnodiniaceae Amphidinium Amphidinium spp. Ochrophyta Bacillariophyceae Naviculales Amphipleuraceae Amphiprora Amphiprora spp. Bacillariophyta Bacillariophyceae Thalassiophysales Catenulaceae Amphora Amphora spp. Cyanobacteria Cyanophyceae Nostocales Aphanizomenonaceae Anabaenopsis Anabaenopsis milleri Cyanobacteria Cyanophyceae Oscillatoriales Coleofasciculaceae Anagnostidinema Anagnostidinema amphibium Anagnostidinema Cyanobacteria Cyanophyceae Oscillatoriales Coleofasciculaceae Anagnostidinema lemmermannii Cyanobacteria Cyanophyceae Oscillatoriales Microcoleaceae Annamia Annamia toxica Cyanobacteria Cyanophyceae Nostocales Aphanizomenonaceae Aphanizomenon Aphanizomenon flos-aquae -
Harmful Algae 91 (2020) 101587
Harmful Algae 91 (2020) 101587 Contents lists available at ScienceDirect Harmful Algae journal homepage: www.elsevier.com/locate/hal Review Progress and promise of omics for predicting the impacts of climate change T on harmful algal blooms Gwenn M.M. Hennona,c,*, Sonya T. Dyhrmana,b,* a Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States b Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States c College of Fisheries and Ocean Sciences University of Alaska Fairbanks Fairbanks, AK, United States ARTICLE INFO ABSTRACT Keywords: Climate change is predicted to increase the severity and prevalence of harmful algal blooms (HABs). In the past Genomics twenty years, omics techniques such as genomics, transcriptomics, proteomics and metabolomics have trans- Transcriptomics formed that data landscape of many fields including the study of HABs. Advances in technology have facilitated Proteomics the creation of many publicly available omics datasets that are complementary and shed new light on the Metabolomics mechanisms of HAB formation and toxin production. Genomics have been used to reveal differences in toxicity Climate change and nutritional requirements, while transcriptomics and proteomics have been used to explore HAB species Phytoplankton Harmful algae responses to environmental stressors, and metabolomics can reveal mechanisms of allelopathy and toxicity. In Cyanobacteria this review, we explore how omics data may be leveraged to improve predictions of how climate change will impact HAB dynamics. We also highlight important gaps in our knowledge of HAB prediction, which include swimming behaviors, microbial interactions and evolution that can be addressed by future studies with omics tools. Lastly, we discuss approaches to incorporate current omics datasets into predictive numerical models that may enhance HAB prediction in a changing world. -
Are Blastocystis Species Clinically Relevant to Humans?
Are Blastocystis species clinically relevant to humans? Robyn Anne Nagel MB, BS, FRACP A thesis submitted for the degree of Doctor of Philosophy at the University of Queensland in 2015 School of Veterinary Science Title page Culture of human faecal specimen Blastocystis organisms, vacuolated and granular forms, Photographed RAN: x40 magnification, polarised light ii Abstract Blastocystis spp. are the most common enteric parasites found in human stool and yet, the life cycle of the organism is unknown and the clinical relevance uncertain. Robust cysts transmit infection, and many animals carry the parasite. Infection in humans has been linked to Irritable bowel syndrome (IBS). Although Blastocystis carriage is much higher in IBS patients, studies have not been able to confirm Blastocystis spp. are the direct cause of symptoms. Moreover, eradication is often unsuccessful. A number of approaches were utilised in order to investigate the clinical relevance of Blastocystis spp. in human IBS patients. Deconvolutional microscopy with time-lapse imaging and fluorescent spectroscopy of xenic cultures of Blastocystis spp. from IBS patients and healthy individuals was performed. Green autofluorescence (GAF), most prominently in the 557/576 emission spectra, was observed in the vacuolated, granular, amoebic and cystic Blastocystis forms. This first report of GAF in Blastocystis showed that a Blastocystis-specific fluorescein-conjugated antibody could be partially distinguished from GAF. Surface pores of 1m in diameter were observed cyclically opening and closing over 24 hours and may have nutritional or motility functions. Vacuolated forms, extruded a viscous material slowly over 12 hours, a process likely involving osmoregulation. Tear- shaped granules were observed exiting from the surface of an amoebic form but their identity and function could not be elucidated. -
Neoproterozoic Origin and Multiple Transitions to Macroscopic Growth in Green Seaweeds
Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds Andrea Del Cortonaa,b,c,d,1, Christopher J. Jacksone, François Bucchinib,c, Michiel Van Belb,c, Sofie D’hondta, f g h i,j,k e Pavel Skaloud , Charles F. Delwiche , Andrew H. Knoll , John A. Raven , Heroen Verbruggen , Klaas Vandepoeleb,c,d,1,2, Olivier De Clercka,1,2, and Frederik Leliaerta,l,1,2 aDepartment of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium; bDepartment of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium; cVlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium; dBioinformatics Institute Ghent, Ghent University, 9052 Zwijnaarde, Belgium; eSchool of Biosciences, University of Melbourne, Melbourne, VIC 3010, Australia; fDepartment of Botany, Faculty of Science, Charles University, CZ-12800 Prague 2, Czech Republic; gDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742; hDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; iDivision of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, United Kingdom; jSchool of Biological Sciences, University of Western Australia, WA 6009, Australia; kClimate Change Cluster, University of Technology, Ultimo, NSW 2006, Australia; and lMeise Botanic Garden, 1860 Meise, Belgium Edited by Pamela S. Soltis, University of Florida, Gainesville, FL, and approved December 13, 2019 (received for review June 11, 2019) The Neoproterozoic Era records the transition from a largely clear interpretation of how many times and when green seaweeds bacterial to a predominantly eukaryotic phototrophic world, creat- emerged from unicellular ancestors (8). ing the foundation for the complex benthic ecosystems that have There is general consensus that an early split in the evolution sustained Metazoa from the Ediacaran Period onward. -
Eukaryotes Blastocystis Species and Other Microbial Cluster Assembly
Evolution of the Cytosolic Iron-Sulfur Cluster Assembly Machinery in Blastocystis Species and Other Microbial Eukaryotes Anastasios D. Tsaousis, Eleni Gentekaki, Laura Eme, Daniel Gaston and Andrew J. Roger Eukaryotic Cell 2014, 13(1):143. DOI: 10.1128/EC.00158-13. Published Ahead of Print 15 November 2013. Downloaded from Updated information and services can be found at: http://ec.asm.org/content/13/1/143 http://ec.asm.org/ These include: SUPPLEMENTAL MATERIAL Supplemental material REFERENCES This article cites 50 articles, 28 of which can be accessed free at: http://ec.asm.org/content/13/1/143#ref-list-1 on February 24, 2014 by Dalhousie University CONTENT ALERTS Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more» Information about commercial reprint orders: http://journals.asm.org/site/misc/reprints.xhtml To subscribe to to another ASM Journal go to: http://journals.asm.org/site/subscriptions/ Evolution of the Cytosolic Iron-Sulfur Cluster Assembly Machinery in Blastocystis Species and Other Microbial Eukaryotes Anastasios D. Tsaousis,a,b Eleni Gentekaki,a Laura Eme,a Daniel Gaston,a Andrew J. Rogera ‹Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Department of Biochemistry and Molecular Biology, Halifax, Nova Scotia, Canadaa; Laboratory of Molecular and Evolutionary Parasitology, School of Biosciences, University of Kent, Canterbury, United Kingdomb The cytosolic iron/sulfur cluster assembly (CIA) machinery is responsible for the assembly of cytosolic and nuclear iron/sulfur clusters, cofactors that are vital for all living cells. This machinery is uniquely found in eukaryotes and consists of at least eight Downloaded from proteins in opisthokont lineages, such as animals and fungi. -
Ectocarpus: an Evo‑Devo Model for the Brown Algae Susana M
Coelho et al. EvoDevo (2020) 11:19 https://doi.org/10.1186/s13227-020-00164-9 EvoDevo REVIEW Open Access Ectocarpus: an evo-devo model for the brown algae Susana M. Coelho1* , Akira F. Peters2, Dieter Müller3 and J. Mark Cock1 Abstract Ectocarpus is a genus of flamentous, marine brown algae. Brown algae belong to the stramenopiles, a large super- group of organisms that are only distantly related to animals, land plants and fungi. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity. For many years, little information was available concerning the molecular mechanisms underlying multicellular development in the brown algae, but this situation has changed with the emergence of Ectocarpus as a model brown alga. Here we summarise some of the main questions that are being addressed and areas of study using Ectocarpus as a model organism and discuss how the genomic information, genetic tools and molecular approaches available for this organism are being employed to explore developmental questions in an evolutionary context. Keywords: Ectocarpus, Life-cycle, Sex determination, Gametophyte, Sporophyte, Brown algae, Marine, Complex multicellularity, Phaeoviruses Natural habitat and life cycle Ectocarpus is a cosmopolitan genus, occurring world- Ectocarpus is a genus of small, flamentous, multicellu- wide in temperate and subtropical regions, and has been lar, marine brown algae within the order Ectocarpales. collected on all continents except Antarctica [1]. It is pre- Brown algae belong to the stramenopiles (or Heter- sent mainly on rocky shores where it grows on abiotic okonta) (Fig. 1a), a large eukaryotic supergroup that (rocks, pebbles, dead shells) and biotic (other algae, sea- is only distantly related to animals, plants and fungi. -
Lateral Gene Transfer of Anion-Conducting Channelrhodopsins Between Green Algae and Giant Viruses
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.15.042127; this version posted April 23, 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. 1 5 Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses Andrey Rozenberg 1,5, Johannes Oppermann 2,5, Jonas Wietek 2,3, Rodrigo Gaston Fernandez Lahore 2, Ruth-Anne Sandaa 4, Gunnar Bratbak 4, Peter Hegemann 2,6, and Oded 10 Béjà 1,6 1Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel. 2Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, Berlin 10115, Germany. 3Present address: Department of Neurobiology, Weizmann 15 Institute of Science, Rehovot 7610001, Israel. 4Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway. 5These authors contributed equally: Andrey Rozenberg, Johannes Oppermann. 6These authors jointly supervised this work: Peter Hegemann, Oded Béjà. e-mail: [email protected] ; [email protected] 20 ABSTRACT Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity 1,2. Four ChR families are currently known. Green algal 3–5 and cryptophyte 6 cation-conducting ChRs (CCRs), cryptophyte anion-conducting ChRs (ACRs) 7, and the MerMAID ChRs 8. Here we 25 report the discovery of a new family of phylogenetically distinct ChRs encoded by marine giant viruses and acquired from their unicellular green algal prasinophyte hosts. -
A Distinct Lineage of Giant Viruses Brings a Rhodopsin Photosystem to Unicellular Marine Predators
A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators David M. Needhama,1, Susumu Yoshizawab,1, Toshiaki Hosakac,1, Camille Poiriera,d, Chang Jae Choia,d, Elisabeth Hehenbergera,d, Nicholas A. T. Irwine, Susanne Wilkena,2, Cheuk-Man Yunga,d, Charles Bachya,3, Rika Kuriharaf, Yu Nakajimab, Keiichi Kojimaf, Tomomi Kimura-Someyac, Guy Leonardg, Rex R. Malmstromh, Daniel R. Mendei, Daniel K. Olsoni, Yuki Sudof, Sebastian Sudeka, Thomas A. Richardsg, Edward F. DeLongi, Patrick J. Keelinge, Alyson E. Santoroj, Mikako Shirouzuc, Wataru Iwasakib,k,4, and Alexandra Z. Wordena,d,4 aMonterey Bay Aquarium Research Institute, Moss Landing, CA 95039; bAtmosphere & Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan; cLaboratory for Protein Functional & Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan; dOcean EcoSystems Biology Unit, GEOMAR Helmholtz Centre for Ocean Research, 24105 Kiel, Germany; eDepartment of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; fGraduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan; gLiving Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4SB, United Kingdom; hDepartment of Energy Joint Genome Institute, Walnut Creek, CA 94598; iDaniel K. Inouye Center for Microbial Oceanography, University of Hawaii, Manoa, Honolulu, HI 96822; jDepartment of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106; and kDepartment of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0032, Japan Edited by W. Ford Doolittle, Dalhousie University, Halifax, Canada, and approved August 8, 2019 (received for review May 27, 2019) Giant viruses are remarkable for their large genomes, often rivaling genomes that range up to 2.4 Mb (Fig. -
Neoproterozoic Origin and Multiple Transitions to Macroscopic Growth in Green Seaweeds
bioRxiv preprint doi: https://doi.org/10.1101/668475; this version posted June 12, 2019. 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. Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds Andrea Del Cortonaa,b,c,d,1, Christopher J. Jacksone, François Bucchinib,c, Michiel Van Belb,c, Sofie D’hondta, Pavel Škaloudf, Charles F. Delwicheg, Andrew H. Knollh, John A. Raveni,j,k, Heroen Verbruggene, Klaas Vandepoeleb,c,d,1,2, Olivier De Clercka,1,2 Frederik Leliaerta,l,1,2 aDepartment of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium bDepartment of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium cVIB Center for Plant Systems Biology, Technologiepark 71, 9052 Zwijnaarde, Belgium dBioinformatics Institute Ghent, Ghent University, Technologiepark 71, 9052 Zwijnaarde, Belgium eSchool of Biosciences, University of Melbourne, Melbourne, Victoria, Australia fDepartment of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12800 Prague 2, Czech Republic gDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA hDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, USA. iDivision of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK jSchool of Biological Sciences, University of Western Australia (M048), 35 Stirling Highway, WA 6009, Australia kClimate Change Cluster, University of Technology, Ultimo, NSW 2006, Australia lMeise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium 1To whom correspondence may be addressed. Email [email protected], [email protected], [email protected] or [email protected]. -
Physiological Responses of Aureoumbra Lagunensis and Synechococcus Sp
Harmful Algae 6 (2007) 48–55 www.elsevier.com/locate/hal Physiological responses of Aureoumbra lagunensis and Synechococcus sp. to nitrogen addition in a mesocosm experiment Hudson R. DeYoe a,*, Edward J. Buskey b, Frank J. Jochem c a Department of Biology, University of Texas-Pan American, 1201 W. University Dr., Edinburg, TX 78541, United States b University of Texas Marine Science Institute, Port Aransas, TX 78373, United States c Florida International University, Marine Biology Program, North Miami, FL 33181, United States Received 7 March 2006; received in revised form 16 May 2006; accepted 6 June 2006 Abstract Aureoumbra lagunensis is the causative organism of the Texas brown tide and is notable because it dominated the Laguna Madre ecosystem from 1990 to 1997. This species is unusual because it has the highest known critical nitrogen to phosphorus ratio (N:P) for any microalgae ranging from 115 to 260, far higher than the 16N:1P Redfield ratio. Because of its high N:P ratio, Aureoumbra should be expected to respond to N additions that would not stimulate the growth of competitors having the Redfield ratio. To evaluate this prediction, a mesocosm experiment was performed in the Laguna Madre, a South Texas coastal lagoon, in which a mixed Aureoumbra–Synechococcus (a cyanobacterium) community was enclosed in 12 mesocosms and subjected to nitrogen addition (6 controls, 6 added ammonium) for 16 days. After day 4, added nitrogen did not significantly increase Aureoumbra specific growth rate but the alga retained dominance throughout the experiment (64–75% of total cell biovolume). In control mesocosms, Aureoumbra became less abundant during the first 4 days of the experiment but rebounded by the end of the experiment and was dominant over Synechococcus. -
HARMFUL ALGAL BLOOMS in COASTAL WATERS: Options for Prevention, Control and Mitigation
Science for Solutions A A Special Joint Report with the Decision Analysis Series No. 10 National Fish and Wildlife Foundation onald F. Boesch, Anderson, Rita A dra %: Shumway, . Tesf er, Terry E. February 1997 U.S. DEPARTMENT OF COMMERCE U.S. DEPARTMENT OF THE INTERIOR William M. Daley, Secretary Bruce Babbitt, Secretary The Decision Analysis Series has been established by NOAA's Coastal Ocean Program (COP) to present documents for coastal resource decision makers which contain analytical treatments of major issues or topics. The issues, topics, and principal investigators have been selected through an extensive peer review process. To learn more about the COP or the Decision Analysis Series, please write: NOAA Coastal Ocean Office 1315 East West Highway Silver Spring, MD 209 10 phone: 301-71 3-3338 fax: 30 1-7 13-4044 Cover photo: The upper portion of photo depicts a brown tide event in an inlet along the eastern end of Long Island, New York, during Summer 7986. The blue water is Block lsland Sound. Photo courtesy of L. Cosper. Science for Solutions NOAA COASTAL OCEAN PROGRAM Special Joint Report with the Decision Analysis Series No. 10 National Fish and WildlifeFoundation HARMFUL ALGAL BLOOMS IN COASTAL WATERS: Options for Prevention, Control and Mitigation Donald F. Boesch, Donald M. Anderson, Rita A. Horner Sandra E. Shumway, Patricia A. Tester, Terry E. Whitledge February 1997 National Oceanic and Atmospheric Administration National Fish and Wildlife Foundation D. James Baker, Under Secretary Amos S. Eno, Executive Director Coastal Ocean Office Donald Scavia, Director This ~ublicationshould be cited as: Boesch, Donald F. -
Controlled Sampling of Ribosomally Active Protistan Diversity in Sediment-Surface Layers Identifies Putative Players in the Marine Carbon Sink
The ISME Journal (2020) 14:984–998 https://doi.org/10.1038/s41396-019-0581-y ARTICLE Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink 1,2 1 1 3 3 Raquel Rodríguez-Martínez ● Guy Leonard ● David S. Milner ● Sebastian Sudek ● Mike Conway ● 1 1 4,5 6 7 Karen Moore ● Theresa Hudson ● Frédéric Mahé ● Patrick J. Keeling ● Alyson E. Santoro ● 3,8 1,9 Alexandra Z. Worden ● Thomas A. Richards Received: 6 October 2019 / Revised: 4 December 2019 / Accepted: 17 December 2019 / Published online: 9 January 2020 © The Author(s) 2020. This article is published with open access Abstract Marine sediments are one of the largest carbon reservoir on Earth, yet the microbial communities, especially the eukaryotes, that drive these ecosystems are poorly characterised. Here, we report implementation of a sampling system that enables injection of reagents into sediments at depth, allowing for preservation of RNA in situ. Using the RNA templates recovered, we investigate the ‘ribosomally active’ eukaryotic diversity present in sediments close to the water/sediment interface. We 1234567890();,: 1234567890();,: demonstrate that in situ preservation leads to recovery of a significantly altered community profile. Using SSU rRNA amplicon sequencing, we investigated the community structure in these environments, demonstrating a wide diversity and high relative abundance of stramenopiles and alveolates, specifically: Bacillariophyta (diatoms), labyrinthulomycetes and ciliates. The identification of abundant diatom rRNA molecules is consistent with microscopy-based studies, but demonstrates that these algae can also be exported to the sediment as active cells as opposed to dead forms.