Scales of Temporal and Spatial Variability in the Distribution of Harmful Algae Species in the Indian River Lagoon, Florida, USA
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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. -
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 -
The Toxic Dinoflagellate Alexandrium Minutum Impairs the Performance Of
The toxic dinoflagellate Alexandrium minutum impairs the performance of oyster embryos and larvae Justine Castrec, Helene Hegaret, Matthias Huber, Jacqueline Le Grand, Arnaud Huvet, Kevin Tallec, Myrina Boulais, Philippe Soudant, Caroline Fabioux To cite this version: Justine Castrec, Helene Hegaret, Matthias Huber, Jacqueline Le Grand, Arnaud Huvet, et al.. The toxic dinoflagellate Alexandrium minutum impairs the performance of oyster embryos and larvae. Harmful Algae, Elsevier, 2020, 92, pp.101744. 10.1016/j.hal.2020.101744. hal-02879884 HAL Id: hal-02879884 https://hal.archives-ouvertes.fr/hal-02879884 Submitted on 24 Jun 2020 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. 1 The toxic dinoflagellate Alexandrium minutum impairs the performance of oyster 2 embryos and larvae 3 Justine Castrec1, Hélène Hégaret1, Matthias Huber2, Jacqueline Le Grand2, Arnaud Huvet2, 4 Kevin Tallec2, Myrina Boulais1, Philippe Soudant1, and Caroline Fabioux1. 5 1 Univ Brest, CNRS, IRD, Ifremer, LEMAR, F-29280 Plouzane, France 6 2 Ifremer, Univ Brest, CNRS, IRD, LEMAR, F-29280 Plouzane, France 7 * Corresponding author: [email protected] 8 Abstract 9 The dinoflagellate genus Alexandrium comprises species that produce highly potent 10 neurotoxins known as paralytic shellfish toxins (PST), and bioactive extracellular compounds 11 (BEC) of unknown structure and ecological significance. -
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. -
De Rijk, L?, Caers, A,, Van De Peer, Y. & De Wachter, R. 1998. Database
BLANCHARD & HICKS-THE APICOMPLEXAN PLASTID 375 De Rijk, l?, Caers, A,, Van de Peer, Y. & De Wachter, R. 1998. Database gorad, L. & Vasil, I. K. (ed.), Cell Culture and Somatic Cell Genetics on the structure of large ribosomal subunit RNA. Nucl. Acids. Rex, of Plants, Vol7A: The molecular biology of plastids. Academic Press, 26: 183- 186. San Diego. p. 5-53. Deveraux, J., Haeberli, l? & Smithies, 0. 1984. A comprehensive set of Palmer, J. D. & Delwiche, C. E 1996. Second-hand chloroplasts and sequence analysis programs for the VAX. Nucl. Acids. Rex, 12:387-395. the case of the disappearing nucleus. Proc. Natl. Acad. Sci. USA, 93: Eaga, N. & Lang-Unnasch, N. 1995. Phylogeny of the large extrachro- 7432-7435. mosomal DNA of organisms in the phylum Apicomplexa. J. Euk. Popadic, A,, Rusch, D., Peterson, M., Rogers, B. T. & Kaufman, T. C. Microbiol,, 42:679-684. 1996. Origin of the arthropod mandible. Nature, 380:395. Fichera, M. E. & Roos, D. S. 1997. A plastid organelle as a drug target Preiser, l?, Williamson, D. H. & Wilson, R. J. M. 1995. Transfer-RNA in apicomplexan parasites. Nature, 390:407-409. genes transcribed from the plastid-like DNA of Plasmodium falci- Gardner, M. J., Williamson, D. H. & Wilson, R. J. M. 1991. A circular parum. Nucl. Acids Res., 23:4329-4336. DNA in malaria parasites encodes an RNA polymerase like that of Reith. M. & Munholland, J. 1993. A high-resolution gene map of the prokaryotes and chloroplasts. Mol. Biochem. Parasitiol., 44: 1 15-123. chloroplast genome of the red alga Porphyra purpurea. Plant Cell, Gardner, M. -
Recent Dinoflagellate Cysts from the Chesapeake Estuary (Maryland and Virginia, U.S.A.): Taxonomy and Ecological Preferences
Recent dinoflagellate cysts from the Chesapeake estuary (Maryland and Virginia, U.S.A.): taxonomy and ecological preferences. Tycho Van Hauwaert Academic year 2015–2016 Master’s dissertation submitted in partial fulfillment of the requirements for the degree of Master in Science in Geology Promotor: Prof. Dr. S. Louwye Co-promotor: Dr. K. Mertens Tutor: P. Gurdebeke Jury: Dr. T. Verleye, Dr. E. Verleyen Picture on the cover An exceptionally dense bloom of Alexandrium monilatum was observed in lower Chesapeake Bay along the north shore of the York River between Sarah's Creek and the Perrin River on 17 August 2015. Credit: W. Vogelbein/VIMS ii ACKNOWLEDGEMENTS First of all I want to thank my promoters, Prof. Dr. S. Louwye and Dr. K. Mertens. They introduced me into the wonderful world of dinoflagellates and the dinocysts due to the course Advanced Micropaleontology. I did not have hesitated long to choose a subject within the research unit of paleontology. Thank you for the proofreading, help with identification and many discussions. A special mention for Pieter Gurdebeke. This appreciation you can imagine as a 22-minutes standing ovation for the small talks and jokes only! If you include the assistance in the thesis, I would not dare to calculate the time of applause. I remember when we were discussing the subject during the fieldtrip to the Alps in September. We have come a long way and I am pleased with the result. Thank you very much for helping me with the preparation of slides, identification of dinocysts, some computer programs, proofreading of the different chapters and many more! When I am back from my trip to Canada, I would like to discuss it with a (small) bottle of beer. -
Molecular Phylogeny of Sinophysis: Evaluating the Possible Early 2 3 Q1 Evolutionary History of Dinophysoid Dinoflagellates 4 5 M
1 Molecular phylogeny of Sinophysis: Evaluating the possible early 2 3 Q1 evolutionary history of dinophysoid dinoflagellates 4 5 M. HOPPENRATH1,2*, N. CHOME´ RAT3 & B. LEANDER2 6 1 7 Forschungsinstitut Senckenberg, Deutsches Zentrum fu¨r Marine Biodiversita¨tsforschung 8 (DZMB), Su¨dstrand 44, D-26382 Wilhelmshaven, Germany 9 2 10 Departments of Zoology and Botany, University of British Columbia, Canadian Institute 11 for Advanced Research, Program in Integrated Microbial Biodiversity, Vancouver, 12 BC, V67 1Z4, Canada 13 3 14 IFREMER, LER FBN Station de Concarneau, 13 rue de Ke´rose, 29187 15 Concarneau Cedex, France 16 17 *Corresponding author (e-mail: [email protected]) 18 19 20 Abstract: Dinophysoids are a group of thecate dinoflagellates with a very distinctive thecal plate 21 arrangement involving a sagittal suture: the so-called dinophysoid tabulation pattern. Although the number and layout of the thecal plates is highly conserved, the morphological diversity within the 22 group is outstandingly high for dinoflagellates. Previous hypotheses about character evolution 23 within dinophysoids based on comparative morphology alone are currently being evaluated by 24 molecular phylogenetic studies. Sinophysis is especially significant within the context of these 25 hypotheses because several features within this genus approximate the inferred ancestral states 26 for dinophysoids as a whole, such as a (benthic) sand-dwelling lifestyle, a relatively streamlined 27 theca and a heterotrophic mode of nutrition. We generated and analysed small subunit (SSU) 28 rDNA sequences for five different species of Sinophysis, including the type species (S. ebriola, 29 S. stenosoma, S. grandis, S. verruculosa and S. microcephala). We also generated SSU rDNA 30 sequences from the planktonic dinophysoid Oxyphysis (O. -
Phytoplankton Biomass and Composition in a Well-Flushed, Sub-Tropical Estuary: the Contrasting Effects of Hydrology, Nutrient Lo
Marine Environmental Research 112 (2015) 9e20 Contents lists available at ScienceDirect Marine Environmental Research journal homepage: www.elsevier.com/locate/marenvrev Phytoplankton biomass and composition in a well-flushed, sub-tropical estuary: The contrasting effects of hydrology, nutrient loads and allochthonous influences * J.A. Hart a, E.J. Phlips a, , S. Badylak a, N. Dix b, K. Petrinec b, A.L. Mathews c, W. Green d, A. Srifa a a Fisheries and Aquatic Sciences Program, SFRC, University of Florida, 7922 NW 71st Street, Gainesville, FL 32653, USA b Guana Tolomato Matanzas National Estuarine Research Reserve, 505 Guana River Road, Ponte Vedra, FL 32082, USA c Georgia Southern University, Department of Biology, Statesboro, GA 30460, USA d St. Johns River Water Management District, 4049 Reid Street, Palatka, FL 32177, USA article info abstract Article history: The primary objective of this study was to examine trends in phytoplankton biomass and species Received 10 March 2015 composition under varying nutrient load and hydrologic regimes in the Guana Tolomato Matanzas es- Received in revised form tuary (GTM), a well-flushed sub-tropical estuary located on the northeast coast of Florida. The GTM 28 July 2015 contains both regions of significant human influence and pristine areas with only modest development, Accepted 31 August 2015 providing a test case for comparing and contrasting phytoplankton community dynamics under varying Available online 4 September 2015 degrees of nutrient load. Water temperature, salinity, Secchi disk depth, nutrient concentrations and chlorophyll concentrations were determined on a monthly basis from 2002 to 2012 at three represen- Keywords: Guana Tolomato Matanzas estuary tative sampling sites in the GTM. -
New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life
bioRxiv preprint doi: https://doi.org/10.1101/403329; this version posted August 30, 2018. 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. New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life Jürgen F. H. Strassert1, Mahwash Jamy1, Alexander P. Mylnikov2, Denis V. Tikhonenkov2, Fabien Burki1,* 1Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden 2Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Yaroslavl Region, Russia *Corresponding author: E-mail: [email protected] Keywords: TSAR, Telonemia, phylogenomics, eukaryotes, tree of life, protists bioRxiv preprint doi: https://doi.org/10.1101/403329; this version posted August 30, 2018. 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. Abstract The broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these ‘orphan’ groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. -
Chesapeake Bay Harmful Algal Blooms Overview of Emerging Issues
Chesapeake Bay Harmful Algal Blooms Overview of Emerging Issues Peter Tango USGS@CBPO Chesapeake Bay Monitoring Coordinator Toxics WG meeting 2/13/2019 1990s/early 2000s: 12 Toxin-producing phytoplankton recognized for Chesapeake Bay (Marshall 1996) • Diatoms: • Amphora coffeaformis • Pseudo-nitszschia pseudodelicatissima • P. seriata, • P. multiseries (pre-1985) • Dinoflagellates: • Cochlodinium heteroblatum • Dinophysis acuminata, D. acuta, D. caudata, D. fortii, D. norvegica, • Gyrodinium aureolum • Pfiesteria piscicida • Prorocentrum minimum • Alexandrium catenella (pre-1985) • Gonyaulax polyedra ((pre-1985) • 708 total phytoplankton taxa recognized in our tidal waters (Marshall 1994) Phytoplankton diversity in Chesapeake Bay today • > 1400 species (Marshall et al. 2005) • < 2% potentially toxic • ~1% proven toxic activity N 0 10 20 30 km Chesapeake Bay and Watershed HABs: What’s new? • Diatoms: Didymo (aka Rock snot) Ecosystem disruptor (nontoxic) • Toxic dinoflagellates • Alexandrium monilatum (oyster/fish killing Rock snot CBP A. monilatum. VIMS toxins in Chesapeake Bay) • Karlodinium micrum (fish tissue dissolves) • Raphidophytes (2+ possibly toxic spp.) • Not previous described among the A. monilatum. York River, VIMS Potomac River blue-greens Sassafras River July 2003 potentially toxic plankton community September 2003, Smith Point area Photo by Connie Goulet > 1.5 million cells/ml • Cyanobacteria • Microcystis aeruginosa (Hepatotoxic) • Anabaena spp. (Neurotoxic) • Aphanizomenon (Hepato+Neurotoxic) • Cylindrospermopsis (Hepatotoxic) • 708 total phytoplankton taxa recognized in our tidal waters (Marshall 1994) • UPDATE: 1434 total phytoplankton taxa recognized (Marshall et al. 2005) Blooms: Species importances range across all seasons. We have potentially toxic plankton species. Are they actively toxic? Where, when, how often? Karlotoxin associated fish kill Bloom and crab jubilee Corsica River 2005 Toxic bloom and bird deaths: Early cyanotoxin history in the bay region • Tisdale (1931a,b) and Veldee (1931) Am. -
Alexandrium Monilatum in the Lower Chesapeake Bay: Sediment Cyst Distribution and Potential Health Impacts on Crassostrea Virginica
W&M ScholarWorks Dissertations, Theses, and Masters Projects Theses, Dissertations, & Master Projects 2016 Alexandrium Monilatum in the Lower Chesapeake Bay: Sediment Cyst Distribution and Potential Health Impacts on Crassostrea Virginica Sarah Pease College of William and Mary - Virginia Institute of Marine Science, [email protected] Follow this and additional works at: https://scholarworks.wm.edu/etd Part of the Aquaculture and Fisheries Commons, Ecology and Evolutionary Biology Commons, and the Marine Biology Commons Recommended Citation Pease, Sarah, "Alexandrium Monilatum in the Lower Chesapeake Bay: Sediment Cyst Distribution and Potential Health Impacts on Crassostrea Virginica" (2016). Dissertations, Theses, and Masters Projects. Paper 1477068141. http://doi.org/10.21220/V5C30T This Thesis is brought to you for free and open access by the Theses, Dissertations, & Master Projects at W&M ScholarWorks. It has been accepted for inclusion in Dissertations, Theses, and Masters Projects by an authorized administrator of W&M ScholarWorks. For more information, please contact [email protected]. Alexandrium monilatum in the Lower Chesapeake Bay: Sediment Cyst Distribution and Potential Health Impacts on Crassostrea virginica ______________ A Thesis Presented to The Faculty of the School of Marine Science The College of William and Mary in Virginia In Partial Fulfillment of the Requirements for the Degree of Master of Science ______________ by Sarah K. D. Pease 2016 APPROVAL SHEET This thesis is submitted in partial fulfillment of the requirements for the degree of Master of Science _________________________________ Sarah K. D. Pease Approved, by the Committee, August 2016 __________________________________ Kimberly S. Reece, Ph.D. Committee Co-Chairman/Co-Advisor __________________________________ Wolfgang K. Vogelbein, Ph.D. -
Cell Lysis of a Phagotrophic Dinoflagellate, Polykrikos Kofoidii Feeding on Alexandrium Tamarense
Plankton Biol. Ecol. 47 (2): 134-136,2000 plankton biology & ecology f The Plankton Society of Japan 2(100 Note Cell lysis of a phagotrophic dinoflagellate, Polykrikos kofoidii feeding on Alexandrium tamarense Hyun-Jin Cho1 & Kazumi Matsuoka2 'Graduate School of Marine Science and Engineering, Nagasaki University, 1-14 Bunkyo-inachi, Nagasaki 852-8521. Japan 2Laboratory of Coastal Environmental Sciences, Faculty of Fisheries. Nagasaki University. 1-14 Bunkyo-machi, Nagasaki 852-8521. Japan Received 9 December 1999; accepted 10 April 2000 In many cases, phytoplankton blooms terminate suddenly dinoflagellate, Alexandrium tamarense (Lebour) Balech. within a few days. For bloom-forming phytoplankton, grazing P. kofoidii was collected from Isahaya Bay in western is one of the major factors in the decline of blooms as is sexual Kyushu, Japan, on 3 November, 1998. We isolated actively reproduction to produce non-dividing gametes and planozy- swimming P. kofoidii using a capillary pipette and individually gotes (Anderson et al. 1983; Frost 1991). Matsuoka et al. transferred them into multi-well tissue culture plates contain (2000) reported growth rates of a phagotrophic dinoflagellate, ing a dense suspension of the autotrophic dinoflagellate, Polykrikos kofoidii Chatton, using several dinoflagellate Gymnodinium catenatum Graham (approximately 700 cells species as food organisms. They noted that P. kofoidii showed ml"1) isolated from a bloom near Amakusa Island, western various feeding and growth responses to strains of Alexan Japan, 1997. The P. kofoidii were cultured at 20°C with con drium and Prorocentrum. This fact suggests that for ecological stant lighting to a density of 60 indiv. ml"1, and then starved control of phytoplankton blooms, we should collect infor until no G.