Resilience to Temperature and Ph Changes in a Future Climate Change Scenario
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Molecular Underpinnings and Biogeochemical Consequences of Enhanced 8 Diatom Growth in a Warming Southern Ocean
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.01.177865; this version posted July 2, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 2 3 4 Main Manuscript for: 5 6 7 Molecular underpinnings and biogeochemical consequences of enhanced 8 diatom growth in a warming Southern Ocean 9 10 11 Loay Jabrea, Andrew E. Allenb,c*, J. Scott P. McCaina, John P. McCrowb, Nancy Tenenbaumd, 12 Jenna L. Spackeene, Rachel E. Siplere,f, Beverley R. Greeng, Deborah A. Bronke,h, David A. 13 Hutchinsd*, Erin M. Bertranda,*# 14 a Dept. of Biology, Dalhousie University, 1355 Oxford Street, PO BOX 15000, Life Sciences 15 Center, Halifax, NS, Canada, B3H 4R2 16 b Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037, USA 17 c Integrative Oceanography Division, Scripps Institution of Oceanography, University of 18 California, San Diego, La Jolla, CA 92037, USA 19 d University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA 20 e Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, VA, 23062, 21 USA 22 f Memorial University of Newfoundland, 0 Marine Drive, Ocean Sciences Centre, St. John’s, NL, 23 Canada, A1A 4A8 24 g Dept. of Botany, University of British Columbia, #3200-6270 University Boulevard, Vancouver, 25 BC, Canada, V6T 1Z4 26 h Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME 04544, USA 27 *Corresponding Authors. -
Diatomic Compounds in the Soils of Bee-Farm and Nearby Territories in Samarskaya Oblast
BIO Web of Conferences 27, 00036 (2020) https://doi.org/10.1051/bioconf/20202700036 FIES 2020 Diatomic compounds in the soils of bee-farm and nearby territories in Samarskaya oblast N.Ye. Zemskova1,*, A.I. Fazlutdinova2, V.N. Sattarov2 and L.M. Safiullinа2 1Samara State Agrarian University, Ust-Kinelskiy, Samarskaya oblast, 446442, Russia 2Bashkir State Pedagogical University n.a. M. Akmulla, Ufa, 450008, Russia Abstract. This article sheds light on the role diatomic algae in soils play in the assessment of bee farm and nearby territories in four soil and landscape zones in Samarskaya Oblast. The community of diatomic algae is characterized by low species diversity, of which 23 taxons were found. The most often found species are represented by Hantzschia amphioxys (Ehrenberg) Grunow in Cleve & Grunow and Luticola mutica (Kützing) D.G.Mann in Round et al. The maximum of phyla (18) were found in the buffer (transient) zone; in the wooded steppe zone, 11 species were recorded; in the steppe – 2 species, and in the dry steppe zone no species of diatomic algae were found. The qualitative and quantitative characteristics of diatomic algae communities in various biotopes depend on the natural and climate features of a territory and the degree of the anthropogenic impact on the soil and vegetation, which is proved by the fact that high species wealth signifies that the ecosystem is stable and resilient to the changing conditions in the environment, while poor algal flora is less resilient due to the lower degree of diversity. 1 Introduction Diatomic algae play a special role in habitats with extreme conditions [6, 7]. -
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 -
Analysis of Transposable Elements and Protein Divergence Across Diatoms
Analysis of Transposable Elements and Protein Divergence across Diatoms Nina Denne, Illinois Mathematics and Science Academy Matthew Parks, Norm Wickett, & Matthew Johnson, Chicago Botanic Garden IMSAloquium – 4/26/2017 IMSAloquium 2017 1 Outline • Topic 1: Introduction to Diatoms • Topic 2: Introduction to Transposable Elements • Topic 3: Introduction to Protein Divergence • Topic 4: Methods • Topic 5: Transposable Element Results • Topic 6: Protein Divergence Results • Topic 7: Discussion IMSAloquium 2017 2 Diatoms • Responsible for up to 20% of total global photosynthesis • 3 diatom genomes have been sequenced: Thalassiosira pseudonana, Phaeodactylum tricornutum, Fragiliariopsis cylindrus (closest relative: Nannochloropsis gaditana) • How do these diatom genomes compare to Psammoneis japonica in terms of transposable elements and protein divergence? Topic: Introduction to Diatoms - IMSAloquium 2017 3 Diatoms Us! Topic: Introduction to Diatoms IMSAloquium 2017 4 Nannochloropsis gaditana Thalassiosira pseudonana Psammoneis japonica Phaeodactylum tricornutum Fragilariopsis cylindrus Topic: Introduction to Diatoms - IMSAloquium 2017 5 Transposable Elements • DNA sequences that can excise themselves and reinsert themselves in the genome • Regulate gene expression • Two main classes: • 1. Class 1 transposons (retrotransposons) • 2. Class 2 transposons (DNA transposons) • Diatom-specific lineages: CoDiI and CoDiII • Important in understanding genome function and evolution Topic: Transposable Element Introduction - IMSAloquium 2017 6 Protein -
Proceedings of the Fourth Polar Diatom Colloquium
PROCEEDINGS OF THE FOURTH POLAR DIATOM COLLOQUIUM STOCKHOLMS UNIVERSITET DEPARTMENT OF QUATERNARY RESEARCH STOCKHOLM UNIVERSITY AUGUST 24 -28, 1992 BYRD POLAR RESEARCH CENTER T h i Ohio S t ft t « Unlvarilty Byrd Polar Research Center Miscellaneous Series M-323 Fourth Polar Diatom Colloquium Proceedings BYRD POLAR RESEARCH CENTER The Ohio State University Columbus, Ohio 43210, USA PROCEEDINGS OF THE FOURTH POLAR DIATOM COLLOQUIUM AUGUST 24 - 28, 1992 DEPARTMENT OF QUATERNARY RESEARCH STOCKHOLM UNIVERSITY ODENGATAN 63 STOCKHOLM SWEDEN BYRD POLAR RESEARCH CENTER THE OHIO STATE UNIVERSITY COLUMBUS, OHIO 43210 USA Organizing Committee: Urve Miller Anders Wasell Amy Leventer Includes: Agenda Abstracts Attendee List Byrd Polar Research Center Miscellaneous Series M-323 Fourth Polar Diatom Colloquium Proceedings Compiled in 1993 by the BYRD POLAR RESEARCH CENTER Material in this document may be copied without restraint for library, abstract service, education, or personal research purposes. This report may be cited as: Leventer, A. (ed.), 1993. Proceedings of Che Fourth Polar Diatom Colloquium, Department of Quaternary Research, Stockholm University, Stockholm, Sweden, August24-28, 1992. BPRC Misc. Series M-323, Byrd Polar Research Center, Columbus, 72 pp. This report is distributed by: Publications Distribution Program GOLDTHWAIT POLAR LIBRARY Byrd Polar Research Center The Ohio State University Columbus, OH 43210-1002 Mail order requests will be in voiced for the cost of shipping and handling, 1 ii TABLE OF CONTENTS Page Tabic of Contents iii Acknowledgments iv Abstract v Program « vi Microscope Sessions vii Session 1 - Leader Heinz Kldser 1 Cecilie Helium 2 Sung-Ho Kang 4 Heinz KJoser 6 Ryszard Ligowski 8 Harvey Marchant (2) 11 Vladmir Nikolaev 14 UliZielinski 15 Session 2 - Leader Michelle De Seve 16 General Summary 17 Lloyd BurckJe 18 Martine Lapointe 20 Amy Leventer 21 Yelena Polyakova 22 Michelle De Seve 24 Ute Treppke 25 Kerstin Williams 27 Session 3 - Leader David Harwood 28 Lloyd Burckle 29 Martha Ferrario 30 Sung-Ho Kang . -
The Evolution of Silicon Transporters in Diatoms1
CORE Metadata, citation and similar papers at core.ac.uk Provided by Woods Hole Open Access Server J. Phycol. 52, 716–731 (2016) © 2016 The Authors. Journal of Phycology published by Wiley Periodicals, Inc. on behalf of Phycological Society of America. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. DOI: 10.1111/jpy.12441 THE EVOLUTION OF SILICON TRANSPORTERS IN DIATOMS1 Colleen A. Durkin3 Moss Landing Marine Laboratories, 8272 Moss Landing Road, Moss Landing California 95039, USA Julie A. Koester Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington North Carolina 28403, USA Sara J. Bender2 Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole Massachusetts 02543, USA and E. Virginia Armbrust School of Oceanography, University of Washington, Seattle Washington 98195, USA Diatoms are highly productive single-celled algae perhaps their dominant ability to take up silicic acid that form an intricately patterned silica cell wall after from seawater in diverse environmental conditions. every cell division. They take up and utilize silicic Key index words: diatoms; gene family; molecular acid from seawater via silicon transporter (SIT) evolution; nutrients; silicon; transporter proteins. This study examined the evolution of the SIT gene family -
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. -
Transcriptomic and Proteomic Responses of the Oceanic Diatom Pseudo-Nitzschia Granii to Iron Limitation
Environmental Microbiology (2018) 20(8), 3109–3126 doi:10.1111/1462-2920.14386 Transcriptomic and proteomic responses of the oceanic diatom Pseudo-nitzschia granii to iron limitation Natalie R Cohen ,1,2 Weida Gong ,1 in low iron regions and rapidly bloom to outcompete Dawn M. Moran,2 Matthew R. McIlvin,2 Mak A. Saito2 other diatom taxa following iron enrichment. and Adrian Marchetti 1* 1 Department of Marine Sciences, University of North Introduction Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA. fi 2Marine Chemistry and Geochemistry Department, In the coastal Northeast (NE) Paci c Ocean, high phyto- Woods Hole Oceanographic Institution, Woods Hole, plankton biomass is fueled by upwelling of nutrient-rich MA, 02543, USA. deep ocean waters as well as the merging of comple- mentary water masses where coastal nitrate-poor, iron- rich waters meet oceanic nitrate-rich, iron-poor waters Summary (Ribalet et al., 2010). Further offshore, in the middle of Diatoms are a highly successful group of photosyn- the subpolar Alaskan gyre, chronic iron limitation of phy- thetic protists that often thrive under adverse envi- toplankton growth is well-characterized with occasional ronmental conditions. Members of the genus Pseudo- blooms occurring when ephemeral iron enters surface nitzschia are ecologically important diatoms which waters via atmospheric deposition of continental dust or are able to subsist during periods of chronic iron lim- volcanic activity (Lam et al., 2006; Lam and Bishop, itation and form dense blooms following iron fertiliza- 2008; Olgun et al. 2013). Iron fertilization experiments tion events. The cellular strategies within diatoms have demonstrated that the introduction of bioavailable that orchestrate these physiological responses to iron to these high-nutrient, low-chlorophyll (HNLC) waters variable iron concentrations remain largely uncharac- creates diatom blooms, often dominated by the pennate terized. -
2016 National Algal Biofuels Technology Review
National Algal Biofuels Technology Review Bioenergy Technologies Office June 2016 National Algal Biofuels Technology Review U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Bioenergy Technologies Office June 2016 Review Editors: Amanda Barry,1,5 Alexis Wolfe,2 Christine English,3,5 Colleen Ruddick,4 and Devinn Lambert5 2010 National Algal Biofuels Technology Roadmap: eere.energy.gov/bioenergy/pdfs/algal_biofuels_roadmap.pdf A complete list of roadmap and review contributors is available in the appendix. Suggested Citation for this Review: DOE (U.S. Department of Energy). 2016. National Algal Biofuels Technology Review. U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy, Bioenergy Technologies Office. Visit bioenergy.energy.gov for more information. 1 Los Alamos National Laboratory 2 Oak Ridge Institute for Science and Education 3 National Renewable Energy Laboratory 4 BCS, Incorporated 5 Bioenergy Technologies Office This report is being disseminated by the U.S. Department of Energy. As such, the document was prepared in compliance with Section 515 of the Treasury and General Government Appropriations Act for Fiscal Year 2001 (Public Law No. 106-554) and information quality guidelines issued by the Department of Energy. Further, this report could be “influential scientific information” as that term is defined in the Office of Management and Budget’s Information Quality Bulletin for Peer Review (Bulletin). This report has been peer reviewed pursuant to section II.2 of the Bulletin. Cover photo courtesy of Qualitas Health, Inc. BIOENERGY TECHNOLOGIES OFFICE Preface Thank you for your interest in the U.S. Department of Energy (DOE) Bioenergy Technologies Office’s (BETO’s) National Algal Biofuels Technology Review. -
UC San Diego UC San Diego Previously Published Works
UC San Diego UC San Diego Previously Published Works Title Diversity of the diatom genus Fragilariopsis in the Argentine Sea and Antarctic waters: morphology, distribution and abundance Permalink https://escholarship.org/uc/item/5p2517zr Journal Polar Biology, 33(11) ISSN 1432-2056 Authors Cefarelli, Adrián O. Ferrario, Martha E. Almandoz, Gastón O. et al. Publication Date 2010-11-01 DOI 10.1007/s00300-010-0794-z Peer reviewed eScholarship.org Powered by the California Digital Library University of California Polar Biol (2010) 33:1463–1484 DOI 10.1007/s00300-010-0794-z ORIGINAL PAPER Diversity of the diatom genus Fragilariopsis in the Argentine Sea and Antarctic waters: morphology, distribution and abundance Adria´n O. Cefarelli • Martha E. Ferrario • Gasto´n O. Almandoz • Adria´n G. Atencio • Rut Akselman • Marı´a Vernet Received: 9 October 2009 / Revised: 2 March 2010 / Accepted: 12 March 2010 / Published online: 16 October 2010 Ó The Author(s) 2010. This article is published with open access at Springerlink.com Abstract Fragilariopsis species composition and abun- Drake Passage and twelve in the Weddell Sea. F. curta, dance from the Argentine Sea and Antarctic waters were F. kerguelensis, F. pseudonana and F. rhombica were analyzed using light and electron microscopy. Twelve present everywhere. species (F. curta, F. cylindrus, F. kerguelensis, F. nana, F. obliquecostata, F. peragallii, F. pseudonana, F. rhombica, Keywords Phytoplankton Á Diatom Á Fragilariopsis Á F. ritscheri, F. separanda, F. sublinearis and F. vanheurckii) Antarctica Á Argentine Sea are described and compared with samples from the Frengu- elli Collection, Museo de La Plata, Argentina. F. peragallii was examined for the first time using electron microscopy, Introduction and F. -
Diversity of the Diatom Genus Fragilariopsis in the Argentine Sea and Antarctic Waters: Morphology, Distribution and Abundance
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/228758431 Diversity of the diatom genus Fragilariopsis in the Argentine Sea and Antarctic waters: Morphology, distribution and abundance Article in Polar Biology · November 2010 DOI: 10.1007/s00300-010-0794-z CITATIONS READS 47 1,068 6 authors, including: Adrián O. Cefarelli Martha Elba Ferrario Centro de Investigaciones y Transferencia Golfo San Jorge, CONICET, Argentina Universidad Nacional de La Plata 33 PUBLICATIONS 261 CITATIONS 100 PUBLICATIONS 2,088 CITATIONS SEE PROFILE SEE PROFILE Gastón O. Almandoz Adrian Atencio Universidad Nacional de La Plata Departamento General de Irrigacion 53 PUBLICATIONS 947 CITATIONS 13 PUBLICATIONS 290 CITATIONS SEE PROFILE SEE PROFILE Some of the authors of this publication are also working on these related projects: Red Tide View project Evaluación de la presencia de microplásticos en ambientes y organismos costeros del Golfo San Jorge - Mar Argentino View project All content following this page was uploaded by Gastón O. Almandoz on 04 August 2014. The user has requested enhancement of the downloaded file. Polar Biol (2010) 33:1463–1484 DOI 10.1007/s00300-010-0794-z ORIGINAL PAPER Diversity of the diatom genus Fragilariopsis in the Argentine Sea and Antarctic waters: morphology, distribution and abundance Adria´n O. Cefarelli • Martha E. Ferrario • Gasto´n O. Almandoz • Adria´n G. Atencio • Rut Akselman • Marı´a Vernet Received: 9 October 2009 / Revised: 2 March 2010 / Accepted: 12 March 2010 / Published online: 16 October 2010 Ó The Author(s) 2010. This article is published with open access at Springerlink.com Abstract Fragilariopsis species composition and abun- Drake Passage and twelve in the Weddell Sea. -
Taxonomy and Diversity of a Little-Known Diatom Genus Simonsenia (Bacillariaceae) in the Marine Littoral: Novel Taxa from the Yellow Sea and the Gulf of Mexico
Plant Ecology and Evolution 152 (2): 248–261, 2019 https://doi.org/10.5091/plecevo.2019.1614 REGULAR PAPER Taxonomy and diversity of a little-known diatom genus Simonsenia (Bacillariaceae) in the marine littoral: novel taxa from the Yellow Sea and the Gulf of Mexico Byoung-Seok Kim1,8,*, Andrzej Witkowski2,8, Jong-Gyu Park3, Chunlian Li4,2, Rosa Trobajo5, David G. Mann5,6, So-Yeon Kim1, Matt Ashworth7, Małgorzata Bąk2 & Romain Gastineau2 1Department of Oceanography, College of Ocean Science and Engineering, Kunsan National University, Gunsan 54150, Republic of Korea 2Palaeoceanology Unit, Faculty of Geosciences, Natural Sciences Education and Research Centre, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland 3Department of Marine Life and Applied Sciences, College of Ocean Science and Engineering, Kunsan National University, Gunsan 54150, Republic of Korea 4Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou 510631, China 5Institute of Agriculture and Food Research and Technology (IRTA), Sant Carles de la Ràpita, E-43540, Spain 6Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, Scotland, UK 7UTEX Culture Collection of Algae, Department of Molecular Biosciences, University of Texas at Austin, 205 W. 24th St. MS C0930 Austin, Texas 78712, United States 8Both authors contributed equally to this work *Author for correspondence: [email protected] Background and aims – The diatom genus Simonsenia has been considered for some time a minor taxon, limited in its distribution to fresh and slightly brackish waters. Recently, knowledge of its diversity and geographic distribution has been enhanced with new species described from brackish-marine waters of the southern Iberian Peninsula and from inland freshwaters of South China, and here we report novel Simonsenia from fully marine waters.