A Review of Selected Aspects of Coccolithophore Biology with Implications for Paleobiodiversity Estimation
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Overcalcified Forms of the Coccolithophore Emiliania Huxleyi in High CO2 Waters Are Not Pre-Adapted to Ocean Acidification
Biogeosciences Discuss., https://doi.org/10.5194/bg-2017-303 Manuscript under review for journal Biogeosciences Discussion started: 6 September 2017 c Author(s) 2017. CC BY 4.0 License. Overcalcified forms of the coccolithophore Emiliania huxleyi in high CO2 waters are not pre-adapted to ocean acidification. Peter von Dassow1,2,3*, Francisco Díaz-Rosas1,2, El Mahdi Bendif4, Juan-Diego Gaitán-Espitia5, Daniella Mella-Flores1, Sebastian Rokitta6, Uwe John6, and Rodrigo Torres7,8 5 1 Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile. 2 Instituto Milenio de Oceanografía de Chile. 3 UMI 3614, Evolutionary Biology and Ecology of Algae, CNRS-UPMC Sorbonne Universités, PUCCh, UACH. 4 Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, UK. 5 CSIRO Oceans and Atmosphere, GPO Box 1538, Hobart 7001, TAS, Australia. 10 6 Marine Biogeosciences | PhytoChange Alfred Wegener Institute – Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany. 7 Centro de Investigación en Ecosistemas de la Patagonia (CIEP), Coyhaique, Chile. 8 Centro de Investigación: Dinámica de Ecosistemas marinos de Altas Latitudes (IDEAL), Punta Arenas, Chile. Correspondence to: Peter von Dassow ([email protected]) 15 Abstract. Marine multicellular organisms inhabiting waters with natural high fluctuations in pH appear more tolerant to acidification than conspecifics occurring in nearby stable waters, suggesting that environments of fluctuating pH hold genetic reservoirs for adaptation of key groups to ocean acidification (OA). The abundant and cosmopolitan calcifying phytoplankton Emiliania huxleyi exhibits a range of morphotypes with varying degrees of coccolith mineralization. We show that E. huxleyi populations in the naturally acidified upwelling waters of the Eastern South Pacific, where pH drops below 20 7.8 as is predicted for the global surface ocean by the year 2100, are dominated by exceptionally overcalcified morphotypes whose distal coccolith shield can be almost solid calcite. -
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. -
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. -
An Explanation for the 18O Excess in Noelaerhabdaceae Coccolith Calcite
Available online at www.sciencedirect.com ScienceDirect Geochimica et Cosmochimica Acta 189 (2016) 132–142 www.elsevier.com/locate/gca An explanation for the 18O excess in Noelaerhabdaceae coccolith calcite M. Hermoso a,⇑, F. Minoletti b,c, G. Aloisi d,e, M. Bonifacie f, H.L.O. McClelland a,1, N. Labourdette b,c, P. Renforth g, C. Chaduteau f, R.E.M. Rickaby a a University of Oxford – Department of Earth Sciences, South Parks Road, Oxford OX1 3AN, United Kingdom b Sorbonne Universite´s, UPMC Universite´ Paris 06 – Institut de Sciences de la Terre de Paris (ISTeP), 4 Place Jussieu, 75252 Paris Cedex 05, France c CNRS – UMR 7193 ISTeP, 4 Place Jussieu, 75252 Paris Cedex 05, France d Sorbonne Universite´s, UPMC Universite´ Paris 06 – UMR 7159 LOCEAN, 4 Place Jussieu, 75005 Paris, France e CNRS – UMR 7159 LOCEAN, 4 Place Jussieu, 75005 Paris, France f Institut de Physique du Globe de Paris, Sorbonne Paris Cite´, Universite´ Paris-Diderot, UMR CNRS 7154, 1 rue Jussieu, 75238 Paris Cedex, France g Cardiff University – School of Earth and Ocean Sciences, Parks Place, Cardiff CF10 3AT, United Kingdom Received 10 November 2015; accepted in revised form 11 June 2016; available online 18 June 2016 Abstract Coccoliths have dominated the sedimentary archive in the pelagic environment since the Jurassic. The biominerals pro- duced by the coccolithophores are ideally placed to infer sea surface temperatures from their oxygen isotopic composition, as calcification in this photosynthetic algal group only occurs in the sunlit surface waters. In the present study, we dissect the isotopic mechanisms contributing to the ‘‘vital effect”, which overprints the oceanic temperatures recorded in coccolith calcite. -
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. -
A Persistent Giant Algal Virus, with a Unique Morphology, Encodes An
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.30.228163; this version posted January 13, 2021. 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 A persistent giant algal virus, with a unique morphology, encodes an 2 unprecedented number of genes involved in energy metabolism 3 4 Romain Blanc-Mathieu1,2, Håkon Dahle3, Antje Hofgaard4, David Brandt5, Hiroki 5 Ban1, Jörn Kalinowski5, Hiroyuki Ogata1 and Ruth-Anne Sandaa6* 6 7 1: Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011, Japan 8 2: Laboratoire de Physiologie Cellulaire & Végétale, CEA, Univ. Grenoble Alpes, 9 CNRS, INRA, IRIG, Grenoble, France 10 3: Department of Biological Sciences and K.G. Jebsen Center for Deep Sea Research, 11 University of Bergen, Bergen, Norway 12 4: Department of Biosciences, University of Oslo, Norway 13 5: Center for Biotechnology, Universität Bielefeld, Bielefeld, 33615, Germany 14 6: Department of Biological Sciences, University of Bergen, Bergen, Norway 15 *Corresponding author: Ruth-Anne Sandaa, +47 55584646, [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.30.228163; this version posted January 13, 2021. 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. 16 Abstract 17 Viruses have long been viewed as entities possessing extremely limited metabolic 18 capacities. -
Available Generic Names for Trilobites
AVAILABLE GENERIC NAMES FOR TRILOBITES P.A. JELL AND J.M. ADRAIN Jell, P.A. & Adrain, J.M. 30 8 2002: Available generic names for trilobites. Memoirs of the Queensland Museum 48(2): 331-553. Brisbane. ISSN0079-8835. Aconsolidated list of available generic names introduced since the beginning of the binomial nomenclature system for trilobites is presented for the first time. Each entry is accompanied by the author and date of availability, by the name of the type species, by a lithostratigraphic or biostratigraphic and geographic reference for the type species, by a family assignment and by an age indication of the type species at the Period level (e.g. MCAM, LDEV). A second listing of these names is taxonomically arranged in families with the families listed alphabetically, higher level classification being outside the scope of this work. We also provide a list of names that have apparently been applied to trilobites but which remain nomina nuda within the ICZN definition. Peter A. Jell, Queensland Museum, PO Box 3300, South Brisbane, Queensland 4101, Australia; Jonathan M. Adrain, Department of Geoscience, 121 Trowbridge Hall, Univ- ersity of Iowa, Iowa City, Iowa 52242, USA; 1 August 2002. p Trilobites, generic names, checklist. Trilobite fossils attracted the attention of could find. This list was copied on an early spirit humans in different parts of the world from the stencil machine to some 20 or more trilobite very beginning, probably even prehistoric times. workers around the world, principally those who In the 1700s various European natural historians would author the 1959 Treatise edition. Weller began systematic study of living and fossil also drew on this compilation for his Presidential organisms including trilobites. -
Seasonal and Depth Variations in Molecular and Isotopic Alkenone Composition of Sinking Particles from the Western Title North Pacific
Seasonal and depth variations in molecular and isotopic alkenone composition of sinking particles from the western Title North Pacific Author(s) Yamamoto, Masanobu; Shimamoto, Akifumi; Fukuhara, Tatsuo; Naraoka, Hiroshi; Tanaka, Yuichiro; Nishimura, Akira Deep Sea Research Part I : Oceanographic Research Papers, 54(9), 1571-1592 Citation https://doi.org/10.1016/j.dsr.2007.05.012 Issue Date 2007-09 Doc URL http://hdl.handle.net/2115/28776 Type article (author version) File Information DSR54-9.pdf Instructions for use Hokkaido University Collection of Scholarly and Academic Papers : HUSCAP Seasonal and depth variations in molecular and isotopic alkenone composition of sinking particles from the western North Pacific Masanobu Yamamoto1,*, Akifumi Shimamoto2, Tatsuo Fukuhara2, Hiroshi Naraoka3, Yuichiro Tanaka4 and Akira Nishimura4 1Faculty of Environmental Earth Science, Hokkaido University, Sapporo 060-0810, Japan. 2The General Environmental Technos Co., LTD., Osaka 541-0052, Japan. 3Department of Earth Sciences, Okayama University, Okayama 700-8530, Japan. 4National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8567, Japan *Corresponding author; [email protected] Abstract: Seasonal and depth variations in alkenone flux and molecular and isotopic composition of sinking particles were examined using a 21-month time-series sediment trap experiment at a mooring station WCT-2 (39°N, 147°E) in the mid-latitude NW Pacific to assess the influences of seasonality, production depth, and degradation in the K’ water column on the alkenone unsaturation index U 37. Analysis of the underlying sediments was also conducted to evaluate the effects of alkenone degradation at the 1 K’ K’ water-sediment interface on U 37. -
Coccolithophore Distribution in the Mediterranean Sea and Relate A
Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Ocean Sci. Discuss., 11, 613–653, 2014 Open Access www.ocean-sci-discuss.net/11/613/2014/ Ocean Science OSD doi:10.5194/osd-11-613-2014 Discussions © Author(s) 2014. CC Attribution 3.0 License. 11, 613–653, 2014 This discussion paper is/has been under review for the journal Ocean Science (OS). Coccolithophore Please refer to the corresponding final paper in OS if available. distribution in the Mediterranean Sea Is coccolithophore distribution in the A. M. Oviedo et al. Mediterranean Sea related to seawater carbonate chemistry? Title Page Abstract Introduction A. M. Oviedo1, P. Ziveri1,2, M. Álvarez3, and T. Tanhua4 Conclusions References 1Institute of Environmental Science and Technology (ICTA), Universitat Autonoma de Barcelona (UAB), 08193 Bellaterra, Spain Tables Figures 2Earth & Climate Cluster, Department of Earth Sciences, FALW, Vrije Universiteit Amsterdam, FALW, HV1081 Amsterdam, the Netherlands J I 3IEO – Instituto Espanol de Oceanografia, Apd. 130, A Coruna, 15001, Spain 4GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Marine Biogeochemistry, J I Duesternbrooker Weg 20, 24105 Kiel, Germany Back Close Received: 31 December 2013 – Accepted: 15 January 2014 – Published: 20 February 2014 Full Screen / Esc Correspondence to: A. M. Oviedo ([email protected]) Published by Copernicus Publications on behalf of the European Geosciences Union. Printer-friendly Version Interactive Discussion 613 Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Abstract OSD The Mediterranean Sea is considered a “hot-spot” for climate change, being char- acterized by oligotrophic to ultra-oligotrophic waters and rapidly changing carbonate 11, 613–653, 2014 chemistry. Coccolithophores are considered a dominant phytoplankton group in these 5 waters. -
Review of the Center for Computational Sciences, University of Tsukuba 2020
Review of the Center for Computational Sciences, University of Tsukuba 2020 筑波大学計算科学研究センター 外部評価報告書 September 2020 2020 年 9月 Center for Computational Sciences University of Tsukuba Review of the Center for Computational Sciences, University of Tsukuba 2014-2019 Foreword This volume contains the Report of the External Review for Center for Computational Scineces (CCS), University of Tsukuba, which was carried out in FY2019. The objective of the External Review was to evaluate the research activities of CCS during the period from FY2014 to FY2019 since the previous external review which was held in FY2013, and the future strategy and plans. Originally formed as the Center for Computational Physics (CCP) in 1992, the CCS was reorganized, expanded and relaunched under its current name in April 2004. The mission of the Center for Computational Sciences (CCS) is the promotion of "Multidisciplinary Computational Sciences" through enhanced cooperation between, and the fusion of, computational and computer sciences. The most important characteristics of the research collaboration in the CCS is “codesigning” where the needs from application fields and seeds from system technologies to make a balanced and optimized system development as well as application program development. As a unique research center where both computational and computer scientists work together, our codesigning for advanced High Performance Computing (HPC) research has been continued from the beginning until today. The CCS has developed several supercomputers, and conducted computational sciences in the areas of particle physics, astrophysics, nuclear physics, materials science, life science, environmental science, high performance computing technology, and information science including database technology and computational media. Also, the CCS plays a significant role as a nation-wide joint-use facility that provides computational resources for external scientific researchers in all of these areas all over the world. -
The Coccolithophore Family Calciosoleniaceae with Report of A
The coccolithophore family Calciosoleniaceae with report of a new species: Calciosolenia subtropicus from the southern Indian Ocean Shramik Patil, Rahul Mohan, Syed Jafar, Sahina Gazi, Pallavi Choudhari, Xavier Crosta To cite this version: Shramik Patil, Rahul Mohan, Syed Jafar, Sahina Gazi, Pallavi Choudhari, et al.. The coccolithophore family Calciosoleniaceae with report of a new species: Calciosolenia subtropicus from the southern Indian Ocean. Micropaleontology, Micropaleontology Press, 2019. hal-02323185 HAL Id: hal-02323185 https://hal.archives-ouvertes.fr/hal-02323185 Submitted on 22 Oct 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. The coccolithophore family Calciosoleniaceae with report of a new species: Calciosolenia subtropicus from the southern Indian Ocean Shramik Patil1, Rahul Mohan1, Syed A. Jafar2, Sahina Gazi1, Pallavi Choudhari1 and Xavier Crosta3 1National Centre for Polar and Ocean Research (NCPOR), Headland Sada, Vasco-da-Gama, Goa-403804, India email: [email protected] 2Flat 5-B, Whispering Meadows, Haralur Road, Bangalore-560 102, India 3UMR-CNRS 5805 EPOC, Université de Bordeaux, Allée Geoffroy Saint Hilaire, 33615 Pessac Cedex, France ABSTRACT: The families Calciosoleniaceae, Syracosphaeraceae and Rhabdosphaeraceae belong to the order Syracosphaerales and constitute a significant component of extant coccolithophore species, sharing similar ultrastructural bauplans. -
Within-Arctic Horizontal Gene Transfer As a Driver of Convergent Evolution in Distantly Related 1 Microalgae 2 Richard G. Do
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454568; this version posted August 2, 2021. 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 Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related 2 microalgae 3 Richard G. Dorrell*+1,2, Alan Kuo3*, Zoltan Füssy4, Elisabeth Richardson5,6, Asaf Salamov3, Nikola 4 Zarevski,1,2,7 Nastasia J. Freyria8, Federico M. Ibarbalz1,2,9, Jerry Jenkins3,10, Juan Jose Pierella 5 Karlusich1,2, Andrei Stecca Steindorff3, Robyn E. Edgar8, Lori Handley10, Kathleen Lail3, Anna Lipzen3, 6 Vincent Lombard11, John McFarlane5, Charlotte Nef1,2, Anna M.G. Novák Vanclová1,2, Yi Peng3, Chris 7 Plott10, Marianne Potvin8, Fabio Rocha Jimenez Vieira1,2, Kerrie Barry3, Joel B. Dacks5, Colomban de 8 Vargas2,12, Bernard Henrissat11,13, Eric Pelletier2,14, Jeremy Schmutz3,10, Patrick Wincker2,14, Chris 9 Bowler1,2, Igor V. Grigoriev3,15, and Connie Lovejoy+8 10 11 1 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, 12 INSERM, Université PSL, 75005 Paris, France 13 2CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, 14 FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France 15 3 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 16 Cyclotron Road, Berkeley,