DOCSLIB.ORG

UC San Diego UC San Diego Previously Published Works

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
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. pseudonana was recorded for the first time in Argentinean shelf waters. New information on the girdle The Argentine Sea, the Polar Front and the Weddell Sea are view is included, except for the species F. curta, F. cylindrus characterized by high primary productivity and rich phy- and F. nana, for which information already existed. In the toplankton communities (Longhurst 1998; Romero et al. Argentine Sea, F. pseudonana was the most abundant 2006; Schloss et al. 2007). Phytoplankton are the main Fragilariopsis species, and in Antarctic waters, F. curta was source of organic carbon in the ocean and are subject to high most abundant. Of the twelve species of Fragilariopsis spatial variability and strong seasonality (Fischer et al. documented, four occurred in the Argentine Sea, nine in the 2002). The abundance, composition and cell size distribu- tion of phytoplankton communities influence the flow of organic carbon in pelagic waters (Schloss and Estrada A. O. Cefarelli (&) Á M. E. Ferrario Á G. O. Almandoz Á 1994). Large phytoplankton organisms (microplankton, A. G. Atencio [20 lm) are commonly associated with productive areas in Departamento Cientı´fico Ficologı´a, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del the Southern Ocean, while smaller flagellates (nanoplank- Bosque s/n, 1900 La Plata, Argentina ton, 2–20 lm) dominate areas of lower productivity (Fryxell e-mail: [email protected] 1989; Kang and Fryxell 1993). Diatoms in chains and Phaeocystis antarctica Karsten are found at the ice edge in M. E. Ferrario Á G. O. Almandoz Á A. G. Atencio CONICET, Consejo Nacional de Investigaciones Cientı´ficas y the spring as well as at oceanic fronts (Kang et al. 2001; Te´cnicas, Av. Rivadavia 1917 (1033), Buenos Aires, Argentina Krell et al. 2005). Diatoms such as Fragilariopsis curta (van Heurck) Hustedt and F. cylindrus (Grunow ex Cleve) R. Akselman Frenguelli can dominate the water column, sea ice and ice- Instituto Nacional de Investigacio´n y Desarrollo Pesquero, V. Ocampo 1, Escollera Norte, B7602HSA Mar del Plata, edge communities (Garrison et al. 1987; Garrison and Buck Argentina 1989; Kang and Fryxell 1993; Socal et al. 1997; Hegseth and von Quillfeldt 2002). Nanoplankton is usually charac- M. Vernet terized by cryptomonads, single cell Phaeocystis antarc- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, tica, Pyramimonas spp. and small diatom species (Garibotti La Jolla, CA 92093-0218, USA et al. 2003). 123 1464 Polar Biol (2010) 33:1463–1484 The predominance of diatoms in the Southern Ocean has elliptical-linear-lanceolate, and isopolar or heteropolar in been well documented and was first described in early valve view. The canal raphe is markedly eccentric, not research expeditions (Hooker 1844). Productive areas, such raised above the level of the valve and without poroids in as the Western Antarctic Peninsula (Walsh et al. 2001; the outer wall (Hasle 1965, 1993; Round et al. 1990). The Garibotti et al. 2003; Pre´zelin et al. 2004), the Weddell Sea valve striae are separated by robust interstriae and gener- (Fryxell and Kendrick 1988), Prydz Bay (Kopczyn´ska et al. ally have two rows of poroids (rarely more than two and 1995), the Bellingshausen Sea (Barlow et al. 1998; van sometimes only one). In general, the striae are parallel, Leeuwe et al. 1998) and the Ross Sea (Arrigo et al. 1999), except near the poles (Round et al. 1990; Hasle and tend to be rich in diatoms (Kopczyn´ska et al. 2007; Syvertsen 1997). The valve mantle can be unperforated or Kozlowski 2008). Productive waters of the Argentine Sea can have striae with one or more rows of poroids. Girdle (Southwestern South Atlantic) are also rich in diatoms bands are unperforated or show one or more rows of por- (e.g., Carreto et al. 1981; Akselman 1996; Almandoz et al. oids (Hasle 1965; Medlin and Sims 1993). In general, there 2007). Diatoms can be identified by microscopy, pigment is little information on the girdle view of the different content or genetic analyses. The need for improved meth- Fragilariopsis species. The cells have two chloroplasts, ods to identify diatoms as well as additional information to one at each side of the median transapical plain (Hasle and improve the use of existing techniques is an ongoing Syvertsen 1997). research effort. Diatom samples from Antarctica and Argentina, col- Fragilariopsis Hustedt is a marine diatom genus that lected by Dr. Joaquı´n Frenguelli (1883–1958) and others, includes planktonic, a few benthic and some ice-associated are catalogued and compiled as the ‘‘Coleccio´nde species (Hasle and Medlin 1990; Round et al. 1990). Many Diatomeas Argentinas Dr. J. Frenguelli’’. The collection is of them are well preserved in marine sediments and are located at the Museo de La Plata, La Plata, Argentina. used in paleoceanography for past productivity estimates Permanent slides (2,435) are catalogued and organized by (e.g., Zielinski and Gersonde 1997; Abelmann et al. 2006). sample (Ferrario et al. 1995). With 459 new taxa (genera, Fragilariopsis has a wide geographical distribution but is species, varieties and forms) and 38 type materials from mainly found in polar waters, especially Antarctica, where Antarctica, Frenguelli’s collection is frequently consulted many species can be found, usually in great abundance for taxonomic studies (e.g., Hasle 1964, 1965; Simonsen (Frenguelli 1943; Frenguelli and Orlando 1958, 1959; 1974; Ferrario et al. 2008; Fernandes and Sar 2009). As Hasle and Medlin 1990; Round et al. 1990). However, the collection includes multiple Fragilariopsis species, F. pseudonana (Hasle) Hasle is a cosmopolitan species, we consulted it for this study (Frenguelli 1943, 1960; and F. doliolus (Wallich) Medlin and Sims is restricted to Frenguelli and Orlando 1958, 1959). warm waters (Hasle 1976; Medlin and Sims 1993; Hasle The objective of this study was to identify and describe and Syvertsen 1997). Some Fragilariopsis species are the Fragilariopsis diatom species found in neritic and found in the Southwestern Atlantic Ocean (Brandini et al. oceanic surface waters of the Argentine Sea, Drake Passage 2000; Romero and Hensen 2002; Olguı´n et. al 2006), but and Weddell Sea by light and electron microscopy. Twelve their occurrence in Argentine shelf waters is poorly docu- species were documented. Previous descriptions on Frag- mented (Ferrario and Galva´n 1989; Vouilloud 2003). ilariopsis species were expanded, and important details on The genus Fragilariopsis was established by Hustedt in girdle view were provided for the first time. F. peragallii 1913 by separating Fragilariopsis from the genus Fragi- (Hasle) Cremer was examined for the first time using laria Lyngbye. In 1972, Hasle reduced Fragilariopsis to a electron microscopy. Species relative abundance and con- section of the genus Nitzschia Hassall, arguing that a real centration were given and compared with abundance of difference between these genera did not exist. In 1990, other diatom species and total phytoplankton. Round et al. preferred to give Fragilariopsis generic status in view of the enormous diversity already present in Nitzschia and considering that Fragilariopsis appeared to Materials and methods be a natural group. Later, in 1993, Hasle recognized Fragilariopsis to generic status, emending its diagnosis and The present work is based on the analysis of phytoplankton making new combinations. However, the molecular anal- samples collected in the South Atlantic and Antarctic yses indicated that Fragilariopsis and Pseudo-nitzschia are waters. During the expedition ARGAU I Project ‘‘Coop- very closely related genera and they might be congeneric eration Program between France and ARGentina for the (Lundholm et al. 2002). The cells in Fragilariopsis are study of the AUstral Atlantic Ocean’’ (19–26 February usually united by the whole or the majority of the valve 2001), 36 quantitative and qualitative samples were col- face into flat, ribbon-like colonies; single cells appear only lected onboard the icebreaker ARA Almirante Irizar along occasionally. The frustules are rectangular in girdle view, three north–south transects: (1) continental shelf of the 123 Polar Biol (2010) 33:1463–1484 1465 Argentine Sea (AS), (2) Drake Passage (DP) and (3) Quantitative samples from ARGAU I were collected Weddell Sea (WS) (Fig.
Load more

Recommended publications
  • 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.
    [Show full text]
  • 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].
    [Show full text]
  • 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
    [Show full text]
  • 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
    [Show full text]
  • Resilience to Temperature and Ph Changes in a Future Climate Change Scenario
    Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Biogeosciences Discuss., 12, 4627–4654, 2015 www.biogeosciences-discuss.net/12/4627/2015/ doi:10.5194/bgd-12-4627-2015 BGD © Author(s) 2015. CC Attribution 3.0 License. 12, 4627–4654, 2015 This discussion paper is/has been under review for the journal Biogeosciences (BG). Resilience to Please refer to the corresponding final paper in BG if available. temperature and pH changes in a future Resilience to temperature and pH climate change changes in a future climate change scenario M. Pan£i¢ et al. scenario in six strains of the polar diatom Fragilariopsis cylindrus Title Page Abstract Introduction M. Pan£i¢1,2, P. J. Hansen3, A. Tammilehto1, and N. Lundholm1 Conclusions References 1Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark Tables Figures 2National Institute of Aquatic Resources, DTU Aqua, Section for Marine Ecology and Oceanography, Technical University of Denmark, Charlottenlund, Denmark 3Marine Biological Section, University of Copenhagen, Helsingør, Denmark J I Received: 12 February 2015 – Accepted: 6 March 2015 – Published: 20 March 2015 J I Correspondence to: M. Pan£i¢ ([email protected]) Back Close Published by Copernicus Publications on behalf of the European Geosciences Union. Full Screen / Esc Printer-friendly Version Interactive Discussion 4627 Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Abstract BGD The effects of ocean acidification and increased temperature on physiology of six strains of the polar diatom Fragilariopsis cylindrus from Greenland were investigated. 12, 4627–4654, 2015 Experiments were performed under manipulated pH levels (8.0, 7.7, 7.4, and 7.1) and ◦ 5 different temperatures (1, 5 and 8 C) to simulate changes from present to plausible Resilience to future levels.
    [Show full text]
  • 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 .
    [Show full text]
  • 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
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]