1
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Millette NC, Gast RJ, Luo JY, Moeller HV, Stamieszkin K, Andersen KH, Brownlee EF, Cohen NR, Duhamel S, Dutkiewicz S, Glibert PM, Johnson MD, Leles SG, Maloney AE, Mcmanus GB, Poulton N, Princiotta SD, Sanders RW, Wilken S. Mixoplankton and mixotrophy: future research priorities. J Plankton Res 2023; 45:576-596. [PMID: 37483910 PMCID: PMC10361813 DOI: 10.1093/plankt/fbad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/14/2023] [Indexed: 07/25/2023]
Abstract
Phago-mixotrophy, the combination of photoautotrophy and phagotrophy in mixoplankton, organisms that can combine both trophic strategies, have gained increasing attention over the past decade. It is now recognized that a substantial number of protistan plankton species engage in phago-mixotrophy to obtain nutrients for growth and reproduction under a range of environmental conditions. Unfortunately, our current understanding of mixoplankton in aquatic systems significantly lags behind our understanding of zooplankton and phytoplankton, limiting our ability to fully comprehend the role of mixoplankton (and phago-mixotrophy) in the plankton food web and biogeochemical cycling. Here, we put forward five research directions that we believe will lead to major advancement in the field: (i) evolution: understanding mixotrophy in the context of the evolutionary transition from phagotrophy to photoautotrophy; (ii) traits and trade-offs: identifying the key traits and trade-offs constraining mixotrophic metabolisms; (iii) biogeography: large-scale patterns of mixoplankton distribution; (iv) biogeochemistry and trophic transfer: understanding mixoplankton as conduits of nutrients and energy; and (v) in situ methods: improving the identification of in situ mixoplankton and their phago-mixotrophic activity.
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Affiliation(s)
| | - Rebecca J Gast
- Woods Hole Oceanographic Institution, 266 Woods Hole Rd, Woods Hole, MA 02543, USA
| | - Jessica Y Luo
- NOAA Geophysical Fluid Dynamics Laboratory, 201 Forrestal Rd., Princeton, NJ 08540, USA
| | - Holly V Moeller
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, 1120 Noble Hall, Santa Barbara, CA 93106, USA
| | - Karen Stamieszkin
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Dr., East Boothbay, ME 04544, USA
| | - Ken H Andersen
- Center for Ocean Life, Natl. Inst. of Aquatic Resources, Technical University of Denmark, Kemitorvet, Bygning 202, Kongens Lyngby 2840, Denmark
| | - Emily F Brownlee
- Department of Biology, St. Mary’s College of Maryland, 18952 E. Fisher Road, St. Mary’s City, MD 20686, USA
| | - Natalie R Cohen
- Skidaway Institute of Oceanography, University of Georgia, 10 Ocean Science Circle, Savannah, GA 31411, USA
| | - Solange Duhamel
- Department of Molecular and Cellular Biology, The University of Arizona, 1007 E Lowell Street, Tucson, AZ 85721, USA
| | - Stephanie Dutkiewicz
- Center for Global Change Science, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02874, USA
| | - Patricia M Glibert
- Horn Point Laboratory, University of Maryland Center for Environmental Science, 2020 Horns Point Rd, Cambridge, MD 21613, USA
| | - Matthew D Johnson
- Woods Hole Oceanographic Institution, 266 Woods Hole Rd, Woods Hole, MA 02543, USA
| | - Suzana G Leles
- Department of Marine and Environmental Biology, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA
| | - Ashley E Maloney
- Geosciences Department, Princeton University, Guyot Hall, Princeton, NJ 08544, USA
| | - George B Mcmanus
- Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Rd., Groton, CT 06340, USA
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Dr., East Boothbay, ME 04544, USA
| | - Sarah D Princiotta
- Biology Department, Pennsylvania State University, Schuylkill Campus, 200 University Drive, Schuylkill Haven, PA 17972, USA
| | - Robert W Sanders
- Department of Biology, Temple University, 1900 N. 12th St., Philadelphia, PA 19122, USA
| | - Susanne Wilken
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
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2
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Balch WM, Drapeau DT, Poulton N, Archer SD, Cartisano C, Burnell C, Godrijan J. Osmotrophy of dissolved organic compounds by coccolithophore populations: Fixation into particulate organic and inorganic carbon. Sci Adv 2023; 9:eadf6973. [PMID: 37224255 DOI: 10.1126/sciadv.adf6973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/19/2023] [Indexed: 05/26/2023]
Abstract
Coccolithophores are typically thought of as photoautotrophs, yet a few genera inhabit sub-euphotic environments with insufficient light for photosynthesis, suggesting that other carbon acquisition strategies are likely. Field experiments were performed in the northwest Atlantic (a region with potentially abundant coccolithophores). Phytoplankton populations were incubated with 14C-labeled dissolved organic carbon (DOC) compounds, acetate, mannitol, and glycerol. Coccolithophores were sorted from these populations 24 hours later using flow cytometry, and DOC uptake was measured. DOC uptake rates were as high as 10-15 moles cell-1 day-1, slow relative to photosynthesis rates (10-12 moles cell-1 day-1). Growth rates on the organic compounds were low, suggesting that osmotrophy plays more of a survival strategy in low-light situations. Assimilated DOC was found in both particulate organic carbon and calcite coccoliths (particulate inorganic carbon), suggesting that osmotrophic uptake of DOC into coccolithophore calcite is a small but notable part of the biological carbon pump and alkalinity pump paradigms.
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Affiliation(s)
- William M Balch
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Dr., East Boothbay, ME 04544, USA
| | - David T Drapeau
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Dr., East Boothbay, ME 04544, USA
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Dr., East Boothbay, ME 04544, USA
| | - Stephen D Archer
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Dr., East Boothbay, ME 04544, USA
| | - Carmen Cartisano
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Dr., East Boothbay, ME 04544, USA
| | - Craig Burnell
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Dr., East Boothbay, ME 04544, USA
| | - Jelena Godrijan
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
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3
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Delmont TO, Gaia M, Hinsinger DD, Frémont P, Vanni C, Fernandez-Guerra A, Eren AM, Kourlaiev A, d'Agata L, Clayssen Q, Villar E, Labadie K, Cruaud C, Poulain J, Da Silva C, Wessner M, Noel B, Aury JM, de Vargas C, Bowler C, Karsenti E, Pelletier E, Wincker P, Jaillon O, Acinas SG, Bork P, Karsenti E, Bowler C, Sardet C, Stemmann L, de Vargas C, Wincker P, Lescot M, Babin M, Gorsky G, Grimsley N, Guidi L, Hingamp P, Jaillon O, Kandels S, Iudicone D, Ogata H, Pesant S, Sullivan MB, Not F, Lee KB, Boss E, Cochrane G, Follows M, Poulton N, Raes J, Sieracki M, Speich S. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean. Cell Genom 2022; 2:100123. [PMID: 36778897 PMCID: PMC9903769 DOI: 10.1016/j.xgen.2022.100123] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 12/10/2021] [Accepted: 04/04/2022] [Indexed: 12/20/2022]
Abstract
Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.
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Affiliation(s)
- Tom O. Delmont
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France,Corresponding author
| | - Morgan Gaia
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Damien D. Hinsinger
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Paul Frémont
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Chiara Vanni
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - A. Murat Eren
- Helmholtz Institute for Functional Marine Biodiversity at Oldenburg, Germany
| | - Artem Kourlaiev
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Leo d'Agata
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Quentin Clayssen
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Emilie Villar
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Corinne Cruaud
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Marc Wessner
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Tara Oceans CoordinatorsSunagawaShinichi12AcinasSilvia G.13BorkPeer141516KarsentiEric171819BowlerChris1718SardetChristian1720StemmannLars1720de VargasColomban1721WinckerPatrick1722LescotMagali1723BabinMarcel1724GorskyGabriel1720GrimsleyNigel172526GuidiLionel1720HingampPascal1723JaillonOlivier1722KandelsStefanie1417IudiconeDaniele27OgataHiroyuki28PesantStéphane2930SullivanMatthew B.313233NotFabrice21LeeKarp-Boss34BossEmmanuel34CochraneGuy35FollowsMichael36PoultonNicole37RaesJeroen383940SierackiMike37SpeichSabrina4142Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, EtH Zürich, Zürich, SwitzerlandDepartment of Marine Biology and Oceanography, Institute of Marine Sciences–CsiC, Barcelona, SpainStructural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, GermanyMax Delbrück Center for Molecular Medicine, Berlin, GermanyDepartment of Bioinformatics, Biocenter, University of Würzburg, Würzburg, GermanyResearch Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOsee, Paris, FranceInstitut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, FranceDirectors’ Research, European Molecular Biology Laboratory, Heidelberg, GermanySorbonne Université, CNRS, Laboratoire D’Océanographie de Villefranche, Villefranche- sur- Mer, FranceSorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, FranceGénomique Métabolique, Genoscope, Institut de Biologie Francois Jacob, Commissariat à l’Énergie Atomique, CNrs, Université Evry, Université Paris- Saclay, Evry, FranceAix Marseille Universit/e, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, FranceDépartement de Biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)–CNRS (France), Université Laval, Quebec, QC, CanadaCNRS UMR 7232, Biologie Intégrative des Organismes Marins, Banyuls- sur- Mer, FranceSorbonne Universités Paris 06, OOB UPMC, Banyuls- sur- Mer, FranceStazione Zoologica Anton Dohrn, Naples, ItalyInstitute for Chemical Research, Kyoto University, Kyoto, JapanPaNGaea, University of Bremen, Bremen, GermanyMaruM, Center for Marine Environmental Sciences, University of Bremen, Bremen, GermanyDepartment of Microbiology, The Ohio State University, Columbus, OH, USADepartment of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USACenter for RNA Biology, The Ohio State University, Columbus, OH, USASchool of Marine Sciences, University of Maine, Orono, ME, USAEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, UKDepartment of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USABigelow Laboratory for Ocean Sciences, East Boothbay, ME, USADepartment of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, BelgiumCenter for the Biology of Disease, VIB KU Leuven, Leuven, BelgiumDepartment of Applied Biological Sciences, Vrije Universiteit Brussel, Brussels, BelgiumDepartment of Geosciences, Laboratoire de Météorologie Dynamique, École Normale Supérieure, Paris, FranceOcean Physics Laboratory, University of Western Brittany, Brest, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France,Sorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, France
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France,Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Eric Karsenti
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France,Sorbonne Université and CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Roscoff, France,Directors’ Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
| | - Olivier Jaillon
- Génomique Métabolique, Genoscope, Institut François-Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057 Evry, France,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75016 Paris, France
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4
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Galbraith D, Loureiro J, Antoniadi I, Bainard J, Bureš P, Cápal P, Castro M, Castro S, Čertner M, Čertnerová D, Chumová Z, Doležel J, Giorgi D, Husband BC, Kolář F, Koutecký P, Kron P, Leitch IJ, Ljung K, Lopes S, Lučanová M, Lucretti S, Ma W, Melzer S, Molnár I, Novák O, Poulton N, Skalický V, Sliwinska E, Šmarda P, Smith TW, Sun G, Talhinhas P, Tárnok A, Temsch EM, Trávníček P, Urfus T. Best practices in plant cytometry. Cytometry A 2021; 99:311-317. [PMID: 33398930 DOI: 10.1002/cyto.a.24295] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 01/19/2023]
Affiliation(s)
- David Galbraith
- School of Plant Sciences, BIO5 Institute, Arizona Cancer Center, Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA.,State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, Henan University, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Kaifeng, China
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Ioanna Antoniadi
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Jillian Bainard
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, CZ, Czech Republic
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Mariana Castro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Sílvia Castro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Dora Čertnerová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Zuzana Chumová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Debora Giorgi
- Green Biotechnology Laboratory, Biotechnology and Agroindustry Division, Casaccia Research Center, ENEA - Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Petr Koutecký
- Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Paul Kron
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Ilia J Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Richmond, UK
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Sara Lopes
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Magdalena Lučanová
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic.,Department of Botany, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Sergio Lucretti
- Green Biotechnology Laboratory, Biotechnology and Agroindustry Division, Casaccia Research Center, ENEA - Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Wen Ma
- School of Plant Sciences, BIO5 Institute, Arizona Cancer Center, Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA.,State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, Henan University, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Kaifeng, China
| | - Susanne Melzer
- Clinical Trial Centre Leipzig, University Leipzig, Leipzig, Germany.,LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czech Republic
| | - Ondřej Novák
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.,Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Nicole Poulton
- Center for Aquatic Cytometry, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - Vladimír Skalický
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, UTP University of Science and Technology, Bydgoszcz, Poland
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, CZ, Czech Republic
| | - Tyler W Smith
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Guiling Sun
- School of Plant Sciences, BIO5 Institute, Arizona Cancer Center, Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA.,State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, Henan University, School of Life Sciences, State Key Laboratory of Crop Stress Adaptation and Improvement, Kaifeng, China
| | - Pedro Talhinhas
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Attila Tárnok
- LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany.,Department of Precision Instruments, Tsinghua University, Beijing, China.,Department for Therapy Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Eva M Temsch
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Pavel Trávníček
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Tomáš Urfus
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
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5
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Benites LF, Poulton N, Labadie K, Sieracki ME, Grimsley N, Piganeau G. Single cell ecogenomics reveals mating types of individual cells and ssDNA viral infections in the smallest photosynthetic eukaryotes. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190089. [PMID: 31587637 DOI: 10.1098/rstb.2019.0089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Planktonic photosynthetic organisms of the class Mamiellophyceae include the smallest eukaryotes (less than 2 µm), are globally distributed and form the basis of coastal marine ecosystems. Eight complete fully annotated 13-22 Mb genomes from three genera, Ostreococcus, Bathycoccus and Micromonas, are available from previously isolated clonal cultured strains and provide an ideal resource to explore the scope and challenges of analysing single cell amplified genomes (SAGs) isolated from a natural environment. We assembled data from 12 SAGs sampled during the Tara Oceans expedition to gain biological insights about their in situ ecology, which might be lost by isolation and strain culture. Although the assembled nuclear genomes were incomplete, they were large enough to infer the mating types of four Ostreococcus SAGs. The systematic occurrence of sequences from the mitochondria and chloroplast, representing less than 3% of the total cell's DNA, intimates that SAGs provide suitable substrates for detection of non-target sequences, such as those of virions. Analysis of the non-Mamiellophyceae assemblies, following filtering out cross-contaminations during the sequencing process, revealed two novel 1.6 and 1.8 kb circular DNA viruses, and the presence of specific Bacterial and Oomycete sequences suggests that these organisms might co-occur with the Mamiellales. This article is part of a discussion meeting issue 'Single cell ecology'.
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Affiliation(s)
- L Felipe Benites
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, 66650 Banyuls-sur-Mer, France
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique, université Paris Saclay, 9105 Evry, France
| | | | - Nigel Grimsley
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, 66650 Banyuls-sur-Mer, France
| | - Gwenael Piganeau
- Integrative Biology of Marine Organisms (BIOM), Sorbonne University, CNRS, Oceanological Observatory of Banyuls, 66650 Banyuls-sur-Mer, France
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6
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Becraft ED, Woyke T, Jarett J, Ivanova N, Godoy-Vitorino F, Poulton N, Brown JM, Brown J, Lau MCY, Onstott T, Eisen JA, Moser D, Stepanauskas R. Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla. Front Microbiol 2017; 8:2264. [PMID: 29234309 PMCID: PMC5712423 DOI: 10.3389/fmicb.2017.02264] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/02/2017] [Indexed: 01/08/2023] Open
Abstract
Recent advances in single-cell genomic and metagenomic techniques have facilitated the discovery of numerous previously unknown, deep branches of the tree of life that lack cultured representatives. Many of these candidate phyla are composed of microorganisms with minimalistic, streamlined genomes lacking some core metabolic pathways, which may contribute to their resistance to growth in pure culture. Here we analyzed single-cell genomes and metagenome bins to show that the "Candidate phylum Rokubacteria," formerly known as SPAM, represents an interesting exception, by having large genomes (6-8 Mbps), high GC content (66-71%), and the potential for a versatile, mixotrophic metabolism. We also observed an unusually high genomic heterogeneity among individual Rokubacteria cells in the studied samples. These features may have contributed to the limited recovery of sequences of this candidate phylum in prior cultivation and metagenomic studies. Our analyses suggest that Rokubacteria are distributed globally in diverse terrestrial ecosystems, including soils, the rhizosphere, volcanic mud, oil wells, aquifers, and the deep subsurface, with no reports from marine environments to date.
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Affiliation(s)
- Eric D Becraft
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Tanja Woyke
- Joint Genome Institute, Walnut Creek, CA, United States
| | | | | | - Filipa Godoy-Vitorino
- Department of Natural Sciences, Inter American University of Puerto Rico, San Juan, Puerto Rico
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Joseph Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - M C Y Lau
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Tullis Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Jonathan A Eisen
- College of Biological Sciences, Genome Center, University of California, Davis, Davis, CA, United States
| | - Duane Moser
- Desert Research Institute, Las Vegas, NV, United States
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7
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Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL, Pesant S, Karsenti E, Wincker P. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Sci Data 2017; 4:170093. [PMID: 28763055 PMCID: PMC5538240 DOI: 10.1038/sdata.2017.93] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/05/2017] [Indexed: 02/01/2023] Open
Abstract
A unique collection of oceanic samples was gathered by the Tara Oceans
expeditions (2009–2013), targeting plankton organisms ranging from viruses to
metazoans, and providing rich environmental context measurements. Thanks to recent advances in
the field of genomics, extensive sequencing has been performed for a deep genomic analysis of
this huge collection of samples. A strategy based on different approaches, such as
metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for
analysis of size-fractionated plankton communities. Here, we provide detailed procedures
applied for genomic data generation, from nucleic acids extraction to sequence production, and
we describe registries of genomics datasets available at the European Nucleotide Archive (ENA,
www.ebi.ac.uk/ena). The association of these metadata to the experimental
procedures applied for their generation will help the scientific community to access these data
and facilitate their analysis. This paper complements other efforts to provide a full
description of experiments and open science resources generated from the Tara
Oceans project, further extending their value for the study of the world’s planktonic
ecosystems.
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Affiliation(s)
- Adriana Alberti
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Julie Poulain
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Stefan Engelen
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Karine Labadie
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Sarah Romac
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Guillaume Albini
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Jean-Marc Aury
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Caroline Belser
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Alexis Bertrand
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Corinne Cruaud
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Corinne Da Silva
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Carole Dossat
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Frédérick Gavory
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Shahinaz Gas
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Julie Guy
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Maud Haquelle
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - E'krame Jacoby
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Olivier Jaillon
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
| | - Arnaud Lemainque
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Eric Pelletier
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
| | - Gaëlle Samson
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | - Mark Wessner
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France
| | | | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Marta Royo-Llonch
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Francisco M Cornejo-Castillo
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Ramiro Logares
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain
| | - Beatriz Fernández-Gómez
- Departament de Biologia Marina i Oceanografia, Institute of Marine Sciences (ICM), CSIC, Barcelona E08003, Spain.,FONDAP Center for Genome Regulation, Moneda 1375, Santiago 8320000, Chile.,Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, El Libano Macul, Santiago 5524, Chile
| | - Chris Bowler
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Clara Amid
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genomes Campus, Hinxton, Cambridge CB10 1 SD, UK
| | - Colomban De Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France.,Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Nigel Grimsley
- CNRS UMR 7232, BIOM, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France.,Sorbonne Universités Paris 06, OOB UPMC, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France
| | - Elodie Desgranges
- CNRS UMR 7232, BIOM, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France.,Sorbonne Universités Paris 06, OOB UPMC, Avenue Pierre Fabre, Banyuls-sur-Mer 66650, France
| | - Stefanie Kandels-Lewis
- Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany.,Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany
| | - Hiroyuki Ogata
- for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine 04544, USA
| | - Michael E Sieracki
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine 04544, USA.,National Science Foundation, Arlington, Virginia 22230, USA
| | | | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio 43210, USA.,Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jennifer R Brum
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Bonnie L Hurwitz
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, Arizona 85719, USA
| | | | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Str. 8, Bremen 28359, Germany.,PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Leobener Str. 8, Bremen 28359, Germany
| | - Eric Karsenti
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, Paris F-75005, France.,Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany.,Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, 181 Chemin du Lazaret, Villefranche-sur-mer F-06230, France
| | - Patrick Wincker
- CEA-Institut de Biologie François Jacob, Genoscope, 2 rue Gaston Crémieux, Evry 91057, France.,CNRS, UMR 8030, Evry CP5706, France.,Université d'Evry, UMR 8030, Evry CP5706, France
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8
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Dashkova V, Malashenkov D, Poulton N, Vorobjev I, Barteneva NS. Imaging flow cytometry for phytoplankton analysis. Methods 2017; 112:188-200. [DOI: 10.1016/j.ymeth.2016.05.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/13/2016] [Indexed: 10/21/2022] Open
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9
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Cetinić I, Poulton N, Slade WH. Characterizing the phytoplankton soup: pump and plumbing effects on the particle assemblage in underway optical seawater systems. Opt Express 2016; 24:20703-20715. [PMID: 27607674 DOI: 10.1364/oe.24.020703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Many optical and biogeochemical data sets, crucial for algorithm development and satellite data validation, are collected using underway seawater systems over the course of research cruises. Phytoplankton and particle size distribution (PSD) in the ocean is a key measurement, required in oceanographic research and ocean optics. Using a data set collected in the North Atlantic, spanning different oceanic water types, we outline the differences observed in concurrent samples collected from two different flow-through systems: a permanently plumbed science seawater supply with an impeller pump, and an independent system with shorter, clean tubing runs and a diaphragm pump. We observed an average of 40% decrease in phytoplankton counts, and significant changes to the PSD in 10-45 µm range, when comparing impeller and diaphragm pump systems. Change in PSD seems to be more dependent on the type of the phytoplankton, than the size, with photosynthetic ciliates displaying the largest decreases in cell counts (78%). Comparison of chlorophyll concentrations across the two systems demonstrated lower sensitivity to sampling system type. Observed changes in several measured biogeochemical parameters (associated with phytoplankton size distribution) using the two sampling systems, should be used as a guide towards building best practices when it comes to the deployment of flow-through systems in the field for examining optics and biogeochemistry. Using optical models, we evaluated potential impact of the observed change in measured phytoplankton size spectra onto scattering measurements, resulting in significant differences between modeled optical properties across systems (~40%). Researchers should be aware of the methods used with previously collected data sets, and take into consideration the potentially significant and highly variable ecosystem-dependent biases in designing field studies in the future.
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10
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Kopf A, Bicak M, Kottmann R, Schnetzer J, Kostadinov I, Lehmann K, Fernandez-Guerra A, Jeanthon C, Rahav E, Ullrich M, Wichels A, Gerdts G, Polymenakou P, Kotoulas G, Siam R, Abdallah RZ, Sonnenschein EC, Cariou T, O'Gara F, Jackson S, Orlic S, Steinke M, Busch J, Duarte B, Caçador I, Canning-Clode J, Bobrova O, Marteinsson V, Reynisson E, Loureiro CM, Luna GM, Quero GM, Löscher CR, Kremp A, DeLorenzo ME, Øvreås L, Tolman J, LaRoche J, Penna A, Frischer M, Davis T, Katherine B, Meyer CP, Ramos S, Magalhães C, Jude-Lemeilleur F, Aguirre-Macedo ML, Wang S, Poulton N, Jones S, Collin R, Fuhrman JA, Conan P, Alonso C, Stambler N, Goodwin K, Yakimov MM, Baltar F, Bodrossy L, Van De Kamp J, Frampton DM, Ostrowski M, Van Ruth P, Malthouse P, Claus S, Deneudt K, Mortelmans J, Pitois S, Wallom D, Salter I, Costa R, Schroeder DC, Kandil MM, Amaral V, Biancalana F, Santana R, Pedrotti ML, Yoshida T, Ogata H, Ingleton T, Munnik K, Rodriguez-Ezpeleta N, Berteaux-Lecellier V, Wecker P, Cancio I, Vaulot D, Bienhold C, Ghazal H, Chaouni B, Essayeh S, Ettamimi S, Zaid EH, Boukhatem N, Bouali A, Chahboune R, Barrijal S, Timinouni M, El Otmani F, Bennani M, Mea M, Todorova N, Karamfilov V, Ten Hoopen P, Cochrane G, L'Haridon S, Bizsel KC, Vezzi A, Lauro FM, Martin P, Jensen RM, Hinks J, Gebbels S, Rosselli R, De Pascale F, Schiavon R, Dos Santos A, Villar E, Pesant S, Cataletto B, Malfatti F, Edirisinghe R, Silveira JAH, Barbier M, Turk V, Tinta T, Fuller WJ, Salihoglu I, Serakinci N, Ergoren MC, Bresnan E, Iriberri J, Nyhus PAF, Bente E, Karlsen HE, Golyshin PN, Gasol JM, Moncheva S, Dzhembekova N, Johnson Z, Sinigalliano CD, Gidley ML, Zingone A, Danovaro R, Tsiamis G, Clark MS, Costa AC, El Bour M, Martins AM, Collins RE, Ducluzeau AL, Martinez J, Costello MJ, Amaral-Zettler LA, Gilbert JA, Davies N, Field D, Glöckner FO. The ocean sampling day consortium. Gigascience 2015; 4:27. [PMID: 26097697 PMCID: PMC4473829 DOI: 10.1186/s13742-015-0066-5] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/06/2015] [Indexed: 11/26/2022] Open
Abstract
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
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Affiliation(s)
- Anna Kopf
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany ; Jacobs University Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany
| | - Mesude Bicak
- University of Oxford, 7 Keble Road, OX1 3QG Oxford, Oxfordshire UK
| | - Renzo Kottmann
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Julia Schnetzer
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany ; Jacobs University Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany
| | - Ivaylo Kostadinov
- Jacobs University Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany
| | - Katja Lehmann
- Centre for Ecology & Hydrology, MacLean Building, Benson Lane, Crowmarsh Gifford, OX10 8BB Wallingford, Oxfordshire UK
| | - Antonio Fernandez-Guerra
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany ; University of Oxford, 7 Keble Road, OX1 3QG Oxford, Oxfordshire UK
| | - Christian Jeanthon
- CNRS & Sorbonne Universités, UPMC Univ Paris 06, Station Biologique, Place Georges Teissier, F-29680 Roscoff, France
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Tel- Shikmona, POB 8030, 31080 Haifa, Israel
| | - Matthias Ullrich
- Jacobs University Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany
| | - Antje Wichels
- Alfred Wegener Institute, Biologische Anstalt Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
| | - Gunnar Gerdts
- Alfred Wegener Institute, Biologische Anstalt Helgoland, Kurpromenade 201, 27498 Helgoland, Germany
| | - Paraskevi Polymenakou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Gournes Pediados, 71500 Heraklion, Crete Greece
| | - Giorgos Kotoulas
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Gournes Pediados, 71500 Heraklion, Crete Greece
| | - Rania Siam
- Biology Department and YJ-Science and Technology Research Center, American University in Cairo, New Cairo, 11835 Cairo Governorate Egypt
| | - Rehab Z Abdallah
- Biology Department and YJ-Science and Technology Research Center, American University in Cairo, New Cairo, 11835 Cairo Governorate Egypt
| | - Eva C Sonnenschein
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet 301, 2800 Kgs., Lyngby, Denmark
| | - Thierry Cariou
- CNRS & Sorbonne Universités, UPMC Univ Paris 06, Station Biologique, Place Georges Teissier, F-29680 Roscoff, France
| | - Fergal O'Gara
- National University of Ireland-University College Cork, Cork, Ireland ; Curtin University, Biomedical Sciences, Perth, Western Australia Australia
| | - Stephen Jackson
- Department of Systems Biology, Technical University of Denmark, Matematiktorvet 301, 2800 Kgs., Lyngby, Denmark
| | - Sandi Orlic
- Ruđer Bošković Institute, Bijenička cesta 54, 10 000, Zagreb, Croatia
| | - Michael Steinke
- School of Biological Sciences, University of Essex, CO4 3SQ Colchester, Essex UK
| | - Julia Busch
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26383 Wilhemshaven, Germany
| | - Bernardo Duarte
- Marine and Environmental Sciences Centre, Faculty of Sciences of the University of Lisbon, Campo Grande 1749-016, Lisbon, Portugal
| | - Isabel Caçador
- Marine and Environmental Sciences Centre, Faculty of Sciences of the University of Lisbon, Campo Grande 1749-016, Lisbon, Portugal
| | - João Canning-Clode
- Marine and Environmental Sciences Centre, Faculty of Sciences of the University of Lisbon, Campo Grande 1749-016, Lisbon, Portugal ; Smithsonian Environmental Research Center, 21037 Edgewater, Maryland USA
| | - Oleksandra Bobrova
- Department of Microbiology, Virology and Biotechnology, Odessa National II Mechnikov University, Dvoryanskaya str.2, 65082 Odessa, Ukraine
| | | | | | - Clara Magalhães Loureiro
- InBio/CIBIO, Departamento de Biologia da Universidade dos Açores, 9501-801 Ponta Delgada, Portugal
| | - Gian Marco Luna
- National Research Council, Institute of Marine Sciences (CNR-ISMAR), Castello 2737/f, Arsenale Tesa 104, 30122 Venezia, Italy
| | - Grazia Marina Quero
- National Research Council, Institute of Marine Sciences (CNR-ISMAR), Castello 2737/f, Arsenale Tesa 104, 30122 Venezia, Italy
| | - Carolin R Löscher
- Institute of Microbiology/ GEOMAR, Am Botanischen Garten 1-9, 24118 Kiel, Germany
| | - Anke Kremp
- Marine Research Centre, Finnish Environment Institute, Erik Palmenin aukio 1, 00560 Helsinki, Finland
| | - Marie E DeLorenzo
- NOAA/National Ocean Service/NCCOS/Center for Coastal Environmental Health & Biomolecular Research Charleston, 29412 South Carolina, USA
| | - Lise Øvreås
- Department of Biology, University of Bergen, Thormøhlensgate 53B, 5020 Bergen, Norway
| | - Jennifer Tolman
- LaRoche Research Group, Department of Biology, Dalhousie University, B3H 4R2 Halifax, Nova Scotia Canada
| | - Julie LaRoche
- LaRoche Research Group, Department of Biology, Dalhousie University, B3H 4R2 Halifax, Nova Scotia Canada
| | - Antonella Penna
- Department of Biomolecular Sciences, University of Urbino, Viale Trieste 296, 61121 Pesaro, Italy
| | - Marc Frischer
- University of Georgia's Skidaway Institute of Oceanography, 10 Ocean Science Circle, 31411 Savannah, Georgia USA
| | - Timothy Davis
- NOAA-Great Lakes Environmental Research Laboratory, 4840 S State Road, 48108 Ann Arbor, Michigan USA
| | - Barker Katherine
- National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, 20013 Washington, DC USA
| | - Christopher P Meyer
- National Museum of Natural History, Smithsonian Institution, 10th and Constitution Avenue NW, 20013 Washington, DC USA
| | - Sandra Ramos
- CIIMAR, Interdisciplinary Center of Environmental and Marine Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - Catarina Magalhães
- CIIMAR, Interdisciplinary Center of Environmental and Marine Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal
| | - Florence Jude-Lemeilleur
- Station Marine d'Arcachon, CNRS & Univ Bordeaux, 2 rue Professeur Jolyet, F-33120 Arcachon, France
| | - Ma Leopoldina Aguirre-Macedo
- Centro de Investigación y de Estudios Avanzados (CINVESTAV), Unidad Mérida, Carretera Antigua a Progreso Km 6 Cordemex, C.P., 97310 Yucatan, Mexico
| | - Shiao Wang
- Department of Biological Sciences, University of Southern Mississippi, 39406 Hattiesburg, Mississippi USA
| | - Nicole Poulton
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, 04544 East Boothbay, Maine USA
| | - Scott Jones
- Smithsonian Marine Station, 701 Seaway Drive, 34949 Fort Pierce, Florida USA
| | - Rachel Collin
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Balboa Ancon, Panama
| | - Jed A Fuhrman
- Wrigley Institute for Environmental Studies and Department of Biological Sciences, University of Southern California, 90089-0371 Los Angeles, California USA
| | - Pascal Conan
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66651 Banyuls sur Mer, France
| | - Cecilia Alonso
- Microbial Ecology of Aquatic Transitional Systems Research Group, Centro Universitario de la Región Este, Universidad de la República, Ruta 15, km 28.500, Rocha, Uruguay
| | - Noga Stambler
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel ; Interuniversity Institute for Marine Sciences in Eilat, 88103 Eilat, Israel
| | - Kelly Goodwin
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, 4301 Rickenbacker Causeway, 33149 Miami, Florida USA
| | - Michael M Yakimov
- Institute for Coastal Marine Environment, IAMC-CNR, Spianata S Raineri, 86 - 98122, Messina, Sicily Italy
| | - Federico Baltar
- Department of Marine Science, University of Otago, PO Box 56, 9054 Dunedin, New Zealand
| | - Levente Bodrossy
- CSIRO Oceans and Atmosphere Flagship, 7000 Hobart, Tasmania Australia
| | - Jodie Van De Kamp
- CSIRO Oceans and Atmosphere Flagship, 7000 Hobart, Tasmania Australia
| | - Dion Mf Frampton
- CSIRO Oceans and Atmosphere Flagship, 7000 Hobart, Tasmania Australia
| | - Martin Ostrowski
- Department of Chemistry and Biomolecular Science, Macquarie University, 2109 Sydney, Australia
| | - Paul Van Ruth
- South Australian Research and Development Institute (SARDI) - Aquatic Sciences, PO Box 120, 5022 Henley Beach, South Australia Australia
| | - Paul Malthouse
- South Australian Research and Development Institute (SARDI) - Aquatic Sciences, PO Box 120, 5022 Henley Beach, South Australia Australia
| | - Simon Claus
- Flanders Marine Institute, InnovOcean site, Wandelaarkaai 7, 8400 Oostende, Belgium
| | - Klaas Deneudt
- Flanders Marine Institute, InnovOcean site, Wandelaarkaai 7, 8400 Oostende, Belgium
| | - Jonas Mortelmans
- Flanders Marine Institute, InnovOcean site, Wandelaarkaai 7, 8400 Oostende, Belgium
| | - Sophie Pitois
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Pakefield Road, NR33 0HT Lowestoft, Suffolk UK
| | - David Wallom
- University of Oxford, 7 Keble Road, OX1 3QG Oxford, Oxfordshire UK
| | - Ian Salter
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66651 Banyuls sur Mer, France ; Alfred-Wegener-Institut-Helmholtz-Zentrum für Polar-und Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Rodrigo Costa
- Microbial Ecology and Evolution Research Group, Centre of Marine Sciences, Algarve University, Gambelas Campus, Building 7, Room 2.77, 8005-139 Faro, Portugal
| | - Declan C Schroeder
- Marine Biological Association of the UK, Citadel Hill, PL1 2PB Plymouth, Devon UK
| | - Mahrous M Kandil
- Soil and Water Science Department, Faculty of Agriculture, Alexandria University, El-Shatbi, 21545 Alexandria, Egypt
| | - Valentina Amaral
- Microbial Ecology of Aquatic Transitional Systems Research Group, Centro Universitario de la Región Este, Universidad de la República, Ruta 15, km 28.500, Rocha, Uruguay
| | - Florencia Biancalana
- Marine Biogeochemistry - Argentine Institute of Oceanography, Camino La Carrindanga Km 7,5, 8000 Florida, Bahia Blanca Argentina
| | - Rafael Santana
- Microbial Ecology of Aquatic Transitional Systems Research Group, Centro Universitario de la Región Este, Universidad de la República, Ruta 15, km 28.500, Rocha, Uruguay
| | - Maria Luiza Pedrotti
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7093, LOV, Observatoire océanologique, F-Villefranche-sur-Mer, Paris, France
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, 606-8502 Sakyo-ku, Kyoto Japan
| | - Hiroyuki Ogata
- Graduate School of Agriculture, Kyoto University, 606-8502 Sakyo-ku, Kyoto Japan
| | - Tim Ingleton
- Waters, Wetlands and Coasts, New South Wales Office of Environment and Heritage, Sydney South 1232, 59-61 Goulburn Street, 2001 PO Box A290, Sydney, New South Wales Australia ; Antarctic and Southern Ocean Studies, University of Tasmania, 7004 Hobart, Tasmania Australia
| | - Kate Munnik
- Lwandle Technologies, Black River Park, Fir Road, 7925 Observatory, Cape Town South Africa
| | | | | | - Patricia Wecker
- CRIOBE, USR3278 CNRS-EPHE-UPVD, LabEx Corail, BP 1013-98729 Papetoai Moorea, French Polynesia
| | - Ibon Cancio
- University of the Basque Country, PO Box 644, E-48080 Bilbao, Basque Country Spain
| | - Daniel Vaulot
- CNRS & Sorbonne Universités, UPMC Univ Paris 06, Station Biologique, Place Georges Teissier, F-29680 Roscoff, France
| | - Christina Bienhold
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany ; Alfred-Wegener-Institut-Helmholtz-Zentrum für Polar-und Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Hassan Ghazal
- Polydisciplinary Faculty of Nador, University Mohammed Premier, Selouane, Nador Morocco ; Laboratory of Genetics and Biotechnology, University Mohammed Premier, Oujda, Morocco
| | - Bouchra Chaouni
- Laboratory of Genetics and Biotechnology, University Mohammed Premier, Oujda, Morocco ; Faculty of Sciences of Rabat, University Mohammed Fifth Rabat, Rabat, Morocco
| | - Soumya Essayeh
- Polydisciplinary Faculty of Nador, University Mohammed Premier, Selouane, Nador Morocco
| | - Sara Ettamimi
- Laboratory of Genetics and Biotechnology, University Mohammed Premier, Oujda, Morocco ; Polydisciplinary Faculty of Taza, University Sidi Mohammed Ben Abdallah, Fes, Morocco
| | - El Houcine Zaid
- Faculty of Sciences of Rabat, University Mohammed Fifth Rabat, Rabat, Morocco
| | - Noureddine Boukhatem
- Laboratory of Genetics and Biotechnology, University Mohammed Premier, Oujda, Morocco
| | - Abderrahim Bouali
- Laboratory of Genetics and Biotechnology, University Mohammed Premier, Oujda, Morocco
| | - Rajaa Chahboune
- Polydisciplinary Faculty of Nador, University Mohammed Premier, Selouane, Nador Morocco ; Faculté des Sciences et Techniques de Tanger, Université Abdelmalek Essaâdi, Tanger, Morocco
| | - Said Barrijal
- Faculté des Sciences et Techniques de Tanger, Université Abdelmalek Essaâdi, Tanger, Morocco
| | - Mohammed Timinouni
- Pasteur Institute of Morocco, 1 Place Louis Pasteur, 20100 Casablanca, Morocco
| | - Fatima El Otmani
- Microbiology, Health and Environment Team, Department of Biology, Faculty of Sciences, Chouaib Doukkali University, Rte Ben Maachou, BP 20 Avenue des Facultés, El Jadida, Morocco
| | - Mohamed Bennani
- Pasteur Institute of Morocco, 1 Place Louis Pasteur, 20100 Casablanca, Morocco
| | - Marianna Mea
- Jacobs University Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany
| | - Nadezhda Todorova
- Institute of Biodiversity and Ecosystem Research (IBER), Bulgarian Academy of Sciences, 2 Gagarin Street, 1113 Sofia, Bulgaria
| | - Ventzislav Karamfilov
- Institute of Biodiversity and Ecosystem Research (IBER), Bulgarian Academy of Sciences, 2 Gagarin Street, 1113 Sofia, Bulgaria
| | - Petra Ten Hoopen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge, Cambridgeshire UK
| | - Guy Cochrane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, CB10 1SD Cambridge, Cambridgeshire UK
| | - Stephane L'Haridon
- Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM), Place Nicolas Copernic, F-29280 Plouzané, France
| | - Kemal Can Bizsel
- Dokuz Eylul University (DEU), Institute of Marine Sciences and Technology (IMST), Baku Bulvard, No: 100, Inciralti, 35340 Izmir, Balcova Turkey
| | - Alessandro Vezzi
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35121 Padova, Italy
| | - Federico M Lauro
- Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Drive, SBS 01N-27, 637551 Singapore, Singapore
| | - Patrick Martin
- Earth Observatory of Singapore, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore, Singapore
| | - Rachelle M Jensen
- Indigo V Expeditions, ONE°15 Marina, #01-01, 11 Cove Drive, Sentosa Cove, 098497 Singapore, Singapore
| | - Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Drive, SBS 01N-27, 637551 Singapore, Singapore
| | - Susan Gebbels
- School of Marine Science and Technology, Newcastle University, Dove Marine Laboratory, Cullercoats, NE30 4PZ Tyne and Wear UK
| | - Riccardo Rosselli
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35121 Padova, Italy
| | - Fabio De Pascale
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35121 Padova, Italy
| | - Riccardo Schiavon
- Department of Biology, University of Padova, Via Ugo Bassi 58/B, 35121 Padova, Italy
| | - Antonina Dos Santos
- IPMA, Department of Sea and Marine Resources, Avenida de Brasília, s/n, 1449-006 Lisboa, Portugal
| | - Emilie Villar
- Aix Marseille Université, CNRS, IGS UMR 7256, 163 Avenue de Luminy, 13288 Marseille, France
| | - Stéphane Pesant
- PANGAEA - Data Publisher for Earth & Environmental Science, MARUM Center for Marine Environmental Sciences, University Bremen, Hochschulring 18, 28359 Bremen, Germany
| | - Bruno Cataletto
- OGS, National Institute of Oceanography and Experimental Geophysics, Via Auguste Piccard, 54, 34151, Santa Croce, Trieste, Italy
| | - Francesca Malfatti
- OGS, National Institute of Oceanography and Experimental Geophysics, Via Auguste Piccard, 54, 34151, Santa Croce, Trieste, Italy
| | - Ranjith Edirisinghe
- Department of Physical Sciences, Faculty of Applied Sciences, Rajarata University of Sri Lanka, Mihintale, Sri Lanka
| | - Jorge A Herrera Silveira
- Department of Biological Sciences, University of Southern Mississippi, 39406 Hattiesburg, Mississippi USA
| | - Michele Barbier
- Mediterranean Science Commission, 16 Bd de Suisse, 98 000 Monaco, Monaco
| | - Valentina Turk
- Marine Biology Station, National Institute of Biology, Fornače 41, 6330 Piran, Slovenia
| | - Tinkara Tinta
- Marine Biology Station, National Institute of Biology, Fornače 41, 6330 Piran, Slovenia
| | - Wayne J Fuller
- Near East University, TRNC Mersin 10, 99138 Nicosia, Northern Cyprus
| | - Ilkay Salihoglu
- Near East University, TRNC Mersin 10, 99138 Nicosia, Northern Cyprus
| | - Nedime Serakinci
- Near East University, TRNC Mersin 10, 99138 Nicosia, Northern Cyprus
| | | | - Eileen Bresnan
- Phytoplankton Ecology, Marine Scotland Marine Laboratory, 375 Victoria Road, AB11 9DB Aberdeen, Aberdeenshire UK
| | - Juan Iriberri
- University of the Basque Country, PO Box 644, E-48080 Bilbao, Basque Country Spain
| | | | - Edvardsen Bente
- Section for Aquatic Biology and Toxicology, Department of Biosciences, University of Oslo, PO Box 1066, 0316 Blindern, Oslo Norway
| | - Hans Erik Karlsen
- Drøbak Field Station, Marine Biology Research station, Biologiveien 2, 1440 Drøbak, Norway
| | - Peter N Golyshin
- School of Biological Sciences, College of Natural Sciences, Bangor University, LL57 2UW Gwynedd, Bangor UK
| | - Josep M Gasol
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar-CSIC, Pg Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya Spain
| | - Snejana Moncheva
- Fridtjof Nansen Institute of Oceanology, First May Street 40, 9000 Varna, Bulgaria
| | - Nina Dzhembekova
- Fridtjof Nansen Institute of Oceanology, First May Street 40, 9000 Varna, Bulgaria
| | - Zackary Johnson
- Nicholas School of the Environment and Biology Department, Duke University, 135 Marine Lab Road, 28516 Beaufort, North Carolina USA
| | - Christopher David Sinigalliano
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, 4301 Rickenbacker Causeway, 33149 Miami, Florida USA
| | - Maribeth Louise Gidley
- NOAA Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, 4301 Rickenbacker Causeway, 33149 Miami, Florida USA ; Cooperative Institute of Marine and Atmospheric Sciences, Rosenstiel School of Marine & Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, 33149 Miami, Florida USA
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Roberto Danovaro
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy ; Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - George Tsiamis
- Department of Environmental and Natural Resources Management, University of Patras, 2 Seferi Street, 301 00 Agrinio, Greece
| | - Melody S Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, CB3 0ET Cambridge, Cambridgeshire UK
| | - Ana Cristina Costa
- InBio/CIBIO, Departamento de Biologia da Universidade dos Açores, 9501-801 Ponta Delgada, Portugal
| | - Monia El Bour
- Institut National des Sciences et Technologies de la Mer (INSTM), 28 rue du 2 mars 1934, 2025 Salammbô, Tunisia
| | - Ana M Martins
- InBio/CIBIO, Departamento de Biologia da Universidade dos Açores, 9501-801 Ponta Delgada, Portugal ; Department of Oceanography and Fisheries, University of the Azores, PT-9901-862 Horta, Portugal
| | - R Eric Collins
- University of Alaska Fairbanks, Box 757220, 99775 Fairbanks, Alaska USA
| | | | - Jonathan Martinez
- University of Hawaii at Manoa, Kewalo Marine Laboratory, 41 Ahui St., Honolulu, 96813 Hawaii, USA
| | - Mark J Costello
- Institute of Marine Science, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Linda A Amaral-Zettler
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, 02543 Massachusetts, USA ; Department of Earth, Environmental, and Planetary Sciences, Brown University, 02912 Providence, Rhode Island USA
| | - Jack A Gilbert
- College of Environmental and Resource Sciences, Zhejiang University, 310058 Hangzhou, China ; Institute for Genomic and Systems Biology, Bioscience Division, Argonne National Laboratory, 9700 South Cass Avenue, 60439 Argonne, Illinois USA ; University of Chicago, 1101 E 57th Street, 60637 Chicago, Illinois USA ; Marine Biological Laboratory, 7 MBL Street, Woods Hole, 02543 Massachusetts, USA
| | - Neil Davies
- Jacobs University Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany ; Gump South Pacific Research Station, University of California Berkeley, BP 244 98728 Moorea, French Polynesia
| | - Dawn Field
- Jacobs University Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany ; University of Oxford, 7 Keble Road, OX1 3QG Oxford, Oxfordshire UK
| | - Frank Oliver Glöckner
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany ; Jacobs University Bremen gGmbH, Campus Ring 1, D-28759 Bremen, Germany
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