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      Genetic tool development in marine protists: emerging model organisms for experimental cell biology

      research-article
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      Nature Methods
      Nature Publishing Group US
      Genetic models, Molecular biology

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          Abstract

          Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.

          Abstract

          This Resource describes genetic tools for microbial eukaryotes, providing a roadmap for developing genetically tractable organisms.

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          Most cited references42

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          Primary Production of the Biosphere: Integrating Terrestrial and Oceanic Components

          C Field (1998)
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            Environmental science. Rethinking the marine carbon cycle: factoring in the multifarious lifestyles of microbes.

            The profound influence of marine plankton on the global carbon cycle has been recognized for decades, particularly for photosynthetic microbes that form the base of ocean food chains. However, a comprehensive model of the carbon cycle is challenged by unicellular eukaryotes (protists) having evolved complex behavioral strategies and organismal interactions that extend far beyond photosynthetic lifestyles. As is also true for multicellular eukaryotes, these strategies and their associated physiological changes are difficult to deduce from genome sequences or gene repertoires—a problem compounded by numerous unknown function proteins. Here, we explore protistan trophic modes in marine food webs and broader biogeochemical influences. We also evaluate approaches that could resolve their activities, link them to biotic and abiotic factors, and integrate them into an ecosystems biology framework.
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              Pan genome of the phytoplankton Emiliania underpins its global distribution

              Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.
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                Author and article information

                Contributors
                dranov@paru.cas.cz
                t.mock@uea.ac.uk
                azworden@geomar.de
                jula@paru.cas.cz
                Journal
                Nat Methods
                Nat. Methods
                Nature Methods
                Nature Publishing Group US (New York )
                1548-7091
                1548-7105
                6 April 2020
                6 April 2020
                2020
                : 17
                : 5
                : 481-494
                Affiliations
                [1 ]Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
                [2 ]ISNI 0000000121885934, GRID grid.5335.0, Department of Biochemistry, , University of Cambridge, ; Cambridge, UK
                [3 ]ISNI 0000 0000 9516 4913, GRID grid.296275.d, Bigelow Laboratory for Ocean Sciences, ; East Boothbay, ME USA
                [4 ]ISNI 0000 0004 0424 5398, GRID grid.507636.1, Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, ; Barcelona, Spain
                [5 ]ISNI 0000 0001 0116 3029, GRID grid.270056.6, Monterey Bay Aquarium Research Institute, ; Moss Landing, CA USA
                [6 ]ISNI 0000 0001 2107 4242, GRID grid.266100.3, Integrative Oceanography Division, , Scripps Institution of Oceanography, University of California, ; San Diego, CA USA
                [7 ]GRID grid.469946.0, Microbial and Environmental Genomics, , J. Craig Venter Institute, ; La Jolla, CA USA
                [8 ]ISNI 0000 0001 0740 6917, GRID grid.205975.c, Molecular, Cell and Developmental Biology, , University of California, ; Santa Cruz, CA USA
                [9 ]ISNI 0000 0004 1936 9297, GRID grid.5491.9, The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, , University of Southampton, ; Southampton, UK
                [10 ]ISNI 0000 0004 1937 0060, GRID grid.24434.35, School of Biological Sciences, , University of Nebraska, ; Lincoln, NE USA
                [11 ]GRID grid.452959.6, Gordon and Betty Moore Foundation, ; Palo Alto, CA USA
                [12 ]ISNI 0000 0001 2181 7878, GRID grid.47840.3f, Department of Molecular and Cell Biology, , University of California, ; Berkeley, CA USA
                [13 ]ISNI 0000 0001 2308 1657, GRID grid.462844.8, Sorbonne Université, CNRS UMR7621, Observatoire Océanologique, ; Banyuls sur Mer, France
                [14 ]ISNI 0000 0001 2112 9282, GRID grid.4444.0, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, ; Paris, France
                [15 ]ISNI 0000 0004 1936 8200, GRID grid.55602.34, Centre for Comparative Genomics and Evolutionary Bioinformatics, , Dalhousie University, ; Halifax, Nova Scotia Canada
                [16 ]ISNI 0000 0001 2292 3357, GRID grid.14848.31, Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, , Université de Montréal, ; Montreal, Quebec Canada
                [17 ]ISNI 0000 0001 0726 5157, GRID grid.5734.5, Institute of Cell Biology, University of Bern, ; Bern, Switzerland
                [18 ]ISNI 0000 0004 1936 738X, GRID grid.213876.9, Center for Tropical and Emerging Global Diseases, , University of Georgia, ; Athens, GA USA
                [19 ]ISNI 0000 0001 2216 9681, GRID grid.36425.36, School of Marine and Atmospheric Sciences, , Stony Brook University, ; Stony Brook, NY USA
                [20 ]ISNI 0000 0001 2288 9830, GRID grid.17091.3e, Department of Botany, , University of British Columbia, ; Vancouver, British Columbia Canada
                [21 ]ISNI 0000 0001 0454 4791, GRID grid.33489.35, University of Delaware College of Earth, Ocean and Environment, ; Lewes, DE USA
                [22 ]ISNI 0000 0004 0504 7510, GRID grid.56466.37, Woods Hole Oceanographic Institution, ; Woods Hole, MA USA
                [23 ]ISNI 0000 0001 2157 0406, GRID grid.7870.8, Facultad Ciencias Biológicas, , Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), ; Santiago de Chile, Chile
                [24 ]ISNI 0000 0001 2232 2818, GRID grid.9759.2, School of Biosciences, , University of Kent, Canterbury, ; Kent, UK
                [25 ]ISNI 0000 0001 2232 2818, GRID grid.9759.2, Laboratory of Molecular and Evolutionary Parasitology, , University of Kent, ; Kent, UK
                [26 ]ISNI 0000 0001 2369 4728, GRID grid.20515.33, Graduate School of Life and Environmental Sciences, , University of Tsukuba, ; Ibaraki, Japan
                [27 ]ISNI 0000 0001 2341 2786, GRID grid.116068.8, Department of Mechanical Engineering, , Massachusetts Institute of Technology, ; Boston, MA USA
                [28 ]ISNI 000000041936754X, GRID grid.38142.3c, Department of Organismic and Evolutionary Biology, , Harvard University, ; Cambridge, MA USA
                [29 ]ISNI 0000 0001 2190 4373, GRID grid.7700.0, Centre for Organismal Studies, , University of Heidelberg, ; Heidelberg, Germany
                [30 ]ISNI 0000 0004 1937 116X, GRID grid.4491.8, Department of Parasitology, Faculty of Science, , Charles University, BIOCEV, ; Vestec, Czech Republic
                [31 ]ISNI 0000 0001 2369 4728, GRID grid.20515.33, Faculty of Life and Environmental Sciences, , University of Tsukuba, ; Ibaraki, Japan
                [32 ]ISNI 0000 0001 1092 7967, GRID grid.8273.e, School of Environmental Sciences, , University of East Anglia, ; Norwich, UK
                [33 ]ISNI 0000 0001 2248 6943, GRID grid.69566.3a, Graduate School of Life Sciences, , Tohoku University, ; Sendai, Miyagi Japan
                [34 ]ISNI 0000 0004 0618 8593, GRID grid.419396.0, Division of Environmental Photobiology, , National Institute for Basic Biology, ; Okazaki, Aichi Japan
                [35 ]ISNI 0000 0001 0860 4915, GRID grid.63054.34, Department of Marine Sciences, , University of Connecticut , ; Groton, CT USA
                [36 ]ISNI 0000 0000 9745 6549, GRID grid.5602.1, School of Biosciences and Veterinary Medicine, , University of Camerino, ; Camerino, Italy
                [37 ]ISNI 0000 0004 1763 208X, GRID grid.275033.0, Department of Basic Biology, School of Life Science, , Graduate University for Advanced Studies, ; Okazaki, Aichi Japan
                [38 ]ISNI 0000 0001 2097 3211, GRID grid.10814.3c, Instituto de Biología Molecular y Celular, CONICET, and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, ; Rosario, Argentina
                [39 ]ISNI 0000 0004 1936 8753, GRID grid.137628.9, Center for Genomics and Systems Biology, , New York University, ; New York, NY USA
                [40 ]ISNI 0000 0001 1926 5090, GRID grid.45672.32, Biological and Environmental Science and Engineering Division, , King Abdullah University of Science and Technology, ; Thuwal, Saudi Arabia
                [41 ]ISNI 0000 0001 2173 7691, GRID grid.39158.36, Center for Zoonosis Control, Global Institution for Collaborative Research and Education, , Hokkaido University, ; Sapporo, Japan
                [42 ]ISNI 0000 0001 2216 9681, GRID grid.36425.36, Department of Ecology and Evolution, , Stony Brook University, ; Stony Brook, NY USA
                [43 ]ISNI 0000 0004 0486 8069, GRID grid.254277.1, Lasry Center for Biosciences, , Clark University, ; Worcester, MA USA
                [44 ]ISNI 0000 0004 1937 0247, GRID grid.5841.8, Departament de Genètica Microbiologia i Estadıśtica, , Universitat de Barcelona, ; Barcelona, Spain
                [45 ]ISNI 0000 0000 9601 989X, GRID grid.425902.8, Catalan Institution for Research and Advanced Studies, ; Barcelona, Spain
                [46 ]ISNI 000000041936754X, GRID grid.38142.3c, Department of Systems Biology, , Harvard Medical School, ; Boston, MA USA
                [47 ]ISNI 000000041936754X, GRID grid.38142.3c, Wyss Institute for Biologically Inspired Engineering, Harvard University, ; Boston, MA USA
                [48 ]ISNI 0000 0001 0806 2909, GRID grid.253561.6, Department of Environmental Biotechnology, , Moss Landing Marine Laboratories, ; Moss Landing, CA USA
                [49 ]ISNI 0000 0004 1936 7822, GRID grid.170205.1, Department of Molecular Genetics and Cell Biology, , University of Chicago, ; Chicago, IL USA
                [50 ]ISNI 0000000107068890, GRID grid.20861.3d, Department of Biology, , California Institute of Technology, ; Pasadena, CA USA
                [51 ]GRID grid.507343.6, Instituto Milenio de Oceanografia de Chile, ; Concepción, Chile
                [52 ]ISNI 0000 0004 1764 3555, GRID grid.449133.8, Institute of Oceanography, Minjiang University, ; Fuzhou, China
                [53 ]Ocean EcoSystems Biology Unit, Marine Ecology Division, Helmholtz Centre for Ocean Research, Kiel, Germany
                [54 ]ISNI 0000 0004 1936 8868, GRID grid.4563.4, Present Address: School of Biosciences, , University of Nottingham, ; Sutton Bonington, UK
                [55 ]GRID grid.427807.e, Present Address: AGADA Biosciences Inc., ; Halifax, Nova Scotia Canada
                [56 ]Present Address: Institute de Biologie de l’ENS, Département de biologie, École Normale Supérieure, CNRS, INSERM, Paris, France
                [57 ]ISNI 0000 0001 1014 8330, GRID grid.419495.4, Present Address: Max Planck Institute for Developmental Biology, ; Tübingen, Germany
                Author information
                http://orcid.org/0000-0001-9623-2233
                http://orcid.org/0000-0003-4487-196X
                http://orcid.org/0000-0001-5911-6081
                http://orcid.org/0000-0002-2552-9168
                http://orcid.org/0000-0003-3835-6187
                http://orcid.org/0000-0002-8679-8812
                http://orcid.org/0000-0001-8774-5715
                http://orcid.org/0000-0001-7435-7609
                http://orcid.org/0000-0003-4229-8784
                http://orcid.org/0000-0002-0896-6542
                http://orcid.org/0000-0001-6805-381X
                http://orcid.org/0000-0002-4972-9383
                http://orcid.org/0000-0002-8026-1336
                http://orcid.org/0000-0002-6975-8640
                http://orcid.org/0000-0002-2287-031X
                http://orcid.org/0000-0003-1735-9557
                http://orcid.org/0000-0001-7521-1863
                http://orcid.org/0000-0001-8831-6111
                http://orcid.org/0000-0002-1128-5916
                http://orcid.org/0000-0002-3028-3203
                http://orcid.org/0000-0002-0654-9147
                http://orcid.org/0000-0003-4894-2905
                http://orcid.org/0000-0002-1755-2819
                http://orcid.org/0000-0002-7856-4071
                http://orcid.org/0000-0003-1258-4800
                http://orcid.org/0000-0001-5032-3834
                http://orcid.org/0000-0002-5424-1905
                http://orcid.org/0000-0002-0642-8468
                http://orcid.org/0000-0003-3531-5806
                http://orcid.org/0000-0002-9056-3565
                http://orcid.org/0000-0001-8689-0080
                http://orcid.org/0000-0002-6031-9254
                http://orcid.org/0000-0001-9604-0362
                http://orcid.org/0000-0002-9888-9324
                http://orcid.org/0000-0002-0578-6618
                Article
                796
                10.1038/s41592-020-0796-x
                7200600
                32251396
                aafb791a-5a32-41c1-845c-2a91ab69a5ad
                © The Author(s), under exclusive licence to Springer Nature America, Inc. 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 26 June 2019
                : 2 March 2020
                Funding
                Funded by: FundRef https://doi.org/10.13039/100000936, Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation);
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                © The Author(s), under exclusive licence to Springer Nature America, Inc. 2020

                Life sciences
                genetic models,molecular biology
                Life sciences
                genetic models, molecular biology

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