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Dramburg S, Grittner U, Potapova E, Travaglini A, Tripodi S, Arasi S, Pelosi S, Acar Şahin A, Aggelidis X, Barbalace A, Bourgoin A, Bregu B, Brighetti MA, Caeiro E, Caglayan Sozmen S, Caminiti L, Charpin D, Couto M, Delgado L, Di Rienzo Businco A, Dimier C, Dimou MV, Fonseca JA, Goksel O, Hernandez D, Hernandez Toro CJ, Hoffmann TM, Jang DT, Kalpaklioglu F, Lame B, Llusar R, Makris M, Mazon A, Mesonjesi E, Nieto A, Öztürk AB, Pahus L, Pajno G, Panasiti I, Papadopoulos NG, Pellegrini E, Pereira AM, Pereira M, Pinar NM, Priftanji A, Psarros F, Sackesen C, Sfika I, Suarez J, Thibaudon M, Uguz U, Verdier V, Villella V, Xepapadaki P, Yazici D, Matricardi PM. Heterogeneity of sensitization profiles and clinical phenotypes among patients with seasonal allergic rhinitis in Southern European countries-The @IT.2020 multicenter study. Allergy 2024; 79:908-923. [PMID: 38311961 DOI: 10.1111/all.16029] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 02/06/2024]
Abstract
BACKGROUND Pollen allergy poses a significant health and economic burden in Europe. Disease patterns are relatively homogeneous within Central and Northern European countries. However, no study broadly assessed the features of seasonal allergic rhinitis (SAR) across different Southern European countries with a standardized approach. OBJECTIVE To describe sensitization profiles and clinical phenotypes of pollen allergic patients in nine Southern European cities with a uniform methodological approach. METHODS Within the @IT.2020 multicenter observational study, pediatric and adult patients suffering from SAR were recruited in nine urban study centers located in seven countries. Clinical questionnaires, skin prick tests (SPT) and specific IgE (sIgE) tests with a customized multiplex assay (Euroimmun Labordiagnostika, Lübeck, Germany) were performed. RESULTS Three hundred forty-eight children (mean age 13.1 years, SD: 2.4 years) and 467 adults (mean age 35.7 years SD: 10.0 years) with a predominantly moderate to severe, persistent phenotype of SAR were recruited. Grass pollen major allergenic molecules (Phl p 1 and/or Phl p 5) ranged among the top three sensitizers in all study centers. Sensitization profiles were very heterogeneous, considering that patients in Rome were highly poly-sensitized (sIgE to 3.8 major allergenic molecules per patient), while mono-sensitization was prominent and heterogeneous in other cities, such as Marseille (sIgE to Cup a 1: n = 55/80, 68.8%) and Messina (sIgE to Par j 2: n = 47/82, 57.3%). Co-sensitization to perennial allergens, as well as allergic comorbidities also broadly varied between study centers. CONCLUSIONS In Southern European countries, pollen allergy is heterogeneous in terms of sensitization profiles and clinical manifestations. Despite the complexity, a unique molecular, multiplex, and customized in-vitro IgE test detected relevant sensitization in all study centers. Nevertheless, this geographical diversity in pollen allergic patients imposes localized clinical guidelines and study protocols for clinical trials of SAR in this climatically complex region.
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Affiliation(s)
- S Dramburg
- Department of Pediatric Respiratory Care, Immunology and Intensive Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - U Grittner
- Institute of Biometry and Clinical Epidemiology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - E Potapova
- Department of Pediatric Respiratory Care, Immunology and Intensive Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - A Travaglini
- Department of Biology, Tor Vergata University, Rome, Italy
- Italian Aerobiology Monitoring Network - Italian Aerobiology Association, Rome, Italy
| | - S Tripodi
- Pediatric Allergy Unit, Sandro Pertini Hospital, Rome, Italy
- Allergolology Service, Policlinico Casilino, Rome, Italy
| | - S Arasi
- Department of Pediatric Respiratory Care, Immunology and Intensive Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Pediatric Allergology Unit, Department of Pediatric Medicine, Bambino Gesù Children's Research Hospital (IRCCS), Rome, Italy
| | | | - A Acar Şahin
- Department of Biology, Faculty of Science, Ankara University, Ankara, Turkey
| | - X Aggelidis
- Allergy Unit, 2nd Department of Dermatology and Venereology, National and Kapodistrian University of Athens, University Hospital "Attikon", Athens, Greece
| | - A Barbalace
- Allergy Unit, Department of Pediatrics, University of Messina, Messina, Italy
| | - A Bourgoin
- Department of Pneumonology and Allergy, La Timone Hospital, APHM, Aix-Marseille University, Marseille, France
| | - B Bregu
- Department of Allergology and Clinical Immunology, UHC Mother Teresa, Medical University Tirana, Tirana, Albania
| | - M A Brighetti
- Department of Biology, Tor Vergata University, Rome, Italy
| | - E Caeiro
- MED- Mediterranean Institute for Agriculture, Environment and Development, Institute for Advanced Studies and Research, University of Évora, Évora, Portugal
- Portuguese Society of Allergology and Clinical Immunology, Lisbon, Portugal
| | | | - L Caminiti
- Allergy Unit, Department of Pediatrics, University of Messina, Messina, Italy
| | - D Charpin
- Department of Pneumonology and Allergy, La Timone Hospital, APHM, Aix-Marseille University, Marseille, France
| | - M Couto
- Immunoallergology, Hospital CUF Trindade, Porto, Portugal
| | - L Delgado
- Basic and Clinical Immunology Unit, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
- CINTESIS@RISE, MEDCIDS, Faculty of Medicine of the University of Porto, Porto, Portugal
- Allergy Unit, Instituto & Hospital CUF Porto, Porto, Portugal
| | | | - C Dimier
- Department of Pneumonology and Allergy, La Timone Hospital, APHM, Aix-Marseille University, Marseille, France
| | - M V Dimou
- Allergy Department, 2nd Pediatric Clinic, Athens General Children's Hospital "P&A Kyriakou", University of Athens, Athens, Greece
| | - J A Fonseca
- CINTESIS@RISE, MEDCIDS, Faculty of Medicine of the University of Porto, Porto, Portugal
- Allergy Unit, Instituto & Hospital CUF Porto, Porto, Portugal
- MEDCIDS-Department of Community Medicine, Information, and Health Sciences, Faculty of Medicine, University of Porto, Porto, Portugal
| | - O Goksel
- Department of Pulmonary Medicine, Division of Immunology, Allergy and Asthma. Faculty of Medicine, Ege University, Izmir, Turkey
| | - D Hernandez
- Department of Allergy, Health Research Institute Hospital La Fe, Valencia, Spain
| | - C J Hernandez Toro
- Department of Pediatric Respiratory Care, Immunology and Intensive Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute of Biometry and Clinical Epidemiology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - T M Hoffmann
- Department of Pediatric Respiratory Care, Immunology and Intensive Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - D T Jang
- Pediatric Allergy and Pneumology Unit, Children's Hospital La Fe; Health Research Institute La Fe, Valencia, Spain
| | - F Kalpaklioglu
- Department of Immunology and Allergic Diseases, Kırıkkale University School of Medicine, Kırıkkale, Turkey
| | - B Lame
- Department of Allergology and Clinical Immunology, UHC Mother Teresa, Medical University Tirana, Tirana, Albania
| | - R Llusar
- Pediatric Allergy and Pneumology Unit, Children's Hospital La Fe; Health Research Institute La Fe, Valencia, Spain
| | - M Makris
- Allergy Unit, 2nd Department of Dermatology and Venereology, National and Kapodistrian University of Athens, University Hospital "Attikon", Athens, Greece
| | - A Mazon
- Pediatric Allergy and Pneumology Unit, Children's Hospital La Fe; Health Research Institute La Fe, Valencia, Spain
| | - E Mesonjesi
- Department of Allergology and Clinical Immunology, UHC Mother Teresa, Medical University Tirana, Tirana, Albania
| | - A Nieto
- Pediatric Allergy and Pneumology Unit, Children's Hospital La Fe; Health Research Institute La Fe, Valencia, Spain
| | - A B Öztürk
- Division of Allergy and Immunology, Department of Pulmonary Medicine, Arel University, School of Medicine, Istanbul, Turkey
| | - L Pahus
- Aix Marseille Univ, APHM, INSERM CIC 1409, INSERM U1263, INRA 1260 (C2VN), Marseille, France
| | - G Pajno
- Allergy Unit, Department of Pediatrics, University of Messina, Messina, Italy
| | - I Panasiti
- Allergy Unit, Department of Pediatrics, University of Messina, Messina, Italy
| | - N G Papadopoulos
- Allergy Department, 2nd Pediatric Clinic, Athens General Children's Hospital "P&A Kyriakou", University of Athens, Athens, Greece
- Division of Infection, Immunity & Respiratory Medicine, Royal Manchester Children's Hospital, University of Manchester, Manchester, UK
| | - E Pellegrini
- Department of Reggio Calabria, ARPA - Regional Agency for Environmental Protection, Calabria, Italy
| | - A M Pereira
- Allergy Unit, Instituto & Hospital CUF Porto, Porto, Portugal
- MEDCIDS-Department of Community Medicine, Information, and Health Sciences, Faculty of Medicine, University of Porto, Porto, Portugal
| | - M Pereira
- Basic and Clinical Immunology Unit, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
- CINTESIS@RISE, MEDCIDS, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - N M Pinar
- Department of Biology, Faculty of Science, Ankara University, Ankara, Turkey
| | - A Priftanji
- Department of Allergology and Clinical Immunology, UHC Mother Teresa, Medical University Tirana, Tirana, Albania
| | - F Psarros
- Allergy Department, Athens Naval Hospital, Athens, Greece
| | - C Sackesen
- Division of Pediatric Allergy, Koç University School of Medicine, Istanbul, Turkey
| | - I Sfika
- Pediatric Allergy Unit, Sandro Pertini Hospital, Rome, Italy
| | - J Suarez
- Department of Biology of Organisms and Systems, Area of Botany, University of Oviedo, Oviedo, Spain
| | - M Thibaudon
- Réseau National de Surveillance Aérobiologique, Brussieu, France
| | - U Uguz
- Department of Biology, Faculty of Science, Ege University, Izmir, Turkey
| | - V Verdier
- Department of Pneumonology and Allergy, La Timone Hospital, APHM, Aix-Marseille University, Marseille, France
| | - V Villella
- Pediatric Allergy Unit, Sandro Pertini Hospital, Rome, Italy
| | - P Xepapadaki
- Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | - D Yazici
- Cellular and Molecular Medicine, KUTTAM, Graduate School of Health Sciences, Koç University, Istanbul, Turkey
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - P M Matricardi
- Department of Pediatric Respiratory Care, Immunology and Intensive Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
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2
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Rigonato J, Budinich M, Murillo AA, Brandão MC, Pierella Karlusich JJ, Soviadan YD, Gregory AC, Endo H, Kokoszka F, Vik D, Henry N, Frémont P, Labadie K, Zayed AA, Dimier C, Picheral M, Searson S, Poulain J, Kandels S, Pesant S, Karsenti E, Bork P, Bowler C, de Vargas C, Eveillard D, Gehlen M, Iudicone D, Lombard F, Ogata H, Stemmann L, Sullivan MB, Sunagawa S, Wincker P, Chaffron S, Jaillon O. Ocean-wide comparisons of mesopelagic planktonic community structures. ISME Commun 2023; 3:83. [PMID: 37596349 PMCID: PMC10439195 DOI: 10.1038/s43705-023-00279-9] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 06/21/2023] [Accepted: 06/29/2023] [Indexed: 08/20/2023]
Abstract
For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a vast and heterogeneous part of the ocean: the mesopelagic zone. How plankton composition is shaped by environment has been well-explored in the epipelagic but much less in the mesopelagic ocean. Here, we conducted comparative analyses of trans-kingdom community assemblages thriving in the mesopelagic oxygen minimum zone (OMZ), mesopelagic oxic, and their epipelagic counterparts. We identified nine distinct types of intermediate water masses that correlate with variation in mesopelagic community composition. Furthermore, oxygen, NO3- and particle flux together appeared as the main drivers governing these communities. Novel taxonomic signatures emerged from OMZ while a global co-occurrence network analysis showed that about 70% of the abundance of mesopelagic plankton groups is organized into three community modules. One module gathers prokaryotes, pico-eukaryotes and Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from oxic regions, and the two other modules are enriched in OMZ prokaryotes and OMZ pico-eukaryotes, respectively. We hypothesize that OMZ conditions led to a diversification of ecological niches, and thus communities, due to selective pressure from limited resources. Our study further clarifies the interplay between environmental factors in the mesopelagic oxic and OMZ, and the compositional features of communities.
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Affiliation(s)
- Janaina Rigonato
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.
| | - Marko Budinich
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680, Roscoff, France
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Alejandro A Murillo
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Manoela C Brandão
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Juan J Pierella Karlusich
- Institut de Biologie de l'ENS (IBENS), Département de biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Yawouvi Dodji Soviadan
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Ann C Gregory
- Department of Microbiology, The Ohio State University, Columbus, OH, 43214, USA
| | - Hisashi Endo
- Bioinformatics Center, Institute for Chemical Research Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Florian Kokoszka
- Institut de Biologie de l'ENS (IBENS), Département de biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Dean Vik
- Department of Microbiology, The Ohio State University, Columbus, OH, 43214, USA
| | - Nicolas Henry
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680, Roscoff, France
| | - Paul Frémont
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, OH, 43214, USA
| | - Céline Dimier
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Marc Picheral
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Sarah Searson
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany
- Directors' Research European Molecular Biology Laboratory Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | - Eric Karsenti
- Institut de Biologie de l'ENS (IBENS), Département de biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
- Directors' Research European Molecular Biology Laboratory Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Institut de Biologie de l'ENS (IBENS), Département de biologie, Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680, Roscoff, France
| | - Damien Eveillard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Marion Gehlen
- Institut Pierre Simon Laplace, Laboratoire des Sciences du Climat et de l'Environnement, CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette cedex, France
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Fabien Lombard
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Hiroyuki Ogata
- Bioinformatics Center, Institute for Chemical Research Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Lars Stemmann
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, 06230, Villefranche-sur-Mer, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, 43214, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, 43214, USA
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany
- Department of Biology; Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, 8093, Switzerland
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Samuel Chaffron
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France
- Nantes Université, École Centrale Nantes, CNRS, LS2N, UMR 6004, F-44000, Nantes, France
| | - Olivier Jaillon
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 91000, Evry, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016, Paris, France.
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3
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Lombard F, Bourdin G, Pesant S, Agostini S, Baudena A, Boissin E, Cassar N, Clampitt M, Conan P, Da Silva O, Dimier C, Douville E, Elineau A, Fin J, Flores JM, Ghiglione JF, Hume BCC, Jalabert L, John SG, Kelly RL, Koren I, Lin Y, Marie D, McMinds R, Mériguet Z, Metzl N, Paz-García DA, Pedrotti ML, Poulain J, Pujo-Pay M, Ras J, Reverdin G, Romac S, Rouan A, Röttinger E, Vardi A, Voolstra CR, Moulin C, Iwankow G, Banaigs B, Bowler C, de Vargas C, Forcioli D, Furla P, Galand PE, Gilson E, Reynaud S, Sunagawa S, Sullivan MB, Thomas OP, Troublé R, Thurber RV, Wincker P, Zoccola D, Allemand D, Planes S, Boss E, Gorsky G. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems. Sci Data 2023; 10:324. [PMID: 37264023 DOI: 10.1038/s41597-022-01757-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/10/2022] [Indexed: 06/03/2023] Open
Abstract
The Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.
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Affiliation(s)
- Fabien Lombard
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France.
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France.
- Institut Universitaire de France, 75231, Paris, France.
| | - Guillaume Bourdin
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
- School of Marine Sciences, University of Maine, Orono, Maine, 04469, USA
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Alberto Baudena
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Nicolas Cassar
- Nicholas School of the Environment, Duke University, Durham, NC, USA
- Laboratoire des Sciences de l'Environnement Marin, UMR 6539 UBO/CNRS/IRD/IFREMER, Institut Universitaire Européen de la Mer, Brest, France
| | - Megan Clampitt
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
| | - Pascal Conan
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, 66650, Banyuls Sur Mer, France
- Sorbonne Université, CNRS, OSU STAMAR - UAR2017, 75252 Paris, France
| | - Ophélie Da Silva
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Céline Dimier
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Amanda Elineau
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Jonathan Fin
- Laboratoire LOCEAN/IPSL, Sorbonne Université-CNRS-IRD-MNHN, Paris, 75005, France
| | - J Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, Rehovot, Israel
| | - Jean-François Ghiglione
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, 66650, Banyuls Sur Mer, France
| | | | - Laetitia Jalabert
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Seth G John
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
| | - Rachel L Kelly
- Department of Earth Science, University of Southern California, Los Angeles, CA, USA
| | - Ilan Koren
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, Rehovot, Israel
| | - Yajuan Lin
- Nicholas School of the Environment, Duke University, Durham, NC, USA
- Laboratoire des Sciences de l'Environnement Marin, UMR 6539 UBO/CNRS/IRD/IFREMER, Institut Universitaire Européen de la Mer, Brest, France
- Environmental Research Center, Duke Kunshan University, Kunshan, China
| | - Dominique Marie
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, AD2M, Roscoff, France
| | - Ryan McMinds
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Maison de la Modélisation, de la Simulation et des Interactions (MSI), Nice, France
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Zoé Mériguet
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Nicolas Metzl
- Laboratoire LOCEAN/IPSL, Sorbonne Université-CNRS-IRD-MNHN, Paris, 75005, France
| | - David A Paz-García
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Baja California Sur, 23096, México
| | - Maria Luiza Pedrotti
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Mireille Pujo-Pay
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne, LOMIC, 66650, Banyuls Sur Mer, France
| | - Joséphine Ras
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
| | - Gilles Reverdin
- Laboratoire LOCEAN/IPSL, Sorbonne Université-CNRS-IRD-MNHN, Paris, 75005, France
| | - Sarah Romac
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, AD2M, Roscoff, France
| | - Alice Rouan
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
| | - Eric Röttinger
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
| | - Assaf Vardi
- Weizmann Institute of Science, Department of Plant and Environmental Science, Rehovot, Israel
| | | | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Chris Bowler
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Colomban de Vargas
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, AD2M, Roscoff, France
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
| | - Pierre E Galand
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, UMR 8222, LECOB, Banyuls-sur-Mer, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Institut Fédératif de Recherche - Ressources Marines (IFR MARRES), Nice, France
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
- Department of Medical Genetics, CHU, Nice, France
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Antoine, Monaco
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zurich, Switzerland
| | - Matthew B Sullivan
- Department of Microbiology and Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road, Galway, Ireland
| | | | | | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Antoine, Monaco
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé Université Côte d'Azur - Centre Scientifique de Monaco, Nice, Monaco
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, MC-98000, Antoine, Monaco
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, Maine, 04469, USA
| | - Gaby Gorsky
- Sorbonne Université, Laboratoire d'Océanographie de Villefranche, UMR 7093, CNRS, Institut de la Mer de Villefranche, 06230, Villefranche sur mer, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 75000, Paris, France
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4
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Bonnet S, Benavides M, Le Moigne FAC, Camps M, Torremocha A, Grosso O, Dimier C, Spungin D, Berman-Frank I, Garczarek L, Cornejo-Castillo FM. Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean. ISME J 2023; 17:47-58. [PMID: 36163270 PMCID: PMC9750961 DOI: 10.1038/s41396-022-01319-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/25/2022] [Accepted: 09/06/2022] [Indexed: 11/09/2022]
Abstract
Diazotrophs are widespread microorganisms that alleviate nitrogen limitation in 60% of our oceans, thereby regulating marine productivity. Yet, the group-specific contribution of diazotrophs to organic matter export has not been quantified, which so far has impeded an accurate assessment of their impact on the biological carbon pump. Here, we examine the fate of five groups of globally-distributed diazotrophs by using an original combination of mesopelagic particle sampling devices across the subtropical South Pacific Ocean. We demonstrate that cyanobacterial and non-cyanobacterial diazotrophs are exported down to 1000 m depth. Surprisingly, group-specific export turnover rates point to a more efficient export of small unicellular cyanobacterial diazotrophs (UCYN) relative to the larger and filamentous Trichodesmium. Phycoerythrin-containing UCYN-B and UCYN-C-like cells were recurrently found embedded in large (>50 µm) organic aggregates or organized into clusters of tens to hundreds of cells linked by an extracellular matrix, presumably facilitating their export. Beyond the South Pacific, our data are supported by analysis of the Tara Oceans metagenomes collected in other ocean basins, extending the scope of our results globally. We show that, when diazotrophs are found in the euphotic zone, they are also systematically present in mesopelagic waters, suggesting their transport to the deep ocean. We thus conclude that diazotrophs are a significant part of the carbon sequestered in the deep ocean and, therefore, they need to be accounted in regional and global estimates of export.
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Affiliation(s)
- Sophie Bonnet
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.
| | - Mar Benavides
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France ,grid.5399.60000 0001 2176 4817Turing Center for Living Systems, Aix-Marseille University, 13009 Marseille, France
| | - Frédéric A. C. Le Moigne
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France ,grid.463763.30000 0004 0638 0577LEMAR, Laboratoire des sciences de l’environnement marin, UMR6539, CNRS, UBO, IFREMER, IRD, 29280 Plouzané, Technopôle Brest-Iroise France
| | - Mercedes Camps
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Antoine Torremocha
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Olivier Grosso
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Céline Dimier
- grid.499565.20000 0004 0366 8890Laboratoire d’Océanographie de Villefranche (LOV), Sorbonne Université, CNRS, 06230 Villefranche sur mer, France
| | - Dina Spungin
- grid.18098.380000 0004 1937 0562University of Haifa, The Leon H. Charney School of Marine Sciences, Haifa, 3498838 Israel
| | - Ilana Berman-Frank
- grid.18098.380000 0004 1937 0562University of Haifa, The Leon H. Charney School of Marine Sciences, Haifa, 3498838 Israel
| | - Laurence Garczarek
- grid.464101.60000 0001 2203 0006Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Francisco M. Cornejo-Castillo
- grid.464101.60000 0001 2203 0006Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France ,grid.418218.60000 0004 1793 765XInstitut de Ciènces del Mar (ICM-CSIC), E08003 Barcelona, Spain
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5
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Richter DJ, Watteaux R, Vannier T, Leconte J, Frémont P, Reygondeau G, Maillet N, Henry N, Benoit G, Da Silva O, Delmont TO, Fernàndez-Guerra A, Suweis S, Narci R, Berney C, Eveillard D, Gavory F, Guidi L, Labadie K, Mahieu E, Poulain J, Romac S, Roux S, Dimier C, Kandels S, Picheral M, Searson S, Pesant S, Aury JM, Brum JR, Lemaitre C, Pelletier E, Bork P, Sunagawa S, Lombard F, Karp-Boss L, Bowler C, Sullivan MB, Karsenti E, Mariadassou M, Probert I, Peterlongo P, Wincker P, de Vargas C, Ribera d'Alcalà M, Iudicone D, Jaillon O. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. eLife 2022; 11:78129. [PMID: 35920817 PMCID: PMC9348854 DOI: 10.7554/elife.78129] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 02/23/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the ‘seascape’) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton. Oceans are brimming with life invisible to our eyes, a myriad of species of bacteria, viruses and other microscopic organisms essential for the health of the planet. These ‘marine plankton’ are unable to swim against currents and should therefore be constantly on the move, yet previous studies have suggested that distinct species of plankton may in fact inhabit different oceanic regions. However, proving this theory has been challenging; collecting plankton is logistically difficult, and it is often impossible to distinguish between species simply by examining them under a microscope. However, within the last decade, a research schooner called Tara has travelled the globe to gather thousands of plankton samples. At the same time, advances in genomics have made it possible to identify species based only on fragments of their DNA sequence. To understand the hidden geography of plankton communities in Earth’s oceans, Richter et al. pored over DNA from the Tara Oceans expedition. This revealed that, despite being unable to resist the flow of water, various planktonic species which live close to the surface manage to occupy distinct, stable provinces shaped by currents. Different sizes of plankton are distributed in different sized provinces, with the smallest organisms tending to inhabit the smallest areas. Comparing DNA similarities and speeds of currents at the ocean surface revealed how these might stretch and mix plankton communities. Plankton play a critical role in the health of the ocean and the chemical cycles of planet Earth. These results could allow deeper investigation by marine modellers, ecologists, and evolutionary biologists. Meanwhile, work is already underway to investigate how climate change might impact this hidden geography.
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Affiliation(s)
- Daniel J Richter
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Romain Watteaux
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,CEA, DAM, DIF, F-91297, Arpajon Cedex, France
| | - Thomas Vannier
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO UM, Marseille, France
| | - Jade Leconte
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Paul Frémont
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Gabriel Reygondeau
- Changing Ocean Research Unit, Institute for the Oceans and Fisheries, University of British Columbia. Aquatic Ecosystems Research Lab, Vancouver, Canada.,Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Nicolas Maillet
- Institut pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Nicolas Henry
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Gaëtan Benoit
- Univ Rennes, CNRS, Inria, IRISA-UMR 6074, Rennes, France
| | - Ophélie Da Silva
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Oceanographie de Villefranche, LOV, Villefranche-sur-Mer, France
| | - Tom O Delmont
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Antonio Fernàndez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Samir Suweis
- Dipartimento di Fisica e Astronomia 'G. Galilei' & CNISM, INFN, Università di Padova, Padova, Italy
| | - Romain Narci
- MaIAGE, INRAE, Université Paris-Saclay, Jouy-en-Josas, France
| | - Cédric Berney
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Damien Eveillard
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Nantes Université, Ecole Centrale Nantes, CNRS, LS2N, Nantes, France
| | - Frederick Gavory
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Lionel Guidi
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Oceanographie de Villefranche, LOV, Villefranche-sur-Mer, France
| | - Karine Labadie
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Eric Mahieu
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, United States
| | - Céline Dimier
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Directors' Research European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marc Picheral
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Oceanographie de Villefranche, LOV, Villefranche-sur-Mer, France
| | - Sarah Searson
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Oceanographie de Villefranche, LOV, Villefranche-sur-Mer, France
| | | | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Jennifer R Brum
- Department of Microbiology, The Ohio State University, Columbus, United States.,Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, United States
| | | | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Yonsei Frontier Lab, Yonsei University, Seoul, Republic of Korea.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg, Zurich, Switzerland
| | - Fabien Lombard
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Sorbonne Universités, CNRS, Laboratoire d'Oceanographie de Villefranche, LOV, Villefranche-sur-Mer, France.,Institut Universitaire de France (IUF), Paris, France
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, United States
| | - Chris Bowler
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, United States.,EMERGE Biology Integration Institute, The Ohio State University, Columbus, United States.,Center of Microbiome Science, The Ohio State University, Columbus, United States.,Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, United States
| | - Eric Karsenti
- Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France.,Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Directors' Research European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Ian Probert
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | | | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
| | | | | | - Olivier Jaillon
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France.,Research Federation for the study of Global Ocean systems ecology and evolution, FR2O22/Tara GOSEE, Paris, France
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6
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Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sánchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Acinas SG, Babin M, Bork P, Bowler C, de Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome. Cell 2020; 179:1068-1083.e21. [PMID: 31730850 PMCID: PMC6912165 DOI: 10.1016/j.cell.2019.10.014] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 07/26/2019] [Accepted: 10/11/2019] [Indexed: 12/02/2022]
Abstract
Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. Video Abstract
A catalog of 47 million genes was generated from 370 globally distributed metagenomes Meta-omics data integration disentangled the mechanisms of changes in transcript pools Transcript pool changes of metabolic marker genes show distinct mechanistic patterns Community turnover as a response to ocean warming may be strongest in polar regions
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Affiliation(s)
- Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid 28223, Spain; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Miguelangel Cuenca
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Christopher M Field
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Corinne Cruaud
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Stefan Engelen
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Ann C Gregory
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Karine Labadie
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Claudie Marec
- Département de biologie, Université Laval, QC G1V 0A6, Canada; Laboratoire d'Oceanographie Physique et Spatiale, UMR 6523, CNRS-IFREMER-IRD-UBO, Plouzané, France
| | - Eric Pelletier
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Simon Roux
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Hideya Uehara
- Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan; Hewlett-Packard Japan, 2-2-1, Ojima, Koto-ku, Tokyo 136-8711, Japan
| | - Ahmed A Zayed
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Margaux Carmichael
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Céline Dimier
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Joannie Ferland
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Marc Picheral
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, Villefranche-sur-mer 06230, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow 117997, Russia
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Barcelona 08003, Spain
| | - Marcel Babin
- Takuvik Joint International Laboratory, CNRS-Université Laval, QC G1V 0A6, Canada
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany; Max Delbrück Centre for Molecular Medicine, Berlin 13125, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg 97074, Germany
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France
| | - Lionel Guidi
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Sorbonne Université & CNRS, UMR 7144 (AD2M), ECOMAP, Station Biologique de Roscoff, Place Georges Teissier, Roscoff 29680, France; Department of Oceanography, University of Hawaii, Honolulu, HI 96822, USA
| | - Pascal Hingamp
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France; Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | | | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME 04469, USA
| | - Eric Karsenti
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris 75005, France; Directors' Research European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto Univerisity, Gokasho, Uji 611-0011, Japan
| | - Stephane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | | | - Matthew B Sullivan
- Department of Microbiology, the Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, the Ohio State University, Columbus, OH 43214, USA; Center for RNA Biology, the Ohio State University, Columbus, OH 43214, USA
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 Rue Michel-Ange, Paris 75016, France
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich 8093, Switzerland.
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7
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Ibarbalz FM, Henry N, Brandão MC, Martini S, Busseni G, Byrne H, Coelho LP, Endo H, Gasol JM, Gregory AC, Mahé F, Rigonato J, Royo-Llonch M, Salazar G, Sanz-Sáez I, Scalco E, Soviadan D, Zayed AA, Zingone A, Labadie K, Ferland J, Marec C, Kandels S, Picheral M, Dimier C, Poulain J, Pisarev S, Carmichael M, Pesant S, Babin M, Boss E, Iudicone D, Jaillon O, Acinas SG, Ogata H, Pelletier E, Stemmann L, Sullivan MB, Sunagawa S, Bopp L, de Vargas C, Karp-Boss L, Wincker P, Lombard F, Bowler C, Zinger L. Global Trends in Marine Plankton Diversity across Kingdoms of Life. Cell 2020; 179:1084-1097.e21. [PMID: 31730851 PMCID: PMC6912166 DOI: 10.1016/j.cell.2019.10.008] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/22/2019] [Accepted: 10/07/2019] [Indexed: 12/31/2022]
Abstract
The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation. Video Abstract
Most epipelagic planktonic groups exhibit a poleward decline of diversity No latitudinal diversity gradient was observed below the photic zone Temperature emerges as the best predictor of epipelagic plankton diversity Global warming may increase plankton diversity, particularly at high latitudes
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Affiliation(s)
- Federico M Ibarbalz
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Nicolas Henry
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Manoela C Brandão
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Séverine Martini
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Greta Busseni
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Hannah Byrne
- Department of Earth and Planetary Sciences, Harvard University, 20 Oxford St., Cambridge, MA 02138, USA
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Hisashi Endo
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain; Centre for Marine Ecosystems Research, Edith Cowan University, Joondalup, WA, Australia
| | - Ann C Gregory
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Frédéric Mahé
- CIRAD, UMR BGPI, 34398, Montpellier, France; BGPI, Université Montpellier, CIRAD, IRD, Montpellier SupAgro, Montpellier, France
| | - Janaina Rigonato
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Guillem Salazar
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Isabel Sanz-Sáez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Dodji Soviadan
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Ahmed A Zayed
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Énergie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Joannie Ferland
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Claudie Marec
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany; Directors' Research European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Marc Picheral
- Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Céline Dimier
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology of the Russian Academy of Sciences, 36 Nakhimovsky Prosp., 117997 Moscow, Russia
| | - Margaux Carmichael
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France
| | - Stéphane Pesant
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany; PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany
| | | | - Marcel Babin
- Takuvik Joint International Laboratory (UMI3376), Université Laval (Canada) - CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Olivier Jaillon
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49 Barcelona E08003, Spain
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Eric Pelletier
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Lars Stemmann
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA; Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Laurent Bopp
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; LMD/IPSL, ENS, PSL Research University, École Polytechnique, Sorbonne Université, CNRS, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, 29680 Roscoff, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Patrick Wincker
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France; Sorbonne Université, CNRS, UMR 7093, Institut de la Mer de Villefranche-sur-Mer, Laboratoire d'Océanographie de Villefranche, 06230 Villefranche-sur-Mer, France
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France; Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France.
| | - Lucie Zinger
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France.
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8
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Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B, Alberti A, Ardyna M, Arkhipova K, Carmichael M, Cruaud C, Dimier C, Domínguez-Huerta G, Ferland J, Kandels S, Liu Y, Marec C, Pesant S, Picheral M, Pisarev S, Poulain J, Tremblay JÉ, Vik D, Babin M, Bowler C, Culley AI, de Vargas C, Dutilh BE, Iudicone D, Karp-Boss L, Roux S, Sunagawa S, Wincker P, Sullivan MB. Marine DNA Viral Macro- and Microdiversity from Pole to Pole. Cell 2019; 177:1109-1123.e14. [PMID: 31031001 PMCID: PMC6525058 DOI: 10.1016/j.cell.2019.03.040] [Citation(s) in RCA: 367] [Impact Index Per Article: 73.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/05/2019] [Accepted: 03/20/2019] [Indexed: 01/04/2023]
Abstract
Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.
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Affiliation(s)
- Ann C Gregory
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Nádia Conceição-Neto
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, KU Leuven-University of Leuven, Leuven, Belgium; Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory for Clinical and Epidemiological Virology, KU Leuven-University of Leuven, Leuven, Belgium
| | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, UK
| | - Ben Bolduc
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Mathieu Ardyna
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, 06230 Villefranche-sur-mer, France
| | - Ksenia Arkhipova
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
| | - Margaux Carmichael
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M ECOMAP, 29680 Roscoff, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Corinne Cruaud
- CEA-Institut de Biologie François Jacob, Genoscope, Evry 91057, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Céline Dimier
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, 06230 Villefranche-sur-mer, France; Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | | | - Joannie Ferland
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)-CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Stefanie Kandels
- Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; Directors' Research, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Yunxiao Liu
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Claudie Marec
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)-CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Stéphane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, 28359 Bremen, Germany; MARUM, Bremen University, 28359 Bremen, Germany
| | - Marc Picheral
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefanche, LOV, 06230 Villefranche-sur-mer, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Sergey Pisarev
- Shirshov Institute of Oceanology of Russian Academy of Sciences, 36 Nakhimovsky prosp, 117997 Moscow, Russia
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Jean-Éric Tremblay
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)-CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Dean Vik
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Marcel Babin
- Département de biologie, Québec Océan and Takuvik Joint International Laboratory (UMI 3376), Université Laval (Canada)-CNRS (France), Université Laval, Québec, QC G1V 0A6, Canada
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Alexander I Culley
- Département de biochimie, microbiologie et bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M ECOMAP, 29680 Roscoff, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Simon Roux
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, 8093 Zurich, Switzerland
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA.
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9
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Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaqué D, Bork P, Acinas SG, Wincker P, Sullivan MB. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 2016; 537:689-693. [PMID: 27654921 DOI: 10.1038/nature19366] [Citation(s) in RCA: 447] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 08/12/2016] [Indexed: 12/26/2022]
Abstract
Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting 'global ocean virome' dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups). This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.
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Affiliation(s)
- Simon Roux
- 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
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands
- Department of Marine Biology, Federal University of Rio de Janeiro, Rio de Janeiro, CEP 21941-902, Brazil
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna, A-1090 Vienna, Austria
- Austrian Polar Research Institute, A-1090 Vienna, Austria
| | - Bonnie T Poulos
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Natalie Solonenko
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Elena Lara
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC Barcelona E0800, Spain
- Institute of Marine Sciences (CNR-ISMAR), National Research Council, 30122 Venezia, Italy
| | - Julie Poulain
- CEA - Institut de Génomique, GENOSCOPE, 91057 Evry, France
| | - Stéphane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, 28359 Bremen, Germany
- MARUM, Bremen University, 28359 Bremen, Germany
| | - Stefanie Kandels-Lewis
- Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Directors' Research, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Céline Dimier
- CNRS, UMR 7144, EPEP, Station Biologique de Roscoff, 29680 Roscoff, France
- Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, 29680 Roscoff, France
- Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, Paris Sciences et Lettres Research University, CNRS UMR 8197, INSERM U1024, F-75005 Paris, France
| | - Marc Picheral
- CNRS, UMR 7093, Laboratoire d'océanographie de Villefranche, Observatoire Océanologique, 06230 Villefranche-sur-mer, France
- Sorbonne Universités, UPMC Université Paris 06, UMR 7093, Observatoire Océanologique, 06230 Villefranche-sur-mer, France
| | - Sarah Searson
- CNRS, UMR 7093, Laboratoire d'océanographie de Villefranche, Observatoire Océanologique, 06230 Villefranche-sur-mer, France
- Sorbonne Universités, UPMC Université Paris 06, UMR 7093, Observatoire Océanologique, 06230 Villefranche-sur-mer, France
| | - Corinne Cruaud
- CEA - Institut de Génomique, GENOSCOPE, 91057 Evry, France
| | | | - Carlos M Duarte
- Mediterranean Institute of Advanced Studies, CSIC-UiB, 21-07190 Esporles, Mallorca, Spain
- King Abdullah University of Science and Technology, Red Sea Research Center, Thuwal 23955-6900, Saudi Arabia
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC Barcelona E0800, Spain
| | - Dolors Vaqué
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC Barcelona E0800, Spain
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM), CSIC Barcelona E0800, Spain
| | - Patrick Wincker
- CEA - Institut de Génomique, GENOSCOPE, 91057 Evry, France
- CNRS, UMR 8030, 91057 Evry, France
- Université d'Evry, UMR 8030, 91057 Evry, France
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, Ohio 43210, USA
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10
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Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, Coelho LP, Espinoza JCI, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G. Plankton networks driving carbon export in the oligotrophic ocean. Nature 2016; 532:465-470. [PMID: 26863193 PMCID: PMC4851848 DOI: 10.1038/nature16942] [Citation(s) in RCA: 311] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 12/18/2015] [Indexed: 01/02/2023]
Abstract
The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterised. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria, alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of just a few bacterial and viral genes can predict most of the variability in carbon export in these regions.
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Affiliation(s)
- Lionel Guidi
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, Villefranche-sur-Mer, France.,Department of Oceanography, University of Hawaii, Honolulu, Hawaii, USA
| | - Samuel Chaffron
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.,Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium.,Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Lucie Bittner
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Institut de Biologie Paris-Seine (IBPS), Evolution Paris Seine, F-75005, Paris, France.,Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005 Paris, France.,Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Damien Eveillard
- LINA UMR 6241, Université de Nantes, EMN, CNRS, 44322 Nantes, France
| | | | - Simon Roux
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Youssef Darzi
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.,Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium
| | - Stephane Audic
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Léo Berline
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, Villefranche-sur-Mer, France
| | - Jennifer Brum
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | | | - Shruti Malviya
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005 Paris, France
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Céline Dimier
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Stefanie Kandels-Lewis
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany.,Directors' Research European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg Germany
| | - Marc Picheral
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, Villefranche-sur-Mer, France
| | - Julie Poulain
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry France
| | - Sarah Searson
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, Villefranche-sur-Mer, France.,Department of Oceanography, University of Hawaii, Honolulu, Hawaii, USA
| | | | - Lars Stemmann
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, Villefranche-sur-Mer, France
| | - Fabrice Not
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Pascal Hingamp
- Aix Marseille Université CNRS IGS UMR 7256 13288 Marseille France
| | - Sabrina Speich
- Department of Geosciences, Laboratoire de Météorologie Dynamique (LMD), Ecole Normale Supérieure, 24 rue Lhomond 75231 Paris Cedex 05 France
| | - Mick Follows
- Dept of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, USA
| | - Lee Karp-Boss
- School of Marine Sciences, University of Maine, Orono, USA
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, USA
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Stephane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Jean Weissenbach
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry France.,CNRS, UMR 8030, CP5706, Evry France.,Université d'Evry, UMR 8030, CP5706, Evry France
| | - Patrick Wincker
- CEA - Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry France.,CNRS, UMR 8030, CP5706, Evry France.,Université d'Evry, UMR 8030, CP5706, Evry France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC Pg. Marítim de la Barceloneta 37-49 Barcelona E08003 Spain
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany.,Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany
| | - Colomban de Vargas
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.,Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium.,Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - 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, F-75005 Paris, France.,Directors' Research European Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg Germany
| | - 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, F-75005 Paris, France
| | - Gabriel Gorsky
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire d'oceanographie de Villefranche (LOV), Observatoire Océanologique, Villefranche-sur-Mer, France
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11
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Le Bescot N, Mahé F, Audic S, Dimier C, Garet MJ, Poulain J, Wincker P, de Vargas C, Siano R. Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding. Environ Microbiol 2015; 18:609-26. [DOI: 10.1111/1462-2920.13039] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 08/25/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Noan Le Bescot
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
| | - Frédéric Mahé
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
- Department of Ecology; Technische Universität Kaiserslautern; Erwin-Schrödinger Str. 14 D-67663 Kaiserslautern Germany
| | - Stéphane Audic
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
| | - Céline Dimier
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
| | - Marie-José Garet
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
| | - Julie Poulain
- Centre National de Séquençage; CEA-Institut de Génomique, GENOSCOPE; Evry Cedex France
| | - Patrick Wincker
- Centre National de Séquençage; CEA-Institut de Génomique, GENOSCOPE; Evry Cedex France
- Université d'Evry, UMR 8030; rue Gaston Crémieux CP5706 91057 Evry Cedex France
- Centre National de la Recherche Scientifique (CNRS), UMR 8030; rue Gaston Crémieux CP5706 91057 Evry Cedex France
| | - Colomban de Vargas
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
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12
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Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F, Bittner L, Darzi Y, Wang J, Audic S, Berline L, Bontempi G, Cabello AM, Coppola L, Cornejo-Castillo FM, d'Ovidio F, De Meester L, Ferrera I, Garet-Delmas MJ, Guidi L, Lara E, Pesant S, Royo-Llonch M, Salazar G, Sánchez P, Sebastian M, Souffreau C, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Gorsky G, Not F, Ogata H, Speich S, Stemmann L, Weissenbach J, Wincker P, Acinas SG, Sunagawa S, Bork P, Sullivan MB, Karsenti E, Bowler C, de Vargas C, Raes J. Ocean plankton. Determinants of community structure in the global plankton interactome. Science 2015; 348:1262073. [PMID: 25999517 DOI: 10.1126/science.1262073] [Citation(s) in RCA: 472] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated network-generated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models.
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Affiliation(s)
- Gipsi Lima-Mendez
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Karoline Faust
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Nicolas Henry
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Johan Decelle
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Sébastien Colin
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France
| | - Fabrizio Carcillo
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium. Interuniversity Institute of Bioinformatics in Brussels (IB), ULB Machine Learning Group, Computer Science Department, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Samuel Chaffron
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | | | - Simon Roux
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Flora Vincent
- VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France
| | - Lucie Bittner
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France. Institut de Biologie Paris-Seine, CNRS FR3631, F-75005, Paris, France
| | - Youssef Darzi
- VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jun Wang
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium
| | - Stéphane Audic
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Léo Berline
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Gianluca Bontempi
- Interuniversity Institute of Bioinformatics in Brussels (IB), ULB Machine Learning Group, Computer Science Department, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ana M Cabello
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Laurent Coppola
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Francesco d'Ovidio
- Sorbonne Universités, UPMC, Université Paris 06, CNRS-Institut pour la Recherche et le Développement-Muséum National d'Histoire Naturelle, Laboratoire d'Océanographie et du Climat: Expérimentations et Approches Numériques (LOCEAN) Laboratory, 4 Place Jussieu, 75005, Paris, France
| | - Luc De Meester
- KU Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Charles Deberiotstraat 32, 3000 Leuven
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Marie-José Garet-Delmas
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Lionel Guidi
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Elena Lara
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Stéphane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Hochschulring 18, 28359 Bremen, Germany. MARUM, Center for Marine Environmental Sciences, University of Bremen, Hochschulring 18, 28359 Bremen, Germany
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Guillem Salazar
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Marta Sebastian
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Caroline Souffreau
- KU Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Charles Deberiotstraat 32, 3000 Leuven
| | - Céline Dimier
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France
| | - Marc Picheral
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Sarah Searson
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Stefanie Kandels-Lewis
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Directors' Research, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Gabriel Gorsky
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Fabrice Not
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, 611-0011 Kyoto, Japan
| | - Sabrina Speich
- Department of Geosciences, Laboratoire de Météorologie Dynamique (LMD), Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France. Laboratoire de Physique des Océan, Université de Bretagne Occidentale (UBO)-Institut Universaire Européen de la Mer (IUEM), Palce Copernic, 29820 Polouzané, France
| | - Lars Stemmann
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Paris 06, UMR 7093, Laboratoire d'Océanographie de Villefranche (LOV), Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Jean Weissenbach
- Commissariat à l'Énergie Atomique (CEA), Genoscope, 2 rue Gaston Crémieux, 91000 Evry, France. CNRS, UMR 8030, 2 rue Gaston Crémieux, 91000 Evry, France. Université d'Evry, UMR 8030, CP5706 Evry, France
| | - Patrick Wincker
- Commissariat à l'Énergie Atomique (CEA), Genoscope, 2 rue Gaston Crémieux, 91000 Evry, France. CNRS, UMR 8030, 2 rue Gaston Crémieux, 91000 Evry, France. Université d'Evry, UMR 8030, CP5706 Evry, France
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Eric Karsenti
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France. Directors' Research, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Chris Bowler
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), Inserm U1024, CNRS UMR 8197, Paris, F-75005 France.
| | - Colomban de Vargas
- Station Biologique de Roscoff, CNRS, UMR 7144, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France.
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute KU Leuven, Herestraat 49, 3000 Leuven, Belgium. VIB Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences (DBIT) Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
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13
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Villar E, Farrant GK, Follows M, Garczarek L, Speich S, Audic S, Bittner L, Blanke B, Brum JR, Brunet C, Casotti R, Chase A, Dolan JR, d'Ortenzio F, Gattuso JP, Grima N, Guidi L, Hill CN, Jahn O, Jamet JL, Le Goff H, Lepoivre C, Malviya S, Pelletier E, Romagnan JB, Roux S, Santini S, Scalco E, Schwenck SM, Tanaka A, Testor P, Vannier T, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Acinas SG, Bork P, Boss E, de Vargas C, Gorsky G, Ogata H, Pesant S, Sullivan MB, Sunagawa S, Wincker P, Karsenti E, Bowler C, Not F, Hingamp P, Iudicone D. Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport. Science 2015; 348:1261447. [PMID: 25999514 DOI: 10.1126/science.1261447] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic.
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Affiliation(s)
- Emilie Villar
- Aix Marseille Université, CNRS, IGS UMR 7256, 13288 Marseille, France.
| | - Gregory K Farrant
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Michael Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Laurence Garczarek
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Sabrina Speich
- Laboratoire de Physique des Océans (LPO) UMR 6523 CNRS-Ifremer-IRD-UBO, Plouzané, France. Department of Geosciences, Laboratoire de Météorologie Dynamique (LMD) UMR 8539, Ecole Normale Supérieure, 24 Rue Lhomond, 75231 Paris Cedex 05, France
| | - Stéphane Audic
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Lucie Bittner
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Bruno Blanke
- Laboratoire de Physique des Océans (LPO) UMR 6523 CNRS-Ifremer-IRD-UBO, Plouzané, France
| | - Jennifer R Brum
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | | | | | - Alison Chase
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - John R Dolan
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Fabrizio d'Ortenzio
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Jean-Pierre Gattuso
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Nicolas Grima
- Laboratoire de Physique des Océans (LPO) UMR 6523 CNRS-Ifremer-IRD-UBO, Plouzané, France
| | - Lionel Guidi
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Christopher N Hill
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Oliver Jahn
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jean-Louis Jamet
- Université de Toulon, Laboratoire PROTEE-EBMA E.A. 3819, BP 20132, 83957 La Garde Cedex, France
| | - Hervé Le Goff
- CNRS, UMR 7159, Laboratoire d'Océanographie et du Climat LOCEAN, 4 Place Jussieu, 75005 Paris, France
| | - Cyrille Lepoivre
- Aix Marseille Université, CNRS, IGS UMR 7256, 13288 Marseille, France
| | - Shruti Malviya
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Eric Pelletier
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Jean-Baptiste Romagnan
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Simon Roux
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sébastien Santini
- Aix Marseille Université, CNRS, IGS UMR 7256, 13288 Marseille, France
| | - Eleonora Scalco
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Sarah M Schwenck
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Atsuko Tanaka
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Pierre Testor
- CNRS, UMR 7159, Laboratoire d'Océanographie et du Climat LOCEAN, 4 Place Jussieu, 75005 Paris, France
| | - Thomas Vannier
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Flora Vincent
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Adriana Zingone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Céline Dimier
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Marc Picheral
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Sarah Searson
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Stefanie Kandels-Lewis
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM), CSIC, Passeig Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Colomban de Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Gabriel Gorsky
- Sorbonne Universités, UPMC Université Paris 06, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France. INSU-CNRS, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-Mer, France
| | - Hiroyuki Ogata
- Aix Marseille Université, CNRS, IGS UMR 7256, 13288 Marseille, France
| | - Stéphane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany. MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Patrick Wincker
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Genoscope, 2 Rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Eric Karsenti
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Chris Bowler
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France.
| | - Fabrice Not
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, Université Pierre et Marie Curie UPMC, Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France.
| | - Pascal Hingamp
- Aix Marseille Université, CNRS, IGS UMR 7256, 13288 Marseille, France.
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.
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14
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Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P. Ocean plankton. Structure and function of the global ocean microbiome. Science 2015; 348:1261359. [PMID: 25999513 DOI: 10.1126/science.1261359] [Citation(s) in RCA: 1348] [Impact Index Per Article: 149.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.
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Affiliation(s)
- Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Samuel Chaffron
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jens Roat Kultima
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Karine Labadie
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Guillem Salazar
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Bardya Djahanschiri
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Daniel R Mende
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Adriana Alberti
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Francisco M Cornejo-Castillo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Paul I Costea
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Corinne Cruaud
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Francesco d'Ovidio
- Sorbonne Universités, UPMC, Université Paris 06, CNRS-IRD-MNHN, LOCEAN Laboratory, 4 Place Jussieu, 75005 Paris France
| | - Stefan Engelen
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Isabel Ferrera
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Josep M Gasol
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Lionel Guidi
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Falk Hildebrand
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Florian Kokoszka
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Laboratoire de Physique des Océans UBO-IUEM, Place Copernic 29820 Plouzané, France
| | - Cyrille Lepoivre
- Aix Marseille Université CNRS IGS UMR 7256, 13288 Marseille, France
| | - Gipsi Lima-Mendez
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Julie Poulain
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Bonnie T Poulos
- Department of Ecology and Evolutionary Biology, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA
| | - Marta Royo-Llonch
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain
| | - Hugo Sarmento
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain. Department of Hydrobiology, Federal University of São Carlos (UFSCar), Rodovia Washington Luiz, 13565-905 São Carlos, São Paulo, Brazil
| | - Sara Vieira-Silva
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Céline Dimier
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Marc Picheral
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Sarah Searson
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Stefanie Kandels-Lewis
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Chris Bowler
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France
| | - Colomban de Vargas
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Gabriel Gorsky
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Nigel Grimsley
- CNRS UMR 7232, BIOM, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France. Sorbonne Universités Paris 06, OOB UPMC, Avenue du Fontaulé, 66650 Banyuls-sur-Mer, France
| | - Pascal Hingamp
- Aix Marseille Université CNRS IGS UMR 7256, 13288 Marseille, France
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Olivier Jaillon
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Fabrice Not
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-001, Japan
| | - Stephane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science, University of Bremen, Bremen, Germany. MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Sabrina Speich
- Department of Geosciences, Laboratoire de Météorologie Dynamique (LMD), Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France. Laboratoire de Physique des Océans UBO-IUEM, Place Copernic, 29820 Plouzané, France
| | - Lars Stemmann
- CNRS, UMR 7093, Laboratoire d'Océanographie de Villefranche-sur-Mer, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France. Sorbonne Universités, UPMC Université Paris 06, UMR 7093, LOV, Observatoire Océanologique, F-06230 Villefranche-sur-mer, France
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA
| | - Jean Weissenbach
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Patrick Wincker
- CEA-Institut de Génomique, GENOSCOPE, 2 rue Gaston Crémieux, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Eric Karsenti
- Ecole Normale Supérieure, Institut de Biologie de l'ENS (IBENS), and Inserm U1024, and CNRS UMR 8197, F-75005 Paris, France. Directors' Research, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. Center for the Biology of Disease, VIB, Herestraat 49, 3000 Leuven, Belgium. Department of Applied Biological Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Marítim de la Barceloneta, 37-49, Barcelona E08003, Spain.
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany.
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Pesant S, Not F, Picheral M, Kandels-Lewis S, Le Bescot N, Gorsky G, Iudicone D, Karsenti E, Speich S, Troublé R, Dimier C, Searson S. Open science resources for the discovery and analysis of Tara Oceans data. Sci Data 2015; 2:150023. [PMID: 26029378 PMCID: PMC4443879 DOI: 10.1038/sdata.2015.23] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 04/27/2015] [Indexed: 11/29/2022] Open
Abstract
The Tara Oceans expedition (2009–2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. The interpretation of such an extensive collection of samples in their ecological context requires means to explore, assess and access raw and validated data sets. To address this challenge, the Tara Oceans Consortium offers open science resources, including the use of open access archives for nucleotides (ENA) and for environmental, biogeochemical, taxonomic and morphological data (PANGAEA), and the development of on line discovery tools and collaborative annotation tools for sequences and images. Here, we present an overview of Tara Oceans Data, and we provide detailed registries (data sets) of all campaigns (from port-to-port), stations and sampling events.
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Affiliation(s)
- Stéphane Pesant
- PANGAEA, Data Publisher for Earth and Environmental Science , 28359 Bremen, Germany ; MARUM, Center for Marine Environmental Sciences, Universität Bremen , 28359 Bremen, Germany
| | - Fabrice Not
- CNRS, UMR 7144, Station Biologique de Roscoff , 29680 Roscoff, France ; Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff , 29680 Roscoff, France
| | - Marc Picheral
- CNRS, UMR 7093, Observatoire Océanologique de Villefranche-sur-Mer (OOV) , 06230 Villefranche/mer, France ; Sorbonne Universités, UPMC Univ Paris 06, UMR 7093, Observatoire Océanologique de Villefranche-sur-Mer (OOV) , 06230, Villefranche/mer, France
| | - Stefanie Kandels-Lewis
- Structural and Computational Biology, European Molecular Biology Laboratory , Meyerhofstr. 1, 69117 Heidelberg, Germany ; Directors' Research, European Molecular Biology Laboratory Meyerhofstrasse 1 , 69117 Heidelberg, Germany
| | - Noan Le Bescot
- CNRS, UMR 7144, Station Biologique de Roscoff , 29680 Roscoff, France
| | - Gabriel Gorsky
- CNRS, UMR 7093, Observatoire Océanologique de Villefranche-sur-Mer (OOV) , 06230 Villefranche/mer, France ; Sorbonne Universités, UPMC Univ Paris 06, UMR 7093, Observatoire Océanologique de Villefranche-sur-Mer (OOV) , 06230, Villefranche/mer, France
| | - Daniele Iudicone
- Laboratory of Ecology and Evolution of Plankton, Stazione Zoologica Anton Dohrn , 80121 Naples, Italy
| | - Eric Karsenti
- Directors' Research, European Molecular Biology Laboratory Meyerhofstrasse 1 , 69117 Heidelberg, Germany ; Environmental and Evolutionary Genomics Section, Institut de Biologie de l'Ecole Normale Supérieure, CNRS, UMR 8197, Institut National de la Santé et de la Recherche Médicale U1024, Ecole Normale Supérieure , 75005 Paris, France
| | - Sabrina Speich
- Department of Geosciences, Laboratoire de Météorologie Dynamique (LMD), Ecole Normale Supérieure , 75005, Paris, France ; Laboratoire de Physique des Océan, UBO-IUEM , 29280 Polouzané, France
| | - Romain Troublé
- Tara Expéditions, Base Tara , 11 boulevard Bourdon, 75004 Paris, France
| | - Céline Dimier
- CNRS, UMR 7144, Station Biologique de Roscoff , 29680 Roscoff, France
| | - Sarah Searson
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff , 29680 Roscoff, France ; Department of Oceanography, University of Hawaii at Manoa , Honolulu, HI 96822, USA
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16
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de Vargas C, Audic S, Henry N, Decelle J, Mahe F, Logares R, Lara E, Berney C, Le Bescot N, Probert I, Carmichael M, Poulain J, Romac S, Colin S, Aury JM, Bittner L, Chaffron S, Dunthorn M, Engelen S, Flegontova O, Guidi L, Horak A, Jaillon O, Lima-Mendez G, Luke J, Malviya S, Morard R, Mulot M, Scalco E, Siano R, Vincent F, Zingone A, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Acinas SG, Bork P, Bowler C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Not F, Ogata H, Pesant S, Raes J, Sieracki ME, Speich S, Stemmann L, Sunagawa S, Weissenbach J, Wincker P, Karsenti E, Boss E, Follows M, Karp-Boss L, Krzic U, Reynaud EG, Sardet C, Sullivan MB, Velayoudon D. Eukaryotic plankton diversity in the sunlit ocean. Science 2015; 348:1261605. [DOI: 10.1126/science.1261605] [Citation(s) in RCA: 1138] [Impact Index Per Article: 126.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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